The Latest Technologies in Agriculture and Plant Sciences

INTRODUCTION
Agriculture is an integrated field that allows us to experiment in any area. It

plays a crucial role in human life and its existence. There are many molecular
breeding techniques that can be used in the improvement of agriculture.
There has been improvement in the transformation techniques to enhance
the phenotype of the crops. Agrobacterium mediated transformation is
one such important method that can be used in crop improvement. Plant
molecular analysis has led to the development of plant genomics and
this has raised the research standards in silico. This has enabled several
researchers to collaborate real time and get the benefits of technology.
Recombinant technology is another important area that gave use genetically
modified plants with better yields. This technology is satisfying the needs
of the ever-growing population worldwide. This technology allowed us to
use both natural combinations and traditional breeding techniques for the
enhancement of crop traits.
Microarray technology is another essential technology that can be used
to analyze and store huge amounts of biological data. This can be considered
as an important breakthrough in plant and agricultural research. The data
stored can be shared with several scientists all over the globe via the internet
and some of the databases are free to use. The high yielding varieties can
be observed in the drought and disease resistant plants and this comes with
the advancements in genetic engineering and associated tools. Agriculture
is meant to satisfy the food demands of the present generation and should
also help the future generations in the same manner and this purpose can
be satisfied by practicing sustainable methods of agriculture. Though
2 The Latest Technologies in Agriculture and Plant Sciences
technology improves the quality of life, it is essential to follow sustainable

agriculture.
Climate change is decreasing agricultural yields and this is an important
area that needs to be addressed. It left us with limited options and we cannot
cope up with the detrimental effects of climate change with the technology
we have. It is important to opt for climate resilient agriculture to keep the
cycle going forward. We are in need of integrated technological solutions
that can enhance crop yields with limited effects on climate. This can be done
with the use of environmentally friendly tools and techniques frequently.
Plant breeding exists in almost all the areas of crop science and research and
this can be treated as an important approach towards improvement of the
crop breeds and yields.
CHAPTER 1
INTRODUCTION TO ADVANCES
IN PLANT AND AGRICULTURAL
RESEARCH
CONTENTS
1.1 Introduction.......................................................................................... 6
1.2 Defining Diversity and Diversity Management...................................... 7
1.1 INTRODUCTION
In today’s world, technology has played a significant role in how we live,
communicate, travel, and interact. The rapid advancement of technology is
having a significant impact on all industries, particularly agriculture. Most
developing economies rely heavily on agriculture. Agriculture is undertaking
a major transition as a result of digitalization today. Robots, drones, and
machine learning are among the new technologies that are meant to assist
farmers increase productivity and yield (Roldán et al., 2017). Emerging
technologies have already shown to be an important factor in agriculture’s
long-term viability and profitability. For most countries, agriculture has
been the most important industry for economic development. It includes
everything from tiny enterprises to giant corporations to multinational
corporations. Agriculture encompasses more than just farming and
ranching, which are its primary sources of income. Agribusiness is also
the industry that converts agricultural commodities into consumer goods
(Macrae, Henning, & Hill, 1993). Food processing, packaging, shipping,
retail, preparation, and consumption at home all play a role in getting
goods to consumers. Agriculture has gone through a number of changes.
Mechanization has recently changed farming by replacing horses with
tractors. Today, technology is being accepted at an increasing rate, to the
point where it has become an unavoidable requirement for every farmer,
particularly in wealthy countries. There is insufficient land on the planet to
support today’s global population utilizing yesterday’s technologies.
Figure 1.1: Agriculture.
Source: https://www.croplife.com/management/get-ready-for-agriculture-3-0/
Introduction to advances in Plant and Agricultural Research 5
Agriculture, (Figure 1.1) like every other element of our modern life, is being
influenced by technology. In its most elementary form, technology can be
defined as a set of skills that enable us to create items and machines to meet
our requirements. Agriculture technology, commonly known as AgTech, has
revolutionized the business in recent years. Farming technology is assisting
farmers in increasing efficiency and production. Harvest automation,
autonomous tractors, planting and weeding, and drones are just a few of
the primary technologies used by farms. Technology is altering the field
of livestock management, which operates poultry farms, dairy farms, cattle
ranches, and other livestock-related agribusinesses, according to recent
developments. Livestock provides us with essential renewable natural
resources that we require on a daily basis.
In the coming years, emerging technologies have the potential to
completely revolutionize the agricultural environment. On a small and large
scale, emerging technologies ranging from robots to machine language have
totally altered modern agriculture. They'll take farming to new heights.
Farms are finding it cost-effective to strategically deploy sensors around
their land in order to reap a variety of benefits. Farmers can observe their
crops from anywhere in the world thanks to sensors and image recognition
technology. Agriculture benefits from sensors since they allow for real-time
traceability (Ko, Kwak, & Song, 2014). They would provide a real-time
picture of the current state of a farm, forest, or body of water. They assist in
the management and monitoring of livestock and crop production. They also
contribute to the farm's environmental sustainability by conserving water,
controlling erosion, and lowering fertilizer levels in local rivers and lakes.
Vertical farming has made its way to the city. Indoor vertical farming is
the process of producing vegetables in a closed and regulated environment,
layered one on top of the other (Benke & Tomkins, 2017). Artificial lights
are utilized in place of natural sunlight in the growing process. Within a
decade, vertical farming will not only be technically possible, but also
commercially viable. It is a type of urban agriculture that produces food
in layers that are vertically stacked. It isn't only restricted to metropolitan
settings. It can be applied to any condition in order to make better use of
available land. Vertical farming can boost agricultural yields, overcome land
constraints, and lessen farming's environmental impact. This is often referred
to as "ecological agriculture” (Kiley-Worthington, 1981). Organic farming
is environmentally benign and does not cause harm to the environment. It
is thought to be a greater alternative to chemical-based farming. Organic
farming, often known as organic agriculture, is a type of farming that
avoids the use of artificial fertilizers and pesticides to a considerable extent

(Leifeld, 2012). It's a system that keeps soils, ecosystems, and humans
healthy. It bans genetically modified and animal cloned items, as well as
industrial herbicides and fertilizers. It has a one-of-a-kind place in the
world's agricultural systems. Organic farming's major purpose is to create
businesses that are both sustainable and environmentally friendly. Crop
rotations, crop diversification, crop residues, animal manures, legumes,
green manures, off-farm organic wastes, bio-fertilizers, and mechanized
cultivation are all encouraged in organic farming.
1.2 TECHNOLOGY
Technology has continuously played an important part in how we live our
lives. It has an impact on how we interact, travel, and even eat. Agricultural
technological advancements are transforming the way we grow food and
manage its production. In agriculture, the ultimate purpose of technology
is to increase yields, shorten harvest periods, and reduce expenses and
environmental effects. Emerging technologies have a significant impact not
just on small-scale farming, but also on the large-scale food distribution
system. As new technology is integrated into modern farming, output
improves and supply chain management becomes easier. Automation is
the actual emphasis of agricultural technological advancements, and it is
already in use on farms all over the world. Modern automation has gone a
long way since the days of mechanical timers, and it now requires relatively
little human intervention. From seed to sale, systems are being developed to
monitor, feed, and harvest crops. Automation incorporates a wide range of
sensors, computers, feeding mechanisms, and, of course, robots. Complete
automation is a nearly self-contained system that can manage all of the
farm's day-to-day operations (Edan, Han, & Kondo, 2009; Jha, Doshi, Patel,
& Shah, 2019). It virtually eliminates the need for human staffing, which
can be beneficial or detrimental depending on your perspective. A huge
network of sensors is one of automation's most valuable assets.
The backbone of future automated farming is likely to be crop, air, and soil
sensors. While today's sensors can determine fundamental parameters such as
pH, sensors of the future will be able to do much more. Not only will soil and
crop sensors be able to read nutrient levels and EC, but they will also be able
to undertake more extensive analysis utilizing infrared, electromagnetic, and
acoustic methods. More data allows crop growers to break from traditional
feed plans and embrace a more as-needed approach, saving time and money.
Equipment sensors will also be utilized to convey information from smart
technology to a central control unit in order to warn of potential mechanical
breakdowns. A sensor will be constantly interacting with a centrally
managed artificial intelligence system for almost any metric that can be
measured. Artificial intelligence, or AI, will improve the adaptability of
automated systems to changing environments. Furthermore, AI agricultural
systems will be capable of analyzing, diagnosing, and prescribing suitable
crop treatment regimens at a level of efficiency unequalled by humans.
When we talk about AI, we're not talking about The Terminator. For the
time being, AI is merely a sophisticated computer system that can adapt
to new inputs. Agriculture AI technologies help farmers better coordinate
mechanical systems, establish feed plans, identify sickness, and boost yields
and productivity. Drones are one of the more intriguing technologies that AI
will coordinate in agriculture.
1.3 ARTIFICIAL INTELLIGENCE

Drones (Figure 1.2) are becoming more common and are presently controlled
by the Federal Aviation Administration (FAA) in the United States (Puri,
Nayyar, & Raja, 2017). They appear to have far more practical applications
than anyone could have expected. Farmers may use a surveillance drone to
fly over acres of crops and gather images and video in real-time. In the winter,
they can also be used to monitor crop temperatures. Drones are currently
being utilized on farms not only for observation but also for application.
Drones that spray crops are one of the newest types of unmanned aerial
vehicles (UAVs) that can be found on today’s farms. Drones that spray
pesticides or fertilizers on crops are unaffected by difficult terrain (Adão et
al., 2017). Modern farming is also being influenced by autonomous robots.
Figure 1.2: Drones.
Source: https://archive.factordaily.com/drones-for-precision-agriculture-in-
india/
Farms of the future may not require people to cultivate crops at all.
Drone-like autonomous robots are now being employed to undertake duties
such as seed planting, crop tending, and harvesting. Drones are beginning to
appear on the market in a number of configurations. Drone tractors, micro-
seed planters, and weed-eating robots are all progressively making their
way into the agricultural mainstream. The concept is to construct a group
of autonomous robots controlled by a central AI that eliminates human
error and adjusts to changing conditions to maximize yields, reduce time,
and boost efficiency. Farming devices that are automated work similarly to
self-driving cars. GPS technology, which accurately controls their locations
and functions, keeps them in sync. Precision agriculture is a larger trend
in farming that includes the use of GPS technology. Satellite farming and
site-specific crop management are two terms used to describe precision
agriculture (SSCM)(Ahmad & Mahdi, 2018). Precision agriculture
combines the most precise topography data with sensor data on the ground
to produce a precise picture of crop requirements. It is divided into four
stages: data collection, variable analysis, strategy development, and practice
implementation. Finally, precision agriculture aims to maximize efficiency
by analyzing data precisely and using cutting-edge technologies.
Changes in the global economy are converting American agriculture into

a mission to improve public health, social well-being, and the environment
in addition to efficient food and fiber production. Recent technological
advancements will make it easier for agriculture to realize its full potential
in terms of providing a wide range of societal benefits. However, in order
for that vision to become a reality, the agricultural research system must
seize new possibilities and form new collaborations, as well as possess the
leadership necessary to meet agriculture’s complex and diversified duties
in the twenty-first century. Food and fiber production has been the primary
public need addressed by the United States agriculture during the previous
century, and agricultural research has centered on increasing the productivity
of agronomical important crops and livestock. The productivity of that
endeavor can be seen in such productivity gains as the tripling of corn yields
over the last 50 years and a 2.5-fold increase in overall productivity, as well as
the low average percentage of consumer income spent on food in the United
States (Ning & Reed, 1995)outflow, and reinvestment. Cultural linkages,
trading blocs, host market size, tax considerations, exchange differentials,
and host market growth rates are found to be significant determinants of DFI
in food manufacturing. Wage rate differentials were found to be important
in the position and reinvested equations, but not in the outflow equation.
Thus, cheap labor may not be as important in attracting DFI as in the past.
© 1995 by John Wiley & Sons, Inc.”,”container-title”:”Agribusiness”,”D
OI”:”10.1002/1520-6297(199501/02. Those increases have been fueled
by scientific breakthroughs in plant and animal genetics, plant and animal
nutrition, and livestock health, as well as the practical application of those
breakthroughs in production systems.
Simultaneously, significant advances in public opinion have widened the
scope of agricultural research to encompass environmental, human health,
and community aims. Agriculture’s link to the food and fiber system, the
environment, and the fabric of American society will be altered by changing
public attitudes and wants, which will provide new market opportunities.
Agriculture’s capacities will be revolutionized as the speed of scientific
discovery and technological advancement accelerates.
The link between agriculture and public health has never been more
obvious, necessary, or promising. The increased public concern in food
safety indicates an understanding of this connection. Foodborne disease
is becoming more common in the United States. Furthermore, due to the
rising percentage of the US population over 65, a growing number of
people infected with HIV, and a growing number of people receiving bone
marrow or organ transplants, as well as patients receiving chemotherapy or

immunosuppressive drugs, a growing percentage of the populace is becoming
vulnerable to opportunistic infections, including foodborne pathogens (Shiels
et al., 2011)an increasing number of HIV-infected people are at risk of non-
AIDS-defining cancers that typically occur at older ages. We estimated the
annual number of cancers in the HIV-infected population, both with and
without AIDS, in the United States.Incidence rates for individual cancer
types were obtained from the HIV/AIDS Cancer Match Study by linking 15
HIV and cancer registries in the United States. Estimated counts of the US
HIV-infected and AIDS populations were obtained from Centers for Disease
Control and Prevention surveillance data. We obtained estimated counts of
AIDS-defining (ie, Kaposi sarcoma, non-Hodgkin lymphoma, and cervical
cancer. Increased mobility of animals, people, and products into the food
system is introducing new and unknown dangers. Some animal production
methods, such as those with larger animal densities and mechanized systems
that disseminate food, water, and other inputs and outputs, may increase
human exposure to infectious disease, according to epidemiologic studies.
Because of problems with food security, and the fragility of our
agricultural resources, public awareness of food safety is at an all-time
high. This sensitivity is part of a bigger trend in which people are becoming
more interested in where their food comes from. Several well-publicized
foodborne pathogen outbreaks have raised concerns about disease origins
and mitigation. The discovery of genetically modified corn in human
food products that have been approved for human consumption has raised
concerns about food traceability and accountability. These and other factors
have contributed to the explosive growth in consumer demand for organic
and low-input agricultural goods during the last decade.
Another significant shift is taking place in American society’s perception
of the relationship between agriculture and the environment. Through the
twentieth century, a number of public policies were established in an attempt
to mitigate the negative environmental effects of agricultural intensification
and widespread pesticide and fertilizer use. The public, on the other hand,
is now demanding agriculture to go further and provide environmental
advantages. Lands are projected to play a larger role in supplying clean
water, mitigating global climate change, protecting biological diversity, and
maintaining rural amenities like open space and recreational activities. Indeed,
in some locations, the national demand for environmental and recreational
services from the land is likely to overtake food needs. There is also a higher
level of public awareness and concern about global environmental change
and concerns, such as natural-resource depletion, desertification, climate
change, and biodiversity loss.
1.4 GENOMICS
The use of genomic technologies (Figure 1.3) is being employed to
investigate the genetic propensity to environmental variables that cause
disease in humans and animals. The techniques will also be used to
characterize the effects of food chemical components on disease conditions,
leading to a better knowledge of the relationship between human health and
nutrition. Collaborations between nutritionists and health-care specialists, as
well as plant scientists, will increasingly lead to the development of foods
that combat diseases and disease predispositions. In the 1990s, advances
in nutrition research broadened our understanding of important nutrients
and their involvement in disease genesis (Milner, 2000). This paved the
way not just for the recent increase in “functional” foods with specialized
nutritional properties, but also for future biotechnology-based creation of
nutritionally fortified foods. Advances in animal nutrition and genetics
have resulted in significant gains in efficiency and quality in the dairy,
livestock, poultry, and industries, which are predicted to boost US animal
agriculture’s future competitiveness. Animal feeds should be developed to
match the genetics of the animals as cloning of farm animals progresses to
commercial use, resulting in more effective growth and meat production,
augmented compatibility of meat with human nutritional needs, and reduced
waste and pollution from animal production facilities. Advances in disease
identification and control, such as the introduction of vaccinations and other
preventives in feed, will reduce bacterial, fungal, and viral contamination
of animal products, boosting production efficiency and food safety even
further.
Figure 1.3: Genomic technologies.
Source: https://www.sciencedirect.com/science/article/abs/pii/
S0167779917300318
Global data on natural resources, as well as the tools for managing,
manipulating, and using them, are fast evolving, allowing ideas that could
not previously be tested to be explored. Farms, forests, and rangelands
will benefit from tools that incorporate spatially referenced and satellite-
based remotely sensed data into decision support systems. Large new
datasets have provided the foundation for better epidemiologic techniques
to understanding, preventing, and reducing disease outbreaks. Massive
datasets are now routinely transferred and manipulated among academics.
Synthetic data analysis that was before unachievable has become possible
thanks to Internet access to various databases at the same time. Advances
in the social sciences have led to a more comprehensive knowledge of the
social and economic linkages between the agricultural and non-farm sectors.
New analytic and modeling approaches, for example, have made it possible
to compare the effects of various policy alternatives in addressing a wide
range of social goals. Trade and immigration trends may now be studied
demographically, economically, and environmentally thanks to the growth
of information resources. Modeling approaches for assessing how changing
economic conditions affect land-use decisions and ecologic conditions are
expected to yield significant insights into the determinants of environmental

quality and the effectiveness of various policy approaches.
Food safety and food acceptance have gained a new human dimension
because of the social and communication sciences. The mixing of
biomedical and social sciences can be seen in risk assessment, risk
communication, consumer education, and human behavior and attitudes.
With the introduction of genetically modified crops and animals, the human
components of contemporary agriculture and related studies have become
even more important.
Few contemporary economic shifts have matched the effects of
globalization in the last quarter of the twentieth century. In addition to
handling their highly productive resource base, American farmers must
also respond to changing consumer demands for products and services, as
well as manage technology, capital, and labor in internationally integrated
marketplaces. Even if global population growth slows, demand for animal
products will skyrocket as incomes rise in less-developed nations, creating
new market opportunities and global problems for agricultural systems.
Agriculture in the United States will need to maintain its technological
leadership and long-term productivity increases to remain competitive in
this global economy. This will necessitate the development of new and more
complex information management technologies and systems. Advances
in information technology and genomic sciences have opened up new
research opportunities to help agriculture provide higher-quality products
and services. However, as the global nature of possible threats posed by
new technology becomes better known, a more thorough assessment of such
risks is required.
The global trend of countries exporting and importing an increasing
share of products, services, production inputs, and intellectual property
will have significant implications for national economies, society, and
the environment. In order to offer a solid, scientific basis for policies
and programs that address such consequences in the United States, more
research is required. Such research must be comprehensive, looking at all
of globalization’s implications as well as the environmental, social, and
economic trade-offs that policymakers will face. One of the most important
concerns that research should address is the relative advantages and costs of
investing in various types of research, including societal and environmental
research. The task of correcting policy distortions that bias incentives in
global agriculture is a second concern.
1.5 IPR
Improved knowledge of how global changes in IPR laws affect the public
research agenda is a related field of research. Changes in technology, legal
judgments, and international agreements have enhanced the return on
investment and international spill overs from privately supported agricultural
and food research. In agricultural research, partnerships, joint ventures, and
other collaborations between public and private institutions are becoming
more widespread. Such collaborations increase funding for some types of
research and improve the chances of commercialization and application of
new technologies, but they also raise questions about whether private-sector
interests are playing an excessive role in determining research priorities.
Although such concerns are not unique to agriculture, the rapid pace of
development in agricultural research institutes and biotechnology poses a
number of unanswered difficulties.
In order to increase the efficacy and specificity of gene-transfer
technologies, the public sector must also invest in research. The development
of techniques for modifying plant and animal genomes, the construction of
models and systems that integrate basic knowledge about plants and animals
into gene selection, and the synthesizing of findings on gene mapping and
the protein expression related with quantitative traits are all examples of
important research. The current state of knowledge about physiologic
systems and metabolic pathways does not allow for precise genetic
modifications. Greater precision and predictability are required due to the
expenses of genetic alterations, particularly in animals. To build quantitative
and dynamic models of interactions in physiologic and metabolic systems,
collaboration between experimentalists and modelers will be critical; this
will allow scientists to make particular changes and better comprehend
the ramifications for the entire organism. Finally, the application of
genomics-based techniques to environmental challenges is unlikely to be a
high commercial priority, thus it should be included in the public sector’s
portfolio. Advances in agricultural genomics as a result of the above-
mentioned research will create new information resources and needs, hence
expanding the use of bioinformatics in agriculture for acquiring, processing,
storing, distributing, analyzing, and interpreting biologic data.
1.6 PRECISION AGRICULTURE

Precision agriculture (Figure 1.4) is another cutting-edge technology that
has the potential to boost productivity while also benefiting the environment.
Tracking productivity and adapting inputs to fit the specific demands of sub
acre areas in individual fields are part of this spatially explicit approach
to crop management. Precision agriculture technology has advanced faster
than its practical implementation in recent years. We need practical decision-
making tools that allow farmers to alter the timing and quantity of seed,
fertilizer, water, and pesticides to maximize productivity while minimizing
waste and negative environmental effects. Integrating experimental findings
into decision-support systems and underlying models for crop, animal, and
environmental systems will require close collaboration among experimental
scientists, statisticians, economists, engineers, and systems analysts.
Figure 1.4: Precision Agriculture.
Source: https://www.arcweb.com/blog/iot-steps-smart-farming-precision-agri-
culture
Understanding the whole range of potential repercussions of new
technologies and practices pertaining to social, economic, health,
environmental, and ethical as well as their worldwide implications, is critical
for quality research and technology transfer. New technologies frequently
hold great promise for improving people’s lives. They do, however, present
critical considerations concerning environmental and health dangers,
reward and risk distribution, and public principles and ethics. Exploring
such queries early in the R&D process will help to focus technological
development efforts on those that are most likely to benefit the public. The
development of genetically modified food has brought new questions about
the proper amount of health and environmental scrutiny, product labeling,
and public communication. Differences in attitudes and values among
different parts of society, as well as among scientists with varying levels of
competence, have been highlighted in public discourse. Similar challenges
will arise as new technology and methods emerge. The usage of recombinant
bovine somatotropin (Growth hormone) in dairy cattle, the development
of antibiotic resistance as a result of antimicrobial use in the livestock and
dairy industries are some examples.
Because research on transgenic crops has far outpaced research on
pleiotropic and other unintended consequences, there is widespread public
and scientific support for establishing a government-sponsored program to
investigate queries about food allergens and toxicants that are improbable to
be pursued by the private sector.
Figure 1.5: Bioactive compounds.
Source: https://www.researchgate.net/publication/349348618_Natural_Bioac-
tive_Compounds_Useful_in_Clinical_Management_of_Metabolic_Syndrome/
figures
The development of an animal model of food allergenicity in humans, for

example, would be accelerated by a vigorous federally financed study. Once
these questions are answered, it may be feasible to pinpoint the mechanisms
by which certain proteins induce allergies or harmful consequences, as well
as devise novel ways to mitigate the risk associated with these proteins.
Developing biotechnological ways to inactivate allergic or harmful chemicals
in meals could be one of the strategies. In an increasingly integrated global
economy, scientific advancements offer new options to control plant and
animal health. They include novel epidemiology, risk assessment, and risk
management methods to better comprehend the threats posed by wildlife or
growing international plant and animal trade. Using genetic approaches to
improve disease resistance in plants and animals could result in significant
savings in processing and manufacturing costs, as well as a reduction in the
usage of antibiotics in animal production. Basic research on biotechnology
applications will be required for such applied research.
1.7 BIOACTIVE COMPOUNDS

Carotenoids, flavonoids, plant sterols, omega-3 fatty acids, allyl and diallyl
sulphides, indoles, and phenolic acids are examples of bioactive components
found naturally in many foods, particularly fruits and vegetables(Rice-Evans
& Miller, 1996). These food components (Figure 1.5) require a scientific
understanding of their chemistry, metabolism, and health impacts. In order
to estimate and track dietary intakes, it is also necessary to quantify the
amounts of these components in foods and incorporate the information into
food-composition databases. The Agricultural Research Service should
keep putting together databases on carotenoids, flavonoids, and other
bioactive chemicals. Human genetics-based nutrition research will lay the
groundwork for better understanding the metabolic fate of nutrients and the
biochemical roles of dietary components such as macronutrients, vitamins,
minerals, bioactive components, and pharmacologic agents. It will also
explain how and why people’s requirements for and utilization of specific
food components differ. Disease prevention and reducing exposure to
physiologically hazardous chemicals in plant and animal products are major
applications of this knowledge. The genetic underpinnings of such variance
are unknown. Researchers have discovered a small number of particular
genes that influence how the human body uses certain food components.
Many features of how genes interact with one another and the environment
to produce certain nutritional or disease consequences are also unknown.
Improved knowledge of how genes influence individual dietary status

and disease risk could help shape public-health policies in the future. A
deeper understanding of how genes affect the body’s storage and use of
food calories, for example, would substantially aid attempts to design
effective food and nutrition policies aimed at correcting our nation’s obesity
epidemic(“Obesity — United States, 1999–2010,” n.d.). Given the likely rapid
introduction of transgenic foods into the marketplace in the coming years,
and the possibility that some of the intended and unintended compositional
changes may disproportionately affect genetically susceptible populations,
there is a pressing need to speed up research into gene-bioactive compound
interactions in food and dietary supplements. Indeed, there may be value
in arranging this research in some way that prioritizes researching genetic
interactions with chemicals that are consumed by the biggest number of
people or have the highest potential for causing negative outcomes.
The public’s perception of the relationship between agriculture and
the environment is changing dramatically. Whereas previous public
policies aimed to reduce the negative environmental effects of agricultural
practices, such as pollution, today’s and tomorrow’s policies will go even
further in realizing agriculture’s potential to provide broad environmental
benefits, such as clean water, carbon sequestration, and biodiversity
conservation. Agricultural research must thus fulfill two roles: establishing
environmentally-friendly farming practices and advancing innovative
land and natural resource management practices that will improve the
environment. Integrating recent conceptual advancements from the ecologic
and social sciences can help both pursuits. In the face of rising pressures on
global land, water, and genetic resources, as well as global environmental
change, agricultural research conducted in the United States can help bring
worldwide environmental benefits and inform international environmental
agreements.
The use of genomics to generate new crop cultivars and livestock strains
has the potential to improve environmental compatibility in a variety of
ways. Improving plant nutrient usage, as well as the efficiency of nutrient
digestion and use in cattle, could reduce fertilizer requirements and keep
surplus nitrogen and phosphorus out of waterways. Increasing the efficiency
with which main crops use water would lower agricultural water demands.
Pesticide and fungicide application rates should be reduced for plants
and animals that are more resistant to pests or diseases. Related research
should focus on applying biotechnology to environmental concerns as well
as assessing related environmental dangers, such as the possible spread of
novel genes and phenotypes into native microbes, plants, and insects. The
transfer of novel genes to microorganisms, in particular, poses a significant
threat to agricultural and natural landscape ecology.
The future of agricultural research will be difficult to predict. The rising
economic, social, and environmental demands on agriculture provide a
difficult context in which to plan research. Although these demands increase
the potential for increased societal returns from agricultural research, they
also place a strain on the system’s ability in a variety of ways. With limited
resources, there will be trade-offs between research goals that must be
handled. Traditional and new players in the agricultural research system will
send contradictory messages. Occasionally, research is required to address
trade-offs or perceived trade-offs among the numerous demands placed
on the agricultural system. Researchers may be enlisted to help mitigate
the unintended consequences of food and agriculture policies. Established
agricultural research methodologies and partnerships must develop to meet
new demands without losing their unique value. Only by long-term vision,
leadership, and political will can those tensions in the research agenda be
managed.
For the improvement of plant varieties, plant breeders primarily rely
on phenotypic selection. However, the introduction of molecular markers
made it possible to more directly pick favorable features. Molecular
markers, primarily DNA markers, are segments of an organism’s genome
that are used to identify a larger portion of the genome. The genome is the
totality of genes in an organism, and genomics is the study of the entire
genome, which includes both structural and functional aspects of genomics.
Restriction fragment length polymorphism was the first DNA-based genetic
marker. A molecular marker can be found within a gene of interest or related
to a gene that controls a trait of interest. Plant breeding can now utilize
easily detectable DNA markers for marker-assisted selection (MAS) to
generate superior varieties based on the genotype of plants rather than only
the phenotype. Furthermore, DNA markers are employed in germplasm
evaluation, genetic diagnostics, phylogenetic analysis, genome organization
research, and transformant screening. Marker-assisted backcrossing,
marker-assisted recurrent selection, advanced backcross-quantitative trait
loci, and gene pyramiding are the most common MAS breeding procedures
for introgression of genes from breeding lines or wild relatives to cultivated
species. Disease and pest resistance are the primary breeding objectives
for which MAS is currently used in crops, followed by yield improvement,
quality attributes, and abiotic stress resistance.
Plant genomics encompasses both scientific and applied aspects, and

includes structural and functional genomes. The comprehension of genes
to genomes has improved due to the rapid evolution of novel technologies,
particularly the introduction of bioinformatics. Genomic analysis,
proteomics, transcriptomics, genome sequencing, and metabolomics are
examples of ‘omics’ technologies (Morgante & Salamini, 2003). Genomic
technology, in particular, is revolutionizing breeding practice, resulting in
‘genomics-assisted breeding,’ which improves the efficiency of breeding
for the enhancement of agronomical desirable traits. Plant breeding using
genomics technologies is sometimes referred to as molecular breeding.
Furthermore, genomics facilitates plant biotechnology by increasing the
number of native target genes. Many agronomic features are controlled by
genes whose functions are unknown, but which can be mapped and cloned
using genetic mapping. In addition, various novel technologies have been
developed, such as next-generation sequencing (NGS), Solexa Illumina,
applied biosystems (ABI) solid and high-throughput marker genotyping
technologies]. Marker-assisted selection (MAS) has been a technology used
by agricultural businesses and research institutes to generate new superior
varieties, allowing for a breeding program based on plant genotype rather
than only phenotypic.
Genomics is a technique that uses molecular characterization and whole
genome cloning to understand the structure, function, and evolution of genes
in order to answer all fundamental biological issues. It involves combining
biology, engineering, bioinformatics, and statistics to solve the sequence of
a complicated genome and then mining the sequence data in silico to extract
biological insights. Fine-scale genetic mapping and efforts to discover the
whole DNA sequence of organisms are both parts of this field. Although
the sequence of DNA is important in genomics, it is only the beginning of
a large-scale genome investigation. The placement/sequence of bases in a
DNA strand is known as the genome/DNA sequence. The life cycle of an
organism, its developmental program, disease resistance or susceptibility,
and how similar various organisms are all revealed by genome sequence
information. Genomes are chosen for sequencing based on a variety of
factors, including genome size, cost, and relevance to human–animal disease
transmission and agriculture, among others.
Figure 1.6: Molecular markers.
Source: https://link.springer.com/chapter/10.1007/978-94-017-9996-6_2
1.8 MARKERS
The first step in molecular marker (Figure 1.6) research is the isolation of
DNA. Fresh, lyophilized, preserved, or dead material can all be used to
extract DNA; however, fresh material is best for extracting high-quality
DNA. At the end of each DNA isolation procedure, there are three possible
outcomes: (i) There is no DNA; (ii) DNA has been degraded; and (iii)
DNA appears as whitish thin threads and that means good-quality DNA or
brownish threads (DNA oxidized by pollutants such phenolic chemicals).
The most commonly employed hybridization-based DNA marker is RFLP.
RFLP markers were originally utilized in 1975 to detect DNA polymorphisms
for genetic mapping of adenovirus serotypes with temperature-sensitive
mutations. These markers were later employed for human genome mapping
and, more recently, plant genomics. Restriction enzymes can be used to cut
genomic DNA and identify RFLPs. When the DNA is digested, each of
these enzymes recognizes a distinct recognition sequence in the genome,
which is often palindromic and results in restriction fragments of a specific
length. Changes in these sequences, such as point mutations, insertions, and
deletions, result in DNA fragments of various sizes and molecular weights.
Agarose gel electrophoresis is used to separate these fragments based on
their size, and Southern blots with specific probes are used to analyze them.
The co-dominant nature of RFLP markers and their great repeatability are
their key advantages. However, RFLP analysis has various drawbacks,
including the need for relatively high quality and quantity of DNA, the need
for probe libraries, the inability to automate the process, the fact that it is
arduous and time-consuming, and the need for radioactively labeled probes.
RAPD markers are made by using PCR on random DNA segments with
single, often 10-mer primers of any nucleotide sequence. The primers attach
to complementary sample DNA sequences, and a stretch of DNA is amplified
when the primers bind to the sample DNA in close proximity for effective
PCR. Gel electrophoresis is used to visualize the DNA amplification results.
No previous information of the genome sequence is mandatory because
the primers are chosen at random. The genome is supposed to be sampled
at random, and this approach is particularly beneficial when testing loci
throughout a full genome. The technical simplicity of RAPD markers, as
well as their independence from any preceding DNA sequence information,
are two of its biggest advantages. While the polymorphisms are simply
recognized as the presence or lack of a band of a specific molecular weight,
there is no information on heterozygosis, i.e., dominant inheritance, and
RAPDs have some repeatability issues.
RFLP and RAPD methodologies are combined in the AFLP methodology.
It is based on restriction fragment amplification using selective PCR.
After digesting genomic DNA, oligonucleotide adapters or specified
short oligonucleotide sequences are ligated to both ends of the restriction
fragments. Second, the fragments are amplified selectively, with the adapter
and restriction site sequences serving as primer binding sites in future PCR
operations. Because the ends of the primers extend 1–4 bp into restriction
fragments, only those fragments whose ends are fully complementary to the
ends of the selective primers are amplified. Finally, gel electrophoresis is used
to separate the amplified fragments, which are then seen by autoradiography,
silver staining or fluorescence. In comparison to RFLPs, AFLP technology
allows for the detection of higher amounts of polymorphisms. AFLPs are

also more reproducible than RAPDs. However, AFLP is a difficult technique
to master because it necessitates the use of polyacrylamide gels for detection,
as well as higher equipment investments. Because diploid homozygous
candidates create a more intense peak than heterozygous individuals for
a single character, scoring AFLP polymorphisms as co-dominant marker
locus is achievable in some situations. It will take specialized algorithms and
software packages to detect such markers and score them as co-dominant.
The technique of establishing the precise order of nucleotides within a
DNA molecule is known as DNA sequencing. It refers to any technology
that is used to determine the order of four bases in a strand of DNA: adenine,
guanine, cytosine, and thymine. Rapid DNA sequencing tools have sped
up biological and medical research tremendously. Modern DNA sequencing
technology has aided in the sequencing of entire genome sequences because
of the high speed of sequencing(Dabney & Meyer, 2012). The primer attaches
to the end of the sequenced DNA. The primer-coated DNA is separated into
four reaction mixes. All four dNTPs and one of the four dideoxy analogues
or ddNTPs are present in each reaction combination. Because the hydroxyl
in the dideoxy sugar has been replaced by a hydrogen moiety, the chain
cannot be extended further. As a result, the dideoxy analogue serves as a
unique chain-termination reagent. Depending on the amount of ddNTP
in the mixture, variable-length fragments are generated. Using a tagged
radioactive or fluorescent primer is also known.
1.9 PYROSEQUENCING
Pyrosequencing (Figure 1.7) detects individual nucleotides added to nascent
DNA by using luciferase to emit light, and the combined data is utilized
to generate sequence readouts. Mostafa Ronaghi and Pal Nyren invented
the approach in 1996 at the Royal Institute of Technology in Stockholm
(Mikeska, Felsberg, Hewitt, & Dobrovic, 2011). It varies from Sanger
sequencing in that it uses pyrophosphate on the nucleotide base rather
than chain termination with dideoxynucleotides to detect pyrophosphate
release. The sequencing in pyrosequencing is done by extending a primed
template with polymerase. At each cycle, single nucleotides are added. The
integration of the nucleotide supplied to the polymerase reaction with the
nucleotide on the template creates a luciferase-based light reaction. After
that, the reaction chamber is cleansed, and the cycle is repeated. Functional
genomics is a branch of genomics that studies the roles and interactions of
genes and proteins. Its goal is to learn how the genome works at different
stages of development and in diverse environments. Functional genomics
focuses on gene transcription, translation, and protein–protein interactions,
i.e., it uses high-throughput approaches rather than a more traditional 'gene-
by-gene' approach to answer questions regarding the function of DNA at the
level of genes, RNA transcripts, and protein products.
Figure 1.7: Pyrosequencing.
Source: https://www.researchgate.net/publication/306030603_Current_mo-
lecular_methods_for_the_detection_of_hepatitis_B_virus_quasispecies/
figures?lo=1
The use of antisense RNA technology to limit gene expression is a potent
technique. Synthetically manufactured complementary molecules attach to
messenger RNA (mRNA) in this method, effectively preventing the last step
of protein production. An antisense nucleic acid sequence base couples with
its matching sense RNA strand and stops it from being translated into a
protein, according to the theory. The original sequence of the DNA or RNA
molecule is referred to as sense.’ The complementary sequence of DNA or
RNA molecules is referred to as ‘antisense.’
Figure 1.8: Small interfering RNAs.
Source: https://www.researchgate.net/publication/333048593_Oncogenic_Sig-
naling_in_Tumorigenesis_and_Applications_of_siRNA_Nanotherapeutics_in_
Breast_Cancer/figures?lo=1
Small interfering RNAs (siRNAs) (Figure 1.8) and microRNAs
(miRNAs) are small RNAs that are produced by processing longer double-
stranded RNA (dsRNA). RNase III, a member of the RNase III family of
dsRNA-specific ribonucleases, cleaves dsRNA in an ATP-dependent manner
(Kesharwani, Gajbhiye, & Jain, 2012). Dicer enzymes are essential for the
production of these two RNAi effectors. Exportin-5 transports the precursor
miRNA (pre-miRNA) to the cytoplasm, where it is cleaved into miRNA
duplexes by Dicer, a dsRNA-specific ribonuclease. The mature single-
stranded miRNA is integrated into an RNA-induced silencing complex
when the duplexes’ strands are separated.
A DNA microarray is also known as a DNA chip, genomic chip, or
biochip is a solid-surface collection of tiny DNA patches. Each DNA patch
on the solid surface comprises probe picomoles, which are picomoles of a
specific DNA sequence. Southern blotting and hybridization, in which target
DNA is bonded to a substrate and then probed with a known DNA sequence,
gave rise to microarray technology. The essential premise of DNA microarray
is a hybridization between two DNA strands, which takes advantage of
the ability of single strands of DNA to establish hydrogen bonds between
complementary base pairs. To count the relative abundance of nucleic acid

sequences, hybridization of the probe to the target is commonly identified and
quantified by detecting fluorophore, silver, or chemiluminescence-labeled
targets. A DNA microarray can be used to perceive SNPs by measuring
changes in expression levels. Thousands of genes are simultaneously
tracked in gene expression profiling tests to examine the impact of various
therapies. By comparing gene expression in infected cells or tissues to that
in uninfected cells or tissues, microarray-based gene expression profiling
can be utilized to recognize genes whose expression varies in response to
pathogens of other organisms. By comparing genome content in different
cells or closely related organisms, a DNA microarray may aid in comparing
different genomes.
1.10 PLANT BREEDING

Molecular plant breeding (Figure 1.9) strives to increase crop variety in
terms of yield, quality, and resistance by utilizing the most recent advances
in genetics and genomics. With the use of genomics techniques, we are
learning more about the relationship between genotype and phenotype.
The identification of genetic markers linked with the trait of interest is
one of the most important uses of genomics directly related to breeding.
Molecular characterization is vital for unearthing species’ histories, such as
their evolution from wild ancestors, and classifying them into appropriate
groups based on genetic diversity, distinctiveness, and population structure.
This is especially crucial when morphological markers have failed to
provide correct results or the results have been deceptive. For example,
morphological features have classed the rice lines Azucena and PR 304 as
indices, despite the fact that they behave like japonicas in crossing tests.
When molecular markers are used to analyze these samples, it is evident that
they are japonicas (Yang, Su, Wu, Wang, & Hu, 2011).
Quantitative variation is regulated by multiple QTL, each having
a modest effect, in the bulk of traits of interest. In diverse habitats and
seasons, minor QTL have an uneven QTL effect. Even if the effect of these
minor QTL is consistent, MABC introgression into the desired genotype
becomes incredibly challenging because more progenies are needed to
select acceptable lines. MARS can be used to pyramid superior alleles at
several loci/QTL in a single genotype in such instances. MARS is based on
the discovery of trait-associated markers and the estimate of their impact.
This method entails a series of marker-based selection cycles, which
include (i) identifying F2 progenies with favorable alleles for most QTL;
(ii) recombination of the selected progenies with the selfed ones; and (iii)
repeating these two cycles (Swamy, Vikram, Dixit, Ahmed, & Kumar, 2011).
When prior QTL information is known, MARS is used more frequently, and
the response reduces as knowledge of the several minor QTLs associated with
the characteristic of interest declines. Genomic advances have the potential
to accelerate the development of crops with promising agronomic features.
Agriculture genomics is the use of genetics in agriculture to increase crop
and livestock production productivity and sustainability.
Figure 1.9: Molecular plant breeding.
Source: https://www.researchgate.net/publication/346580221_Conventional_
Breeding_Molecular_Breeding_and_Speed_Breeding_Brave_Approaches_to_
Revamp_the_Production_of_Cereal_Crops/figures?lo=1
There has been a great increase in genomic resources available,

including expressed sequence tags (ESTs), BAC end sequence, genetic
sequence polymorphisms, gene expression profiling, whole-genome (re)
sequencing, and genome-wide association studies, thanks to the combination
of traditional and high-throughput sequencing platforms. With the advent of
genomic sequencing and the development of bioinformatics tools, we are
moving away from single gene studies and toward whole-genome analysis,
which provides a more comprehensive understanding of how all genes
interact.
Almost every species-specific genome can be read for a reasonable
price, opening up a world of possibilities for targeted crop breeding. In
addition, genomics is playing an increasingly important role in biodiversity
conservation. Advanced genomics aids in the identification of the genome
segments that are responsible for adaptability. It can also increase our grasp
of microevolution by better comprehending natural selection, mutation, and
recombination. Understanding the structure, organization, and dynamics of
genomes in plant species can reveal how genes have been altered to respond
to environmental restrictions through natural and artificial selection, as well
as the potential for manipulating them for crop development. In agriculture,
traditional breeding relies solely on phenotypic selection. Comparative
genomics approaches were successful for discovering homologues/
orthologues or cloning species-specific genes utilizing sequence conservation
from model plant systems before genomic sequence for model plants
became available. RNA transcription, protein modification, and calcium
signaling were among the functional categories assigned to genes encoding
MRPs. In Arabidopsis and soybean, MRPs were discovered to be primarily
responsible for drought and salinity stress. It can be challenging to predict
gene function purely based on similarity to other genes.
In addition to generating reference genomes, high-throughput sequencing
technology has made it possible to resequence genomes from the same
species but different accessions in order to detect genomic diversity. Large-
scale marker segregation data on mapping populations have been generated
using genotyping technologies, resulting in detailed genetic maps. We can
use the genome sequence to find genome-wide molecular markers such
as functional markers, candidate genes, and breeding prediction markers.
Duckweeds are promising plants for removing pollutants from wastewater
and digesting them into renewable biofuel. Varied ecotypes of the same
duckweed species have been found to have different biochemical and
physiological features.
CHAPTER 2
ADVANCES IN PLANT RESEARCH
CONTENTS
1.1 Introduction.......................................................................................... 6
2.1 INTRODUCTION
In the modern molecular breeding of crops, plant genetic engineering has
become one of the most essential molecular techniques. Significant progress
has been attained in the development of novel and efficient transformation
methods in plants over the previous decade(Ghosh et al., 2018). Despite the
availability of a number of DNA delivery techniques, both Agrobacterium-
and biolistic-mediated transformation remain the most popular. Particularly
impressive progress has been made in Agrobacterium-mediated
transformation of cereals and other resistant dicot species. Other transgenic-
enabling technologies, such as marker-free transgenics, gene targeting, and
chromosomal engineering, have evolved in the meantime. Although the
transformation of some plant species or elite germplasm remains a challenge,
further progress in transformation technology is expected because the
mechanisms governing regeneration and transformation processes are now
better understood and are being applied in designing better transformation
methods enabling technologies. Advances in plant biotechnology are already
aiding developing countries and should continue to do so in the future. Cotton
that is insect-resistant and contains a natural pesticide protein from Bacillus
thuringiensis (Bt cotton) is giving increased yields, lower insecticide costs,
and less health hazards to millions of farmers. Many additional valuable
plant biotechnology products that can benefit farmers and consumers are in
the research and development pipelines of developing-country institutions,
and should be available to farmers in the near future.
At all levels of organization, from single to large multicellular organisms,
biological systems are dynamic in space and time. Understanding the
mechanisms of life requires being able to visualize and measure how
biological processes develop. Imaging tools are continually being created
across the complete spectrum of biological organization, revolutionizing
how we observe the inner workings of cells, tissues, organs, and whole
organisms. Many improvements in imaging techniques were first developed
in animal systems, with numerous benefits to the area of plant imaging.
Plants, on the other hand, differ from animals in a number of ways: their
development is normally slower, their cells do not migrate, and their cell
walls, plastids, and vacuoles present unique imaging issues. As a result,
plant-optimized methodologies have been developed to enable functional
imaging of plant processes at various scales, allowing researchers to gain a
better understanding of how plants work as multicellular animals.
Advances in Plant Research 31
2.2 IMAGING TECHNOLOGY

The evolution of imaging technology (Figure 2.1) requires the development
and use of novel microscopy methods. Light sheet imaging of tissues
and organs, as well as two-photon microscopy enabling long-term three-
dimensional and deep-tissue imaging, are examples of exceptional
breakthroughs(Lu, Dao, Liu, He, & Shang, 2020). Other key topics that
have been discussed elsewhere include super-resolution and single-particle
imaging, as well as artificial intelligence–based denoizing.
Figure 2.1: Imaging technology.
Source: https://medium.com/remote-sensing-in-agriculture/hyperspectral-im-
aging-in-agriculture-befa83cafaa7
Quantification of cell characteristics in time-resolved datasets that can
be very large is at the cutting edge of functional plant imaging. Their method
uses neural networks to evaluate images captured by a light sheet microscope,
revealing that during the first two rounds of lateral root formation, cells
integrate growth and division to accurately partition their volume upon
division. In many species, including human brains, two-photon imaging
is one of the most potent approaches for whole organ and deep-tissue
cellular imaging. Laser cell ablation for two-photon imaging employing a
multiphoton laser is also described as a tool for studying individual cell
functions and resolving cell-to-cell communications in deep tissues. Vacuole
dynamics are controlled by several genetic pathways, and this dynamic
behavior is crucial for their directional migration from the apical to the basal
region of the zygote, according to genetic and pharmacological dissection
using quantitative two-photon microscopy.
Users investigating plant development and physiological responses at
the cellular level benefit greatly from the invention and implementation of
innovative sensors, reporters, and probes. Until now, genetically encoded
sensors and indications have served as effective molecular tools. Oxygen
sensors are divided into two types: direct and indirect. Direct sensors bind
oxygen, whereas indirect sensors require additional components. Internal
oxygen concentrations are not in balance, resulting in strong O2 gradients
in plant tissues. Oxygen sensors are thus extremely useful for studying
O2 responses in a variety of physiological processes and throughout plant
development. A subset of root meristem cells was discovered to have a
rapid increase in cytosolic calcium levels among cell populations. When
investigating plant development, seeing the cell cycle of individual cells
in plant tissues has been a major challenge. While various histochemical
techniques have traditionally allowed for the recording of cell-cycle status
in fixed tissues, new genetically encoded reporters such as Cytrap and Plant
Cell Cycle Indicator now allow for cell cycle progression to be tracked in
living plant tissues such as root and shoot meristems(Yokoyama, Hirakawa,
Hayashi, Sakamoto, & Matsunaga, 2016)we focused on the proliferating
cell nuclear antigen (PCNA.
Chemistry-enabled imaging is another promising area of research, with
innovative and widely applicable fluorescent compounds being produced at
the intersection of biology and chemistry. N-aryl pyrido cyanine (N-aryl-PC)
derivatives, also known as the Kakshine series, are super, cell-permeable

DNA staining dyes that are useful for two-photon, super-resolution, and
time-gated imaging of living cells. Chemistry-enabled probes utilizing
fluorescent chemicals, especially in plant cells, have challenges with precise
labeling and cell permeability when compared to genetically encoded
probes using fluorescent proteins. Fluorescent substances, on the other hand,
may be able to overcome issues such as photostability and the availability
of excitation wavelengths for fluorescent molecules. The development of
chemistry-enabled probes will allow for novel plant imaging methodologies.
Plant biotechnology is now at the forefront of fields such as alternative
energy, which includes biogas production, bioremediation, which involves
the use of natural products to treat human diseases, sustainable agriculture,
which includes organic farming practices, and genetic engineering of crop
plants to make them more productive and effective in dealing with biotic
and abiotic stresses. Biotechnology’s major tool set includes genomics,
proteomics, metabolomics, and systems biology, among other molecular
biology techniques. Its goal is to create a cost-effective way to produce
specially designed plants that can be cultivated in a safe environment and
used in agricultural, medical, and industrial applications.
2.3 MICROBIAL INTERACTIONS

Microbial interactions with plants (Figure 2.2) have both good and
detrimental effects, and they play an important part in ecosystem processes.
Plant diseases are caused by negative interactions between microorganisms
(bacteria and fungus), which pose a global danger to agriculture.
Positive interactions, on the other hand, have positive consequences in
pharmacological, biotechnological, and agricultural applications. Research
has recently concentrated on understanding the complicated molecular
mechanisms of host-pathogen interactions in order to produce microbe-
based fertilizers (bioprotectants), phyto sanitizers, and rhizosphere microbe
management for increased nutrient absorption and disease control. The
current research is aimed at elucidating the mechanisms of host-pathogen
interaction in order to promote sustainable agriculture.
Figure 2.2: Microbial interactions with plants.
Source: https://www.cell.com/trends/plant-science/fulltext/S1360-
1385(20)30272-7
Pesticide use that is both consistent and judicious results in insect
resistance, the elimination of beneficial species, and an increase in residual
problems, posing a hazard to human health and its ecological partners in the
living biome. The need of the future is to develop an environmentally friendly
approach to combating insect pests that can regulate pest populations by
exploring naturally occurring botanicals such as plant extracts, insecticidal
plants, and plant essential oils that can be used as repellents, antifeedants,
insecticides, molluscicides, and other pest control agents. The findings of
this study overwhelmingly validated the action of a significant number of
plants. As a result, these observations will be valuable in the collecting of
plants for laboratory and field research studies, which could eventually lead
to the commercialization of plant biopesticides.
Figure 2.3: Plant growth-promoting bacteria.
Source: https://microbewiki.kenyon.edu/images/0/06/Nrmico1129-f1.gif
2.4 PLANT GROWTH- PROMOTING BACTERIA

Plant growth-promoting bacteria (PGPB) (Figure 2.3) and plant symbionts
have been used to improve plant performance for centuries. However,
inoculation with microorganisms was not linked to increased plant growth.
Rhizobia inoculants have been economically manufactured for almost
120 years, since the discovery of rhizobia in 1886, primarily in developed
countries (Furseth, Conley, & Ané, 2012). Inoculant technology, particularly
with PGPB, has minimal or little impact on family farm productivity in the
vast majority of developing nations because inoculants are not used, are
of poor quality, or are handmade. Surprisingly, and most likely as a result
of the potential for small companies to produce inoculants at a lower cost
than expensive chemical fertilizers and pesticides, many practical studies
of a variety of crops were conducted in developing countries, such as the
Indian subcontinent, Vietnam, and on cereals and legumes in Latin America,
primarily in Argentina and Mexico, as well as in Africa.
For most PGPB species, the bacteria population rapidly drops once
suspensions of bacteria are introduced into the soil without a suitable carrier.
This characteristic, when combined with low bacterial biomass production,
difficulty maintaining movement in the rhizosphere, and the physiological
phase of the bacteria at application time, can hinder the rhizosphere from
building up a large enough PGPB population. The natural variability of the
soil is a major problem, as introduced bacteria frequently fail to find an open
niche in the soil. These unprotected, inoculated bacteria must compete with
the local microflora, which is frequently more suited, and survive predation
by soil microfauna. As a result, one of the important functions of inoculant
formulation is to offer more favorable niches well as physical protection
for a long time, in order to inhibit the spread of introduced bacteria. Field-
scale inoculants must be designed to give a consistent source of bacteria
that survives in the soil and becomes available to crops when needed. Many
inoculants do not accomplish this, despite the fact that it is the primary goal
of inoculant development. When it comes to inoculating plants with PGPB
(including rhizobia), the first goal is to locate the optimal bacteria strain
or microbial consortia for the desired effect on the target crop. The next
stage is to develop a customized inoculant formulation for the target crop as
well as a feasible application method that takes into account the producers’
restrictions.
In practice, the inoculant’s potential success is determined by the
formulation and application method used. Many beneficial strains have
been identified in the scientific literature but have yet to be commercialized,
possibly due to incorrect formulation. The majority of the research focused
on specific genera, such as Rhizobia and Azospirillum, field performance
of several PGPBs, availability of diverse PGPBs and their modes of action,
fertilizer reduction through inoculants, and possible marketing. Despite
the fact that some evaluations covered formulations and practical elements
of inoculants briefly, none of these recent reviews focused on that area.
Bacterial isolates are particular bacterial strains like PGPB or rhizobia that
can boost plant development after inoculation. The abiotic substrate like
solid, liquid, or gel employed in the formulation process is referred to as the

“carrier.”
Formulation refers to the process of combining the carrier with the
bacterial strain in a laboratory or industrial setting. The term “inoculant”
refers to the finished result of a formulation that includes a carrier, bacterial
agent, or a group of microorganisms. The practice of measuring defined
quality characteristics of the inoculant is referred to as “quality control.”
“Quality assurance” is a broad assessment of whether quality control
procedures and strategies are accomplishing their goals. The amount of
viable and effective cells capable of nodulating plants and fixing nitrogen of
the intended strain given by the inoculant at point-of-sale is defined as the
quality of the inoculant in legumes. Similar characteristics apply to PGPB,
with a greater focus on contaminant-free inoculants.
Plant biology in the twenty-first century is and will remain substantially
different from that of the twentieth century. The use of genomics approaches
to uncover the genetic blueprints for plant species, as well as resolving
genome differences in thousands of people at the population level, has been
a driving force behind this. Since the first plant genome sequence, that of
Arabidopsis thaliana, was published in 2000, genomics technology has
advanced significantly(Platt et al., 2010). Researchers in plant genomics
have adopted new algorithms, tools, and methodologies to generate
genome, transcriptome, and epigenome datasets for model and crop species,
allowing for deep conclusions into plant biology. The capacity to create
de novo transcriptome assemblies offers another way to get around these
stubborn species' complicated genomes and into their gene space. The field
of genomics is being propelled forward by technological advancements in
sequencing platforms; nevertheless, software and algorithm development
have lagged behind lower sequencing costs, increased throughput, and
higher quality. Sequencing platforms are expected to enhance the length
and quality of their output, as well as the complementing algorithms and
bioinformatics software required to manage huge, repetitive genomes. Our
understanding of plant biology will continue to increase exponentially in
the future.
2.5 GENETIC CODE

The genetic code (Figure 2.4) is the foundation of all biological life. As a
result, access to the core DNA sequence, i.e., the genome, and how genes
are encoded within it has become an important resource in biology. Despite
the fact that plant genome sequencing lags behind that of microbial and
mammalian systems, genomics and the associated data are widely used
in plant science sub-disciplines such as agronomy, biochemistry, forestry,
genetics, horticulture, pathology, and systematics. In addition to de novo
genome sequencing, sequencing technologies and associated bioinformatic
and computational processes enable the determination of the transcriptome
and epigenome or modified DNA and chromatin state, as well as genome
such as the complement of exons and regulatory regions.
Figure 2.4: Genetic code.
Source: https://www.genome.gov/sites/default/files/tg/en/illustration/genetic_
code.jpg
Challenges in genomics, particularly for plants, are presented in order

to promote awareness of the field's current limits among the larger plant
community. To familiarise readers with these resources, new computational
methodologies for addressing the bulk of sequencing data sets are explored.
The introduction of automated sequencing methods that combined
dideoxy chain termination with fluorescent molecules, often known as
Sanger sequencing, in the early 1990s signaled the beginning of genomics
(Loit et al., n.d.). The first large-scale gene discovery attempt by sequencing,
i.e., expressed sequence tags (ESTs), was made possible by this technology.
The finding of genes from discrete tissues of interest was made possible
by single-end sequencing of cDNA clones. Plant biologists accepted
this strategy, which included sequencing ESTs from the model species
Arabidopsis thaliana, despite its initial controversy. The National Center for
Biotechnology database of ESTs or dbEST now has sequences for 733 plant
species, demonstrating the interest in and utility of single-pass sequences for
transcribed genes in plants(Sayers et al., 2011). The bacterium Haemophilus
influenzae had the first de novo sequenced genome of a free-living
organism. This ground-breaking achievement was made possible by Sanger-
based sequencing technology, which showed that whole-genome shotgun
sequencing or WGS, in which the genome was randomly fragmented, cloned
into a plasmid vector, paired-end sequenced, and the reads were assembled
using computational algorithms, was possible. This was shortly followed by
a second bacterial WGS effort using Mycobacterium genitalium, proving
that this method could be replicated. Although WGS was successful for
small microorganisms, it was not possible to apply this approach to larger
eukaryotes due to assembly issues. Thus, in the 1990s, early eukaryotic
genome WGS studies required the fragmentation of the genome into huge
portions such as cosmids, bacterial artificial chromosomes (BAC), and yeast
artificial chromosomes (YAC), which were then shotgun sequenced per
clone (Balloux et al., 2018).
2.6 PESTS AND DISEASES

Plants are constantly exposed to biotic challenges such as pests and diseases,
as well as abiotic stresses such as intense light, UV radiation, drought, salt,
and extremely high or low temperatures. Surprisingly, earlier exposure to
most stimuli makes plants more tolerant of later exposures, a process known
as acclimatization. The memory of most stresses is linked to epigenetic
modifications, according to research conducted over the previous two
decades. Heat stress induces cell injury and death by damaging membrane
proteins, denaturing and inactivating different enzymes, and accumulating
reactive oxygen species. Thermosensors are installed in plants to detect
particular changes and trigger protection mechanisms. Phytochrome and
calcium signaling are important in detecting abrupt temperature changes
and activating signaling cascades that lead to the synthesis of heat shock
proteins (HSPs), which keep protein unfolding under control. Heat shock
factors (HSFs) are transcription factors that detect thermosensor activity and
cause HSP production. HSF epigenetic changes are thought to be a crucial
component of thermal tolerance acquisition (TAT). Despite breakthroughs
in understanding the mechanism of thermomemory development, it is
unknown if plants have systemic activated thermal protection, such as that
seen in pathogen infection in the form of systemic acquired resistance (SAR).
Bioreactors are devices that can maintain a biologically active environment
while conducting aerobic or anaerobic biochemical processes. Bioreactors
are a good alternative to traditional plant tissue and cell culture (PTCC)
methods because of their stability, operating ease, better nutrient uptake
capacity, time and cost-effectiveness, and significant amounts of biomass
output. Bioreactors are used in a variety of plant research applications and
have evolved over time. Such advancements in technology have resulted in
outstanding breakthroughs in the field of PTCC.
2.7 SENSITIVITY
Plant sensitivity to mechanical stress has long been thought to be an artefact
of plant hardening in harsh settings, a curiosity of useful plants adapted
for insectivory, or an avoidance of grazing herbivores. Wind, rain, hail, and
animal movements are examples of mechanical stress vectors seen in nature.
Pruning, pinching, and clipping are all physical injuries to plants used in
production agricultural and landscape operations. Air turbulence created
by urban high-rise structures permanently entrains trees and shrubs to the
growth behaviors of natural plants found on seacoasts and mountain slopes.
Wind as a powerful element restricting plant development has taken a long
time to gain acceptance. Because wind and precipitation are not constantly
present and because numerous environmental stress variables mix with
the wind in the outside environment, it is easy to ignore the mechanical
impact of wind and precipitation on plant structure and development habits.
Mechanical stress is frequently masked or negated by the effects of other
environmental stress factors on plants. Airborne sea salt, desiccation, and
evaporative chilling are all natural causes that can cause distress. It is only
possible to separate the effects of mechanical stress per se from those of
other environmental stresses such as heat, cold, drought, flooding, and
mineral deficiencies if controlled mechanical stresses like shaking, handling,
flexing are applied to plants growing in the wind-protected confines of a
greenhouse or growth chamber. Plants have a general impact of delaying
internode elongation and inhibiting leaf development, which shrinks plants
in size and mass depending on the stress dose. Internode compression and
lateral enlargement of stems are the hallmarks of thigmotropism. Seismic
stress causes plant responses that are similar, but not always identical, to
thermal stress.
The plants grew substantially more slowly than undamaged controls
when the branch ends of potted chrysanthemums were manually flexed for
a few seconds each day. The flowers of the shorter, stressed plants were
not smaller, but they used far less water than the taller controls, which had
a larger surface area for transpiration. Laboratory shakers can be fitted
with platforms to handle numerous plants to standardize seismic treatment
applications for research, but growers still can’t afford to manually load
and unload a restricted number of platform shakers. In the mid-1970s,
Purdue University constructed a series of automated mechanical oscillatory
shaking (AMOS) devices to serve as a prototype for shaking devices with
commercial potential(Latimer, 1998).
Early morning was the most efficient period for shaking, according to
research on chrysanthemum height control using AMOS, and isomorphism
obeys the law of reciprocity. Plants of the ‘Alaska’ pea (Pisum sativum
L.) was shrunk by daily shaking on a gyratory platform shaker, which also
reduced the number of pods generated and the quantity of seeds per pod
Shaken pea plants’ seed output was only half that of undisturbed controls
as a result of the combined effect. Mechanical stress has reduced yield in
every crop species studied thus far, either due to a delay in flowering or a
reduction in the size, number, or mass of harvestable components. It was
found that striking the stem tips or shaking the entire shoot of potted potato
plants reduced the size and mass of tubers formed during treatment, but
not the number. Mechanical stress tests with potatoes indicate that shoots,
which receive the major mechanical stress stimuli, can transfer those signals
to below-ground plant components. The fact that localized rubbing of stem
tips has the same growth-retarding effects on potato tubers as more general
shaking treatments applied to the entire shoot calls into question any claim
that stress effects on roots and tubers are caused solely by physical forces
transmitted from shoots to below-ground plant parts. Plant molecular
farming or PMF is a novel field of plant biotechnology in which plants are
genetically modified to produce vast amounts of recombinant medicinal
and industrial proteins. PMF is still struggling to obtain social recognition
as an emerging subset of the biopharmaceutical business, compared to the
well-established production methods that create these high-value proteins in
microbial, yeast, or mammalian expression systems.
2.8 STRESSORS
Plant growth and development are hampered by abiotic and biotic stressors,
which have a negative impact on crop output. Plants have evolved stress-
specific adaptations as well as simultaneous responses to a combination
of abiotic and pathogen stressors. Stress-induced adaptive responses are
dependent on the activation of molecular signaling pathways and intracellular
networks via changing the expression, abundance, and/or post-translational
modification (PTM) of proteins that are predominantly connected with
defense mechanisms. Advanced quantitative proteomic techniques have
improved total proteome and sub-proteome coverage from small amounts
of starting material, as well as characterized PTMs and protein–protein
interactions at the cellular level, providing thorough evidence on organ and
tissue specific regulatory mechanisms responding to a variety of individual
stresses or stress combinations during the plant life cycle. We can focus on
tissue-specific signaling networks that are localised to various organelles
and are involved in stress-related physiological plasticity and adaptive
mechanisms like photosynthetic efficiency, symbiotic nitrogen fixation,
plant growth, tolerance, and common responses to environmental stresses.
We also highlight the present challenges and limitations of proteomics
techniques and data interpretation for non-model organisms, as well as the
advancement of proteomics with main crop species.
To accomplish substantial successes in genomics-driven breeding of key
crops for high productivity and stress tolerance, it is critical to understand all
levels that regulate adaptation mechanisms and the resilience of crop plants
in the context of climate change. Agricultural production systems have
already been impacted by a new pattern of often occurring extreme weather
events. The development of bioinformatics techniques and analytical
instrumentation, in addition to the growing genomic information available
for both model and non-model plants, has made proteomics an essential
approach for revealing major signaling and biochemical pathways of plant

life cycle, interaction with the environment, and responses to abiotic and
biotic stresses. Quantitative profiling, analysis of dynamic post-translational
modifications or PTMs, subcellular localization and compartmentalization,
protein complexes, signaling pathways, and protein–protein interactions are
all examples of high-throughput proteomic studies.
Plant development and productivity are inevitably influenced by
extreme environmental variables such as drought, heat, salinity, cold, or
pathogen infection, which can delay or induce seed germination, restrict
seedling growth, and diminish crop yields when grown in the field or in
the lab. Proteomics research can help uncover nearly every element of
cellular function in plant stress responses, as well as putative links between
protein abundance and/or alteration and plant stress tolerance. Studies using
model plants like Arabidopsis, and sorghum explained the involvement of
proteomics to understand the molecular mechanisms of plant responses
to stresses and signaling pathways linking changes in protein expression
to cellular metabolic events. Major monocotyledonous cereals and
dicotyledonous legumes like maize, wheat, etc. have been widely used to
study quantitative changes in protein abundance related to climate change
due to improvements in diverse proteomic technology platforms that united
classical two-dimensional electrophoresis and gel-based techniques with
mass spectrometry (MS) based quantitative approaches.
Crop plants are subjected to a complex mix of abiotic and biotic
stressors in the agricultural environment. Evidence shows that simultaneous
incidence of multiple stresses affecting crop growth, yield, and physiological
traits can alert plants to activate intricate metabolic pathways involved in
specific programming of gene expression that uniquely respond to different
combinations of stresses, in addition to studying the effects of various
stresses applied individually under laboratory-controlled conditions.
Transcriptome and proteome analysis of various crop plants subjected to
various stress combinations revealed several different signaling pathways
involved in multiple stress-responding mechanisms, implying a complex
regulatory network orchestrated by hormone signals, transcription factors,
reactive oxygen species (ROS), and osmolyte synthesis.
Fundamentally, crop growth is dependent on the efficient synthesis of
energy and nutritious substances, which is regulated by several organs,
each of which is equipped with its own set of cytosolic proteins, hormones,
and metabolites. Plant cells respond differently to abiotic stressors in
various tissues. Organ-specific proteomics, in combination with subcellular

organelle proteomic studies of developmental mechanisms from leaf to
root, can provide more detailed information about cellular mechanisms
that regulate stress response and signal transduction in various organelles.
By assessing spatial and functional sub-proteomes, tissue-targeted seed
proteomic studies of distinct developmental phases under abiotic challenges
have contributed to enhancing our depth of knowledge about the processes
driving seed development, dormancy, and germination.
Pests and diseases have a negative impact on agricultural output and
quality, as well as resource efficiency. Crop protection measures that prevent
such damage and loss can boost productivity and contribute significantly
to food security. The identification of novel disease agents will be aided by
rapid sequencing of nucleic acids from affected plants. Pest outbreaks can
also be detected through biomarkers of infections or crop damage, such as
volatile compounds. Biosensors linked to information networks will allow
for real-time monitoring and surveillance of crops or stored produce, as well
as early detection of emergent problems and invading species. Although the
rapid expansion of the internet, mobile phones, and other communication
networks will give new opportunities, challenges remain in the transmission
of new technologies and information to resource poor farmers in developing
countries. Identifying the genetic and molecular basis of innate plant
immunity has been a significant step forward in plant biology, with the
potential to uncover new targets for intervention using innovative chemical
or genetic manipulation (GM).
2.9 TRANSGENIC CROPS

There should also be options for selecting more responsive crop genotypes
or developing transgenic crops that respond to specific chemical signals or
molecular patterns that can be used to diagnose specific biotic concerns. The
genome sequencing of important crop species and their wild relatives will
vastly extend the gene pool and diversity of genetic resources available to
plant breeders. It should be possible to uncover genomic areas and genes that
give greater long-lasting, quantitative pathogen resistance. High-throughput
phenotyping and efficient selection of resistance features utilizing within-
gene markers will speed up the breeding cycle. Pyramiding or combining
resistance genes with diverse specificities and modes of action will be easier
in using GM methods, lowering the possibility of virulence directional
selection. Genome analysis of plant pathogens and invertebrate pests is
already revealing new genes, gene families, and mechanisms involved in

host colonization and pathogenicity. Comparative genomics of species
with distinct host ranges, eating patterns, and pathogenic lifestyles can help
researchers find new targets for pest control and produce new antimicrobial
medications.
Knowing the natural ecology of pests and pathogens, such as the factors
that determine host placement and interactions with other organisms, will
help us influence behavior or exploit natural enemies or other antagonists
of pest species. Volatile signals will be more frequently exploited to
modify pest behavior, whether they come from natural plant sources or
are produced in transgenic crops. It may also be feasible to alter microbial
communities that regulate pathogen populations and activity, allowing more
effective biocontrol agents to be retained. New knowledge on pest species
suppression methods will be gained by studying the natural variety and
activity of soil and microbial populations in the zones surrounding roots
and seeds. Because of the complexity and diversity of the soil system,
fully effective interventions are improbable, but progress toward integrated
control regimes combining more resistant crop genotypes with focused
management of natural suppressive processes should be made. Improved
understanding of the variables driving pest and pathogen adaptability and
evolution will be required to use new technology and knowledge to build
more durable resistant crops and sustainable disease and pest management
systems. More focus must be placed on translational research and delivery,
as well as devising tactics that are fit for lower-input production systems.
2.10 PROTEOMICS
Proteomics is becoming increasingly relevant for the study of many
different aspects of plant functioning, thanks to the avalanche of genetic
data and advances in analytical technology. Protein studies are critical for
revealing molecular mechanisms underpinning plant growth, development,
and interactions with the environment since proteins are crucial components
of major signaling and metabolic pathways. The proteome of plants is
extremely complex and dynamic. Although much progress must be made
toward the ultimate goal of characterizing all of the proteins in a proteome,
current technologies have opened the door to a plethora of high-throughput
proteomic research to include quantification, PTM, subcellular localization,
and protein–protein interactions. The focus is on recent advancements in
plant protein functional analysis, which pave the way for comprehensive
integration of transcriptomics, metabolomics, and other large-scale “omics”

into systems biology. Plants are constantly attacked by herbivores and
diseases, and as a result, they have developed both constitutive and induced
defenses over time. Both herbivore-induced factors like elicitors, effectors,
and wounds and plant signaling via phytohormone and plant volatiles in
response to arthropod factors trigger and drive the sophisticated signaling
network for plant defense responses.
Interactions between plant and herbivore-derived elicitors and effectors,
followed by fast activation of sophisticated plant signaling cascades, result
in coordination of defense activities against attacking pests. However,
the molecular mechanisms in the hosts that control the balance between
resistance activation and repression are unknown. Despite the large number
of documented plant responses to herbivores, animal-derived defensive
elicitors are rare. Volicitin, a hydroxy fatty acid-amino acid conjugate (FAC),
was discovered in the oral secretions of the beet armyworm and was the
first fully defined herbivore-derived elicitor. The biological roles of FACs
on plants, as well as FAC variation patterns in Lepidoptera species, have
been extensively researched. FACs injected into wounds during feeding,
for example, are rapidly degraded by lipoxygenases in the octadecanoid
pathway, resulting in the formation of additional active elicitors. Due to their
amphiphilic nature, FAC-type elicitors can cause plasma trans-membrane
potential (Vm) depolarization in plant cells. As a result, detergent-like
potential ion fluxes induced by oral secretions cause Vm depolarization and,
as a result, the opening of voltage-dependent Ca2+ channels to transmit the
signal.
Research has been conducted on herbivore secretions, with some
success in identifying other elicitors and herbivore-associated molecules,
such as caeliferins, glucosidase from the cabbage white butterfly, benzyl
cyanides from Pieris brassicae, disulfonyl fatty acids from the American
bird grasshopper. Inceptin and similar peptides are generated from the
regulatory areas of chloroplastic ATP synthase gamma. These peptides
cause the generation of phytohormones to occur quickly and sequentially,
resulting in volatile emissions. In contrast to caterpillars, however, nothing
is known about sucking arthropod oral elicitors like spider mites and aphids.
The release of aphid elicitors like oligogalacturonides due to cell wall
destruction by gel saliva enzymes has recently been postulated to cause Ca2+
influx. Furthermore, plant responses may be elicited by egg deposition. The
egg or egg-associated components of several insects cause plant defensive
responses, though the reaction chemistry has only been identified in bruchid
beetles: long-chain, -monounsaturated C-22 diols and, mono- and di-
unsaturated C-24 diols, mono- or diesterified with 3-hydroxypropanoic acid.
Similarly, powerful elicitors secreted by herbivorous arthropods upon tarsal
contact with a plant may exist.
Although certain diseases inhibit these mechanisms by interfering with
defense-related communication pathways, evidence of such interference in
herbivores is sparse. Herbivorous arthropods, on the other hand, cause a
complex and interconnected array of molecular and physiological reactions
in plants, whether by defoliation or feeding on specific tissues like phloem
or xylem. These reactions may lower host resistance and even limit
photosynthesis. Suppression of host defenses and phenotypic changes in
host plants are common in a wide range of plant-pest particularly plant-
pathogen interactions, and entail the production of chemicals that affect host
cell processes. With Lepidoptera salivary glands, massive proteome and
transcriptome analyzes were conducted, and some of the major components
of saliva were identified. Helicoverpa zea mandibular glands release
salivary glucose oxidase, an enzyme that acts as an effector suppressing
the host plant’s induced defenses by contributing to the initial oxidative
burst of H2O2 observed in herbivore-damaged leaves. Scientists discovered
a link between host range breadth and GOX activity, with more polyphagous
species exhibiting higher GOX levels than species with a more limited host
range.
In Arabidopsis, it was recently discovered that egg-derived elicitors cause
the inhibition of defenses against chewing herbivores. Salicylic acid (SA)
is involved in this mechanism, as indicated by the lack of gene repression
and increased sensitivity in sid2-1 mutants. Distinct plant responses may be
triggered by herbivore species belonging to different feeding guilds, such
as parenchymal cell content feeders and phloem feeders. SA-responsive
gene transcripts accumulated locally and systemically in Arabidopsis plants
infested by the phloem-feeding silver-leaf whitefly, whereas JA and ethylene
dependent RNAs were suppressed or not altered.
B. tabaci was also reported to interfere with Lima bean plants' indirect
defense against spider mites (Tetranychus urticae) by inhibiting the JA
signaling pathway triggered by the latter. Tetranychus evansi inhibits
the induction of the SA and JA signaling pathways in tomato, which are
important in induced plant defenses. Furthermore, significant variations in
features that lead to resistance or susceptibility to JA-dependent defenses
of a host plant, as well as attributes relevant for induction or repression of

JA responses, have been demonstrated within a single herbivore species,
the spider mite T. urticae. Aphids, like plant diseases, send effectors into
their hosts to control host cell processes, allowing plants to be successfully
infested. Plant disease resistance proteins that detect plant pathogens and
those that confer aphid resistance have a nucleotide binding site domain
and leucine rich repeat (LRR) regions in common (Martin, Bogdanove, &
Sessa, 2003). A functional genomics approach based on common features
of plant pathogen effectors was recently devised for the identification of
potential aphid effector proteins from the aphid species Myzus persicae.
M. persicae has 46 potential secreted proteins, according to data mining of
salivary gland expressed sequence tags (ESTs)(Hogenhout & Bos, 2011).
Mp10, for example, generated chlorosis and mildly induced cell death in
Nicotiana benthamiana, as well as suppressing the oxidative burst induced
by the bacterial PAMP flagellin. Furthermore, two potential effectors namely
Mp10 and Mp42 have been identified as lowering aphid performance using
a medium throughput experiment based on transient overexpression in N.
benthamiana, whereas MpC002 improved aphid performance. Overall,
aphid-secreted salivary proteins have characteristics that are similar to plant
pathogen effectors, suggesting that they could act as aphid effectors by
disrupting host cellular processes.
A nitrile-specifier gut protein found in the larvae of various lepidopteran
species, notably Pieris rapae and P. brassicae, detoxifies the breakdown
products of glucosinolates, which are the principal insect deterrents in
Arabidopsis. Furanocoumarins are degraded by the cytochrome P450
monooxygenase gene superfamily in Papilio butterflies, while pyrrolizidine
alkaloids are degraded by the flavin-dependent monooxygenase system of
the arctiid moth Tyria jacobaeae. Plant susceptibility is caused by nematode
effectors. A nematode-secreted peptide and a plant-regulatory protein
were discovered to interact directly. The induced plant defenses against
herbivores appear to be the result of an integrative "cross-talk" between
signaling molecules such as Ca2+ ions, reactive oxygen species (ROS),
protein kinases, JA, cis-12-oxophytodienoic acid (OPDA), SA, ethylene,
and yet unknown octadecanoid family members. Phytohormones, such as
those mentioned above, play a key part in signal transduction in a variety of
signaling pathways. SA, JA, and ethylene are three phytohormones that are
important in monocot and dicot defense. The SA pathway, which is involved
in both locally expressed basal resistance and systemic acquired resistance
(SAR), has been demonstrated to be activated predominantly in response
to biotrophic diseases or insects that cause little damage, such as phloem-

feeding aphids and spider mites. The JA/ethylene route, on the other hand,
is activated in the presence of necrotrophic infections, wounds, and tissue-
damaging insect feeding.
JA is a signaling substance that regulates induced plant responses to
herbivores and pathogen infection by activating several sets of defense
genes. While herbivore resistance is known to be mediated by JA, pathogen
resistance is mostly mediated by SA in plants. Plants, for example, respond
to piercing-sucking herbivores such as aphids, whiteflies, and spider mites by
up-regulating both SA and JA responses simultaneously. In several species of
plants affected with aphids, mRNAs encoding putative proteins that may be
involved in the synthesis of JA and SA are up-regulated, leading to a variety of
plant defense responses, including aphid-dependent blends of plant volatiles
caused by the feeding of various aphid species. Furthermore, JA and SA are
antagonistic and both need for the induced response in response to herbivore
feeding or pathogen attack. JA and SA have antagonistic interactions, and
JA–SA crosstalk is an outstanding illustration of the intricate regulatory
networks that allow the plant to fine-tune individual responses to distinct
pathogens. Although various studies have suggested that JA and SA
have negative interactions in defensive signaling, this crosstalk is highly
dependent on concentration and timing. In N. attenuata, it was discovered
that ethylene plays a key role in the activation of JA-regulated plant defenses
against herbivores. After herbivore attack, JA-ethylene crosstalk limits local
cell development and growth, allowing more resources to be directed to
induce herbivore defenses. By modifying the sensitivity to a second signal
i.e., Ca2+ signal and its downstream responses, ethylene is required for
the simultaneous induction of JA or other signals. After herbivore injury,
ethylene appears to act as a switch, limiting the production of constitutive
defensive chemicals like nicotine while increasing the production of JA
and volatiles. Ethylene has also been shown to contribute to herbivory-
induced terpenoid biosynthesis in Medicago truncatula by influencing both
early signaling events such as cytoplasmic Ca2+ influx and downstream JA-
dependent terpenoid biosynthesis.
Some of these volatiles have the ability to activate defense genes, which
is likely mediated by well-known signaling pathways such as Ca2+ influx,
protein phosphorylation and dephosphorylation, and ROS activity. GLVs
with an unsaturated carbonyl group have been postulated to trigger defense
by acting as reactive electrophile species, while other GLVs that have been
reported to be biologically active lack this pattern. When mechanically
wounded and stimulated with caterpillar regurgitation, corn seedlings

previously exposed to GLVs or terpenoids from nearby plants produced
much more JA and volatile sesquiterpenes than seedlings not subjected to
GLV. Early signaling steps in the cellular response to stress are mediated
by changes in Vm, and exposure to numerous GLVs altered membrane
potentials in intact leaves. It's tempting to think that the intra-membrane
connection of volatiles with membrane proteins, presumably analogous to
insect odorant-binding proteins, causes changes in transmembrane potentials
and, as a result, gene activity. Except for the gaseous hormone ethylene,
nothing is known about such sensory proteins for plant volatiles. Plants
typically respond differently to structurally identical substances, implying
that plants can respond selectively to distinct chemical molecules or even
compounds that differ solely in their stereochemistry. The low-molecular-
weight, lipophilic nature, along with their wide structural variation and high
vapor pressures at ordinary temperatures of many VOCs account for their
significance as chemical information carriers.
Next-generation sequencing (NGS) is transforming genetics and
revealing new information on genome organization, evolution, and function.
The number of plant genomes being sequenced is increasing. However,
obtaining whole genome sequences in large genome species remains
problematic for the time being, owing to the fact that short reads produced by
NGS platforms are insufficient to deal with repeat-rich DNA, which makes
up a substantial percentage of these genomes. In polyploids, which dominate
the plant kingdom, the problem of sequence redundancy is exacerbated.
Flow-cytometry can be used to reduce the complete nuclear genome to
its individual chromosomes, which can help overcome some of these
challenges. This DNA has proven to be suitable for a variety of applications,
including PCR-based physical mapping, in situ hybridization, DNA array
formation, DNA marker creation, BAC library construction, and positional
cloning. When chromosome sorting and NGS are combined, it opens up
possibilities for studying genome organization at the single chromosomal
level, comparative analysis between related species, and validation of whole
genome assemblies. Apart from the primary goal of lowering the template's
complexity, using a chromosome-based technique allows multiple teams to
work in parallel, each analyzing a distinct chromosome.
CHAPTER 3
GENOMICS IN PLANT RESEARCH
CONTENTS
1.1 Introduction.......................................................................................... 6
3.1 INTRODUCTION
Until recently, plant molecular analysis was frequently limited to single genes.
Recent technological advancements have shifted this paradigm, allowing
for the study of genomic organization, expression, and interaction. Genomic
science is the study of how genes and genetic information are structured
inside the genome, as well as the methods for collecting and interpreting
this data and how this arrangement influences their biological performance
(DellaPenna, 1999). Genomic techniques are pervading every part of plant
biology, and because they rely on DNA-coded information, they enable
multi species molecular investigations. Plant genomics is reversing the old
paradigm, which focused on locating genes behind biological functions, and
instead focused on identifying biological functions behind genes. It also
bridges the gap between phenotype and genotype, allowing researchers to
better understand how a gene in the genetic environment and the genetic
networks with which it interacts can affect its activity.
Figure 3.1: Reterotransposons.
Source: https://en.wikipedia.org/wiki/Retrotransposon#/media/
File:Retrotransposons.png
Plant genomes contain a variety of repetitive sequences as well as
retrovirus-like retrotransposons (Figure 3.1) with lengthy terminal repeats
and other retroelements like long interspersed nuclear elements and short-
interspersed nuclear elements. Retroelement insertions are responsible
Genomics in Plant Research 53
for the substantial size disparity between collinear genome segments in

different plant species, as well as the 50 percent or more variability in overall
genome size among species with big genomes, such as maize (Van Bel et al.,
2012). In plants with smaller genomes, they contribute a smaller fraction of
genome size. When other repetitive sequences are taken into consideration,
the corn genome contains about 70% repetitive sequences and 5% protein
encoding regions. 70-80 percent of flowering plants are thought to be the
result of at least one polyploidization event (H. Tang et al., 2008). Many
economically significant plant species, including corn, wheat, potato, and
oat, are polyploids, meaning they have more than one, and in the case of
wheat, three, homologous genomes inside a single species. A considerable
portion of the rice genome is made up of duplicated sequences. The
Arabidopsis genome is split into 24 duplicated segments, each measuring
more than 100 kb(Platt et al., 2010). Through gene duplication and gene
silencing, ancestral polyploidy leads to the creation of genetic variation. In
plants, genome duplication and subsequent divergence is a major source of
protein diversity.
Figure 3.2: Drosophila melanogaster.
Source: https://www.theguardian.com/science/2017/oct/07/fruit-fly-fascina-
tion-nobel-prizes-genetics
3.2 MODEL ORGANISMS

Drosophila melanogaster (Figure 3.2), Caenorhabditis elegans, and
Saccharomyces cerevisiae are model organisms that provide genetic and
molecular insights into the biology of more complex species. The plant
scientific community has embraced model organisms because the genomes
of most plant species are either too vast or too complicated to be thoroughly
studied. They have common characteristics such as being diploid and
suitable for genetic study, being amenable to genetic transformation, having
a relatively tiny genome and a short growth cycle, having widely available
tools and resources, and being the subject of much research. Although
tissue culture techniques encouraged the use of tobacco and petunia,
rice and Arabidopsis are increasingly employed as model organisms for
monocotyledonous and dicotyledonous plants, respectively. Arabidopsis is a
tiny Cruciferae plant that produces seeds in only 6 weeks after being planted.
It has a short genome of 120 Megabytes and only five chromosomes (Lenoir,
Cournoyer, Warwick, Picard, & Deragon, 1997). For genomic analysis,
whole genome sequence, Expressed Sequence Tags (ESTs) collections,
point mutants, and huge populations mutagenized using insertion elements
or transposons or Agrobacterium T-DNA, there are numerous techniques
available. Agrobacterium tumefaciens and biolistics can be used to genetically
modify Arabidopsis on a wide scale. Saturated genetic and physical maps
are two other techniques accessible for this model plant.
Rice, unlike Arabidopsis, is one of the most important cereals on the
planet. Rice is produced in excess of 500 million tonnes per year and is the
staple food for half of the population. Rice is divided into two subspecies:
japonica is grown primarily in Japan, whereas indica is grown primarily
in China and other Asia-Pacific countries. Rice also has a lot of genetic
maps, physical maps, whole genome sequences, and EST collections from
various tissues and stages of development. It has 12 chromosomes and a
genome of 420 megabytes, and it can be transformed using biolistics and A.
tumefaciens, just like Arabidopsis(Goff et al., 2002). Although some recent
successes have been reported, efficient transposon-tagging systems for
gene knockouts and gene detection have yet to be developed for saturation
mutagenesis in rice.
3.3 MOLECULAR MARKERS

The development of molecular markers has enabled the creation of complete
genetic maps for the majority of economically significant plant species.
They detect genetic variation at the DNA level directly. There is a plethora
of molecular marker systems available, however, describing them is beyond
the scope of this work. A genetic map depicts the ordering of molecular
markers along chromosomes as well as the genetic distances between
adjacent molecular markers, which are usually expressed in centiMorgans
(cM). Many experimental populations have been used to create genetic
maps in plants, but the most common are F2, backcrosses, and recombinant
inbred lines. Recombinant inbred lines provide a better genetic resolution
and practical advantages, but they take longer to create. It only takes a few
months to create a genetic map with a 10 cM resolution once a mapping
population has been established. Genetic maps help us understand how
plant genomes are organised, and once we have them, we can use them
to develop practical applications in plant breeding, such as identifying
Quantitative Trait Loci and Marker Assisted Selection. Plant features
that are economically important, such as yield, plant height, and quality
components, have a continuous dispersal rather than discrete classes and are
classified as quantitative traits. Several loci, each with a tiny effect, govern
these features, and different combinations of alleles at these loci might result
in diverse phenotypes.
The identification of genetic areas linked to the phenotypic expression
of a particular characteristic is referred to as loci analysis. Individuals
possessing chromosomal fragments associated with the expression of a
certain phenotype can be assembled into designer genotypes once the
location of such genomic areas is determined. As a result, the presence of
the molecular marker is always linked to the existence of the desired allele.
Genomic maps are also useful for isolating plant genes, because once the
genetic position of a mutation is determined, positional cloning can be used
to try to isolate it. In addition, genetic maps aid in determining the level of
genome collinearity and duplication between species.
Plants play a significant role in providing a large amount of food.
Plants have also been utilized as model organisms to research transposable
elements in heterochromatin and epigenetic regulation and have been chosen
as model organisms to study transposable elements in heterochromatin and
epigenetic control. Because of its importance, plant biology has been studied
extensively since the beginning of human history. Plant biology research has
advanced to new heights. High-throughput sequencing tools have allowed
scientists to exploit the structure of genetic material at the molecular level,
a process called genomics. Because of the rapid increase in sequenced
genomes of many plant species, plant genomics has recently blossomed and
has become the dominant focus in plant research. Plant genome research has
a tremendous impact on the advancement of economically important plants
as well as plant biology. Plant genetic information is open to the public and
updated on a regular basis, creating a fruitful environment for plant research.
3.4 DNA SEQUENCING TECHNOLOGY

The evolution of DNA sequencing technology (Figure 3.3) has been long
and marked by numerous historical events. Nearly all DNA sequence
generation in the last decade has been restricted to capillary-based, semi-
automated applications of Sanger biochemistry and its variants. Over the
years, the area of DNA sequencing has been resurrected and developed due
to various scientific achievements. Due to a variety of factors, these technical
developments finally encouraged the development of fresh experimental
designs for this sector. Finally, in 2005, next-generation sequencing (NGS)
methods were made public (Yohe & Thyagarajan, 2017). They're referred
to as high throughput sequencing technologies because they parallelize
the sequencing process, producing millions of sequences at once at a
substantially cheaper per-base cost than traditional Sanger sequencing.
DNA polymerase is used in the sequencing-by-synthesis platform to
lengthen multiple DNA strands in parallel. This approach employs modified
deoxynucleoside triphosphates or dNTPs with a terminator that stops further
polymerization, allowing DNA polymerase to add only one base to each
developing DNA copy strand. As a result, as extension progresses, the newly
integrated nucleotide or oligonucleotide can be determined. The sequencing-
by-synthesis (SBS) approach underpins the pyrosequencing platform.
It is dependent on the detection of pyrophosphate generated by DNA
polymerase during nucleotide integration to support a series of enzymatic
events that eventually produce light from the cleavage of oxyluciferin by
luciferase. DNA ligase is used to create sequential ligation of dye-labeled
oligonucleotides in the Sequencing-by-ligation platform.
Figure 3.3: DNA sequencing technology.
Source: https://www.sigmaaldrich.com/IN/en/technical-documents/protocol/
genomics/sequencing/sanger-sequencing
The concealed sequence of the target DNA molecule is subsequently
determined using the sensitivity of these amplified DNA fragments. The
hydrogen ions generated during DNA polymerization are detected by an
ion semiconductor-based non-optical sequencing device. The successive
enzymatic breakdown of fluorescently tagged single DNA molecules,
and the detection and identification of the liberated monomer molecules
according to their sequential order in a microstructured channel is the basis
for single-molecule sequencing. Amplification of DNA fragments is not
required before sequencing with a single-molecule sequencer. Individual
nucleotide sequences are identified by variations in the ion current when
the DNA strand passes through a membrane-inserted protein nanopore, one
base at a time.
Figure 3.4: Exome sequencing.
Source: https://www.researchgate.net/publication/235368577_Application_of_
Whole_Exome_Sequencing_to_Identify_Disease-Causing_Variants_in_Inher-
ited_Human_Diseases/figures?lo=1
3.5 EXOME SEQUENCING

Exome sequencing (Figure 3.4) can be used to explore biodiversity, study
host–pathogen interactions, investigate the natural evolution of crops, test
for genetic marker inheritance, provide large-scale genetic resources for
crop improvement, identify genes, and establish the presence of functional
gene sets that are involved in symbiotic or other co-existential systems.
Furthermore, single-base resolution NGS approaches can give epigenomic
information. For example, a study of the A. thaliana epigenome found
that cytosine methylation was highly associated with the location and
abundance of short RNA targets. Genotyping by sequencing or GBS, a high-

throughput and low-cost method for optimizing genotype populations, is
another application of plant genome sequencing. GBS provides a number of
methods for improving genomic map building, particularly the detection of
single nucleotide polymorphisms or SNPs.
GBS showed that there is a favorable correlation between trait-related
genes and 681,257 SNP markers from 2,815 maize inbred accessions
(Romay et al., 2013). It is undeniable that NGSs have been successful in
plant genome research. However, building computer tools for studying
genomic sequences is difficult. Galaxy project is one of the software systems
that allows researchers to employ analysis tools using web-based interfaces
that contain massive amounts of freely available biological data. Artemis
is another free programme accessible from the Sanger Institute. It has a
genome browser as well as an annotation tool. The Broad Institute's Genome
Sequencing and Analysis Program or GSAP provides various more genome
sequence analysis tools. Furthermore, the significant decrease in the cost of
genome sequencing necessitates the quick creation of large database storage
and administration systems. In reality, to meet this demand, a growing
number of plant genome databases have been created.
Plant genomes from non-model and non-crop species can also reveal
information on genome building and flowering plant evolution. Genomes
from Utricularia gibba and Genlisea aurea, for example, can reveal a lot
about genome size variation. Furthermore, the genome of Spirodela polyrhiza
is equivalent in size to that of Arabidopsis, although it only requires 28%
fewer genes to operate normally (W. Wang et al., 2014). In another case, the
genomes of Selaginella moellendorffii and Amborella trichopoda offer key
understandings regarding the trajectory of plant-specific gene families and
the radiance of flowering plants, giving further insights into flowering plant
evolution.
Individual alleles can be recognized, classified, exploited, and tagged
using genomic knowledge, as well as molecular markers can be promoted
and manipulated to track desired alleles in breeding programs. Many genome
sequencing projects in the field of horticultural crops have been carried out for
these reasons, including the Tomato genome sequencing project, the Potato
genome sequencing consortium, the Papaya genome sequencing project, the
Grape genome sequencing project and, ideally, in the near future, many more
will be released in the public domain for scientific purposes. These studies
used sophisticated sequencing technologies in conjunction with traditional
approaches to fully validate the development of high-quality sequences

and cost-effective design. As a result, by providing important resources for
comparative and functional genomic investigations, these whole-genome
sequencing efforts may have a considerable impact on global food security
and bio-energy progress. If present research continues, applications of
genomic science resources to horticultural plant species could have a
significant impact on worldwide human well-being. An increasing number
of genes in plant species have been annotated using a comparative genomics
technique. Several known stress-responsive transcription factors OR TFs in
Arabidopsis and rice, for example, were utilized to properly predict stress-
responsive TFs in soybean, maize, sorghum, barley, and wheat. Furthermore,
not only within plant species, but also between plants and distantly related
prokaryotes, comparative genomics can considerably infer the functionally
linked genes. Knowing the function of the NiaP protein family in bacteria
led to the discovery of its function in plants. Researchers can analyze gene
annotation in freshly sequenced plant species using similar methodologies to
discover functional genes among various plants using comparative analysis.
To store and manage enormous genomic data, substantial computational
resources are required in addition to tools and methodologies for analysis.
Many online platforms for comparative genomic studies among different
plant species have been developed, published, and made available. For
example, the following plant genomic data platforms have recently been
the most representative and widely used. Phytozome is one of the largest
comparison databases for plant species. It offers information on the plant
genome, gene families, and evolutionary history. Only 25 plant genomes
were sequenced and annotated at the start. In its current state, this number
has risen to more than 50 species(Goodstein et al., 2012)and the application
of inexpensive next generation sequencing. To interact with this increasing
body of data, we have developed Phytozome (http://www.phytozome.net.
Phytozome also includes powerful tools for comparing sequences, gene
structures, gene families, and genome architecture. With these tools and a
complete web platform, Phytozome makes plant study accessible to scientists
all around the world. PLAZA is the most user-friendly online platform for
plant comparative genomics. It integrates functional and structural annotation
of all currently available crop plant genomes. PLAZA offers a variety of
interactive tools for studying genes, genome evolution, and gene function
in addition to that massive data set. Pre-computed datasets, intraspecies
dot plots, whole-genome multiple sequence alignments, homologous gene
families, phylogenetic trees, and genomic collinearity between species are

only a few of the tools available.
Figure 3.5: GreenPhylDB.
Source: https://www.researchgate.net/publication/46413750_GreenPhylDB_
v20_Comparative_and_functional_genomics_in_plants/figures?lo=1
3.6 GREENPHYLDB
GreenPhylDB (Figure 3.5) is a public-access web resource that is part of the
South Green Bioinformatics Platform. GreenPhylDB is a database for plant
comparative and functional genomics. At the current release version 4, this
database comprises 37 complete genomes of Plants. Gene predictions of
genomes give a catalogue of gene families from GreenPhylDB, which covers
a large taxonomy of green plants. Its web interfaces are constantly being
improved to make it easier to navigate through information about each gene
or gene family, including gene composition, protein domains, publications,
orthologous gene predictions, and external links. The most recent edition of
this database now allows users to search the entire Gene Oncology database,
which aids gene discovery. PlantsDB is one of the most widely utilized plant
database sites for integrative and comparative plant genome research. Tomato,
Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley, and
wheat have database instances in PlantsDB. Individual plant genomes are

stored and made available through this platform. It’s also outfitted with
cutting-edge bioinformatics tools for visualising synteny, transferring data
from model systems to crops, and comparing and contrasting plant species.
Repeat catalogues and classification systems for all plant species are other
key analysis methodologies generated from PlantsDB.
Figure 3.6: Phylogenomics.
Source: https://www.nature.com/articles/s41467-019-13443-4/figures/1
3.7 PHYLOGENOMICS
Phylogenomics (Figure 3.6) is a type of molecular phylogenetic analysis
that involves using sets of genomic databases to predict gene function
and investigate evolutionary links across species. This definition of
phylogenomics is based on early investigations from the late 1990s when

a scientific hypothesis concerning protein function was published based on
the evolutionary analysis of a gene and its homologs. Phylogenomics has
also been described as a new era of phylogenetic analysis in which more
entire genomes have been sequenced. Plant phylogenomics has an advantage
over other species in that it can find hundreds of low copy number nuclear
genes, making molecular systematics and evolutionary biology much easier
to examine. Plant phylogenomics researchers may now use current NGS
methodologies to learn more about plant genome diversity, such as the nature
and frequency of genome duplication across a variety of plant lineages.
There are two major objectives that phylogenomic research attempts
to achieve. The first step is to use nuclear genomic data to uncover
evolutionary patterns among plant species. The second goal is to come
up with a new theory for the unknown function of plant genes linked to
important divergence events in plant evolution. Genomic data have greater
advantages in evolutionary research than morphological data, which can
be readily misinterpreted, or fossil data, which is frequently fragmented.
Phylogenomics also uses a set of orthologs derived from the genomic
sequence in a phylogenetic context to identify gene and biological process
hypotheses. The main difference between functional phylogenomics and
traditional phylogenetic analysis methods and current functional genomic
methods is that in phylogenomics research, genomic data is mined without
taking into account the phylogenetic context when looking for orthologs or
candidate genes of functional significance.
However, creating the tree of life or phylogeny of all organisms using
phylogenomics as the advanced method, which inferred evolutionary
relationships, remains a contentious subject. Some studies revalidated
the locations of certain plant species in biological taxonomy on a regular
basis in order to obtain the most accurate tree. As a result, due to several
restrictions, such as conflicting techniques and character sets and systematic
errors from simply adding more sequences, determining how to construct
a scientifically important topology remains a challenge. The most difficult
aspect of phylogenomics is determining how to properly handle huge
amounts of genomic data in order to avoid making systematic assumptions.
However, statistical confidence or P-value, which is commonly used in
such phylogenetic issues, was found to be incorrect. The magnitudes of
differences and biological relevance should be given more attention in order
to obtain reliable results. Another option is to improve existing phylogenetic
methods so that phylogenomic links can be inferred with fewer technical

biases and more computing power.
There are two ways to conduct these searches. Searching the internet
using key terms or looking through specific databases relevant to genetic
studies are two options. Despite the fact that the information in these databases
isn't always up to date, the second method is more suitable for obtaining
the finest results. When it comes to plant genome information, there are
four primary genomic project databases to choose from: GOLD or Genomes
Online Database, NCBI genomes, CoGepedia, (Figure 3.7) and plaBi. Gold
is a World Wide Web resource that provides full access to information about
genome and metagenome sequencing efforts, as well as the metadata that
goes with them. GOLD is presently hosted by the JGI DOE Institute, with
version 5 being the most recent release. More than 20,000 studies, 60,000
biosamples, 60,000 sequencing projects, and 50,000 analytic projects are now
stored in the database (Bernal, Ear, & Kyrpides, 2001). GOLD is unique in
that it encompasses not just nuclear and organelle genome research, but also
transcriptome, methylation, exome, and re-sequencing initiatives. Species
from the phyla Chlorophyta and Streptophyta are involved in around 100
and 3,400 completed or continuing initiatives, respectively. GOLD is hand-
curated, with quality-controlled metadata, and fully supports and adheres to
the Genomic Criteria Consortium (GSC) Minimum Information standards.
Figure 3.7: CoGepedia.
Source: https://genomevolution.org/wiki/images/d/d9/CoGe_system_design.
png
NCBI Genomes is an NCBI (National Center for Biotechnology
Information) database that organizes genome-related information such as
sequences, maps, chromosomes, assemblies, and annotations. The NCBI
Genome database gathers genome sequencing initiatives for a given species

and links them to records in the BioProject, Assembly, Nucleotide, and
Protein databases. More than 2,200 eukaryotic genomes have been deposited
so far, with over 200 of them corresponding to plant species. Assembly, a new
database from NCBI, was recently launched. The database keeps track of
changes to assemblies as they are updated by submitting groups throughout
time with a versioned Assembly accession number. The Assembly database
contains metadata such as assembly names, simple assembly statistical
reports, and assembly change history. Users can readily obtain sequence
and annotations for current versions of genome assemblies from the NCBI
genomes FTP site using links in the Assembly resource.
CoGepedia is the wiki page for CoGe, a platform for comparative
genomics research that offers a network of interconnected tools for
managing, analyzing, and visualizing next-generation sequencing data. This
data is organized in a phylogenetic tree made up of roughly 100 species that
have been sequenced (Kim et al., 2016)draft sequences or pseudomolecules
have been published for more than 100 plant genomes including green
algae, in large part due to advances in sequencing technologies. Advanced
DNA sequencing technologies have also conferred new opportunities for
high-throughput low-cost crop genotyping, based on single-nucleotide
polymorphisms (SNPs. plaBi is a plant genome database that includes an
up-to-date tool for determining which plant species have been sequenced.
This data can be viewed from either a chronological or phylogenetic
standpoint. There are also links to the research publications where each
plant genome has been published. Ensembl Plants is an integrative resource
that provides genome-scale information on 39 sequenced plant species,
including 12 dicots, 21 monocots, one moss, one pseudo fern, two green
algae, one red alga, and the genome of Amborella trichopoda, a sister group
to the other angiosperm species. Genome sequence, gene models, functional
annotation, and polymorphism loci are among the data supplied. With the
help of existing genome alignments, a comparative analysis may be done
on the entire genome. Gene families are offered based on an all-versus-all
BLASTP alignment. Under the Plant Compara section, you can find gene
trees that depict the evolutionary history of each gene family.
A genome browser with tracks displays genome sequence and assembly
information, additional gene model and variation datasets, and precomputed
sequence alignments including ESTs, RNA-Seq studies, repetition features,
oligo-probe, and marker sets provides access to the data. Ensembl Plants is
updated four to five times a year and was created in collaboration with the
Gramene database and the transPLANT project, which aims to make it easier
to exchange and integrate plant genome data from disparate sources while
also developing common standards and protocols. Gramene is a curated
online resource for comparative functional genomics in crops and model
plant species, with 45 sequenced reference genomes currently available
in build number 48. Since 2009, Gramene has collaborated with Ensembl
Genomes’ Plants division to develop the genome browser described above,
which uses the Ensembl infrastructure to provide an interface for exploring
genome features, functional ontologies, variation data, and comparative
phylogenomics. Genetic and physical maps with genes, and ESTs and QTLs
location studies of proteins, plant pathways databases like BioCyc and Plant
Reactome platforms, and descriptions of phenotypic features and mutations
are just a few of the tools available in Gramene.
3.8 PLANT GDB

Plant GDB is a website dedicated to the development of reliable genome
annotation methodologies, tools, and standard training sets for plant
genomes. Plant GDB has been providing access to sequence data from
29 plant species since 2012. Plant GDB also includes annotated transcript
assemblies for over 250 plant species, with transcripts mapped to their
relevant genomic context when possible, and is integrated with a number
of sequence analysis tools and web services. Plant GDB is home to a plant
genomics research site that provides easy access to a wealth of research
and training resources. The Plant GDB’s funding was terminated in July
2015, and the website is no longer being updated. Plants DB is a database
created by the Plant Genome Science Board’s plant genomics department.
Plants DB, which presently supports 13 monocot and dicot species, intends
to provide a data and information resource for individual plant species,
particularly complicated Triticeae member genomes. Searches for sequence
similarity can be performed against databases from 18 distinct species
(Duvick et al., 2008)with transcripts mapped to their cognate genomic
context where available, integrated with a variety of sequence analysis tools
and web services. For 14 plant species with emerging or complete genome
sequence, PlantGDB’s genome browsers (xGDB. PlantsDB also serves
as a resource for integrative and comparative plant genome research. The
database framework integrates genome data from model and crop plants
and facilitates knowledge transfer using cutting-edge comparative genomics
tools like CrowsNest, which was developed to visualize and investigate
syntenic relationships between monocot genomes, and the Genome Zipper
concept for an ordered gene annotation in cereals. Plants DB is a member of

the transPLANT consortium.
The Joint Genome Institute’s plant comparative genomics portal,
Phytozome, is part of the Department of Energy’s Joint Genome Institute.
Phytozome’s current release, v10.3, has access to sixty-one sequenced and
annotated plant genomes, 47 of which have been grouped into gene families
at 12 evolutionarily relevant nodes. It contains connections to the individual
pages of the various genomes it hosts, as well as the specific species genomic
sequences compiled in the DOE JGI. There are families of linked genes that
reflect the current descendants of ancestral genes. They were created using
an all-versus-all BLASTP alignment to calculate the evolutionary distance
between every two proteins, reciprocal best hit or synteny analysis to
identify orthologs, and outgroup scores to accrete paralogs. These families
provide quick access to speces-specific orthology/paralogy linkages as well
as information on alterations. Each gene has been annotated with the most
recent PFAM, KOG, KEGG, PANTHER, and GO designations, as well as
its evolutionary history at the sequence, gene structure, gene family, and
genome level. Phytozome also makes the plant genomes it holds accessible
using the JBrowse genome browsers, which are available for all genomes.
PLAZA is a platform established at the University of Ghent for comparative
genomics in plants.
Figure 3.8: PLAZA.
Source: https://www.researchgate.net/publication/294430579_Integration_of_
genomic_data_to_study_genome_evolution_in_plants/figures?lo=1
3.9 PLAZA
PLAZA (Figure 3.8) includes data from Gene Ontology, MapMan,
UniProtKB/Swiss-Prot, PlnTFDB, and PlantTFDB in its extensive structural
and functional annotation of genes. Gene families and subfamilies have
been identified from the over one million genes annotated in the genomes it
contains. First, using an all-against-all BLAST to calculate protein sequence
similarity, and then using graph-based clustering algorithms defined in
TribeMCL and OrthoMCL. Phylogenetic trees to identify physiologically
relevant duplication and speciation events, as well as extensive information
about genome organization to reveal tiny and large genome duplication
events, are also provided in this database. This collection also includes
methods for transferring functional annotation from well-studied plant
genomes to different plant species. Biodiversity International and the
International Cooperation Center for Agricultural Research for Development
collaborated to create GreenPhylDB, a comparative genomics database
(CIRAD). The current version of GreenPhylDB 4.0 has 37 Plantae species,
including one red alga, two green algae, one moss, one lycophyte, one
conifer, the ancestral angiosperm Amborella, 10 monocots, and twenty
eudicot species. Annotated sequences are also grouped into gene families
in this database(Valentin et al., 2020). TribeMCL was used to cluster the
data. This software uses a variety of pairwise similarity matrices derived
from protein-protein BLAST searches with more rigorous standards. After
that, a Markov cluster technique is used to arrange proteins in families at
different levels of clustering using these matrices. The automatic clustering
results are manually annotated with cross-reference databases and examined
using a phylogenetic-based technique to infer homologous relationships.
GreenPhylDB now has 8,347 clusters with more than 5 sequences at level 1,
of which 2,939 are annotated and 4,788 have phylogenetic trees accessible.
This database gives protein domains, orthologous gene predictions, and
important external links for each gene cluster, as well as rapid access to the
gene composition by species(Valentin et al., 2020).
Plant breeding and genetics efforts have historically been driven by
inadvertent plant selection and later cropping, as well as the need and
desire for more food and feed items. Plant genome components were
elucidated, and whole DNA sequences of plant genomes governing the
entire plant life were decoded as a result of the work achieved toward this
goal. Plant genomics aims to develop high-throughput genome-wide-scale
technologies, tools, and methodologies to elucidate the fundamentals of
genetic traits/characteristics, genetic diversities, and by-product production;

to comprehend phenotypic development throughout plant ontogenesis with
genetic by environmental interactions; to map important loci in the genome;
and to speed crop improvement. Plant genomics research has increased
steadily over the last 30 years, thanks to the development of low-cost, high-
throughput DNA sequencing tools that have resulted in the sequencing of
100 plant genomes with far-reaching consequences for plant biology study
and application.
The Plant Kingdom is an important part of our planet's food chain. Plant
domestication by humans happened early in human history, and subsequent
agricultural activity and incidental and purposeful plant breeding resulted
in the development of profitable crop species that provided food and
nourishment for all living organisms, including humans. Plant species are
extremely diverse, with over 300,000 species worldwide. To meet the human
diet needs, humanity currently cultivates 2000 plant species on 15.5 million
square kilometers of agriculturally appropriate land. Crop domestication,
followed by breeding and cultivation, has resulted in the creation of 15
priority crop species that produce more than 90% of food (Rieseberg,
1997). Plants offer clothes and housing materials, and earth ecology, give
medications and treatments for a variety of ailments, provide energy and
biofuels, and have a variety of other important features and uses that help us
comprehend life on our planet.
Plant domestication, combined with the desire and demand for more
food and feed products, has resulted in ongoing breeding and genetics
initiatives. Primitive selection efforts led to the development of methods
for shuffling traits and attributes between plant genotypes via controlled
sexual crosses, which led to the discovery of the genetics of essential crop
characteristics. These progressions have resulted in the creation of superior
crop genotypes, which have aided in the rise of agricultural productivity. For
the past 50 years, the cereal crop yield has increased 2.6 times due to the
Green Revolution, efficient exploitation of plant genetic diversity and plant
germplasm resources, novel cultivar development, and better and appropriate
agrochemical technologies, whereas maize production has increased 5-fold.
There are numerous examples of conventional breeding initiatives that have
been effective. Despite this, food insecurity and human starvation are still
widespread, and they will get substantially worse when the world human
population grows to 9 billion by 2050, with 1 billion people at risk of going
hungry (Evenson & Gollin, 2003). In an era of global climate change, ever-
worsening environmental conditions on Earth, societal globalization, and
technological breakthroughs, there is a desire and need to feed the growing

human population, sustain agricultural production, and face newly emerging
biosecurity challenges.
These events motivated the plant breeding and genetics community
to add precision techniques beyond conventional hybridization, selection,
and cultivation or farming procedures to enhance and power traditional
plant breeding and genetics methods. This is also dictated by the long
history of traditional breeding and crop improvement, which has been
hampered by limitations in phenotypic evaluations, masking the effect
of the environment, the polygenic nature of traits with many unnoticed
minor genetic components, negative genetic correlations between
important agronomic traits, linkages, and distorted segregation problems in
hybridization between diverse genotypes. To solve all of these issues, plant
scientists have attempted to decode the molecular basis of genetic diversity
by cloning and sequencing the genes expressing the desired feature, and then
using these genes in plant breeding as tools for vertical or even horizontal
gene transfers. Plant genome composition has been revealed, and the full
DNA sequences of plant genomes controlling plant ontogenesis have been
decoded. The term genomics was coined by Winkeler in 1920 and is derived
from the term genome, which refers to a haploid collection of chromosomes
(Greilhuber, Doležel, Lysák, &Bennett, 2005). Similarly, plant genomics
is a plant science discipline that aims to decode, characterise, and analyze
the genetic compositions, structures, organizations, and functions of a plant
genome, as well as molecular genetic networks. Plant genomics aims to
develop high-throughput technologies and methodologies to elucidate the
fundamentals of genetic traits or characteristics, genetic diversities, and by-
product production; to understand phenotypic development and to accelerate
genome-wide crop breeding and selection.
Plant genomes research has developed steadily during the last 30 years.
The number of scientific papers on plant genomics research has risen
dramatically, reaching 17,210 in 2015, according to the PubMed database,
with the first increase occurring in 2000-2001 and a large peak occurring
after 2010. The model plant Arabidopsis had the first fully sequenced
plant genome, which was released in 2000. By 2013, around 50 plant
genomes had been fully decoded, and the plant sciences community had
completed more than 100 plant genomes by 2015. Furthermore, the plant
sciences community elaborated on a sequencing vision of 1001 Arabidopsis
accessions and 1000 plant species that will have broad implications for areas
as diverse as evolutionary sciences, plant breeding, and human genetics,
while posing many unexpected challenges and grand tasks (Twyford, 2018).
The reference genomes for plants, including specialized crops, have
been sequenced, resulting in a new paradigm for modern crop development.
Crop breeding has rapidly spread and grown ever more productive and
efficient in the plant genomics era, aided and enhanced by molecular
markers, genetic linkage maps, QTL mapping, association mapping, and
marker-assisted selection approaches in the previous century. This is due
to the availability of large-scale transcriptome and whole-genome reference
sequences; high-throughput SNP markers and cost-effective technologies,
which allow breeders to screen multiple genotypes in a short amount of time
in identification and use of expression QTLs in breeding.
The economical sequencing and resequencing potential for population
individuals of genetic crossings and breeding lines has been the most powerful
driving force for genomics-assisted crop breeding in the plant genomics era.
This allows researchers to more precisely detect and link genetic differences
to phenotypic expressions by accounting for rare allelic variations seen
in crop line populations or germplasm resources. The availability of
SNP markers and automated genotyping systems enabled genome-wide
genotype-to-phenotype associations (GWAS) to be performed. Breeders
utilizing GBS and HTS systems can also genotype their mapping population
and give genomic selections for the specific crops of interest when whole-
genome sequences are not available and SNP markers are only present in
a restricted number. Although genomic selection was first used in animal
breeding, it has lately been effectively applied to a number of plant species,
including studies that used GBS in the context of genomic selection. Most
notably, the use of accessible genomics tools, as well as a vast number of
high-throughput DNA markers and next-generation genotyping platforms,
has enabled breeding by design and virtual breeding approaches for effective
crop development.
The availability of genome sequences and a vast number of SNP marker
collections has tremendously aided crop development efforts by allowing
for the investigation of copy number variants (CNVs) in crop genomes and
their linkages to key traits. Furthermore, despite the hurdles, post-genome
sequencing developments have allowed for the integration and enrichment
of genomic selection with critical proteome and metabolome indicators.
This greatly aided and accelerated the development of complicated crop
traits. As a result of the knowledge gained from plant genetics combined
with proteomic and metabolomic breakthroughs, chemical genomics has
permitted the birth of a novel approach to agriculture. This necessitates

the translation of pharmaceutical industry knowledge and expertise on the
development of personalized medicine to treat each person based on their
reaction to medicinal medications into agriculture. Many plant compounds,
such as herbicides, growth regulators and phytohormones, elicitors, low
molecular metabolites like salicylic acid can be screened for a genetic
response of individual crop genotypes and studied for their mechanism of
action contributing to agricultural productivity. Once discovered, highly
genotype-specific chemical compounds can be produced that have a greater
impact than commonly used "fit-for-all" pesticides, growth stimulators,
and fertilizers. A combination of chemical genomics, proteomics and
metabolomics, genetic engineering, and genomic selection will pave the
way for agriculture that ensures crop production sustainability.
3.10 WEEDS
Weeds have constantly disrupted crop plants since their domestication,
resulting in higher production losses than diseases and pests, necessitating
the use of weed control techniques. Weed control is critical to ensure that
enough food is available for a fast-growing human population. Weed
management strategies that combine chemical weed control or herbicides with
integrated weed management (IWM) approaches can be the most successful
and dependable. The use of herbicides for weed control necessitates the
development of herbicide-resistant (HR) crops as soon as possible. Recent
advances in genome editing technologies, particularly CRISPR-Cas9,
have opened up new opportunities for providing sustainable farming in the
current agricultural business. To date, genome editing has resulted in the
development of numerous non-genetically modified (GM) HR crops that
can play a key role in combating weed problems while also enhancing crop
output to meet rising global food demand. We discuss the chemical way
of weed control, herbicide resistance development approaches, and the
potential benefits and drawbacks of genome editing in herbicide resistance.
By 2050, the global human population is predicted to increase to 10
billion people, putting significant pressure on present agriculture to produce
25–70 percent more food to meet the growing population's nutritional
needs. Global food output must be expanded from 70% to 100% to meet
human food demand. The world's total grain production is currently 2.1
billion metric tonnes, with a yield loss of 200 million metric tonnes, with
weeds accounting for up to 10% of this loss(Hawkes & Lobstein, 2011).
Weeds are the most common of all crop pests, invading crop areas year
after year. Weeds provide a multifaceted problem in every cropping system,
competing for water, space, nutrients, and sunlight, negatively affecting
crop productivity. The most serious consequence is a reduction in the end
product's quality and quantity. Weeds not only carry viruses and insects that
affect crop plants, but they also harm native habitats, putting local animals
and plants at risk. Weeds can quickly spread from their natural environment
to different places around the world due to their rapid growth capability and
adaptation to multiple environments, interfering with crop development and
impairing ecosystem processes. They reduce input usage efficiency, induce
the loss of very fertile soils, and raise cultivation expenses, in addition to
direct and indirect losses.
Weed competition and allelopathy are directly related to agricultural
production reduction. Generally, a 1-kilogram increase in weed growth
corresponds to a 1-kilogram decrease in crop growth(van Heemst, 1985).
Weeds have thus been recognized as serious plant pests since antiquity.
Weeds have always played a part in agricultural plant domestication, leading
to the development of numerous weed management measures. Physical
and manual weeding equipment were used to till the soil to manage weeds
when weed problems first appeared in agriculture. Other strategies were
afterwards adopted, such as biological and cultural approaches. Although
these strategies aid in increasing agricultural output and reducing weed
infestations, they have several drawbacks, including inconsistent weed
control, lower labor availability, and higher labor costs. These approaches
aren't always successful, aren't long-lasting, and can be costly.
Weed management is critical in current agricultural systems to ensure
adequate crop productivity, and the goal is to maximize yield while
lowering costs. Herbicide application became an important aspect of
weed management programs in agriculture as a result of ineffective weed
control. Since its adoption, herbicide technology has provided an effective
and relatively inexpensive means of weed management, reducing severe
financial strain and contributing to increased average production.
Figure 3.9: Herbicides.
Source: https://www.intechopen.com/chapters/49524
3.11 HERBICIDES
Herbicides (Figure 3.9) are currently used extensively as the major weed
control method for agronomic crops. Herbicides can be taken up through leaf
and root absorption, causing phytotoxic effects near the entrance point, or
they can be translocated throughout the plant, depending on the application
method. The active chemicals pass through multiple barriers after foliar
application, including epicuticular waxes and leaf cuticles, before reaching
the apoplast and entering the plant cells. Herbicides can also enter the plant
through the stomata and reach the mesophyll cells. The root hairs and root
tips are the most common sites for uptake in roots. Herbicide absorption
in roots is a two-step process, with the first being quick uptake by bulk
water flow and the second being herbicide diffusion along a concentration
gradient, which is a non-metabolic process. The second step is linked to
the metabolic process, which results in a slower entry and accumulation of
material.
Herbicides can be metabolized by a natural metabolic mechanism of
plant detoxification, which comprises four steps, (a) conversion, which
involves modifying the active components chemically through reduction,
oxidation, oxygenation, and hydrolysis. The compounds become more
hydrophilic and less phytotoxic after functional groups like COOH, OH,
NH2 are introduced. This process is aided by the enzyme Cytochrome P450
monooxygenases (P450). (b) Conjugation, in which herbicide molecules or
metabolites generated from conversion are conjugated with amino acids,
sugars, or the tripeptide Glutathione, increasing their water solubility and
lowering phytotoxicity. Conjugation with glutathione, homo-glutathione or

glucose is one of the most important conjugation pathways seen in most
plants. (c) Secondary conjugation takes place, resulting in non-phytotoxic
molecules. Furthermore, conjugated metabolites are primarily carried into
the vacuole by ABC transporters. (d) Compartmentalization, in which
metabolites from the detoxification process are compartmentalized in the
vacuole and may be associated to insoluble residues formed by cell wall
components such as polysaccharides, lignin, pectin, and protein fractions
(Vencill, 2002).
Figure 3.10: Genome editing techniques.
Source: https://www.nature.com/articles/s41467-018-04252-2/figures/1
Genome editing techniques (Figure 3.10) have been successfully
utilized to target genes in a variety of crop species to improve average
crop yields in order to satisfy the rising needs of the current global food
famine. They can give a cost-effective and environmentally sustainable
agricultural programme to improve cultivars for better quality, higher
yield, disease resistance, and HR. Due to its great efficacy, adaptability,
simplicity, and consistency, this method has transformed the area of crop
breeding in recent years. For HR development in plants, all modern genome
editing technologies have been used, including transcription activator-like
effector nucleases (TALENS), zinc finger nucleases (ZFNS), clustered
regularly interspaced short palindromic repeats (CRISPR), and CRISPR-
associated (Cas) approaches. CRISPR-Cas9 systems are the most effective
and frequently used gene editing approach for inducing trait improvement in
crop plants, including HR. The most recent advancements in genome editing
have resulted in new CRISPR-Cas9 tools, such as base editing, which is
more accurate and efficient, and a promising tool that permits targeted
point alterations via programmable nucleotide substitution. Techniques like
CRISPR-Cas, particularly base editing, have the potential to create non-GM
HR crops. In a few countries, non-GM plants generated with CRISPR-Cas
systems have been exempted from GMO legislation. As a result, genome
editing is now the most suitable alternative to transgenic and conventional
processes for the creation of non-GM HR plants, which can give producers
a cost-effective weed management solution.
3.12 WEED MANAGEMENT

Chemical weed management is the most common approach used worldwide,
therefore the evolution of HR weeds and certain environmental problems
are the restrictions. The discovery of herbicide modes of action as a result
of a revitalized interest in research and development initiatives in the
agrochemical business, as well as academic and government organizations, is
a beneficial development. Recent research has identified natural phytotoxins
owing herbicidal action to novel MOA, after three decades without the
identification of a new herbicide MOA. Lipid Biosynthesis, Plastoquinone
Biosynthesis, and Imidazole Glycerol Phosphate Dehydratase (IGPD)
are among the mechanisms involved in the new mode of action. Natural
phytotoxins, such as sorgoleone, have many MOAs that can effectively
reduce the development of resistance to the target site by inhibiting
photosynthesis in developing seedlings and plants. It plays a role in the
suppression of PSII in vitro, which results in a reduction in plant growth.
It also impacts essential plant processes including water and solute uptake,
inhibits HPPD, and inhibits mitochondrial activities.
CRISPR-Cas9 systems and other genome editing methods have been
known to target multiple genes. Base editing techniques are currently being
utilized to modify TaALS and ACCase genes that provide resistance to
various herbicides. This method could be useful for producing plants that are
more resistant to a variety of herbicides. Bipyrazone is a newly developed
candidate of HPPD inhibiting herbicides that has been reported to reduce
broadleaf weeds in wheat growing areas in China. Bipyrazone was used as
a post-emergence herbicide in the greenhouse and in the field, and it was
found to be operative in controlling broadleaf weeds.
Integrated weed management (IWM), a complete approach to controlling

weeds that combines the application of complementary weed control measures
such as biological control, herbicide application, grazing, and land fallowing,
is now receiving research and financing. IWM has the potential to bring weed
populations under control. It aids in minimizing herbicide resistance selection
pressure, reducing the environmental consequences of specific weed control
strategies, and boosting cropping system sustainability. Despite the fact that
genome editing has resulted in the development of a number of HR crops,
agricultural trials using these crops are rare. HR technology, on the other
hand, can be a key component of IWM. HR crops can be used in IWM to
create a long-term, environmentally beneficial, and economic weed control
solution. HR crops have been the most effective way for farmers to control
weeds during the past two decades. They were available at a period when
weed management was becoming more expensive and time-consuming for
contemporary agriculture, as farm sizes became larger and the number of farm
laborers shrank. Thus, the capacity to manipulate biotechnology to develop
HR crops was a significant scientific breakthrough that revolutionized weed
management by providing a non-chemical weed control option.
HR crops have been developed through a variety of mechanisms,
including altering the plant to induce a mechanism that prevents the
herbicide from reaching a molecular target site, introducing or enhancing
herbicide deactivating or degrading enzymes into the plants, and changing
the plant to induce a mechanism that prevents the herbicide from reaching
a molecular target site. The principal method of natural crop resistance to
targeted herbicides is metabolic inactivation or degradation. HR crops,
including glyphosate-resistant cotton, maize, canola (Brassica napus),
and soybeans (Glycine max), have had a significant impact on weed
management. HR technology has quickly gained widespread usage due to
its ability to contribute to considerable gains in yield and cost savings, as
well as its efficacy and simplicity in weed management. For the creation
of HR in plants, however, a variety of strategies or approaches have been
used, including genome editing. HR crops, despite their efficiency, have
some environmental consequences, such as influencing farming methods,
agronomy, weed management, and biodiversity loss. Herbicides appear to
be inescapable in the current weed environment. Weed management by a
single method, such as herbicides, is, however, impossible. In combination
with IWM, gene-edited HR crops harbouring novel and multiple MOA
could be more successful at controlling weeds and reducing environmental
consequences.
3.13 MUTATION BREEDING

Mutation breeding (Figure 3.11) is a process of inducing heritable mutations
in an organism’s genetic material using chemical, physical (UV rays), or
mobile genetic components. In mutation breeding, there are three types of
mutagenesis: induced mutagenesis, where mutations are induced by radiations
like X-rays, gamma rays, ion beam or chemical mutagen treatment; (ii) site-
directed mutagenesis, which is the method of creating specific mutations at
target sites in a DNA molecule, mainly performed with PCR-based methods,
traditional PCR, and inverse Induced mutagenesis has been used to produce
novel genetic alterations since the 1930s. As a result, various crop plants with
better monogenic features have been created. Chemical mutagenesis and
subsequent herbicide selection create many herbicides tolerant (HT) crops,
such as soybean tolerant to sulfonylurea herbicides, sunflower tolerant to
imidazolinones and sulfonylurea, and wheat tolerant to sulfonylurea.
Figure 3.11: Mutation breeding.
Source: https://www.mdpi.com/2223-7747/8/5/128#
All commercial herbicide-tolerant crop varieties, on the other hand, have

been generated via a single nucleotide change of genes encoding proteins or
enzymes that are targeted by herbicides. Certain HT alleles are heterozygous
for herbicide tolerance induction, while others tend to be homozygous.
Except for the triazine-tolerant mutation, which has pleiotropic alleles, all
commercial HT mutations have incompletely dominant alleles inherited
maternally that are implicated in numerous agronomic aspects. By crossing
with a trait donor, HT characteristics can be introduced into an elite variety.
Induced mutagenesis has a number of flaws, including the fact that the
approach is usually random and unstable, and advantageous mutants are
few and mostly recessive. High population size and efficient mass screening
procedures are required for picking uncommon variants. To reduce
background mutations and eliminate chimaeras, a dense mutation burden
necessitates extensive breeding. Multiple gene variants occurring at the same
time are extremely rare. Furthermore, transcription factors are implicated in
the regulation of many quantitative features, and changes in these genes can
have an impact on the transcriptional function of their downstream targets,
which could explain the effects of quantitative changes. Crop growers had
long preferred mutations at specific places within the plant genome rather
than random non-specific variants such as those caused by chemical or
radiation mutagenesis. As a result, when genetic engineering technology
became available, it became possible to precisely and quickly introduce
particular mutations within the target gene to induce gene suppression or
gene expression.
Plant science has made significant progress in the development of
novel biotechnology-based plant breeding strategies for modifying genetic
and epigenetic variables. Site-specific nucleases and gene-targeting
oligonucleotides can be used to create novel plant products (NPPs) through
cisgenesis, intragenesis, and genome engineering. Zinc finger nucleases,
and Cas9 nucleases linked with clustered, regularly interspaced, short
palindromic repeats are among them. Improved plants and fruit trees free
of transgenesis and cisgenes have resulted via reverse breeding procedures
and backcrossing modified plants with natural kinds. NPPs devoid of viral
sequences and antibiotic genes, and containing solely genetic material
acquired from the species itself or from closely related species, are gaining
in popularity. There is a need for harmonization in the rule and defining
disparities between modified and non-modified plant genomes, as well as
in the differences between regulation and regulatory authorities in various
nations. Plants contain a minimal number of hormones compared to animal
and insect organisms. The complexity of hormone crosstalks among them

is to blame for this. Recent research using Arabidopsis and rice as model
plants has revealed the interplay of a range of signaling molecules with
phytohormone metabolism and signaling.
3.14 ALLERGIES
Allergies in the Western countries in recent decades, and several protein
families have been discovered as factors of allergenicity. So far, four allergen
families (Mal d 1–4) have been found in apple fruit, one of the world’s most
significant fruit crops, including pathogenesis-related proteins, thaumatin-
like proteins, lipid transfer proteins, and profilins (Nomura, Morita,
Ohya, Saito, & Matsumoto, 2012). Furthermore, it has been shown that
patient sensitivity varies depending on apple variety, fruit tissue, culture,
and preservation circumstances, making it more difficult to link genetic,
molecular, and biochemical data to clinical test results. Allergens are
structured in vast families with many distinct isoforms, the role of which to
allergenicity is still largely unknown, according to mapping studies and the
availability of the whole apple genome sequence.
Antibody-based therapies and molecular farming are being investigated
in a growing number of therapeutic modalities. There are currently a variety
of designed formats for antibody molecules as well as many approaches for
raising and adjusting binding specificities. Recombinant secretory IgA can
be expressed in plant cells (sIgA). Humanized antibodies against the herpes
simplex virus HSV-2 can be produced by transgenic soybeans. GM corn
has been shown to produce human antibodies at yields of up to 1 kg per
acre and to maintain antibody activity after 5 years of storage under normal
conditions. A plant that is designed for large seed and high protein production
is clearly favoured for seed production (de Vendômois, Roullier, Cellier, &
Séralini, 2009)MON 810, MON 863. Transgenic tobacco chloroplasts can
create human somatotropin or interferons at 100-fold higher protein levels
than their nuclear transgenic counterparts, with somatotropin accounting for
7% of total plant protein output (Daniell, Lee, Panchal, & Wiebe, 2001)000
copies per cell.
Because of their benefits in terms of cost, feasibility, and scalability
of production, plants are attractive biotechnological instruments for the
synthesis of medicinal proteins and vaccines. Virus-like particles (VLPs)
constituted of single or multiple virus proteins with self-assembly capacity
are one of the most appealing systems of antigen production in plants
among biopharmaceuticals. This is because VLPs have a high immunogenic

capability and are safe to employ as plant-made vaccines against a variety
of human and animal diseases. Furthermore, VLPs do not require lengthy
purification stages or the use of a cold chain, which are both limiting
considerations in the manufacture of traditional vaccinations. These features
enable VLPs to compete as excellent alternative candidate vaccines, either as
simple products or as more complicated platforms for carrying heterologous
immunogenic sequences on their surfaces.
The Euphorbiaceae family is important because it includes commercially
valuable crop species like Jatropha curcas, Manihot esculenta, and Ricinus
communis, all of which have distinct applications. Jatropha is primarily a
biofuel and pharmaceutical crop with the potential to reclaim marginal soils
and reduce erosion and desertification risks, whereas cassava is primarily a
staple food and provides food security, and Ricinus is a crop with growing
economic importance, particularly in the chemical industry. Due to biotic
and abiotic stressors, they are all facing significant challenges. The use of
molecular markers to investigate genetic diversity throws light on nucleotide
polymorphisms and provides information about adaptive processes and
population history. The use of diverse molecular detection techniques to
identify viral infections that affect Euphorbiaceae allows for the development
of protective strategies in situations where multiple species are planted side
by side. Furthermore, studies of miRNAs expressed by viral infections that
affect Euphorbiaceae led to the discovery of RNA silencing suppressors.
The mapping of their targets on the genomes of their host plants revealed
that some of these targets are engaged in plant defense mechanisms.
CHAPTER 4
RECOMBINANT DNA TECHNOLOGY
AND PLANTS
CONTENTS
1.1 Introduction.......................................................................................... 6
4.1 INTRODUCTION
Recombinant DNA technology provides the potential to create genetically
modified plants with desirable features such as higher biotic and abiotic
tolerance in plants, as well as improved flexibility for better survival. In
comparison to natural recombination or traditional breeding methods,
recombinant DNA technology allows for faster, cheaper, and more accurate
insertion of specific features from many sources into the plant genome
(Pappu, Niblett, & Lee, 1995). Furthermore, genetic alteration of both
nuclear and eukaryotic and plastid or prokaryotic-like plant genomes has
produced a transgenic plant with different properties. Genetic engineering
has always been a contentious topic because the balance it seeks to strike
between the benefits to people and the ethical implications is up for dispute.
Concerns in the disciplines of agriculture, medicine, bioremediation, and
biotechnology differ according to the discipline. The main source of concern,
however, is the real or perceived environmental impact of recombinant DNA
technology, particularly the release of genetically modified organisms into
the environment.
The transfer of genes across bacteria of the same Escherichia coli
species pioneered the application of recombinant (r-) DNA technology to
make genetically altered species in the early 1970s. Cohen and colleagues
transferred an insulin production gene into an E. coli plasmid in 1978,
resulting in the world's first genetically engineered organism (GMO)(Rousset
et al., 2021). By 1982, national drug regulatory authorities, including the US
Food and Drug Administration, had given their full approval to this protocol,
allowing for the viable mass production of human insulin, a hormone that
controls blood sugar levels and is produced naturally by beta cells in the
pancreas. This permitted the widespread commercial availability of insulin
at a cost that was reasonable to people with diabetes mellitus types 1 & 2,
who either do not make or metabolize enough insulin.
This demonstration of genetic modification's medical benefits sparked
a trend for molecular cloning technologies to transfer genes expressing
desirable features into another host organism, resulting in desirable qualities.
This currently includes both prokaryotes like bacteria which are relatively
easy to genetically change using r-DNA technology and eukaryotes like
yeast, plants, insects, and mammals comparatively complex to manipulate
via r-DNA technology. In agriculture, the production of genetically modified
crops with the goal of increasing output while also increasing resistance
to plant pests or herbicides appears to have achieved popular support and
Recombinant DNA Technology and Plants 85
is already being used commercially in various countries. The genetically

modified tomato was the first commercially cultivated, genetically edited
crop product to get a license. This was created in 1994 to express the
characteristic of delayed softening of tomato flesh as a practical way to
reduce crop losses after harvest. Ironically, given its brand name, 'Flavr
Savr,' (Figure 4.1) this flopped in the marketplace due to an apparent lack of
taste rather than public apprehension over consuming a genetically altered
food. Nonetheless, the introduction of a genetically modified fruit cleared
the door for the usage of GMOs in food. In the United States, 88 percent of
maize and 93 percent of soybeans are genetically modified, and most of this
ends up in processed foods without being labeled(Kramer & Redenbaugh,
1994).
Figure 4.1: Flavr Savr.
Source: https://alchetron.com/Flavr-Savr#flavr-savr-e610022c-006f-
4709-bad5-b8bd685bd7f-resize-750.jpg
4.2 PESTICIDE RESISTANCE

In some areas, the introduction of pest-resistant brinjal also known as
eggplant or aubergine was met with opposition, despite the popularity of
pest-resistant cotton at the time. The same crystal protein gene (Cry1Ac)
from the soil bacteria Bacillus thuringiensis (Bt) was inserted into the
genome of the host plant expression of which synthesises so-called Bt toxins

that confer resistance to predation by Lepidoptera insects in both attempts
at implementation. However, of the two uses as food and clothing, human
eating was the one that raised concern among the general public. In order
to overcome the initial unpopularity of ingesting Bt-brinjals in developing
nations such as India, Bangladesh, and the Philippines, the benefits of
employing Bt toxin should be emphasised. This would minimize public
scepticism based on the erroneous belief that consuming a plant product
containing a ‘toxin’ is hazardous to humans, regardless of the toxin’s
unrelated target and benign method of action.
The emergence of novel genetic modification techniques (nGMs),
sometimes known as new breeding techniques in other sources, has sparked
debate about their regulation around the world. nGMs are covered to
varied degrees by existing regulatory frameworks for genetically modified
organisms (GMOs). The extent to which nGMs are covered is largely
determined by the regulatory trigger. In general, two different trigger systems
can be recognized, depending on whether the development method was used
or the features of the final product. One important topic is whether regulatory
frameworks based on process or product-oriented triggers are better for
regulating nGM applications. The varying criteria and exceptions utilized to
execute the triggers in the various regulatory frameworks are more decisive
for the regulation of organisms or products, notably nGM applications. In
certain countries, there are talks regarding whether legislative changes are
required to achieve the desired level of nGM regulation. It was identified
that there are five ways for countries wishing to regulate nGM applications
for biosafety, ranging from using existing biosafety frameworks without
changes to enacting new stand-alone laws. International harmonization will
allegedly not be reached in the foreseeable future due to differing degrees of
nGM legislation. Transparency about the regulatory status of specific nGM
products is important in international trade. In most countries, biosafety
frameworks established by particular legislation oversee genetically
modified (GM) crop plants developed using recombinant DNA (rDNA)
technology.
Figure 4.2: Biosafety frameworks.
Source: https://www.researchgate.net/publication/311821383_The_Biosecu-
rity_Approach_A_review_and_evaluation_of_its_application_by_FAO_inter-
nationally_and_in_various_countries/figures
4.3 BIOSAFETY
These biosafety frameworks (Figure 4.2) are typically based on the FAO
and WHO. The OECD’s core principles for food and feed safety, as well as
environmental risk assessments of crops produced by modern biotechnology
are important (Sensi, Fao, Brandenberg, Gosh, & Sonnino, 2011). The
Cartagena Protocol on Biosafety (CPB), formed under the Convention
on Biological Diversity, is particularly significant for the creation and
international harmonization of biosafety regimes. When creating national
biosafety rules, the Parties to the CPB, currently 171 nations, are required to
adopt the Protocol’s stipulations. Genetically engineered plants, particularly
in agriculture, have boosted resistance to hazardous agents, increased
product yield, and demonstrated increased adaptation for better survival.
Furthermore, recombinant medications are now being utilized with
confidence, and commercial approvals are being obtained quickly.
Bioremediation and the treatment of serious diseases are additional common
uses of recombinant DNA technology, gene therapy, and genetic changes.
Because of the rapid growth and wide range of applications in the field of
recombinant DNA technology. Three elements have a significant impact on

human life: food scarcity, health problems, and environmental concerns.
Aside from a clean and safe environment, food and health are essential
human needs. Human food requirements are rapidly increasing as the world’s
population grows at a faster rate. Humans demand food that is both safe
and affordable. Several human-related health conditions cause a substantial
number of deaths around the world. Despite significant efforts, present global
food production falls well short of human needs, and healthcare facilities in
third-world countries are far worse. Rapid industrialization has increased
environmental contamination, and industrial wastes are permitted to mix
directly with water, affecting aquatic marine life and, indirectly, humans.
As a result, modern technology must be used to overcome these difficulties.
Unlike traditional approaches to overcoming agriculture, health,
and environmental issues through breeding, traditional medicines, and
pollutant degradation through conventional techniques, genetic engineering
makes use of modern tools and approaches, such as molecular cloning
and transformation, which are faster and produce more reliable results. In
contrast to conventional breeding, which transfers a large number of both
specific and nonspecific genes to the recipient, genetic engineering simply
delivers a small block of desired genes to the target by various methods
such as biolistic and Agrobacterium-mediated transformation. Homologous
recombination-dependent gene targeting or nuclease-mediated site-specific
genome editing are both used to modify plant genomes. Site-specific
genome integration mediated by recombinases and oligonucleotide-directed
mutagenesis can also be utilized. Changing genetic material outside of an
organism to get enhanced and desired features in living creatures or as their
products is referred to as recombinant DNA technology. This approach
entails inserting DNA fragments from a number of sources into a suitable
vector with a desired gene sequence. Manipulation of an organism’s genome
can be done by adding one or more new genes and regulatory elements,
or by recombining genes and regulatory elements to reduce or prevent the
expression of endogenous genes.
Figure 4.3: Restriction endo-nucleases.
Source: http://www.agrilearner.com/restriction-endonuclease/
Using restriction endo-nucleases (Figure 4.3) for specific target sequence
DNA sites, enzymatic cleavage is used to generate distinct DNA fragments,
which are then joined using DNA ligase activity to fix the desired gene in
the vector. After that, the vector is delivered into a host organism, which
is cultured to create multiple copies of the integrated DNA fragment, and
then clones containing a relevant DNA fragment are selected and harvested.
Paul Berg, Herbert Boyer, Annie Chang, and Stanley Cohen of Stanford
University and the University of California, San Francisco created the
first recombinant DNA (rDNA) molecules in 1973. Regulation and safe
use of rDNA technology were debated in “The Asilomar Conference ‘’ in
1975 (Micklos, Freyer, & Crotty, 2003). Recombinant DNA technologies
to encourage agricultural and medication development took longer than
planned due to unexpected obstacles and barriers to get adequate results,
contrary to scientists’ expectations at the time of Asilomar. Since the mid-
1980s, however, a growing range of goods such as hormones, vaccinations,
therapeutic agents, and diagnostic tools have been produced to improve
health. Recombinant DNA technology provides a rapid way to examine the
genetic expression of mutations induced into eukaryotic genes via cloned
insulin genes inserted into a simian virus fragment.
For nearly two decades, molecular approaches have been utilized to

introduce novel traits into agronomically important plants, such as disease,
insect, and herbicide resistance. Antibiotic resistance genes were exploited
as selection markers in the development of several transgenic plants. The
widespread usage of transgenic plants in agriculture results in a substantial
amount of recombinant DNA in the environment. It has been mentioned as
a concern that an accidental transfer of recombinant genetic material into
the soil microbiota may occur, resulting in increased antibiotic resistance in
bacteria, including human pathogens. Simultaneously, the recombinant and
thus distinct nucleotide sequences of genetically modified organisms’ DNA
allowed for quantitative tracing of DNA from transgenic organisms in the
environment via PCR amplification. High molecular weight DNA has been
detected in areas where free DNA or plant material has been deposited, and
it has been reported to remain in non-sterile soils for months. DNA produced
by eukaryotic and prokaryotic cells is thought to form an extracellular gene
pool that can be accessed by biologically competent bacterial cells that
pick-up DNA and integrate it into their genomes or natural transformation.
Transformation was discovered in non-sterile soils in microcosm tests. There
has been no evidence of recombinant DNA transmission from transgenic
plants to soil microorganisms.
4.4 GENE TRANSFER

Gene transfer from transplastomic tobacco plants to Acinetobacter sp. strain
BD413 was demonstrated when the plants were experimentally coinfected
with Acinetobacter and Ralstonia solanacearum. The nptII gene, which
is found as a selection marker gene in the genomes of various transgenic
plants, was previously utilized to evaluate the conditions for horizontal
plant DNA transfer into competent bacteria. When the recipient cells supply
DNA homology for transgene integration by homologous recombination,
recombinant plant DNA can change competent cells to antibiotic resistance.
In the absence of homology, integration could not be detected. Transgenic
potato plants harbouring nptII as a selection marker was evaluated and
the presence of recombinant DNA in their environment to determine the
level, frequency, and dynamics of DNA spread from plants during growth
was studied. A biomonitoring test based on natural transformation of
Acinetobacter sp. strain BD413 to detect recombinant DNA was employed.
During the DNA uptake process, this species does not distinguish between
its own DNA and foreign DNA. The technique has been used to detect nptII
genes in leaf DNA extracts from a variety of transgenic plants, including

potato, rape, tobacco, tomato, and sugar beet plants. It’s also been used to
detect recombinant DNA from transgenic sugar beet plants in environmental
samples recently. A biomonitoring genetic system was used to make it
more specific for a certain recombinant construct, in this case, the DNA
of a transgenic potato with a nptII-tg4 terminator fusion. All features are
defined by their genetic makeup and how it interacts with the environment.
An organism’s genetic makeup is its genome, which is made up of DNA in
all plants and animals. Genes, or DNA sections that carry the instructions for
generating proteins, are found in the genome. These proteins are responsible
for the plant’s appearance. Genes that convey the instructions for generating
proteins involved in producing the pigments that color petals, for example,
determine the color of flowers.
Transfer of DNA into a plant cell is the initial step in creating a GM plant.
One way for transferring DNA is to cover the surface of small metal particles
with the appropriate DNA segment and then bombard the particles into plant
cells. Using a bacteria or virus is another option. Many viruses and bacteria
transfer their DNA into a host cell as part of their usual life cycle. The most
commonly utilized bacterium for GM plants is Agrobacterium tumefaciens.
The desired gene is introduced into the bacterium, and the bacterial cells
subsequently transfer the new DNA to the plant cells’ genome. The plant
cells that successfully took up the DNA are then developed into a new plant.
Because individual plant cells have the ability to create complete plants,
this is possible. In rare cases, DNA transfer can occur without the need for
human intervention. The sweet potato genome, for example, contains DNA
sequences that were transferred thousands of years ago from Agrobacterium
bacteria.
4.5 CROP ENHANCEMENT

Genetic crop enhancement is achieved through both conventional plant
breeding and genetic modification (GM). For thousands of years, genetic
improvement has been a key component of increased agricultural output.
Plants that can compete for light, water, and nutrients with neighboring
plants, defend themselves from being eaten and digested by animals,
and disseminate their seed across large distances are favored by natural
selection. These features are in direct opposition to agricultural goals, which
call for plants to devote as much of their resources as possible to producing
nutritious, easy-to-harvest goods for human consumption. Because of the
striking disparity between what natural selection has generated and what
produces a productive crop, we’ve utilized traditional breeding methods to
convert plants that compete well in the wild to plants that perform well in
agriculture for thousands of years. As a result, we now have crop types that
are significantly more productive and nutritious than their wild parents, but
less useful in the wild.
Crops can be genetically modified or conventionally modified to add
new traits. This allows us the question whether a plant breeder should use a
GM method rather than a traditional one. Only two conditions must be met
for GM to be used to introduce a new trait into a crop. First, the trait must be
able to be introduced with only a minimal number of genes, and second, it is
required to determine which gene or genes are involved. We understood a lot
less about which plant genes do what when GM technology was introduced,
which limited the number of useful applications for GM in crops. We now
know numerous genes that could help increase sustainable food production,
thanks to advances in our understanding of which plant genes do what. In
certain circumstances, traditional breeding that is, cross-breeding with the
plant that possesses the genes that provide these qualities will be the ideal
strategy to deploy these genes.
In some circumstances, GM, in which scientists extract a gene and insert
it directly into a plant, may be the simplest or only option to use them. There
are two key reasons why GM may be the better option. To begin with, the
desired gene may not exist in a species that may successfully cross with the
crop. It’s possible that the gene came from a different kingdom, such as a
bacterium, or from a different plant species. Many plant species in nature
respond to shade by growing taller, allowing them to compete for light. The
capacity to change their height is based on a specific protein that blocks
stem elongation, and the plant can fine-tune its development by adjusting the
amount of this protein in the stem. As part of the so-called Green Revolution
in the 1960s, dwarf wheat cultivars were developed, drastically increasing
yields. The dwarf wheat types take advantage of a mutation in the gene
encoding the height adjusting protein, which increases the quantity of the
protein in the stem, preventing stem growth. As a result, wheat types devote
more resources to their seeds rather than their stems. As a result, they yield
more and are less likely to be flattened by the wind, which is a primary cause
of yield loss known as lodging.
Concerns have been raised that simply adding new DNA into a plant
genome by genetic modification could have unforeseeable repercussions.
However, as our understanding of genomes has grown, it has become evident
that comparable insertion events occur in all plants on a regular basis. Some
bacteria and viruses, for example, introduce new genes into the genomes
of the plants they infect. Plant genomes have a large number of so-called
‘jumping genes,’ which travel about the genome, re-inserting themselves
in different locations. As a result of these processes, all new crop varieties,
regardless of how they are created, may contain genes placed in previously
unknown locations in the genome and novel genes that have never been
found in the food chain or come from non-plant species. This means that
both GM and non-GM crop varieties may have unintended repercussions
on occasion.
4.6 RESISTANCE
Resistance to the herbicides (glyphosate) in soybeans was the first GM trait
to gain widespread adoption. Herbicide-tolerant crops can also be grown
without using genetically modified seeds. Resistance to wide herbicides
which would normally kill both weeds and crops allows for effective weed
control since the herbicide may be given while the crop is growing without
harming it. Without herbicide-tolerant crops, a variety of herbicides may be
required to eradicate all weeds prior to sowing the crop. Herbicide-tolerant
crops also have the advantage of being able to be planted in weedy fields
because the weeds may be controlled with herbicide. This eliminates the
need for ploughing, resulting in reduced soil erosion. The farmer must
purchase a special herbicide to match the herbicide-tolerant crop, and
this form of control goes against efforts to lessen agriculture’s reliance on
chemical inputs.
The Bacillus thuringiensis (Bt) bacteria creates a toxin family of
proteins that are poisonous to certain insects but not to beneficial insects
or other mammals. In organic farming, Bacillus thuringiensis is utilized
as an insecticide spray. GM has introduced genes for various Bt toxins
into several crops. The usage of Bt toxin genes in crops has prevented
the administration of 450,000 tons of insecticide during the last 20 years,
according to estimates. When weed management is especially effective,
insect biodiversity is lost, according to a large farm scale evaluation of
herbicide-tolerant GM crops undertaken in the UK between 1999 and 2006
(Tu et al., 1998). It didn’t matter if the crop was GM or not; what mattered
was how many weeds remained in the crop. If a tiny portion of agricultural
land is left aside for biodiversity, wildlife damage can be reduced. Another
issue is the growing problem of weeds developing resistance to herbicides
as a result of their misuse. Because recurrent growth of the same herbicide-

tolerant crop requires repeated application of the same pesticide, herbicide-
tolerant crops, whether GM or non-GM, can produce this problem. Rotating
crops resistant to different herbicides or alternating herbicide use with other
weed management techniques is one solution.
Genetic use restriction technology (GURT) is based on seed germination
prevention and was patented by the US government in the 1990s and
licensed by private corporations, including Monsanto. In actuality, the
technology was never proved to perform reliably. Because the plants would
be unable to generate fertile seeds, the notion became known as ‘terminator
seed’ technology(Lombardo, 2014). Because of concerns about the potential
economic impact on farmers who would be unable to conserve seed for
future planting, the United Nations Convention on Biological Diversity
imposed an international embargo on the use of GURTs in 2000.
When there are license limitations in effect, saving seeds for both GM
and non-GM crops is not permitted. Furthermore, farmers and gardeners
will be aware of F1 hybrid types, which are created by crossing two or more
parents and from which seed cannot be stored since they do not breed true.
A 3.5-kb mini-binary vector (pCB301) was created that can be used to clone
DNA segments for transfer into the plant genome. However, conjugation
cannot be used to introduce this into A. tumefaciens since crucial DNA
sequences essential for conjugal transfer have been removed. As a result,
electroporation is used to introduce this. Minivector pCB301 was used
to create a number of derivatives(Xiang, Han, Lutziger, Wang, & Oliver,
1999)the nptIII gene conferring kanamycin resistance in bacteria, both the
right and left T-DNA borders, and a multiple cloning site (MCS. Despite
the fact that A. tumefaciens -mediated gene transfer methods are effective
in a variety of species, monocot plants such as rice, wheat, and maize are
not easily changed. However, protocols for the transformation of maize and
rice by A. tumefaciens -bearing Ti plasmid vectors have been developed by
improving and carefully managing circumstances. Immature corn embryos,
for example, were immersed in an A. tumefaciens cell suspension for a
few minutes before being cultured at room temperature for many days in
the absence of selective pressure. After that, the embryos were placed in
a medium containing a selective antibiotic that allowed only altered plant
cells to proliferate. For a few weeks, these cells were kept in the dark.
Finally, the mass of transformed plant cells was transferred to a different
growth medium containing plant hormones to encourage differentiation and
incubated in the light, allowing entire transgenic plants to be regenerated.
4.7 MARKERS
A plant selectable marker gene, the target gene, right border, an E. coli origin of
DNA replication, and a bacterial selectable marker gene are all present in the
cointegrate vector. Within A. tumefaciens, the cointegrate vector recombines
with a modified or disarmed Ti plasmid that lacks both the tumor-producing
genes and the right border of the T-DNA. To generate a recombinant Ti
plasmid, the whole cloning vector is inserted into the disarmed Ti plasmid.
The disarmed helper Ti plasmid and the cointegrate cloning vector both
have homologous DNA sequences for homologous recombination. The
cloning vector becomes part of the disarmed Ti plasmid, which contains the
vir genes, after recombination. The genetically altered T-DNA region can be
transmitted to plant cells in this cointegrated arrangement. When employing
binary vectors, one practical issue is that their vast size (>10 kb) makes
manipulating them in vitro difficult and cumbersome. Furthermore, bigger
plasmids tend to contain fewer distinct restriction sites for cloning reasons.
For these reasons, developing and using smaller binary vectors is useful.
Based on the DNA sequence of a regularly used binary vector, pBIN19,
it was estimated that more than half of the DNA could be erased without
affecting the vector’s functionality.
E. coli and A. tumefaciens origins of DNA replication or a single broad
host range origin of DNA replication are both present in the binary cloning
vector. Before the vector is delivered into A. tumefaciens, all of the cloning
stages are completed in E. coli. The recipient A. tumefaciens strain possesses
a modified Ti plasmid that contains all of the vir genes but lacks the T-DNA
section, preventing the T-DNA from being transferred. In this system, the vir
gene products are synthesised by the faulty Ti plasmid, which also serves
as a helper plasmid. This allows the T-DNA from the binary cloning vector
to be introduced into the chromosomal DNA of the plant. Because T-DNA
transfer begins at the right border, the selectable marker is normally put
adjacent to the left border. Two plant selectable markers, one adjacent to the
right border and the other adjacent to the left border, have been created into
a few binary vectors.
4.8 GENETIC ENGINEERING

Genetic engineering isn’t merely a continuation of traditional breeding. In
truth, it is vastly different. Conventional breeding, in general, uses a selection
method to create new plant varieties, with the goal of achieving expression
of genetic material already existing within a species. Traditional breeding
makes use of natural processes like sexual and asexual reproduction. The
outcome of traditional breeding accentuates specific traits. These features,
however, are not unique to the species. The features have existed for
millennia within the species’ genetic potential. The primary method of
genetic engineering is the insertion of genetic material, albeit gene insertion
must be followed by selection. This type of insertion isn’t found in nature.
A gene gun, a bacterial vector or a chemical or electrical treatment inserts
genetic material into the host plant cell, which subsequently inserts itself
into the chromosomes of the host plant with the help of genetic components
in the construct. In order for the inserted gene to express itself, engineers
must also include promoter genes from a virus.
Even though the primary purpose is just to implant genetic material
from the same species, this procedure, which uses a gene gun or a similar
technique and a promoter, is vastly different from conventional breeding.
Beyond that, the approach allows for the insertion of genetic material from
hitherto unknown sources. It is now feasible to incorporate genetic material
from species, families, and even kingdoms that were previously unavailable as
sources of genetic material for a specific species, as well as custom-designed
genes that did not exist in nature. As a result, we can construct synthetic life
forms, which would be impossible to achieve through traditional breeding.
It›s intriguing to compare this development to the breakthroughs that led to
the development of synthetic organic compounds in the early 1900s.
4.9 SYNTHETIC CHEMICALS

Synthetic chemicals could be considered a continuation of basic chemistry,
and in some ways they are. Because we hadn’t co-evolved with them for
millennia, many of the effects were negative. PCBs and vinyl chloride, both
carcinogens, were discovered, as were various organochlorine pesticides,
which were discovered to be carcinogens, endocrine disruptors, immune
suppressors, and other issues. These breakthroughs are not identical in many
respects, but the experience with synthetic organic molecules highlights the
potential for unanticipated outcomes when fresh substances are introduced
into the biosphere. This is in contrast to traditional breeding, which only
allows genetic material to be transferred between distinct variants within
a species, between closely related species, or between closely related taxa.
Even extensive crosses and hybridization can’t transport genetic material
much beyond these limitations. The great majority of hybrid crops are
created by mating two genetically pure, i.e., homozygous for all alleles, lines
of the same crop to produce a heterozygous line. To develop a mixed line,

hybrid corn is merely the crossing of two pure corn lines. The trait that is
put into the genome of a host plant can be controlled rather precisely via GE.
However, it is still unable to precisely regulate where the characteristic is
put into the genome or assure stable transgenic expression. Transformation
is the process of inserting foreign genetic material into the host plant genome
via GE and expressing that material. Currently, transformation is carried out
using a number of primitive approaches that result in a random distribution
of genes. Manipulation of bacteria belonging to the genus Agrobacterium
is a common transformation approach. These bacteria are among the few
known to be able to transfer genetic material from a kingdom/phyla to
another. By attaching to plants, transferring bacterial DNA into the plant,
and having that DNA incorporated into the host plant genome, these bacteria
cause disease in plants.
Figure 4.4: Agrobacterium-mediated plant transformation.
Source: https://bioone.org/ContentImages/Journals/arbo.j/2017/15/tab.0186/
graphic/f01_01.jpg
4.10 AGROBACTERIUM
Agrobacterium-mediated plant transformation (Figure 4.4) entails removing
disease inducing genes, keeping the bacterial transfer DNA (T-DNA), and
adding the genetic traits or elements to be transferred into the Agrobacterium.

This genetically modified Agrobacterium, often known as a bacterial truck,
is then mixed with the desired plant cells and allowed to transform or infect
them. Agrobacterium-mediated transformation is most commonly used on
dicots and is difficult to do with grains. Almost all GE-derived agricultural
plants have a potent promoter from the Cauliflower mosaic virus (CaMV
35S promoter), which causes disease in mustard plants in nature. Genes
in plants typically have their own promoters, which ensure that the gene
is turned on at the appropriate time in development and expressed at the
appropriate level, resulting in the production of the desired gene product.
Because viruses are genetic parasites that may infect a plant cell and hijack
its cellular machinery to create several copies of themselves in a short
amount of time, a promoter from a plant virus is employed.
The CaMV 35S promoter is chosen because it is a potent promoter that
leads to transgene hyper-expression, with transgenes expressed at levels
2 to 3 orders of magnitude higher than the organism’s own genes. As a
result, GE requires the use of a foreign promoter, which is not required in
traditional breeding, which includes hybridization and extensive crosses,
and so distinguishes GE from conventional breeding. Indeed, using the
naturally occurring promoter for most of the genes being transferred, the
plant would never be able to recognize and express the inserted gene. As
a result, a plant viral promoter must be used; hence, the widespread use of
a plant viral promoter. Most plant promoters fail to get the gene expressed
at a high enough level to complete the job, which is why the CaMV 35S
promoter was used.
Because of what we’re learning about how plants routinely turn many
genes “off” through a phenomenon known as gene silence, CaMV’s ability
to turn genes “on” is of special concern. Gene silencing appears to be an
important defense against foreign DNA infiltration, especially from disease-
causing organisms, as well as a regulator of normal gene expression. In
the last 5-10 years, scientists have discovered that genetic material can be
transferred between organisms that are unable to reproduce. Horizontal gene
flow or transfer of genes from parent to progeny is a type of lateral movement
of genetic material that occurs in nature more frequently. Horizontal gene
flow has been observed in microorganisms, and it is one of the primary
mechanisms through which antibiotic resistance or pathogenicity is
transmitted between bacteria. Viruses can also insert themselves into the
genomes of their hosts. Horizontal gene flow in plants was formerly thought
to be infrequent or non-existent. Scientists stated in 1998 that genes from a
fungus had infiltrated 48 of the 335 species of terrestrial plants studied, and
that this had happened in 32 distinct cases. They calculated that these genes
had infected higher plants over 1000 times via horizontal transfer.
Genomes are complex; research on other complicated systems has
demonstrated that introducing additional pieces can cause the whole genome
to destabilize. Indeed, normal plant development necessitates an exquisite
coordination of genes, with the appropriate set of genes being turned on
at the appropriate time during development. The plant’s regulation system
should include a method to prevent or minimize unintended disruptions of
such a complexly coordinated system. Post-integration strategies include
gene silencing techniques. Gene silencing was first observed in transgenic
plants, and it was assumed that it only happened with transgenes. Because it
causes instability, it is a substantial hurdle to genetic engineering.
Hyper-methylation of genetic material is one strategy linked with
inhibiting transcription, although the predominant mechanism for post-
transcriptional silencing is the production of aberrant RNA molecules, with
occasional DNA methylation. Indeed, transgene silencing is becoming
a more common occurrence. Several factors have been demonstrated to
impact transgene inactivation, including the insertion of numerous copies of
the transgene, transgene hyper-expression due to the use of the CaMV 35S
promoter, and environmental conditions. Gene instability is far more common
when there are several copies of the transgene and multiple insertion sites.
Because these are hallmarks of direct gene transfer technologies, which are
often utilized on cereals, we can predict more issues in these crops. The
work done in Germany with petunias that were modified with a single gene
from corn to produce a new salmon red bloom was perhaps the earliest,
and most widely studied example of such unstable transgene silencing. The
scientists worked with a line that carried a single copy of the inserted gene
at a single insertion site after converting the petunias.
Outside, 30,000 transgenic petunias with a single gene imparting the
salmon red flower color trait were cultivated and differences were noticed.
Initially, the scientists were looking for naturally occurring mobile elements
that would jump into the color gene, disrupting it and causing a different color
to emerge. These mobile elements were thought to occur at a frequency of 1
in 100 to 1 in 100,000(Meyer et al., 1992). The discovery that a considerable
majority of the plants were either poorly colored, white, had variegated
colors, or had distinct colored sectors of the flower was an unexpected
outcome. Because petunias can produce up to 50 flowers during the growth
season, any alterations in individual plants are immediately visible. During

the season, the quantity of non-salmon red flowers also increased.
Horizontal gene flow is nature's version of genetic engineering. However,
only a small number of microbes appear to be capable of inserting DNA into
plants, and plants have evolved defenses against this. Furthermore, each
insertion is a one-time event, whereas with GE, instead of a single mutant
individual arising, the environment is flooded with many altered plants, each
having DNA from sources that bacteria would never carry normally. GE
is, once again, a quantum leap beyond natural phenomena. The modified
genome is destabilized by the simultaneous introduction of the CaMV
promoter gene to override silencing. The nearly universal adoption of marker
genes that code for antibiotic resistance is another noteworthy difference
between conventional breeding and GE. Such marker genes are required to
aid in the identification of the relatively uncommon occurrences of effective
genetic transformation. The widespread usage of antibiotic resistance genes
raises the possibility that such genes could be horizontally transferred to
bacteria, making them resistant to the antibiotic in question.
It is a way of transferring genes directly into a cell, tissue, organ, or
organism utilizing bacteria. The genes found on the plasmids of the
transformed bacterial strains are transported to the cells and expressed.
Gene delivery can take place either intracellular or extracellular. It has the
ability to express heterologous proteins like antigens, toxins, hormones,
enzymes, etc. encoded by plasmids in a variety of cell types. Invasive strains
with higher cell-to-cell dissemination are more efficient. Integrin receptors
can help improve the effectiveness of bactofection-mediated gene transfer.
Integrin receptors are transmembrane surface receptors found on the surface
of mammalian cells. Lipofectamine-mediated bactofection is another
approach that has been used to improve gene transfer efficiency in E. coli
strains, notably in the transfer of large intact DNA for gene expression.
This approach works with a variety of commonly used bacterial vectors,
including L. monocytogenes and S. typhimurium.
A receptor-mediated procedure allows virus particles with candidate
gene sequences to enter the cell and then into the nuclear genome. The
vector genome goes through a series of intricate steps that result in ds-DNA,
which can either survive as an episome or integrate into the host genome,
and then the candidate gene is expressed. The cell membrane is a film of
amphipathic molecules that separates cells from their surroundings. Only
the controlled exchange of materials between the different components of
a cell and with its immediate surroundings is possible with these physical
structures. DNA is a greater molecular weight anionic polymer that is
hydrophilic and susceptible to nuclease breakdown in biological matrices.
Unless they are helped, they cannot readily penetrate the physical barrier
of the membrane and enter the cells. To assist DNA transport directly to
the cell, a variety of charged chemical compounds can be utilized. These
synthetic substances are delivered near recipient cells, disrupting the cell
membranes, expanding the pore size, and allowing DNA to enter into the
cell. They transfected human cells defective in the enzyme hypoxanthine
guanine phosphoribosyl transferase (HPRT) with entire uncloned genomic
DNA. Selection on HAT media revealed a small number of HPRT-positive
cells with pieces of DNA containing the functional gene. The real method
of DNA uptake had remained a mystery until then. The development of a
tiny DNA/calcium phosphate co-precipitate, which settles onto the cells and
is then internalized, was later discovered to be the key to effective DNA
transfer.
4.11 BIOTECHNOLOGY
Biotechnology can be viewed as a continuation of past plant and animal
breeding techniques that date back thousands of years. Compared to
traditional breeding approaches, the technology produces faster, more
exact findings and allows access to a larger genetic base. When combined
with standard breeding methods, it becomes a powerful weapon. Gene
technology’s precision is enabled by the ability to pinpoint the particular
region of a chromosome that determines any desired attribute. Traditional
breeding operations can be accelerated with this capability by locating seeds
or progeny at an early stage using gene marker technology and breeding
exclusively from them. Genes can also be extracted from one organism
and introduced into another. Transgenesis, or the transfer of genes from
one species to another, allows for the transmission of beneficial genes from
any source to other species or organisms. While conventional breeding
techniques have enhanced pest and disease resistance in Australian crops,
the natural germplasm of these crops lacks resistance to some problems,
according to the Cooperative Research Centre (CRC) for Tropical Plant
Pathology.
The promises of improved production and cheaper input costs are
currently the key attractions of GM crops for farmers. Crops that are disease
and pest resistant require less spraying, and animals that are disease and pest
resistant require less care. As a result, significant chemical, labor, and energy
input costs are reduced. Weed control is improved with herbicide-tolerant
crops, which boosts productivity. It would be feasible to make greater use
of the land if animals and crops were better matched to local conditions and
climate, for example, by being more tolerant of drought, salt, and acid. Crop
types that can make better use of soil nutrients or fix nitrogen could cut
fertilizer expenses. Growers boost their marketing possibilities by providing
higher-quality food to processors and consumers. The National Farmers’
Federation (NFF) stated in its response to the inquiry that herbicide-tolerant
soybeans have reduced overall pesticide consumption by 33% in the United
States. In Canada, herbicide-tolerant canola exhibited increased quality and
yield increases of 10-20% above conventional types. Insecticide use has
decreased by 40-50 percent in Australia because of Bt. cotton(Kilpatrick,
1996). This has resulted in higher survival of beneficial predators and
parasites, as well as a lower risk of endosulfan contamination of cattle on
neighboring ranches, which has previously resulted in their rejection by
export markets.
The fast uptake of GM crops in recent years demonstrates the benefits
of GM crops to farmers. By the end of 1998, 17 nations had approved GM
crops for planting and commercialization(Nap, Metz, Escaler, & Conner,
2003)the global area of commercially grown, genetically modified (GM.
They consisted of 56 different crops, the most popular of which were
squash, corn, canola, cotton, and tomato. GM crops have been accepted
in the United States considerably more quickly than any other technology,
and are also being grown in other nations, including Argentina and Canada.
Gene technology provides growers with new options in the form of new
products derived from existing species. Plants, for example, could one
day be genetically modified to create industrial chemicals. Trees could be
bred to produce wood with qualities similar to wood substitutes such as
steel, aluminum, concrete, and plastic. Farmers will also benefit from the
application of gene technology to reduce pest animal species and exotic
weeds.
In the coming decades, the world’s population is predicted to grow
significantly and become increasingly urbanised, resulting in increased
food demand. According to the AWB, global wheat consumption will
have increased by 38% from present levels by 2020 (Ahmadi-Esfahani
& Stanmore, 1995). Concerns have been raised regarding how the rising
demand for food will be satisfied. Some see GM crops as a way to boost
food security and assist satisfy long-term global food demands that
traditional farming methods can’t achieve. Many enhancements to the plant

and animal meals we eat are possible because of gene technology. Taste,
texture, appearance, consistency, storage properties, and nutritional content
are all likely to be improved. Nutritional quality will be the most important
enhancement of these traits. Pesticide-tolerant GM plants allow for greater
herbicide use than conventional cultivars. This is already occurring, and it
may contribute to a loss of diversity among all types of life on land, as
well as in the water and soil surrounding GM plants. Crop plants that are
herbicide-tolerant are more prone to escape into the wild. Pollen drift from
herbicide-tolerant crops to similar wild species, such as canola, could result
in the emergence of super weeds, which has already occurred in a few cases.
Bt. is present all of the time in GM crops, whereas it is only present on
rare occasions when applied as a spray; it is anticipated that the pesticide’s
presence may lead to a faster build-up of pest resistance and more harm to non-
target and beneficial insects. If crop plants that are better suited to marginal
agricultural areas are produced, more native vegetation may be cleared and
biodiversity may be lost. If terminator technology is employed, terminator
genes may spread to other organisms, resulting in the extinction of species.
GM crops, like other modern crops, are farmed in monocultures. There
are numerous environmental hazards associated with the use of herbicide-
tolerant crops, none of which are unique to GM cultivars. Herbicide-
tolerant crops may also develop weeds in non-farming areas or alternative
agricultural systems. Integrated Weed Management decreases the use of
herbicides, lowering the probability of the above-mentioned consequences.
To more effectively control and minimize potential negative repercussions,
it must be combined with early detection of herbicide-tolerant weeds. Cross-
pollination with closely related species is another way herbicide-tolerant
crops may have an impact on the ecosystem. If the herbicide resistance trait
is passed down to wild populations, it may encourage the growth of weeds.
The Genetic Manipulation Advisory Committee (GMAC) has addressed
concerns regarding the spread of GM material from GM to non-GM crops
through cross-pollination by establishing buffer zones surrounding GM
crops to reduce this risk. While buffer zones surrounding GM crops are
decided on a case-by-case basis, buffer zones around GM canola fields are
typically 400 meters in length. However, pollen from GM canola fields can
be transferred up to 15 kilometers by bees and 160 kilometers by wind.
Concerns have been expressed concerning Bt. cotton cross-pollinating
with conventional cotton or comparable wild species. A genetic obstacle,
according to the CSIRO study, limits the flow of genes from agricultural
cotton to related wild species. Cotton is also naturally self-pollinating, thus

the chances of it spreading to other locations are slim. Pest insects may
evolve resistance to the Bt. gene, resulting in unintended repercussions for
the natural environment. The development of resistance is slowed by the
interbreeding of resistant and vulnerable bugs. Bt. cotton’s impacts on non-
target insects, birds, and animals in the surrounding natural environment are
unknown, and they could harm regional biodiversity.
Several members of the committee expressed worries about the health
effects of eating genetically modified foods. Allergies to soybeans have
reportedly increased in the United Kingdom after the introduction of GM
soybean types. Antibiotic resistant marker genes, which are used with other
genes to trace their transfer from one organism to another, are suspected
of being transmitted to bacteria that cause serious disease. Virus particles
injected to confer virus resistance may also recombine with others in the
environment or in the gastrointestinal system, resulting in the emergence
of new diseases. Increased herbicide use is feasible with herbicide-tolerant
crops; nevertheless, some herbicides, such as glyphosate, are known to
have negative effects on humans. The oestrogen content of soybeans is
likewise altered by glyphosate. The safety of GM food is determined by
the substantially equivalent to its non-GM counterpart. If it is, no additional
testing is required. Only foods that are significantly different are thoroughly
evaluated.
Another disadvantage of adopting gene technology in agriculture is
the potential negative influence on farm revenue and rural communities.
Biotechnology is considered as the most recent cause of agriculture’s
industrialization, which has resulted in lower pricing for agricultural
products and forced farmers off their land. It is feared that the usage of
genetically modified organisms (GMOs) would intensify these trends.
The monopoly of a few multinational corporations over important gene
technology allows them to extract premium pricing for GMOs. Monopolistic
control of GM crops will also contribute to the global trend of declining
agricultural biodiversity by reducing genetic reserves from which future
crop varieties can be generated. It was also widely reported that Monsanto
had begun development on a ‘terminator gene,’ which would prohibit GM
plants from generating viable seeds. The terminator gene will put an end to
it, and farmers will be compelled to buy new seeds every season.
Although Monsanto has stated that terminator technology will not be
used in their seed, major concerns have been raised regarding the impact
of such a system on farmers, particularly in underdeveloped countries.

There are differing perspectives on how to overcome these dangers and
drawbacks. At one end of the spectrum of opinions on this subject is the
belief that few of the hazards will materialize, and that if they do, they will
almost certainly be remedied. Others are less optimistic about the impact
of GMOs in agriculture. At least some of the negative repercussions of
releasing genetically modified organisms into the environment are likely to
be irreversible. It may be difficult to recapture GMOs once they have been
unleashed, given their ability to self-replicate.
Several responses to the investigation offered a more pessimistic
assessment of GMOs’ consequences. They stated that more time is required
to determine the long-term health and environmental repercussions. It is
permissible to invoke the precautionary principle under these circumstances.
This principle emphasizes that when substantial or irreparable damage is
threatened, a lack of complete scientific confidence should not be used as
a justification for delaying cost-effective measures. People’s apprehension
about using gene technology in agriculture reflects, in part, their reaction
to the novel and unexpected, as well as their coming to terms with the
ramifications for how they and their society live. Some people believe that
such processes are in violation of natural laws.
CHAPTER 5
MICROARRAY TECHNOLOGY
CONTENTS
1.1 Introduction.......................................................................................... 6
5.1 INTRODUCTION
Recent technological advancements and the ability to capture, store, and
analyze large amounts of complicated biological data have resulted in
a breakthrough in our knowledge of the systems that control organisms’
development and responses to their surroundings. We’re gathering the
knowledge we need to rationally modify these organisms for specific
goals(Heller, 2002). Microarrays are an early illustration of how high-
throughput technologies can be effectively used with biological research.
Living organisms are currently thought to be made up of a huge number of
diverse biological components that interact in a controlled manner for the
purposes of development and reproduction, as well as mediating appropriate
responses to the environment. The reductionist approach has resulted in a
thorough enumeration and description of these components, which have been
grouped at several levels like organs, tissues, cells, subcellular structures,
genes, and so on. The study of how these components interact has sparked
a lot of attention recently. In terms of data collecting and analysis, the
imposition of specific treatments, and the development and implementation
of specific phenotypic assays, a thorough description of these interactions
relies on efficiencies of scale.
If we approach the problem of defining the performance of a biological
system in the most abstract way possible, we discover that collecting a large
number of formally independent measurements of the system across as many
different treatment states as is reasonably possible will eventually provide
a comprehensive description of the regulatory mechanisms governing the
system’s behavior and responses. On a practical level, this necessitates
highly parallel, precise tests as well as assay platforms that can handle
high sample throughput while remaining cost-effective. The availability of
appropriate data processing and storage resources to handle the resulting
data stream is also critical to success.
Microarrays (Figure 5.1) are one of the earliest instances of an
experimental platform that meets these criteria, and they have had an
important impact on our understanding of live organisms. This effect has
previously been observed in model organisms, and it is now spreading to
agriculturally relevant species, such as crops. The sort of data obtained
with this technology is determined by three factors: sequences immobilized
on the arrays, the nature of the hybridization targets used, and the
hybridization circumstances. Probes have traditionally been built using
known or expected gene sequences, and hence are both particular to and
Microarray Technology 109
limited by this information. Microarrays have recently been built so that

individual oligonucleotide elements increasingly tile the chromosomal
sequences, thanks to the availability of higher probe densities. This method
gives unbiased information about the complete genome’s transcriptional
activity, allowing for the discovery of new transcription units as well as the
verification of established gene models. Recent estimates of the disparity
between the 1% to 2% of all base pairs that correspond to the exons of
annotated human protein-coding genes and the approximately 93 percent of
genomic sequences that can be transcribed highlight the importance of this
latter approach to probe design.
The study of targets formed from transcripts has been the most popular
application of microarrays. They’ve recently been used to hybridize
targets obtained from genomic DNA, providing information on changes
in transcriptional activity sites, promoter binding, chromatin state, and
overall polymorphism across genotypes. Microarrays are used to profile
gene expression by separating messenger RNA (mRNA) and turning
it into fluorescent targets, such as DNA or RNA, with or without rounds
of amplification and it depends on the amounts of starting materials. The
microarrays are then hybridized with the targets. Hybridization is often done
pair-wise, with targets tagged with spectrally distinct fluorochromes whose
contributions to fluorescence hybridization may be separated by scanning
at different excitation and emission wavelengths. The two-color approach
is excellent for removing biases produced by changes between slides, such
as spot sizes that are inconsistent. Expression profiling and comparisons are
made across different treatments of biological samples; these treatments can
represent different genotypes, individuals, developmental stages, organs,
tissues, and cell types, or they can represent different biotic or abiotic
treatments imposed on the biological samples. All parts of microarray
experiments require appropriate statistical design and analysis, as well as
proficiency in developing and using this platform.
5.2 MICROARRAYS
Some scientists have deemed the usage of microarrays with predetermined
array elements obsolete, citing recent developments in methods for detecting
transcriptional activity. However, this conclusion is premature. These
statements overlook the importance of the huge number of array elements in
defining the cellular transcriptional state, as they give basically orthogonal
or distinct signals. Indeed, taken to its logical conclusion, many applications
do not require knowledge of which transcripts are represented on individual

microarrays.
Figure 5.1: Microarrays.
Source: https://www.researchgate.net/publication/26888549_Basic_Concepts_
of_Microarrays_and_Potential_Applications_in_Clinical_Microbiology/fig-
ures
The information provided by the array elements is adequate to cluster and
so characterize different cellular and therapeutic states of that organism as
long as they are specific to the experimental organism, produce statistically
significant signals, and do not cross hybridize. Microarrays’ tremendous
dimensionality calls into question efforts to standardize microarray
experiments through the adoption of “MIAME” methods. Minimal
standards, by definition, lack the richness and breadth of information seen
in microarray data sets.
Recently, academics have compiled a concise list of broad network
deductions. Combining data types that indicate diverse aspects of functional
connections between genes yields the most insightful results. Interactions
inferred by orthologies in distinct organisms, and interactions implied by
occupancy of the same metabolic pathways are among them. The genes
linked with distinct metabolic pathways have higher transcript levels
than genes associated with diverse metabolic pathways. Co-expression
analysis was used to link a significant number of Arabidopsis genes of
unclear function to clusters of known function genes. Expanding the term
reaction beyond its conventional biochemical definition to include other

interactions such as protein-protein and protein-DNA interactions, as well
as translocation events involving the movement of molecules between
subcellular compartments, allows for a more comprehensive representation
of biological processes in Arabidopsis. This wide definition resulted in the
production of curated pathways that span roughly 8% of the Arabidopsis
proteome, with the objective of representing all major biological activities.
This method can be used on any plant species (Mergner et al., 2020)proteomes
and phosphoproteomes of 30 tissues of the model plant Arabidopsis thaliana.
Our analysis provides initial answers to how many genes exist as proteins
(more than 18,000.
The identification of potential genes involved in cell-wall biosynthesis,
glucosinolate biosynthesis, and pollen development are only a few
instances of practical findings made possible by clustering investigations.
Through knock-out analysis and ectopic expression, the regulatory roles of
these genes, which encode R2R3-Myb transcription factors, were further
defined. Glucosinolates, which are found in the Brassicaceae family, are
antioxidative, anticarcinogenic, and antimicrobial compounds that play an
important role in pest and pathogen control. They are also of agricultural
and biomedical interest due to their antioxidative, anticarcinogenic, and
antimicrobial properties. The genes discovered in the first and third cases
have ramifications for biofuel production and plant breeding techniques,
respectively.
The retrieval of relevant data from databases remains a challenge, and
populating databases with various data kinds is difficult to automate. Format
compatibility is still elusive. Importantly, progress in silico appears to be
hampered by the fact that there is less information about the biological
roles of proteins and genes accessible for plants than for mammals. Some
scientists offered in-depth studies of the good and negative aspects of using
coexpression analysis on Web-based microarray data sets. However, one of
the greatest obstacles to implementing such approaches is the scarcity of
genetic information for the vast majority of crop species.
The way biologists do research has altered as a result of genomics.
Whole genome sequence information from numerous species has become
available in recent years. Not just model organisms, but also commercially
important species such as crops, human and plant infections, are among these
organisms. The focus of the post-genome era, with the help of genomics,
will be on using systematic ways to speed gene discovery by connecting
phenotypes with gene sequence and expression data in a high-throughput

manner. The two most often utilized platforms for gene expression analysis
are GeneChip high-density oligonucleotide probe arrays (Figure 5.2) and
cDNA microarrays. Because of its reproducibility and precision, as well as
the ability to analyze medium-throughput samples, GeneChip microarrays
are widely employed for large-scale genome profiling. Because of their
flexibility and inexpensive cost, cDNA microarrays are commonly utilized
for more targeted expression monitoring and other applications.
The transcriptome of plant model systems may be profiled on a massive
scale using GeneChip technology. Profiling data reveal a possible relationship
between a specific attribute and genes whose expression varies in that
particular biological activity based on pairwise comparisons of samples.
Furthermore, data mining across multiple experiments in a database aids in
the discovery of gene expression regulatory networks and the assignment of
probable roles to genes that have yet to be identified (Dalma‐Weiszhausz,
Warrington, Tanimoto, & Miyada, 2006).
Figure 5.2: GeneChip high-density oligonucleotide probe arrays.
Source: https://www.researchgate.net/publication/26888549_Basic_Concepts_
of_Microarrays_and_Potential_Applications_in_Clinical_Microbiology/
figures?lo=1
As a result, they provide a plethora of opportunities for plant development

using both traditional and molecular methods. Model systems are
commonly utilized in agricultural genomics for gene finding investigations.
Arabidopsis and rice are the model plants for this purpose. Arabidopsis is
a dicotyledonous plant with a small genome, a short life span, and a high
sensitivity to genetic changes; as a result, it has been widely employed in
molecular genetics research. The recently completed genome map provides
the first glimpse into the organization and regulation of the plant genome.
Rice, too, has a tiny genome with a lot of sequence similarity and synteny
to other monocotyledonous plants, particularly cereal crops. The recently
finished genome sequence project not only allows researchers to investigate
gene activities in this vital food crop, but it also allows them to adapt the
genes discovered in wheat, maize, and barley to other cereal species.
5.3 ARABIDOPSIS
One-third of the Arabidopsis genome is represented by the Arabidopsis
genome array, which has 160,000 perfect and mismatched probe sets for
8300 genes. Each probe is a 25 mer oligonucleotide with a surface area of
24m2. All of the probes can now be arranged in a 1.28 cm2 area(Yamada
et al., 2003). This array has been used to classify circadian regulated plant
genes; to analyze transcription patterns and uncover constitutive and
organ specific promoters, and to dissect the photoreceptor phytochrome. A
signaling pathways. Increased gene coverage per array not only allows for
whole genome expression analysis, but it also reduces the volume of material
necessary for microarray tests, as well as the cost and labor associated with
them. Genome expression analysis currently necessitates the use of a series
of arrays to cover a genome, especially for organisms with more complicated
genomes. Simulation research was done to evaluate outcomes with and
without mismatch probes in the probe set in order to maximize the capacity
of the GeneChip array. Because similar results were obtained as a result of
this work, changes to the rice genome array design were made. Mismatch
probes were removed from the rice GeneChip array, and the feature size
of each probe was lowered from 24 to 20 m2. Due to these changes, probe
sets for around 24,000 rice genes may now be found in the same array area
(Dalma‐Weiszhausz et al., 2006).
The quality of the original RNA samples has a significant impact on
the microarray findings. Controlling sample quality from many laboratories
becomes one of the most difficult tasks for a centralized facility. Biological
samples are subjected to stringent quality tests to solve this problem.

Varying RNA extraction procedures are known to produce different
sample quality, which can alter microarray results. A uniform sample
preparation protocol was devised to ensure the quality of the data, and it
was recommended to globally spread collaborators. Both spectrophotometer
assay and electrophoresis utilizing either conventional gel electrophoresis
or a BioAnalyzer were used to monitor the RNA samples received. Other
procedures, such as setting up biochemical reactions and data archiving,
were monitored with additional quality assay steps. In addition, through a
web-based interface, full sample information was collected and maintained
with the expression data.
The lack of available genetic information, especially for non-model
crops, is the main difficulty in applying microarray technology to agricultural
research. Three techniques can be used to overcome these obstacles. Because
many essential or significant genes in plants are preserved, model systems
can be utilized to identify them. Putative orthologs of these genes can be
found and isolated in economically relevant crops using sequence similarity
searches. Several vegetable crops, such as sugar beets and Brassicas, have
been studied using this method to uncover genes. 2. Microarray technology
is based on hybridization. Cross-species hybridization can be used to use a
microarray developed for a model system for closely related species. The
practicality of such a heterologous system is determined by the balance
of specific and non-specific hybridization. The sequence similarity and
abundance of the hybridising targets determine the hybridization efficiency,
which is utilized to represent the abundance level of the hybridized transcripts.
Genomic DNA can be tagged and applied to an array to find relevant probes,
which often hybridise to both model species and near relatives, to remove
the noise caused by sequence variations. Using this method, a considerable
number of the probes in the rice GeneChip array were shown to be usable
to detect gene expression in maize and barley. After administering plant
hormones like gibberellin or abscisic acid to barley aleurone cells, changes
in gene expression of landmark genes including GAMyb and a-amylases
were identified. The application of genomic arrays to non-model crops
broadens their scope.
Figure 5.3: cDNA microarray.
Source: https://www.mun.ca/biology/scarr/cDNA_microarray_Assay_of_
Gene_Expression.html
5.4 CDNA MICROARRAY

To create a cDNA microarray (Figure 5.3) for a given crop, it is important
to follow certain steps. Because they do not need previous knowledge of
genomic sequences, cDNA microarrays are beneficial for non-model systems.
Whole genome expression analysis may be difficult with this method due
to constraints in source clones and fabrication; it does give a fast way to
examine gene expression at the transcription level in parallel. Furthermore,
when comparing expression data among various kinds in species with a
high polymorphism frequency in their genome, such as maize, the bigger
probes used in the DNA microarray are preferable to the oligonucleotide
probes used in the GeneChip microarray. In any facility, a system with high-
throughput potential for cDNA microarrays was established.
Another example of how the cDNA microarray can be used is to quickly
confirm differentially expressed genes discovered using various transcription
profiling techniques. cDNA fingerprinting has a wide gene coverage,
excellent sensitivity, and is not dependent on genome sequence knowledge.
It has been widely utilized for non-model systems due to these advantages.
However, confirming that the gene segment reporting differential expression

has been found is still a time-consuming process. To speed up the validation
process, the discovered differentially expressed gene fragments were cloned
and spotted onto a glass slide using a cDNA microarray in a huge parallel
test. The results revealed a strong link between the two technologies. The
cDNA microarray confirmed 41 of 48 randomly selected differentially
expressed gene segments, whereas three were slightly confirmed.
DNA microarrays were first described in 1995 for analyzing large-scale
gene expression patterns at the same time(“Use of a CDNA Microarray
to Analyze Gene Expression Patterns in Human Cancer,” 1996). They’ve
risen to popularity in several fields of biological research since then, and
are currently playing an increasingly vital role in diagnostics, genetics,
pharmacology, cancer, and other biomedical research, among others. The
use of DNA microarrays in plant disease detection and identification,
particularly viruses, viroids, and phytoplasmas is evident. They are
particularly dangerous because of their difficulty in detecting and identifying
them. Many quarantine and certification procedures exist, particularly in
industrialized nations, to avoid the entry of these infections into a country
during international germplasm movement and to regulate and decrease their
spread within a country. Biological indexing, immunological techniques,
molecular hybridization, polymerase chain reaction (PCR), and/or reverse
transcription (RT)-PCR are now used to detect these infections.
DNA microarrays were first unveiled in 1995, and biologists have
been fascinated by this technology ever since. It is a great tool for genetic
study since it can display the expression of thousands of genes at the same
time. It is now used in genomics for sequence analysis, gene expression
studies, gene typing, and large-scale polymorphism screening; biomedical
research for understanding cancer, infectious diseases, and genetic diseases;
clinical diagnostics; and drug discovery and development. It was anticipated
that there will be simultaneous detection and identification of many plant
viruses, viroids, and other plant diseases using DNA microarrays due to the
explosion of information resulting from plant virus and viroids sequencing.
These approaches show how to use probes that are detected by a signal,
whether radioactive or fluorescent. However, in recent years, a number of
technologies have been developed that allow massive parallel investigation
of hybridization events by applying vast numbers of DNA oligonucleotides
to surfaces in ordered two-dimensional arrays. Along with techniques such
as quantitative PCR and microarrays were presented as a tool for assessing
the levels of gene expression of numerous genes in a high throughput
analysis. The underpinning idea of DNA microarray is base-pairing of

complementary sequences via hybridization. A target DNA or RNA can
hybridise to a complementary DNA probe on the array due to DNA binding.
Thousands of cDNAs or oligonucleotides make up each probe, each one
specific for a gene, DNA sequence, or RNA sequence of interest. An array is
a collection of samples arranged in a logical sequence. It provides a platform
for comparing known and unknown nucleic acid samples using base-pairing
criteria and automating the identification process. A few nano-itres of DNA
probes are deposited on a solid support to create each array. The printing
is done by a robot, which enables for repetitive spotting of identical spots.
The size of the sample spots determines whether an array is classified as
a macroarray or a microarray. Macroarrays have sample spot sizes of 300
metres or more. Microarray sample spots are typically less than 200 m in
diameter, and these arrays frequently have thousands of dots (Brazma et
al., 2001)one limitation has been the lack of standards for presenting and
exchanging such data. Here we present a proposal, the Minimum Information
About a Microarray Experiment (MIAME.
Microarrays having a density of less than 100 spots per cm2 are sometimes
referred to as low-density. Low-density arrays are available from a variety
of commercial sources or can be made in-house by research organizations.
For low-density arrays, a glass surface is frequently used. Plain glass, which
is usually prepared before use, binds poorly to nucleic acids. Poly-L-lysine
is frequently employed for this purpose because it binds molecules through
ionic interactions. The glass substrate can alternatively be coated with
saline, which binds to the probe DNA covalently and prevents it from being
removed throughout the hybridization and washing procedures. Glass slides
for detecting radioactively tagged nucleic acids can be coated with a nylon
membrane to which DNA probes are covalently cross-linked using UV light.
The DNA put to the array’s surface might be plasmids with 500-5,000 bases,
complementary DNA with several hundred bases, PCR products with 100-
500 base pairs, or synthetic oligonucleotides with an amino or Thiol group
on their 5’ end (Quackenbush, 2001)2001.
Microarrays with a density of 1,000-10,000 spots per cm2 or greater
are referred to as high-density. The phrase DNA chip is commonly used to
describe such high-density arrays. Chemically modified glass or silicon are
commonly utilized as the immobilization substrate for high-density DNA
arrays. The technological breakthrough represented by DNA microarray
technology is its massive parallel nature, or the ability to apply thousands
of nucleotides in an ordered array to a surface, allowing simultaneous

investigation of thousands of distinct sequences.
Short or long oligonucleotides, cDNAs, chromosomes, entire organisms,
or others with known identities can all be used as probes. Standard
technologies like restriction enzymes, cloning, and PCR can be used to make
the probes. They can also be bought individually or mounted to chips, glass
slides, or nylon supports. Purchased and generated cDNA or oligonucleotide
probe libraries are available. Thousands of these cDNAs or oligonucleotides
make up each probe, each one specific for a gene, DNA sequence, or RNA
sequence of interest. The baker’s yeast Saccharomyces cerevisiae was
used to create arrays containing oligonucleotides representing known
genes. More than 65,000 DNA synthesis characteristics were included in
oligonucleotide arrays. Because oligonucleotides are intrinsically only of
known sequences, cDNAs can have the advantage of being unknown, an
experiment utilizing cDNAs could potentially help identify the function of
hitherto uncharacterized and un-sequenced genes, including viral genome
genes.
Microarrays have become a significant tool for studying gene
expression in people, animals, plants, and microbes on a global scale. cDNA
and oligonucleotide arrays, when used in the context of a well-designed
experiment, can allow high throughput, concurrent analysis of transcript
abundance for hundreds, if not thousands, of genes. Despite widespread
acceptance, however, the use of microarrays as a tool to better understand
processes of interest to plant physiologists is still under investigation.
Microarrays are being used to evaluate gene expression in plants exposed to
experimental manipulations of air temperature, and aluminum concentration
in the root zone based on the results. Characterizing transcript profiles for
various post-treatment sampling periods and categorizing genes with common
response patterns using hierarchical clustering approaches are important
parts of analysis. Furthermore, microarrays are revealing developmental
changes in gene expression linked to fiber and root extension in cotton and
maize, respectively. Microarrays are a powerful tool for plant physiologists
interested in the characterization and identification of individual genes and
gene families with potential applications in agriculture, horticulture, and
forestry, despite the fact that much work remains to be done.
5.5 COTTON FIBERS

Cotton fibers are single-celled trichomes that distinguish them from the
developing cotton ovule’s epidermal layer. They proceed through a rapid cell
expansion phase, then a secondary cell wall deposition phase, and eventually
maturity. Cotton fibers are thus unique in that they are one of the longest and
fastest-expanding plant cells, making them a useful experimental system for
studying fundamental processes in plant biology. Cotton fiber elongation
begins on the day of anthesis and ends around 21 days later, overlying with
the onset of secondary cell wall generation, according to research. During
this time of development, many genes are known to be transcriptionally
regulated. However, progress in identifying genes responsible for cell
elongation has been modest. The considerable time it takes to regenerate
transgenic cotton lines and the absence of adequate transient assay techniques
have hampered such research. Using mutants with altered fiber elongation
kinetics is one technique to get around these problems and study more about
the molecular mechanisms that control cell elongation in growing cotton
fibers.
The difference in mature fiber length in the Pilose mutant was related
mostly to changed growth rate, not to early termination or late commencement
of the elongation period, according to fiber length measurements taken
throughout development. The researchers employed cDNA microarrays to
explore the underlying molecular pathways that were responsible for the
decreased growth found in Pilose fiber using this as their model system.
Cotton cDNA microarrays contained 4875 cDNAs from isolated fibers
7–10 days after anthesis, constituting a unigene collection of expressed
sequence tags (ESTs)(Wu et al., 2007). On each slide, each probe was
duplicated twice. Cotton and non-plant sequences were also spotted in each
replication to assess non-specific hybridization aided by the cDNA probes’
poly-T tails. One of the most stimulating discoveries was that four separate
targets on the cotton cDNA array representing expansins exhibited a five-
fold decrease in expression for Pilose mutant fibers. Expansins are cell wall
proteins that affect the mechanical characteristics of cell walls through pH-
dependent mechanisms, resulting in cell wall loosening and turgor-driven
cell expansion.
According to the findings, expansins are one of the most significantly
repressed gene families in elongating Pilose fibers as a result of lower
cell development rates. Two expansin genes called GhExp1 and GhExp2
produced transcripts that are unique to growing cotton ovules, suggesting that
GhExp1 may be involved in cell wall extension during cotton fiber formation.
However, the question is whether the suppression of expansins is the major
and exclusive determinant of shorter fiber length in the Pilose mutant using
data from their microarrays. Profilin, an auxiliary protein of actin filaments,
was decreased in Pilose. Profilins have a variety of biological functions and
influence the actin cytoskeleton in different ways. This finding backs up the
theory that the Pilose phenotype is caused by a combination of processes,
including both expansins and cytoskeleton dynamics. These concepts
will need to be explored more in future studies. To better understand the
mechanisms that underpin the changed phenotype, plans are now underway
to construct comprehensive time-series expression profiles for both control
and Pilose mutants. The researchers at the University of Missouri presented
an overview of a project in which microarrays were used to characterize
gene expression for root elongation in maize for understanding the molecular
mechanisms of fiber elongation in cotton.
5.6 MOLECULAR ANALYSIS

The molecular analysis of gene expression under stress exposure of plants
is one of the most common applications of microarrays in plant physiology.
Under uniform light and moisture conditions, cold stress (5°C) and a heat
shock (32°C) treatment were used. At 1, 2, 4, 8, and 12 hours after the start
of each treatment, leaf samples were obtained from treatment and control
plants, and mRNA was extracted, labeled, and hybridized to the array. Four
distinct groups of reactions emerged from the hierarchical clustering of
genes that showed at least an eight-fold shift in response to cold stress. The
upregulated genes were separated into two groups: one in which transcript
levels increased at first and subsequently declined over time, and the other in
which transcript levels increased continuously during the treatment period.
Cold stress, circadian rhythms, and drought tolerance, lipid metabolism, and
different membrane transporters and transcription factors were among the
genes identified.
Downregulated genes were also split into two groups: one in which
transcript levels progressively declined and subsequently increased, and the
other in which transcript levels decreased continuously throughout time.
Photosynthesis, cell and cell wall development, cellular signaling, and
several genes with unclear functions were all downregulated. Hierarchical
clustering of genes with a 4-fold change in expression revealed four separate
classes of reaction in the instance of heat shock. Upregulated genes were
separated into two categories, the first of which had the highest transcript
levels during the first hour of treatment and thereafter declined. The
majority of these genes were heat shock proteins. After 2 hours of treatment,
transcript abundance was also high, and many of the genes in this second
group were connected to defense. Genes involved with growth inhibition
or auxin-repressed protein and cell signaling were among the 30 transcripts
that were downregulated. Northern blot tests confirmed many of these
expression patterns, the function of particular genes up- and downregulated
by light freezing and heat-shock treatments will be investigated further in
future investigations. These findings point to the prospect of discovering
new genes involved in heat and cold temperature responses, as well as the
temporary nature of these responses. The highly up- and downregulated
proteins with unknown functions are of special relevance in this regard.
Furthermore, these studies could provide insight into the coordinated,
multigenic responses to temperature stress, as well as the identification of
master regulators that could be used as future genetic engineering targets.
5.7 TRANSCRIPT PROFILING

Transcript profiling (Figure 5.4) can help researchers find candidate genes
underpinning quantitative trait loci (QTLs) for yield and other agronomic
variables in agricultural plants grown under a variety of environments.
There’s a lot of interest in utilizing DNA microarrays to track gene
expression profiles in crops that have limited soil water availability. Stress-
inducible genes can be easily found in plants exposed to fast dehydration.
Researchers identified 44 drought-inducible genes in Arabidopsis following
a 2 h dehydration using microarrays containing 1300 full-length cDNAs.
Some researchers recently used cDNA microarrays to identify large-scale
changes in transcript abundance for barley exposed to rapid drought shock
treatments (van Dongen et al., 2009). Research that imposes slower, more
realistic rates of dehydration, as well as studies that compare the ensuing
gene expression profiles to those from plants exposed to drought-shock
therapies, are needed.
Plants were grown in sand until they reached the four-leaf stage, at which
point water was withheld by removing them from the sand and allowing
them to dehydrate for six hours. In a second, more traditional ‘water-stress’
experiment, potted plants were grown in a greenhouse until they reached the
four-leaf stage, then water was incrementally withheld for 11 days until the
moisture content of the soil mix dropped to around 40% of maximal water-
holding capacity.
Figure 5.4: Transcript profiling.
Source: https://www.semanticscholar.org/paper/Microarray-technology%3A-
beyond-transcript-profiling-Hoheisel/5198b8b18713f831e321b3b9ac9bbb21c
9a03e86/figure/1
mRNA was extracted, labeled, and hybridized to microarrays comprising
1463 DNA elements generated from barley cDNA libraries from tissues of
treated and control plants. Signal intensity differences between control and
treatment plants greater than 2.2 times in two replicated tests were considered
significant. Microarray analysis of mRNA isolated from water-shock and
control tissues generally verified the alterations in transcript expression
levels. Under rapid drought stress, over 15% of all transcripts were either
upregulated or downregulated. Jasmonate-responsive, late-embryogenesis-
abundant (LEA), and ABA-responsive proteins were among the transcripts
that showed considerable overexpression.

Aluminum toxicity inhibits root elongation as its principal consequence.
Different species or crop cultivars may react to aluminum in different ways,
and these reactions may have a genetic or molecular basis. Plants (some)
detoxify aluminum in the rhizosphere by producing organic acids that chelate
the metal before it is absorbed by the roots, while others detoxify aluminum
internally by building complexes with organic acids. Unfortunately, the
precise process by which plants tolerate metals in general, and aluminum
in particular, remains completely unknown for the vast majority of plants.
cDNA microarrays were used to assess differences in gene expression for
tolerant and susceptible cultivars exposed to aluminum in understanding
the molecular mechanisms associated with aluminum tolerance in wheat
(Triticum aestivum L.).
In hydroponic culture, seedlings of the cultivar Chisholm that are Al
sensitive and its isogenic line Chisholm-T (Al-tolerant) were developed.
Chisholm-aluminum T’s tolerance is developed from the Al-tolerant cultivar.
Three-day-old seedlings were given an aluminum concentration of 10 mg/l,
which was high but not fatal. The seedlings were cleaned and moved to
deionized water after twenty-four hours. The roots of aluminum-stressed
and control plants were stained with haematoxylin for 15 minutes. The
deposition of a high level of aluminum in roots is indicated by high-intensity
staining. The roots of Chisholm-T and Atlass 66 were mildly stained 24
hours after exposure to aluminum, whereas the roots of the Aluminum-
sensitive cultivar Chisholm were quite black. Suppression subtractive
hybridization was performed to identify transcripts that changed between
cultivars following exposure to aluminum, which was used to produce the
microarrays used. This method was employed to create subtracted cDNA
libraries by combining normalization and subtraction into a single step.
The array revealed sequence tags from 1628 differentially expressed cDNA
clones. At 6 hr, 1 day, 3 days, and 7 days following aluminum stress, the
arrays were hybridized with cDNA from Chisholm-T and Chisholm roots.
In a single reaction, the microarray approach is utilized to detect numerous
diseases infecting plants simultaneously. As a probe, virus-specific oligos
immobilized on a membrane or glass slide are used in this procedure. Total
RNA from infected plants is transcribed to cDNA and amplified by PCR
using pathogen-specific primers, which are then labeled with appropriate
molecules for detection. After that, the amplified and labeled products are
placed on the array and allowed to hybridize. Following washing, the array
will be produced according to the label applied, and the outcome will be
visualized using a CCD and appropriate software.
5.8 GM CROPS
The debate about genetically modified (GM) plants and their potential
influence on human health contrasts with the implicit acceptance of other
modified plants that aren’t classified as GM products like varieties raised
through conventional breeding such as mutagenesis. We can compare the
level of transcriptome alteration that occurs during transgenesis versus
mutant breeding for rice improvement. The observed modification was
more extensive in mutagenized plants than in transgenic plants in all of
the situations studied. The safety evaluation of modified plant types can be
done on a case-by-case basis, rather than being limited to foods obtained
through genetic engineering. Thousands of years ago, plant breeding began
with the unintentional selection of seeds from plants with superior quality
and productivity. People began to use deliberate interbreeding or crossing
of closely or distantly related species to develop novel crops with desirable
traits when sexual plant reproduction was discovered in the 17th century.
Plant breeders and geneticists began to employ mutagenesis to rapidly
develop and increase diversity in crop species and ultimately change plant
features after discovering that x-rays induced mutations in the fruit fly
Drosophila melanogaster and barley at the turn of the twentieth century.
Classic mutagenesis’ high efficiency has been well documented, and its
global influence on agricultural development has also been assessed.
Advancements in molecular biology techniques have paved the way
for the development of genetic engineering since the 1970s, allowing
agricultural cultivars to reach the next level of genetic gain. This technology
allows researchers to identify, isolate, and transfer a gene of interest from
any type of organism to plant cells. Tissue culture is used to regenerate
transformed plants from these cells. In contrast to the widespread acceptance
of food items derived from traditional plant breeding, the potential benefits
of this new technology have been largely ignored due to the intense debate
over food safety. Despite the lack of universal methods for assessing the
potentially harmful effects of genetic modification, the FAO and the European
Food Safety Authority recommend that macro, micro, and anti-nutrients,
toxins, allergens, and secondary metabolites are evaluated using targeted
approaches. Some molecular profiling methods have also been developed to
boost the odds of finding unwanted consequences. Microarrays are one of

the profiling approaches described. This method enables the simultaneous
monitoring of thousands of genes.
Pearson’s correlation between samples revealed that duplicate samples
always clustered together and modified genotypes always grouped with
their respective unmodified controls after hierarchical clustering of
microarray data of transgenic, mutagenized, and control plants. Genetically
stable samples like the transgenic single-chain variable fragment or ScFv
and mutant Estrela A are more closely associated with their corresponding
controls than unstable samples, regardless of the type of breeding method
used. Transgenic Nipponbare is also more closely connected to its control in
unstable lines than the line acquired with 100-Gy-irradiation. In the unstable
mutagenized rice line, 11,267 genes displayed differential expression,
whereas only 2,318 genes were discovered in the non-stable transgenic line,
as seen in volcano plots (Nishizawa et al., 1999).
Because down-regulation of a nitrilase-associated protein was
discovered in the mutant line, some differentially expressed genes found
in the stable Estrela A line can be linked to a lower indole-3-acetic acid
(IAA) content. Nitrilases are enzymes involved in the production of IAA, a
plant hormone that belongs to the auxin family of plant growth regulators.
Because the phosphatidylinositol signaling pathway is also involved in
plant responses to hormones like auxins, the enzyme phosphatidylinositol
3-kinase, which belongs to the signal transduction functional group, could
be linked to this predicted lower IAA level. It was discovered that, a group
of genes involved in protein modifications whose altered transcription could
be linked to the lower IAA concentration. This group included one F-box
domain-containing protein and the ubiquitin carboxyl-terminal hydrolase,
both of which are involved in ubiquitination. F-box proteins are adaptor
components of the SKP1-CUL1-F-box protein complex, a modular E3
ubiquitin ligase that engages in phosphorylation-mediated ubiquitination.
Protein ubiquitination is a precise technique for regulating gene function
by sending tagged proteins to the proteasome for degradation, and it has
been proposed as a key control system in desiccation resistance. Because
auxin regulates transcription by stimulating the degradation of a family of
transcriptional repressors known as Aux/IAA proteins, which is dependent
on an ubiquitin protein ligase known as SCF, the downregulation of these
2 proteins could be explained by a drop in auxin levels. The F-box protein
TIR1 attaches to the Aux/IAA proteins in the presence of auxin, resulting in
their ubiquitination and destruction.
One copy of the CBF1 gene is present in the unstable transgenic line
Nipponbare GM. C-repeat binding factors (CBFs) regulate the expression
of several stress-inducible genes by interacting with the cis-acting
dehydration-responsive element-DRE. Despite the fact that the BCBF1
gene is controlled by a stress-inducible promoter. As a result, the differential
expression of stress-related genes seen in research might be due to either
the stress induced by the Agrobacterium-mediated genetic change or, at
least in part, the inserted CBF1 transcription factor. To further elucidate
this point, we can look for DRE core motifs in the promoters of the top 50
differentially expressed genes. We can observe that nearly all of the top 50
genes had several DRE core motifs in their promoter regions. As a result,
it appears that the differential expression of these genes is primarily due
to the transgene incorporated. This finding emphasizes the significance of
carefully examining transformants with inserted transcription factor-coding
genes.
Microarray technology is increasingly being used in the agro-food branch,
as it is in other disciplines in the biological sciences, to address basic and
applied research concerns. The goal of this chapter is to provide an overview
of microarray technology’s application in agricultural research by focusing
on one of the most pressing challenges in modern agriculture biotechnology:
the generation of genetically modified crops. Microarrays can be used to
investigate any form of interaction in which the arrayed material can be
properly deposited and the binding reagent can be hybridized and directly or
indirectly labeled, or its binding can be identified in another way. Microarrays
were first used to mimic Southern and northern blot investigations, but
they have a lot of potential for studying other kinds of interactions, such
as those between proteins and proteins and other substrates. Protein-based
microarray applications were originally developed shortly after DNA-based
microarrays were released, but their progress has been much slower since
then. Developing protein microarrays as part of our functional genomics
study has long been a goal of mine. However, like many others, we initially
focused on nucleic acid-based microarrays because we thought they were
more well-established and easier to perform.
CHAPTER 6
DROUGHT RESISTANT PLANTS
CONTENTS
1.1 Introduction.......................................................................................... 6
6.1 INTRODUCTION
Drought is the leading source of agricultural loss around the world, posing
a serious danger to food security. Plant biotechnology is now one of the
most promising fields in terms of producing crops that can provide high
yields in water-scarce environments. The key response pathways to drought
stress have been discovered through studies on Arabidopsis thaliana plants,
and numerous drought resistance genes have already been put into crops(S.
Wang et al., 2004). So far, most plants with increased drought resistance have
had lower agricultural yields, indicating that new techniques to uncoupling
drought resistance from plant development are still needed. Brassinosteroid
(BR) hormone receptors use tissue-specific pathways to mediate various
developmental responses during root growth. Boosting BR receptors in
vascular plant tissues offers drought resistance without compromising
growth in Arabidopsis, providing a unique opportunity to examine the
mechanisms that confer drought resistance in plants with cellular specificity.
6.2 DROUGHT
Drought is described in agronomy as the absence of water that impacts
plant development and survival, resulting in lower crop yields. The broadest
definition of drought stress in plant science is the same as the definition
of water deficit, which occurs when transpiration exceeds water intake.
This will be due to a deficiency of water, but it could also be due to higher
salinity or osmotic pressure. The water loss from the cell, or dehydration,
is the first process during drought stress, according to molecular biology.
Dehydration normally causes osmotic and hormone-related signals, with
abscisic acid (ABA) playing a key role in the latter. These signals trigger
a response that can be divided into three categories. They are drought
escape (DE), dehydration avoidance (DA), and dehydration. DE is a plant’s
attempt to speed up flowering time before drought threatens its existence.
This response is prevalent in annual plants, including the model species
Arabidopsis thaliana (Arabidopsis), and cereal plant breeders use it to their
advantage.
Even amid water scarcity, the plant can maintain a high relative water
in dehydration avoidance. This is accomplished by physiological and
morphological responses such as reduced transpiration via ABA-mediated
stomatal closure, deposition of cuticular waxes, and a slower life cycle for
the plant. Dehydration avoidance usually results in plant survival by delaying
plant growth and, as a result, senescence and mortality. This approach
Drought Resistant Plants 129
arose in response to moderate, transient drought stress, in which the plant

falls into developmental hibernation until the next rain. While dehydration
avoidance is helpful in boosting plant survival, it often comes with growth
and yield losses, which are, of course, substantial drawbacks for crop
breeders. Dehydration tolerance, on the other hand, is the ability of a plant
to sustain its activities in a dehydrated state by increasing the production of
sugars, osmoprotectants, antioxidants, and reactive oxygen species (ROS)
scavengers through modulation of plant metabolism. The modulation of
the GA-signaling molecule DELLA, a pathway that integrates multiple
hormones and stress-related pathways usually activates these responses.
DE and early flowering cultivars with quicker life cycles are attractive
from an agronomic standpoint because an expected changeover to the
reproductive stage could allow grain filling prior to the beginning of the
seasonal terminal drought. A shortened crop season also minimizes the
demand for agricultural inputs such as fertilizers and pesticides and may
make double cropping possible i.e., the farming of two different crops in
the same field within the same year. Crops that flower too early, on the other
hand, will have their yield reduced. Despite the fact that DE is a growing
research subject in crop science, no biotechnologically enhanced crops that
use DE as a drought resistant characteristic exist. Still, it’s been suggested
that DE may be used to produce fast-growing, early-flowering grain varieties,
which would be particularly advantageous in temperate climates like the
Mediterranean, where terminal dryness is likely to damage plants near the
end of the crop season. Furthermore, OsFTL10, one of the 13 Blooming
locust-like (FTL) genes listed in the rice genome, has recently been found
to be triggered by both drought stress and GA, and when overexpressed
in transgenic rice plants, promotes early flowering and enhances drought
tolerance. However, because these transgenic rice lines were not evaluated
in a field trial, it is unknown whether altering FTL genes could result in grain
kinds that perform well in both dry and wet circumstances and provide high
yields(Sharma et al., 2019). Nonetheless, manipulating the DE route could
be a novel and effective method, especially given the extremely changeable
nature of water availability. Due to the fact that DE includes specific tissues
like leaf, phloem and cell types like phloem companion cells, FD-expressing
SAM cells, it may be able to build drought-resistant plants by manipulating
these plant components and tailoring DE to the various climatic conditions.
6.3 STOMATA
Stomata, which are apertures on the surface of a plant’s aerial section,
are surrounded by two specialized guard cells that change their turgor
pressure to open and close the pore. Stomata are important for CO2 uptake
in photosynthetic organs and are tightly controlled by a molecular process
that permits plants to take in CO2 while limiting water loss. Manipulation
of stomatal quantity, size, and control was one of the first tactics used by
scientists to create drought-resistant plants. In water-stressed situations,
the major hormone signal that causes stomatal closure is ABA. The CLE25
peptide is translocated to the leaves, where it binds to barely any meristem
(BAM) receptors, causing ABA buildup and stomatal closure in the leaves.
Increasing stomatal responses in response to drought by manipulating ABA
sensitivity could help plants survive. Condensed photosynthetic activity
as a result of low CO2 uptake, on the other hand, is usually deleterious to
carbon assimilation and has a negative impact on crop yield. Furthermore,
evaporation of water through stomatal pores keeps plants from overheating.
Reduced stomata capacity may not be a viable way to improve drought
resistance while maintaining yield and biomass production in a natural
environment because drought is likely to be followed by warm temperatures.
It was discovered that constitutive expression of AtNF-YB1 in
Arabidopsis enhanced the survival rate of transgenic seedlings in an early
attempt to generate drought-resistant plants. Nuclear factors Y (NF-Y) are
heterotrimeric transcription factors that regulate a variety of developmental
pathways, including stomatal responses via modulation of the ABA
signaling pathway, and have conserved functions in Arabidopsis and cereals
during flowering. Under the direction of the rice actin 1 promoter, one
maize homolog of AtNF-YB1, ZmNF-YB2, was expressed constitutively.
In a greenhouse experiment, maize transgenic plants had a higher survival
rate, showing the functional conservation between Arabidopsis and maize
NF-YBs. Due to a combination of greater stomatal conductance, cooler leaf
temperatures, higher chlorophyll content, and a delayed onset of senescence,
the transgenic plants were also drought resistant in field trials. Nonetheless,
despite encouraging findings in field testing, with the highest performing line
having a 50% increase in yield relative to controls under extreme drought
circumstances, these transgenic lines were never commercialized, possibly
because yield in watered conditions was severely affected.
Manipulation of stomatal kinetics, or more precisely, enhancing the
speed of stomatal responses, could prevent the trade-off between stomatal
conductance and drought tolerance. The expression of a synthetic blue
light–induced K+ channel 1 (BLINK1) under the control of the strong

guard cell–specific promoter pMYB60 recently improved plant stomatal
dynamics (Cosentino et al., 2015). This significantly sped up stomatal
responses, resulting in plants that responded to changing light conditions
more quickly. When compared to control plants, Arabidopsis WUE i.e.,
biomass per transpired water was improved without reducing carbon fixation
rates, resulting in a 2.2-fold increase in total biomass in transgenic plants
maintained in water-deficit circumstances. It is yet to be investigated if this
strategy would be effective in open-field crops, or whether the extra biomass
would result in a higher yield. Overall, altering stomata physiological
behavior is a great breakthrough that has yet to be applied to crops (Kenney,
McKay, Richards, & Juenger, 2014).
In the Alxa Desert of China, the distribution characteristics of Na+, K+, and
free proline were studied in succulent xerophytes Haloxylon ammodendron
and Zygophyllum xanthoxylum; xerophytes Artemisia sphaerocephala and
Caragana korshinskii; and mesophytes Agriophyllum squarrosum and
Corispermum mongolicum. The findings revealed that mesophytes and
xerophytes were salt-free species, with Na+ values ranging from 1.5 to 3.8
percent lower than succulent xerophytes. K+ concentrations were 1.3–2.7
times higher in Agriophyllum squarrosum and Corispermum mongolicum
than in Artemisia sphaerocephala and Caragana korshinskii. Agriophyllum
squarrosum and Corispermum mongolicum had K+ concentrations in their
stems that were 1.8 and 2.2 times higher than in their roots, respectively. Water
transport over a soil–plant gradient may be aided by mesophytes accumulating
substantial amounts of K+ in their stems. Large amounts of K+ and free
proline were collected by the xerophytes. Their proline concentrations were
6.0–16.0 times greater in the total plant than in mesophytes, and 1.8–25.0
times higher in succulent xerophytes. Proline concentrations increased by
3.1 and 10.5 times in Artemisia sphaerocephala from roots to stems and
stems to leaves, respectively. Caragana korshinskii had a similar pattern. As
a result, xerophytes’ accumulation of K+ and free proline may play a role
in drought adaptation(S. Wang et al., 2004). Haloxylon ammodendron and
Zygophyllum xanthoxylum, two succulent xerophytes, were found as salt
diluting species that absorbed a lot of Na+ from their roots and carried it to the
leaves and photosynthesizing branches. Even at low soil salinities, succulent
xerophytes gathered more Na+ than K+ for osmotic adjustment, resulting in
the root systems having the lowest selective absorption and selective transport
capacities. This implies that accumulating Na+ rather than excluding it could
be one of the most successful methods for succulent xerophytes to adapt to
arid settings.
The main reason for C. polygonoides productivity differences appears

to be changes in soil water content and nutrients. The competitive effect
of D. sindicum grass, which appears to have a larger competitive effect
on resource usage, was blamed for lower plant growth in FGP and SDP
habitats. The variation in D. sindicum grass density and root biomass, which
was negatively linked with growth increments and soil water, was explained
by differences in growth and biomass production. The findings show that
surface vegetation has an impact on C. polygonoide productivity through
modifying soil resource availability. As a result, proper water management
will be useful to increase the productivity and population of this species
under the afforestation programme.
Figure 6.1: Drought-resistant crop.
Source: https://www.frontiersin.org/files/Articles/483633/fpls-10-01676-HT-
ML-r1/image_m/fpls-10-01676-g001.jpg
6.4 DROUGHT RESISTANT CROPS

Fully drought-resistant crop plants (Figure 6.1) would be beneficial, but
selection breeding has not produced them. Genetic modification of species
by the introduction of genes is claimed, predominantly, to have given drought
resistance. Experiments in soil with cessation of watering demonstrate
drought resistance in GM plants as later stress development than in wild-
type (WT) plants. This is caused by slower total water loss from the GM
plants which have smaller total leaf area (LA) and/or decreased stomatal
conductance (gs), associated with thicker laminae or denser mesophyll
and smaller cells. Non-linear soil water characteristics result in extreme
stress symptoms in WT before GM plants. Then, WT and GM plants are
overwatered: faster and better recovery of GM plants is taken to show their
greater drought resistance.
Mechanisms targeted in the genetic modification are then, incorrectly,
considered responsible for the drought resistance. However, this is not valid
as the initial conditions in WT and GM plants are not comparable. GM plants
exhibit a form of ‘drought resistance’ for which the term ‘delayed stress
onset’ is introduced. Claims that specific alterations to metabolism give
drought resistance are not critically demonstrated, and experimental tests are
suggested. Small LA and gs may not decrease productivity in well-watered
plants under laboratory conditions but may in the field. Optimization of GM
traits to the environment has not been analyzed critically and is required in
field trials, for example of recently released oilseed rape and maize which
show drought resistance, probably due to delayed stress. Current evidence is
that GM plants may not be better able to cope with drought than selection-
bred cultivars.
Molecular biology techniques have offered the possibility of directly
altering the genomes of higher plants for more than 30 years to change their
metabolism and improve growth and yield under adverse environmental
conditions to better serve human needs. One of the main areas has been
to overcome abiotic environmental factors that restrict agricultural
productivity, such as long generation times. Drought, or a shortage of water,
has a significant detrimental influence on plant and crop productivity. The
goal has been to genetically engineer drought-resistant plants. The terms
genetic engineering or modification have been used to describe the processes
of modifying plants. Hybridization, cell fusion, and tobacco transformation
with a drought-inducible histone gene were all used to try to find and
transmit genes responsible for DR between species. Drought-induced gene
expression in plants has influenced the course of drought research ever since.
As a result, candidate genes that are likely to confer DR in crop species have
been found.
Many types of genes and their control, such as gene promoters and
transcription factors, are thought to have a wide range of consequences and
benefits. Proponents of genetic engineering believe that the mechanisms
impacting agricultural output caused by drought are well understood, and
that the constraints can be alleviated by correct metabolic improvements
via genome modification (GM). GM makes a strong case for being based
on precise knowledge of mechanisms and the ability to manipulate key
metabolic processes to produce a precise outcome and to improve both
absolute and relative crop production per area of land surface, as well as to
improve water use efficiency (WUE) when water is scarce and thus mitigate
or even eliminate drought effects. Despite scientific and practical evidence
to the contrary, there is a general, pervasive ethos in the GM literature that
natural selection has not adequately provided DR plants and that GM is
the only way to achieve the desired changes because selective breeding
is incapable of doing so in any reasonable time scale. Claims in the GM
literature that GM plants have resulted in the development of DR plants
must be investigated.
The social and economic importance of increasing productivity under
water scarcity is huge, and producing true drought-resistant plants would
be a major accomplishment. The world’s present human population is 7
billion, and it is predicted to grow to 10 or possibly 12 billion by 2050,
necessitating the production of food, fiber, and energy(Bloom, 2011).
Agriculture is practiced in many regions across the world where water
availability is typically insufficient compared to evapotranspiration from
crops, resulting in crops receiving insufficient water to reach their genetic
potential production. Drought is a big issue in the long run, but it also
reduces agricultural output in the near run, even when other conditions are
favorable, and can have severe economic and social effects. Water supply
varies greatly at different times during the growth and development of
specific crops, and the consequences can be highly unique. Plant processes,
from genome to growth and production and that means total biomass as
well as economic yield and quality of crops are highly reliant on water and
are extremely vulnerable to drought; losses are difficult to estimate but are
undoubtedly in the millions of tonnes with significant economic value.
During the introduction of agriculture, advantageous plant traits, as

well as the discovery and application of applicable technology, increased
yields of basic crops. Despite what may have been a tendency to select
for productive genotypes in dry environments, crops nevertheless rely
considerably on water. More recent selection breeding based on scientific
principles has not resulted in drought-resistant crops, but has resulted in
smaller improvements; for example, using carbon isotope differentiation in
wheat breeding improved yields by 5% with a 50% yield reduction and by
10% with a 75% yield reduction(McLaughlin & Adams Kszos, 2005)a native
perennial warm-season grass, as a dedicated energy crop is reviewed. The
programmatic objectives were to identify the best varieties and management
practices to optimize productivity, while developing an understanding of
the basis for long-term improvement of switchgrass through breeding and
sustainable production in conventional agroecosystems. This research has
reduced the projected production cost of switchgrass by about 25% ($8–
9Mg−1. Evolved systems allow crops to continue to produce despite severe
water shortages, and they lay the groundwork for further improvement
through selective breeding and molecular genetics data. In contrast, certain
GM publications give the idea that GM plants are ‘DR’ and thus unaffected
by water scarcity.
6.5 GM TECHNOLOGY
GM technology has been justified based on its potential to produce DR
crops faster and more efficiently than selective breeding, hence alleviating
food shortages. The potential for GM to boost food production in drought-
prone locations, such as developing economies in Africa, has received
special attention, despite the fact that the chances of even moderate success
are slim. There have been a lot of claims that GM would produce DR crops.
They stand in contrast to the belief that GM technology will not improve
drought tolerance. Despite this, the prospect for speedy fulfillment of the
objectives has resulted in significant adjustments in research funding and
education in favor of GM technology. Drought has not resulted in greater
yields despite massive investments in GM by public entities and, in particular,
major corporations. There is still a body of opinion emphasizing the need
to understand the effects of water supply and deficits on plant mechanisms
from genome to yield including GM technology, of altering plant and crop
responses and thus improving plant processes like photosynthesis and
crop production. As evidenced by analysis of quantitative trait loci in DR
breeding, the latter is clearly a function not merely of the genome, but of the
entire complex plant system. Understanding requires a focus on the details of
mechanisms, but it is also necessary to consider the entire system. However,
very specific genome interventions produce drought resistance in the lab
but have yet to produce clear evidence of significant improvements in crops
under drought in the field, and those concerned with crops have high doubts
about the ability of GM approaches to provide drought resistance.
Drought, salinity, cold, and other abiotic stressors have a significant
impact on plant output. Plant yields of essential major crops can be reduced
by up to 50% as a result of these stressors(Mahajan & Tuteja, 2005). Abiotic
stress-related genes or other transcription factors (TFs) have multiple
functions, such as increasing proline content, decreasing transpiration rate
by closing stomata, increasing the production of some important stress-
related protective enzymes, and so on, and thus increasing abiotic stress
tolerance. Many transcription factors (TFs) and other stress-related genes
have been discovered, described, and applied to a variety of essential
cultivated plants to protect them against drought and other abiotic stresses.
Transgenic plants outperform non-transgenic plants in terms of morpho-
biochemical and physiological performance. Wheat, rice, tomato, soybean,
cotton, and a variety of other genetically modified plants have been designed
to withstand drought stress. Researchers are increasingly turning to the
effectively engineered clustered regularly interspaced short palindromic
repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system to modify
plant genomes for natural resistance to a variety of abiotic stressors. It is
the leader in genomic editing by precise methods, with little or no effect on
plant growth and development.
6.6 SOYBEAN
Soybean is the economically important oilseed crop on the planet. Soybeans
that have been processed are also the most common source of vegetable
oil and protein feed. Soybeans contain secondary metabolites such as
isoflavones, saponins, phytic acid, oligosaccharides, and phytoestrogens in
addition to macronutrients and minerals. In 2007, global soybean production
was estimated to be around 219.8 million metric tonnes (mmt). The United
States produced the most soybeans (70.4 million tonnes), followed by Brazil
(61 million tonnes), Argentina (47 million tonnes), and China (14.3 million
tonnes)(Manavalan, Guttikonda, Phan Tran, & Nguyen, 2009). While
soybeans have long been used in Japan to make traditional foods like tofu,
miso, shoyu, and vegetable oil, consumption of soybean-based products is

increasing worldwide due to reported health benefits such as cholesterol
reduction, cancer prevention, diabetes and obesity prevention, and protection
against bowel and kidney disease. Soybean is also seen as a promising crop
for biodiesel production. It may also fix atmospheric nitrogen, using only a
small amount of nitrogen fertilizer, which is often the single largest energy
input in agriculture.
Plants are exposed to abiotic and biotic stimuli that have an impact on
their growth and development. Water scarcity, in particular, is expected to
remain a major abiotic issue affecting worldwide crop production. One-
third of the world's population lives in water-stressed areas, and with rising
CO2 levels in the atmosphere and expected climatic changes, droughts may
become more common and severe in the future. It was believed that the
resilience of legume crops to current climatic extremes, such as drought,
excess water, heat, cool weather during grain filling, and early frost, can
forecast their response to future climate change. Drought affects soybean
yields by roughly 40%. During the growing season, soybeans consume
roughly 450–700 mm of water, depending on hybrid traits. It was found that
the most crucial phase for water stress in soybeans is during the blooming
stage and the period following flowering.
6.7 DROUGHT STRESS

Drought stress causes plants to utilize a variety of methods to cope.
Drought escape allows the plant to finish its life cycle while there is
enough water available prior to the commencement of the drought. In
most cases, the life cycle is shorter, and plants produce a few seeds rather
than a complete crop failure. The Early Soybean Planting System, which
is now commonly employed in the southern United States, is an example
of drought resistance. Short season cultivars are planted in March–April in
places where later maturing cultivars have previously been produced in this
way. Early maturing cultivars flower in late April to early May and set pods
in late May, finishing the reproductive stage before the potential drought
period of July–August. Drought avoidance is the second mechanism, and
it entails techniques that help the plant maintain a high-water status during
times of stress, either by efficient water absorption from the roots or by
minimizing evapotranspiration from aerial portions. Drought tolerance is
the third mechanism that permits the plant to sustain turgor and metabolism
even when the water potential is low, for example by protoplasmic
tolerance or the manufacture of osmoprotectants, osmolytes, or suitable

solutes. One of the ways for increasing soybean production is to maintain
optimal transpiration, which leads to higher WUE. Phenology, photoperiod
sensitivity, developmental plasticity, leaf area index, heat tolerance, osmotic
adjustment, early vigor, rooting depth, and rooting density are the features
that have been studied.
The huge diversity of PI lines and cultivars available around the
world provides valuable resources for identifying germplasm that can be
employed in root trait breeding. The time-consuming techniques required
in root separation, as well as the lack of quick screening procedures, are the
key roadblocks to genetically improving root features. Because the most
potential genetic mechanism for enhancing soybean drought tolerance is
a deep taproot system with a moderate quantity of lateral roots to collect
soil water, study in this area is critical. Overall, root characteristics have a
lot of potential for breeding to improve drought resistance. Selection based
on root phenotypic measurement, on the other hand, would be extremely
challenging. Molecular tagging, on the other hand, will make it easier to
breed for root-related features. Another alternative methodology is the
candidate gene approach, which entails selecting a candidate gene for root
traits from public data, obtaining primer sequences to amplify the gene,
uncovering polymorphisms, developing a simple procedure for large-scale
genotyping, identifying a population for association studies, conducting an
association study of the candidate gene with trait phenotype, and finally
verifying the uncovered associations. Under low moisture conditions, this
method proved successful in identifying candidate genes associated with
root number in rice.
Understanding the physiological mechanisms and genetic regulation of
root drought adaptation would aid in the identification of relevant genes and
metabolic pathways for gene-based marker selection or genetic engineering
to generate soybeans with improved root-related attributes. Drought-induced
nitrogen fixing: Thenitrogen (N2) fixation by legumes is highly sensitive
to soil dryness. Soybean not only loses CO2 accumulation and leaf area
development during drought, but its symbiotic N2 fixation is also at risk. It
was found that in dry soils, the supply of N2 for protein formation, which is
the plant’s important seed product, is reduced, resulting in lower crop yields.
Reduced oxygen availability, reduced carbon flux to nodules, decline in
nodule sucrose synthase activity, and an increase in ureides and free amino
acids have all been linked to the inhibition of N2 fixation during drought.
During the first four days of dryness, nitrogenase activity dropped

by 70%, whereas photosynthesis only dropped by 5%. This means that
water stress affects nitrogenase activity in a way that is independent of the
photosynthetic rate. Water deficiency was also discovered to have a direct
impact on nodule activity by increasing resistance to oxygen transport to
the bacteroid. Increased oxygen diffusion resistance, decreased nitrogenase-
linked respiration and enzyme activity, accumulation of respiratory
substrates and oxidized lipids, and up-regulation of antioxidant genes all
show that the respiratory activity of bacteria is impaired in drought, and that
oxidative damage occurs in nodules before any effect on sucrose synthesis
or leghaemoglobin. Soil drying also causes ureides to accumulate in soybean
leaves, which are hypothesised to be nodulation inhibitors. The sensitivity
of N2 fixation in response to soil drying was discovered to have a lot of
genetic diversity. When comparing soybean germplasm with and without
the ability to maintain tissue turgidity, and thus leaf and nodule function,
under drought conditions at the reproductive stage, the germplasm with the
ability to maintain tissue turgidity had the lowest grain yield reduction. The
first step in identifying soybean lines whose N2 fixation is more tolerant of
soil dryness is to test for petiole ureide levels. The variety Jackson, which is
more resistant to N2 fixation in drying soils, has been employed as a parent
for creating drought-tolerant lines.
It’s uncertain if N2 fixation is only regulated at the whole-plant level via a
systemic nitrogen feedback mechanism or if it might also happen at the local
nodule level during drought. There is evidence that a N2 feedback system
involving shoot N2 status can give signaling for biological N2 fixation. A
combination of ureide and aspartic acid levels in nodules, as well as the
transfer of various amino acids from the leaves, may be implicated in a
feedback inhibitory process in soybean. It was found that N2 fixation activity
under drought stress is primarily controlled at the local level rather than by a
systemic N2 signal in a partially droughted split-root system. More research
should be done to better understand the molecular genetics of the processes
that restrict and regulate N2 fixation under drought conditions.
6.8 RAINFALL
Rainfall is becoming less and less irregular as a result of human-caused
climate change, especially in areas where food security is extremely low. The
poor in rural and dry places will be the hardest hit, and will require low-cost,
easily accessible ways to cope with unpredictable weather. This adaptation
will have to account for not only a lack of water and droughts, but also
an increased likelihood of extreme occurrences such as floods. Ecological
approaches to making farms more drought-resistant and adaptable to harsh
events rely on biodiversity and healthy soil. Resilience is the tendency to cope
with and recover from change. Farm output and income are more resilient and
stable when soils are better able to hold soil moisture and decrease erosion,
as well as when biodiversity is increased in the system. Building healthy soil
is critical to assisting farmers in coping with drought. There are a variety of
proven soil-building strategies accessible to farmers right now. Cover crop
residues that protect soils from wind and water erosion, as well as legume
intercrops, manure, and composts that build soil rich in organic matter and
improve soil structure, are all ways to improve water infiltration, hold water
once it gets there, and make nutrients more accessible to plants. It is critical
to boost productivity in rain-fed places where poor farmers apply existing
water and soil conservation knowledge in order to feed people and ensure
ecological resilience. Under a drier and more irregular climate, ecological
farms that work with biodiversity and are knowledge-intensive rather than
chemical input-intensive may be the most resilient options.
Figure 6.2: Drought-resistant crop.
Source: https://www.researchgate.net/profile/Ashkan-Jalilian/post/In_cli-
mate_change_will_the_temperature_increase_be_harmful_to_agricul-
ture_Or_reduced_rainfall/attachment/5c61fd6acfe4a781a57efb82/AS%
3A725255265996800%401549925738200/image/climate-change.jpg
Agriculture will have to adjust to changing rainfall patterns as the

climate changes (Figure 6.2). Water is the most important component of
food production. Human-caused climate change is already leading to less
and more irregular rainfall, particularly in areas with low food security.
Rain-fed farms, which cover 80% of the world’s agriculture, produce more
than 60% of the world’s food. Rain-fed farms provide 95 percent of food
in Sub-Saharan Africa, where climate unpredictability already affects
agricultural production. Climate change will have an impact on river flow
and groundwater in South Asia, where millions of smallholders rely on
irrigated agriculture for survival. Mexico had its driest year in seven decades
in 2009, with major social and economic consequences. It came after a
ten-year drought that had already ravaged the country’s north and western
states. Furthermore, climate models show that as a result of global warming,
Mexico will continue to dry. Climate change will intensify conflicts over
water allocation and the already precarious status of water availability as
temperatures rise and rainfall becomes less and less unpredictable. The poor
in rural and arid areas will be the hardest hit by these changes, and they
will require low-cost, easily available ways to cope with the unpredictable
weather. Since the Neolithic Revolution, which was triggered by the
advent of agriculture 10,000 years ago, humans have been using natural
biodiversity to adapt agriculture to changing conditions (Putterman, 2008).
Diversity farming is the single most significant tool for adapting agriculture
to a changing climate.
The intrinsic diversity and complexity of the world’s farming systems
prevent a single solution from being pursued. Agriculture under a changing
environment necessitates a variety of tactics. We can look at the successes
and evaluate the potential of traditional breeding approaches, such as marker-
assisted selection (MAS), to generate drought-resistant cultivars without the
environmental and food safety issues associated with genetically modified
(GE) crops. Plants have evolved natural ways to cope with drought over
millions of years, with water scarcity being the principal constraint to plant
growth. From improved root growth to control of water loss in leaves, these
mechanisms are complex and diverse. Frequently, developing cultivated
crops under ideal well-watered conditions results in the loss of characteristics
that allow them to cope with less water. The diversity of plant characteristics
available to deal with minimal water in industrially grown crops has been
diminished in the rush to build greater industrial monocultures fuelled by
agrochemicals and enormous irrigation. Crop varieties and wild relatives,
on the other hand, retain this diversity.
Drought and salt are two main environmental challenges that affect
peanut production over the world. Drought stress is thought to be responsible
for a $500 million loss in peanut production per year. Because major peanut-
producing countries like China, India, Nigeria, and the United States are
all experiencing significant water shortages for agricultural irrigation, it is
possible that global peanut production could suffer in the future. Climate
change predictions suggest that extreme weather, notably drought, would
become more frequent in the tropical and subtropical regions of the world,
making peanut production extremely difficult in the future. Peanut is a
popular food in Africa, Asia, and North and South America because it is
one of the most nourishing foods for oil and protein. Reduced peanut output
will raise the price of peanuts and peanut-derived items like peanut butter,
putting people in many nations in a difficult situation. The great challenge
now is to maintain, if not increase, peanut production to meet the demands of
our growing population at a time when the conditions for peanut cultivation
are deteriorating.
Due to the rarity of genes for drought and salt tolerance in existing
peanut germplasms, the traditional method of breeding for drought and
salt-tolerant peanuts has been slow. Gene for drought or salt tolerance is
discovered in a wild peanut relative, introgressing the gene into cultivated
peanut cultivars will be challenging due to the reproductive barrier, not to
mention the lengthy time required for many generations of back-crossing.
With the development of molecular biology, a biotechnology approach
offers a powerful alternative for more efficiently producing drought and salt-
tolerant peanuts. Indeed, several genes that confer drought and salt tolerance
have been introduced into diverse crops and tested in laboratories and in the
field over the last 20 years, with a few of those genes showing significant
potential for commercial release. The DREB/ CBF family of transcription
factor genes, for example, has been widely exploited to improve stress
tolerance in a variety of crops. In the future, this group of genes could be
valuable in developing heat and drought tolerant peanuts. Other sorts of
genes, in addition to transcription factor genes, may be effective in peanut
enhancement. ABA or cytokinin biosynthesis pathways, antioxidation
metabolisms, and stress signal transduction pathways are among the genes
encoded by these genes. In the future, some of these functional genes may
be valuable in enhancing peanut stress tolerance.
We must be able to modify peanuts in order to boost their stress tolerance
using a biotechnology technique. Previous attempts to alter peanuts
utilizing Agrobacterium-mediated gene transfer or biolistic bombardment
were mostly successful. However, the efficiency of these efforts in terms

of transformation was relatively poor, ranging from 0.3 percent to less
than 10%. Researchers developed a peanut transformation process that
raised peanut transformation efficiency to 55% or higher, making peanut
transformation reasonably simple and repeatable. More crucially, this novel
approach appears to be adaptable to a wide range of peanut ecotypes, despite
the fact that it still uses Agrobacterium as a vehicle.
Overexpressing the Arabidopsis vacuolar pyrophosphatase gene AVP1
in transgenic peanut plants increased drought and salt tolerance at the
same time. The proton pump vacuolar pyrophosphatase generates a proton
chemical gradient across vacuolar membranes. For their actions, several
secondary transporters, such as the Na+/H+ antiporter i.e., AtNHX1, rely
on the proton chemical gradient formed by proton pumps like AVP1. Proton
pump activity may be increased by boosting Na+/H+ antiporter activity,
resulting in increased salt tolerance. Overexpression of AVP1 in transgenic
plants increased drought and salt tolerance. The strong root development
produced by enhanced auxin polar transport in transgenic plants was
responsible for the higher drought tolerance in the AVP1- overexpressing
plants. AVP1 and its homologs are overexpressed in various plants, and
in all cases, enhanced drought and salt tolerance have been found. In the
greenhouse, AVP1-overexpressing peanut plants were drought and salt
tolerant, producing more biomass and maintaining greater photosynthetic
rates and transpiration rates under reduced watering and saline conditions.
When plants are exposed to environmental challenges such as high
salt or drought, defense systems are activated. Many investigations have
demonstrated that these defense systems rely on protective processes
triggered by changes in stress gene expression levels. Solanum tuberosum,
an agricultural species, is an autotetraploid with a complex, quantitative
inheritance pattern. Thus, traditional methods of breeding new potato
cultivars that are tolerant of salinity and drought stress are laborious,
complex, and time-consuming, taking between 10 and 15 years on average.
Potato cultivars can be improved faster and more reliably using genetic
engineering techniques. Numerous potato stress genes, including those
that code for functional and regulatory proteins have been isolated and
characterized using homologue gene screening, differential screening,
microarray analysis, and proteome analysis as a first step toward developing
drought and saline tolerant potato plants using molecular breeding methods.
Abiotic stress genes encoding functional proteins including proline
synthesis protein, osmotin-like protein, GPD, trehalose synthesis protein,
and regulatory proteins like StEREBP, CBF, and StRD22 have been used in
various attempts around the world to generate drought- and saline-tolerant
potato plants.
Water is a well-known environmental component and a crucial limiting
factor for plant growth, development, and production. Due to constantly
changing environmental circumstances, plants frequently have a fluctuating
water supply throughout their life cycle. The variability of drought tolerance
among plants of the same species has not been fully explained. Plant responses
to water stress are influenced by plant species, age, growth and development
phases, drought severity and duration, and physical characteristics. There
are recognized differences in drought tolerance among genotypes of plant
species, such as maize, wheat, and triticale. Plants use a variety of strategies
like morphological, physiological, and biochemical to reduce or eliminate
the negative consequences of stress.
It was observed that adding polyethylene glycol (PEG) to a hydroponic
solution causes osmotic stress, which causes changes in the water status of
the tissues and a decrease in plant growth and biomass production. Drought-
resistant genotypes, on average, collect more biomass in their leaves than
susceptible genotypes. Drought-stressed physiological processes include
leaf water content and gas exchange. Reduced CO2 availability owing
to stomatal closure is usually thought to be the cause of a decline in
photosynthesis during mild drought. When dryness lasts for a long time,
however, non-stomatal mechanisms induce a decline in photosynthesis.
Changes in photosynthetic activity are linked to mesophyll cell membrane
degradation, a decrease in chlorophyll concentration, and disruptions in
assimilate synthesis and transport. Photosynthesis limitations caused by
stomatal and non-stomatal mechanisms are dependent on plant species,
stage of development, and leaf age, as well as the duration and degree of
drought stress.
CHAPTER 7
DISEASE RESISTANT PLANTS
CONTENTS
1.1 Introduction.......................................................................................... 6
7.1 INTRODUCTION
Plants face a diverse range of climate-induced biotic and abiotic stresses
in the current era of drastic climate changes such as global warming,
irregular rainfall, and depletion of arable land and water resources. Stress is
a negative situation for plant growth and development that can be produced
by environmental, biological, or both factors (Collinge, Lund, & Thordal-
Christensen, 2008). Concurrent occurrence of two or more different types
of stresses such as drought and salinity, drought and heat are more harmful
to global agricultural productivity under natural settings. Abiotic challenges
that occur at the same time affect plant metabolism and reduce yield more
than abiotic stresses that occur at various phases of growth. Drought and
heat stress in the summer, or drought and salinity stress in the winter, are
instances of coupled abiotic stresses. Pests, diseases, insects, and weeds are
all regulated by abiotic stressors (Figure 7.1).
Figure 7.1: Abiotic stressors.
Source: https://www.mdpi.com/2223-7747/10/2/186#
7.2 WEEDS
Weeds outcompete crops under abiotic stress due to their increased water
consumption efficiency. Abiotic stress has a significant impact on plant
growth, resulting in significant output losses. In most plant species, the
resulting growth reductions can be as much as 50%. The yield of maize
can be lowered by up to 40%, and the yield of wheat can be reduced by up
to 21% with a 40% water reduction. Cowpea yield is also reduced, with
Disease Resistant Plants 147
reductions ranging from 34% to 68% depending on developmental stage

and drought stress (Ashraf & Foolad, 2007). The yield drops in cowpea, an
important crop in Africa and a source of food for millions of farmers, varies
greatly depending on the developmental stage and the intensity of drought
stress. In 2002, it was estimated that soil salinity alone cost more than US$11
billion per year and destroyed about 10% of the world’s arable land, having
a significant impact on global food production and being regarded as the
primary stress affecting worldwide crop yield.
Depending on the number of interacting components, stress is classified
as single, multiple, concurrent, or repeating. Single stress is made up of only
one stress component, whereas multiple individual stressors are made up
of two or more stresses that happen at the same time without overlapping,
and concurrent stresses are made up of two or more stresses that happen
at the same time but with some overlap. Plants are subjected to single or
numerous stresses, which are followed by recovery periods that can be short
or lengthy in duration. At various stages of plant development, several hot
days or repeated bouts of drought and heat stress may occur. The interplay
of multiple stress factors can either increase the plant’s tolerance capacity
or predispose it to a variety of pressures. Drought, for example, promotes
the establishment of Macrophomina phaseolina in the roots of Sorghum
bicolor, resulting in a significant decrease in productivity.
Similarly, in North China, the occurrence of concurrent drought and
cold stress reduces the production of Vitis vinifera. Plants growing in hot,
dry environments, such as arid and semi-arid locations, are frequently
confronted with the development of salinity and heat stress. Cold and
light stressors are the most common in the Mediterranean region, and they
affect plant growth and development. Concurrent cold and ozone stresses,
as well as concurrent salinity and ozone stresses, lower the frost durability
of Triticum aestivum and the production of Cicer arietinum, respectively.
Similarly, the combination of salt and ozone stress contributes to lower yields
in chickpea and rice varieties. Plants are exposed to a variety of concurrent
biotic pressures, similar to abiotic stresses, and are harmed more severely
by the combination of fungal and bacterial infections than by infections with
these pathogens alone. Researchers studied the occurrence of multiple biotic
stressors at the same time and their effects on plant growth and yield. Plants
have evolved a perceptual network that allows them to perceive both biotic
and abiotic stressors at the same time, allowing them to reduce the harmful
effects of stress. Depending on the timing and severity of biotic stresses
such as powdery mildew, rust, and wilt, the impacts of abiotic pressures
such as drought or salinity may lead to either susceptibility or resistance of

plants to biotic stresses such as powdery mildew, rust, and wilt.
The type of the interactions between the stressors, as well as the length
of stress exposure, can have a variety of consequences on plant growth and
overall output.
The magnitude of the impact on crop yield is also determined by the
nature of the interconnections between stressors. For example, abiotic–
abiotic pressures such as concurrent drought and heat stress can result
in higher soil water evaporation, resulting in a lower crop yield. It was
reported that weeds outcompete crops due to their efficient water use
ability during concurrent drought and heat stress, and that the synergistic
effects of drought and heat stress on physiological aspects of plant growth
result in a substantial reduction in crop yield. In tropical and subtropical
conditions, these concurrent stressors produce a significant decline in leaf
water potential and transpiration rate, resulting in increased leaf and canopy
temperature. Concurrent stress-induced increases in transpiration rate have
been shown to alter important physiological processes in plants, according
to several researchers.
Figure 7.2: Drought and heat stress.
Source: https://www.frontiersin.org/files/Articles/388913/fpls-09-01705-HT-
ML/image_m/fpls-09-01705-g004.jpg
Drought and heat stress (Figure 7.2) have a significant impact on

nutrient relationships, slowing growth by limiting nutrient mobility through
diffusion and reducing root mass, number, and growth. Drought and heat
stress damage photopigments and thylakoid membranes, resulting in
decreased chlorophyll biosynthesis and increased chlorophyll breakdown, or
a combination of the two processes. Light reactions in the thylakoid lumen
and light-dependent chemical reactions in the stroma are both affected by the
damage caused by these concurrent stressors. Photosystem II is particularly
susceptible to concurrent stressors, and its activity is considerably altered
or even decreased to zero under severe heat stress. Heat stress promotes
pathogen growth and leads to the emergence of a wide range of bacterial
and fungal diseases, such as tomato wilt caused by Ralstonia solanacearum,
seedling blight and bacterial fruit blotch of cucurbits caused by Acidovorax
avenae, and panicle blight in rice caused by Burkholderia glumae. Heat
stress inhibits plant growth and development while promoting pathogen
growth and reproduction. Heat stress stimulates the growth of many vectors,
boosting the incidence of vector-borne diseases in addition to its promoter
effects on pathogen growth.
Figure 7.3: Salinity and pathogen stress.
Source: https://link.springer.com/article/10.1007/s40502-019-00483-7/fig-
ures/2
Salinity and pathogen stress (Figure 7.3) are another example of

concurrent biotic–abiotic stressors. Pathogen virulence, plant physiology,
and microbial activity in the soil are all influenced by salinity. Salinity
produces increased sporulation in fungus and causes severe Fusarium wilt
in tomatoes. The root system architecture refers to the root system’s spatial
architecture or RSA. In cereals, the genetic regulation of the RSA and its
link to higher output under stress has been thoroughly demonstrated. Roots
facilitate water and nutrient intake, develop symbiotic relationships with
fungi and bacteria, provide anchoring, and serve as storage organs, all of
which are important in crop production. They also serve as the primary
interface for interactions between plants and numerous stress elements, and
they are critical in reducing the damaging effects of stress on plant growth
and development. The organization and structure of the roots, such as their
length and density, dictate the types of interactions that occur between roots
and stress stimuli. Increased root length density (RLD) and a large root
diameter are associated with drought resistance in rice varieties. Drought-
resistant rice varieties have a higher RLD which facilitates access to moisture
in the deeper layers of the soil.
Maize with a higher RLD and fewer lateral roots had a higher
photosynthetic rate, a better plant water status, and more stomatal
conductance under drought stress than maize with a lower RLD and more
lateral roots. The presence of fewer but longer lateral roots resulted in greater
use of water available in deeper levels of the soil due to improved rooting,
allowing the plant to function better under drought stress. The RSA is also
important for preventing pathogen infection in plants. T. aestivum lines
with longer roots were less susceptible to fungal infection with Pythium
debaryanum and Pythium ultimum. The fungal pathogen Rhizoctonia solani
reduced root length, root branching, and root tips, resulting in reduced water
absorption from deeper soil layers. It may be argued that increasing the
RLD can significantly minimize pathogen infection. The RSA is important
in crop plant responses to drought stress and pathogen attack; however,
in field circumstances, drought and pathogen stress frequently occur
simultaneously, resulting in higher plant damage owing to RSA disruption.
Plants that experienced progressive drought with 2 and 4 days of Ralstonia
solanacearum infection were classified as experiencing short-duration (SD)
and long-duration (LD) stress stresses, respectively, in a study of chickpea
plants exposed to concurrent drought and infection with the pathogen
Ralstonia solanacearum (Sinha, Gupta, & Senthil-Kumar, 2017).
7.3 GROWTH AND REPRODUCTION

The pathogen’s growth and reproduction were reduced by SD combined
stress, while there was no difference in LD combined stress. Drought and
the fungus Fusarium solani both inhibited the growth of Phaseolus vulgaris.
Root rot induced by the pathogen is the reason for the lowered growth,
which limited water intake from deeper layers of the soil. Plant size, leaf
area, hydraulic conductance, photosynthetic and transpiration rates have
all been documented to decline when drought and pathogen stress coexist.
Plants’ molecular responses to coupled drought and pathogen stress have
recently been studied in a few major molecular studies. This research has
shown several viable possibilities for improving plant tolerance to mixed
stimuli as well as provided light on plant defense systems against combined
stresses. Methionine gamma lyase and azelaic acid induced 1 are some of the
major candidate genes identified thus far. Genes implicated in the cross talk
between the drought-associated and pathogen infection-associated signaling
pathways contribute to tolerance to combined drought and pathogen stress.
Some studies have suggested that proline and polyamine metabolism play a
role in combined drought and pathogen stress tolerance in A. thaliana and V.
vinifera. The identified candidate genes can be regulated in the right way to
improve tolerance to these combined stresses. Genome editing technologies
such as the CRISPR/Cas9 system can be used to make the changes. By
guiding catalytically inactive dead Cas9 (dCas9) or dCas9 coupled with
transcriptional repressors/activators to the promoter of a gene, CRISPR/
Cas9 can also be utilized to control the transcription of genes of interest.
More study in this field, utilizing various functional genomic techniques,
could reveal plant responses to coupled drought and pathogen stress.
Plants in the field are exposed to a variety of abiotic and biotic
challenges, and to counteract these impacts, they have evolved sophisticated
signaling networks. Plant growth may be affected negatively or favourably
by interactions between the two types of stress conditions. A concurrent
drought, for example, might regulate the interaction of different diseases
and plants in different ways, resulting in pathogen development being
suppressed or increased. As a result, studying the interplay between the two
types of stresses is critical in order to better understand the overall impact
of stress combinations on plants. Several important diseases, such as dry
root rot, powdery mildew, and charcoal rot, are significantly influenced
by concurrent drought conditions, and a mechanistic understanding of the
interactions between pathogen and drought stress can aid in the identification
and development of superior cultivars. Improved crop performance under
combined drought and disease stress necessitates a deeper understanding

of the issues. Transcriptomic research has already begun in an attempt to
comprehend the interconnections.
Drought and pathogen stress on plants have also been combined in well-
designed studies, revealing some elements of drought–pathogen interactions.
To find superior germplasm lines, plant genotypes can be tested for features
like root system architecture, leaf water potential, leaf turgidity, leaf
pubescence, and leaf cuticular waxes. It is critical to develop studies that can
highlight distinct features of interactions between the two different forms of
stress in order to vividly assess the effects of different stress combinations
on plants. A well-designed stress imposition methodology that is similar to
pressures that occur in the field, together with relevant physiological assays
and recently developed genomic technologies, can aid in the discovery of
plant responses to stress combinations. Breeders and field pathologists can
use the knowledge gained from studies on plant responses to combined
drought and disease conditions to better examine the performance of tolerant
genotypes. In areas where the two pressures coexist, further development of
crop simulation models containing a mix of drought and pathogen stress
could aid disease predictions. As a result, collaborative efforts by crop
modeling experts, agronomists, field pathologists, breeders, physiologists,
and molecular biologists can lead to the development of combined stress
tolerant crops that perform well in the field.
Plant diseases are responsible for significant yield losses in most crop
species, putting global food security and sustainability at risk. Plants defend
themselves against pathogen invasion in one of two ways: qualitative or
vertical or total resistance mediated by disease resistance (R) genes,
or quantitative or horizontal or partial resistance regulated by multiple
genes or quantitative disease resistance (QDR) genes. To manage disease
incidence and yield losses, crop resistance to pathogens can be improved
by conventional breeding, marker-assisted breeding (MAB), and transgenic
development. As a result, we need to figure out which genes are involved in
both qualitative and quantitative disease resistance. Major resistance genes
encoding cytoplasmic proteins with nucleotide-binding and leucine-rich
repeat domains or NLR proteins are frequently used to provide qualitative or

complete resistance. These NLR proteins detect pathogen derived chemicals
termed effectors, which are delivered into the host cell by a pathogen and
thereby facilitate infection, either directly or indirectly. After effector
recognition, an NLR protein mediated defense response is triggered, which
includes a hypersensitive response (HR); rapid, localized programmed cell
death at the point of pathogen penetration; and other responses such as ion
flux, an oxidative burst, lipid peroxidation, and cell wall fortification.
7.4 QTL
In other words, many quantitative trait loci (QTLs) (Figure 7.4) govern QDR,
which interact with each other as well as the environment. QTL-mediated
resistance has smaller individual effects than R gene-mediated resistance,
but it is broad-spectrum or non-race specific, and thus is seen as a promising
alternative to less durable race specific resistance for crop improvement.
Pathogen associated molecular pattern (PAMP) triggered immunity (PTI)
and effector-triggered immunity (ETI) are the two major innate immune
responses seen in plants. Activation of mitogen-activated protein kinases
(MAPKs), induction of reactive oxygen species (ROS), callose deposition,
and stimulation of pathogenesis-related (PR) genes are all part of the PTI
response. An early response to pathogen infection is a ROS burst, which
strengthens cell walls by cross-linking glycoproteins and activating defense-
signaling components. To block the host PTI response and produce a
favorable host cell environment, the pathogen releases effector chemicals
into plant cells. Intracellular sensors encoded by resistance (R) genes with
a nucleotide-binding site and leucine-rich repeats (NBS-LRRs) in plants
detect pathogen effectors directly or indirectly, leading to ETI. ETI imparts
significant resistance to specific pathogens, particularly for a specific race,
and elicits a hypersensitive response; but, due to the rapid evolution of
disease effectors, this is not long-lasting.
Figure 7.4: Quantitative trait loci.
Source: https://www.nature.com/articles/35072085
Non-host resistance, or the phenomenon in which most plants are
resistant to most microbial diseases and thus contribute to quantitative
resistance, is influenced by PTI. To find the genetic loci controlling
multiple disease resistance loci, often known as QDR loci, researchers have
utilized linkage analysis, a nested association mapping (NAM) technique,
and genome-wide association studies (GWAS). This technique identifies
loci that contain hundreds of genes and several candidate genes, making
it challenging to pinpoint the causal gene. Multiple connected genes have
been found to underpin a single QDR locus in some circumstances such
as clusters of functionally related defensive genes involved in secretory
processes and cell wall reinforcement. QDR is difficult to genetically
dissect, as are other quantitative traits, and the link between phenotypes
and molecular mechanisms is not well understood. Due to minor genetic
effects, variability in disease severity across different geographical areas,
and lack of uniformity in the evaluation of disease symptoms, map-based
cloning of resistance conferring QTLs has proven to be extremely difficult.
Disease resistance durability is difficult to assess in a short period of time,
and evaluating durability is complicated if the QTLs have distinct genetics.
When a resistance QTL is changed in a highly susceptible background,

for example, it may have a greater effect. Despite the fact that some of
these genes have been used, their usage in elite cultivars has been limited
due to their close association with genes that govern undesired agricultural
properties. Wheat Lr34 lines, for example, produce less grain than Lr34-free
lines, the recessive barley mlo mutant induces early senescence-like leaf
chlorosis. Cloning QDR loci has been difficult due to the minimal influence
of numerous QDR loci and the difficulties of phenotyping disease features
consistently. Tremendous progress has been made in narrowing down
mapped QDR locations to the individual gene level. In recent years, advances
in DNA, RNA, and protein sequencing technology, as well as bioinformatic
analysis of sequencing data, thus allowing us to quickly locate QTLs and
identify candidate genes in many crops for a variety of traits, including
disease resistance. Gene mapping through bulked segregant RNA-seq (BSR-
seq), MutMap, target-enriched X-QTL, genotyping by sequencing (GBS),
indel-seq, and exome aide from these, new genome-editing techniques, such
as zinc-finger nucleases (ZFNs), TAL effector nucleases (TALENs), and the
CRISPR–Cas9 system, have been shown to be promising in simplifying the
process of gene deletion, editing, and insertion in plants, thereby assisting in
the validation of identified candidate genes for traits.
Figure 7.5: CRISPR–Cas9 system.

Source: https://www.researchgate.net/publication/325336648_CRISPR-
Cas9_System_A_Breakthrough_in_Genome_Editing/figures?lo=1
The CRISPR–Cas9 system (Figure 7.5) is now widely regarded as the

preferred way for improving numerous crops for a variety of qualities, as
well as for finding genes of interest. The concept of sustainable agricultural
production was developed to solve the issues posed by the world’s rapidly
increasing human population by boosting crop plant yield and productivity
while avoiding negative environmental effects. The greatest impediment in
realizing the full potential of improved genotypes is environmental stresses,
both biotic and abiotic. Plant diseases, among the different biotic stressors,
pose a significant danger to long-term crop production sustainability. To
acquire persistent resistance against disease-causing infections, various
approaches have been consistently combined, including the use of pesticides,
better agronomic practices, conventional molecular plant breeding, and
genetic modification procedures. Enhancing the resistance of crop plants,
on the other hand, has been proved to be the most successful, long-term, and
cost-efficient technique for dealing with infections.
7.5 RNAI
Plants have evolved numerous complicated strategies to strengthen their own
defensive mechanisms against these diseases during the course of evolution.
When a pathogen attacks, surface-localized pattern recognition receptors
(PRRs) recognize pathogen associated molecular patterns (PAMPs),
activating events that lead to the pathogen’s eradication. As a result, PAMP-
triggered immunity (PTI) is regarded as the first and most important line
of protection against pathogens. The identification of genes implicated in
the pathways responsible for plant–pathogen interactions is complicated by
the huge number of genes involved in PTI. Once the candidate genes have
been identified, they must be introduced into elite germplasms using either
traditional or molecular breeding methods. Modern omics technology has
allowed identifying susceptibility or resistance genes in any species possible,
resulting in a vast number of prospective crop protection targets. However,
the lack of a quick, precise, and efficient gene targeting mechanism in plants
has hampered attempts to confirm these potential genes. Various ways have
been used to transfer genes from wild relatives to domesticated species over
the years. Traditional breeding, on the other hand, takes about 8–10 years
to cascade numerous disease resistance genes into a cultivar. Due to high
pathogenic diversity and quick mutation rates, this extended lifetime might
promote the rapid breakdown of resistant cultivars. Through the silencing of
transcription factor genes, RNA interference (RNAi) based techniques have
been discovered to be effective in regulating the expression of numerous

disease related genes.
However, RNAi transgenics have a number of significant problems.
Transgene expression levels change amongst transgenic lines, so large
populations of plants must be investigated to appropriately identify the set
of plants in which the transgene is highly expressed over generations. Other
problems include the insertion of transgenes into non-target places in the
genome and the introduction of undesired characteristics. Furthermore,
because plants developed using RNAi-based approaches are classified as
transgenics, they must go through stringent regulatory processes before
being commercialised. As a result, more novel biotechnological strategies
that provide crop plants with enhanced plant immunity and permanent broad-
spectrum resistance against pathogens with minimal loss are needed(Dutta,
Banakar, & Rao, 2015)new avenues for engineering resistance have opened
up, with RNA interference being one of them. Induction of RNAi by
delivering double-stranded RNA (dsRNA.
Recent advances in sequence-specific nucleases (SSNs) for introducing
double-strand breaks at target loci have resulted in very precise genome-
editing tools. High-fidelity homologous recombination (HR) or error-prone
nonhomologous end-joining (NHEJ) methods are utilized to repair gene-
specific DNA double-strand breaks (DSBs) induced by SSNs. Furthermore,
unlike RNAi, SSN-based genome editing allows for full knockdown without
the use of foreign DNA. Zinc-finger nucleases (ZFNs), transcription activator-
like effector nucleases (TALENs), and clustered regularly interspaced short
palindromic repeats (CRISPR)/CRISPR-associated proteins are all examples
of SSNs (Cas). CRISPR/Cas9 has been proven to be the most effective SSN
among these technologies. CRISPR was first identified in Escherichia coli
in 1987 by Ishino et al., who discovered a collection of 29 nucleotide repeats
split by non-repetitive short sequences. CRISPR/Cas systems are part of
bacteria and archaea’s adaptive immune systems, which protect them from
invading nucleic acids like viruses by cleaving foreign DNA in a sequence-
dependent way.
The invading pathogen’s DNA or RNA is targeted by CRISPR/ Cas.
Wheat is the world’s second most important cereal crop, behind rice or maize,
and is the most important source of calories and protein in human food,
especially in underdeveloped countries. Over 700 million tonnes of wheat
are harvested annually from approximately 215 million hectares around the
world, which is more than any other crop. Wheat has evolved to a variety of
climates and is cultivated at a variety of elevations and latitudes in irrigated,

severe drought, and moist circumstances. Wheat demand is expected to rise
by 60% by 2050 as the world’s population grows and people’s lifestyles
change. As a result, worldwide average wheat yields per hectare will need
to rise to around 5 tonnes per hectare from the present 3 tonnes per hectare.
Efforts to continuously improve yield and quality are fraught with
difficulties. Unexpected abiotic and biotic challenges, such as abrupt
environmental changes or disease translocation, have posed a threat to
wheat production. Furthermore, urbanization has reduced the amount
of appropriate farmland for wheat farming. Pathogen resurgences have
emerged from the monoculture of current wheat cultivars with little genetic
diversity, posing a threat to wheat supplies. Fifty diseases and pests out
of approximately 200 have been identified as economically important due
to their potential to harm crops and reduce farmer income. Diseases are
expected to cause 18 percent grain output losses, with actual losses of 13
percent with present disease control(Young et al., 2013). Pathogenic fungi,
among other biotic stressors, pose a substantial threat to wheat production.
On the basis of their lifestyle, pathogenic fungi can be divided into two
categories: biotrophic and necrotrophic fungi. Race-specific resistance also
known as seedling resistance and race non-specific resistance are two types
of genetic resistance to rusts. More than 200 rust resistance genes in wheat
or wild relatives have been identified and formally classified; the majority of
them confers race-specific resistance and identified at least 60 of these genes
as SR resistance genes. Sr31 was once one of the most extensively used
race-specific SR resistance genes; however, after testing against Ug99 races
in Kenya, its presence at the International Maize and Wheat Improvement
Center (CIMMYT) has been dramatically reduced. With the introduction of
Ug99, virulence against Sr31 evolved, resulting in susceptibility to SR in the
majority of wheat produced around the world.
7.6 BREEDING PROGRAMS

Breeding programs around the world will benefit from new technologies
such as marker-assisted selection (MAS), genomic selection, transgenics,
and gene editing. MAS has been widely employed in the selection of disease
resistance in wheat in high-income nations, for example, rust resistance
in Australia. Because of the high cost, the lack of diagnostic and reliable
markers, and the high phenotypic selection accuracy, breeding programs
around the world rely on phenotypic selection. Furthermore, using MAS
in conjunction with phenotypic assays is usually recommended to avoid

false positives and poor, agronomically weak plants. In wheat, MAS aids in
the selection of race-specific resistance genes. The transfer of two or more
disease resistance genes in wheat using MAS and traditional backcrossing
methods is known as gene pyramiding. This method takes time and is a
slow method of transferring resistance genes; it is reliant on the availability
of reliable, breeder-friendly markers. Another new wheat technology is the
transfer of gene cassettes or gene stacks also known as gene stacking). As
gene cassettes or gene stacks, desirable combinations of efficient resistance
genes can be assembled and turned into wheat. This could lead to speedier
disease resistance advancements in present high-yielding cultivars. However,
whether the resulting gene-stacked wheat is a cisgenic or transgenic product
is still up for debate. Gene-stacked wheat should be regarded as cisgenic
rather than transgenic because the genes used to build gene cassettes or gene
stacks originate or are derived from wheat or its relatives.
Humans consume or use a variety of cereals, pseudo-cereals, pulses,
oil-yielding plants, fiber-yielding plants, spices, and medicinal plants
around the world. In the fields, all of these diverse groups of plants are
cultivated on a larger scale. These plants are constantly subjected to a
variety of environmental challenges in the field, all of which have an impact
on their growth, development, survival, and subsequent production. These
environmental stresses, which can be divided into two categories: biotic
factors and abiotic variables, have a significant detrimental impact on crop
productivity around the world. Living organisms that have predatory or
symbiotic connections with the host plant are included in the biotic factor.
Fungi, bacteria, nematodes, weeds, insects, parasites, rodents, birds, and
viruses are all members of this class. Phytopathogens cause a variety of
diseases in non-resistant plants by disrupting the plant’s metabolism at the
cellular, molecular, hormonal, and physiological levels, among other biotic
stressors. The most important biological limitation affecting the food usage
component is the vast number of plant diseases. This is evident from the
fact that plant diseases account for global agricultural losses between 20
percent and 45 percent which is supplemented by another 5–10 percent
during postharvest storage with both direct and indirect consequences.
As a result, in order to increase food production, it is critical to develop
and improve already existing high-yield, disease-resistant crop types in
the fields. Furthermore, breeders have improved a variety of crops around
the world for higher yields and stress tolerance, including common bean,
sorghum, wheat, barley, sugarcane, and rice
Breeders have used traditional breeding tactics to add desirable features

from related species to high-yielding variants for ages. Traditional breeding
methods, on the other hand, have a number of drawbacks, including (i) Time
intensive, (ii) being focused on phenotypic evaluation and selection, and
(iii) being difficult to transmit traits with polygenic inheritance. Agricultural
scientists have been using marker-assisted breeding (MAB) to overcome the
limits of traditional breeding strategies. Advances in genomic methodologies
and sequencing, as well as the availability of genome sequences, internet
databases, and a variety of bioinformatics tools, have all aided this MAB
approach. The MAB approach has become indispensable over time because
it focuses on improving overall performance, yield stability, traits such as
stress tolerance, and farmer acceptance.
Crop losses due to disease infestation cost farmers a lot of money all
over the world. To manage diseases in crop plants, scientists and farmers
have long used a variety of traditional and chemical approaches. Chemicals,
primarily fungicides and insecticides, have been used extensively to manage
the disease infestation to some extent, but they come at a cost. Chemical
use not only raises production costs, but it also has a harmful influence on
the environment and the health of both farmers and consumers. Frequently,
pathogens acquire resistance to the fungicides used on them, rendering
them ineffective in controlling the damage that affects agricultural output
and quality. As a result, developing disease-resistant crops is one long-
term method to lessen the impact of crop yield and quality loss due to
plant diseases. Disease resistance breeding has been an important source of
disease control.
The basic definition of disease resistance breeding is the introduction of
disease resistance genes into disease-infected plants. The resistance genes
can come from a natural or artificial source. Disease resistance is divided
into two types: qualitative and quantitative. Quantitative resistance is based
on oligogenic or polygenic inheritance and is governed by additive or partial
dominant genes and is generally race-nonspecific, whereas qualitative
resistance is based on a single dominant or recessive gene, is race-specific,
and usually confers a high level of resistance. Plant breeders place a higher
value on quantitative disease resistance since it is more persistent and has
a broader specificity. Gene-for-gene interaction theory is one of the most
well-known hypotheses about disease resistance and susceptibility. The
hypothesis of gene-for-gene interaction was developed using flax as the host
plant and the fungal rust disease Melampsora lini as the pathogen. Disease
resistance requires a dominant or semi-dominant resistance R gene in the host
plant and a corresponding avirulence (Avr) gene in the pathogen. R genes in

plants are important for detecting pathogen compounds that are particular to
the Avr gene, leading to downstream signal cascades that create defensins,
which drive defense. The hypersensitivity response is typically thought of as
a defense mechanism that initiates a pathogen-host incompatibility reaction.
Disease susceptibility is typically seen in biotrophic pathogens such as
fungus, bacteria, viruses, and nematodes when the R gene or the Avr gene
is mutated or lost completely. In general, the R gene generates proteins that
identify pathogen effectors or modify plant proteins that are the effectors’
targets. The nucleotide binding, leucine-rich repeat (NB-LRR) amino acids
sequence motifs, which are involved in pathogen recognition and related
functions, are the most well-known of the six known classes of R-genes.
Understanding the structural and functional roles of these R genes
can help plants become more disease resistant. Several R genes have
been discovered, isolated, and cloned. Hm1, a maize R gene that causes
resistance to the leaf spot fungus Cochliobolus carbonum, was the first R
gene discovered. Hm1 is a reductase enzyme that detoxifies the HC-toxin
from C. carbonum. R-genes confer an effective defense response in response
to biotrophic pathogen invasion, usually by involvement in a hypersensitive
response, in which tissue directly adjacent to the infection’s location
undergoes rapid programmed cell death. Pto gene, which encodes a serine/
threonine kinase and protects tomato against Pseudomonas syringae, was
another early cloned R gene. RPS2 in Arabidopsis, an NBS/LRR protein
family, is another cloned gene for Pseudomonas syringae.
Traits that can be quantified and have continuous variations are known
as quantitative or metric traits. Quantitative trait loci are loci that influence
the genetics of certain qualities (QTL). The constant variety is due to the
polygenic inheritance of genes with mostly minor additive effects, which
are modified by the environment. Because Mendelian methods of genetic
analysis are ineffective for dissecting these quantitative features, other
quantitative methods are employed to investigate and comprehend them. The
physical localization or mapping of polygenes began with the discovered
relationship between seed coat color and seed size in common beans. The
ability to generate the genomic map of a given species, together with the
development of the linkage idea, leads to the creation of QTL mapping.
Paterson et al. used the restriction fragment length polymorphism in tomato
to map the first QTL in 1988. The use of a mapping population, usually
a bi-parental population derived from the cross of two genetically diverse
parents, a dense marker linkage map for a particular species and genotypic
data (SNPs, SSRs), standard phenotypic measurement, and suitable software

programs, such as R/QTL, QTL Cartographer, and so on, are all common
methods.
Various infections in the environment pose a constant threat to plants.
Some wild plants have an inherent resistance to attack that helps them survive
in the wild. Plants that were domesticated and subsequently developed by
humans to yield good qualities eventually lost their resistance and became
prone to disease attacks. Despite the presence of particular resistance genes,
newly developed pathogen strains can overcome genetic resistance. This
ongoing co-evolution of agricultural plants and their pathogen necessitates
long-term plant breeding efforts to develop new crop varieties or boost
resistance genes in well-adapted kinds. Another source of concern is
the projected rise in climate variability, which could increase pathogen
occurrence in a given area.
For environmental and economic reasons, host plant resistance is
often the most preferable control technique. Until now, conventional plant
breeding methods have aided in the solution of this problem. However,
demand for newer, more resistant crop varieties must be met quickly.
Molecular breeding, also known as marker-assisted breeding (MAB), has
the ability to alleviate this problem and solve it more effectively and quickly
than traditional breeding. Furthermore, without disease manifestation in the
field in MAB, the selection of resistant plants is simple. Marker-assisted
gene pyramiding is a popular strategy for gene stacking within an adapted
variety that avoids the requirement for several pathogen races to be tested in
different conditions. They are separated into tropical pulse crops like pigeon
pea, mung bean, urd bean, cowpea, common bean, and so on and temperate
pulse crops like pigeon pea, mung bean, urd bean, cowpea, common bean,
and so on based on their climatic conditions for growth like chickpea, lentil,
pea, etc. Plant pathogens such as viruses, bacteria, fungi, and pathogenic
weed species cause damage to these pulses. Yellow vein mosaic virus, for
example, is a prevalent issue in tropical legumes such as mung bean, urd
bean, and cowpea. Ascochyta blight causes significant damage to chickpea
and lentil crops. Chickpea and pigeon pea are both susceptible to fusarium
wilt. In subtropical pigeon pea farming, sterility mosaic caused by a virus
is an endemic concern. The creation of resistant cultivars in the above pulse
crops is an immediate requirement to save pulse production from these plant
infections. Recent genome sequencing efforts in major pulse crops have
resulted in massive amounts of marker data and a molecular breeding or
genomics platform. The use of these has aided in the production of less
enhanced variants and has a bright future in the development of disease-

resistant pulse crops.
Previously, great effort was put into improving grain production,
agronomic features, and disease resistance in oat breeding. The complex
oat breeding program’s major goal is to generate new high-yielding winter
and spring types with good grain quality and resistance to the oat disease
complex. Because oats are self-pollinated, the basic breeding technique of
selection, introduction, and hybridization followed by selection is used all
over the world. The oat cultivars grown in the United States during the 1930s
were all introductions or selections from previously introduced cultivars
from other regions of the world. After that, oat breeders used hybridization
extensively to generate high-yielding grain quality with disease resistance
to a wide range of diseases.
Figure 7.6: Genome mapping.
Source: https://www.genome.gov/sites/default/files/tg/en/illustration/genetic_
map.jpg
Gene and genome mapping, (Figure 7.6) as well as understanding
chromosomal behavior and evolution, were all considerably aided by large
crosses between different ploidy species. Oat diseases are still the main cause
of yield and grain quality losses. To date, the main goal of oat breeding has
been to restore disease resistance diversity in cultivated oats by introducing
resistance genes that remained unselected from wild progenitors due to
genetic constraints during domestication. As a result, phytopathological
investigations among the wild oat complex should be prioritised in order

to uncover novel sources of resistance for widening the genetics of farmed
oats(Lee, Tang, Wang, & Paterson, 2013)owing to their propensity for
chromosomal duplication or even triplication in a few cases. Duplicated
genome structures often require both intra- and inter-genome alignments to
unravel their evolutionary history, also providing the means to deduce both
obvious and otherwise-cryptic orthology, paralogy and other relationships
among genes. The burgeoning sets of angiosperm genome sequences
provide the foundation for a host of investigations into the functional and
evolutionary consequences of gene and GD. To provide genome alignments
from a single resource based on uniform standards that have been validated
by empirical studies, we built the Plant Genome Duplication Database
(PGDD; freely available at http://chibba.agtec.uga.edu/duplication/.
Traditional breeding relied on controlled hybridization to generate new
genetic combinations, followed by phenotypic selection in segregating
populations. Traditional breeding techniques are often focused on phenotypic
selection for desirable trait combinations with desired gene combinations.
Traditional breeding strategies have boosted the yielding capacity of major
food crops while also reducing the effectiveness of phenotypic selection
and hindering the identification of superior genotypes due to genotype-
environment interactions. Furthermore, due to the complexity of genes
involved in disease resistance, pathotyping for disease resistance becomes a
tough challenge for plant breeders. Traditional hybridization is a complex and
time-consuming process for introducing a resistance gene into a susceptible
variety from a resistant one. Genetic diversity among agricultural species
has declined throughout time as a result of developmental activities and
industrialization, while diseases and insect pests have evolved continuously
as a result of climatic change. As a result, host resistance has deteriorated,
necessitating the development of breeding variants that combine high yield
and resistance.
The advent of genomics methods and resources has opened up new
horizons in plant breeding since they allow for a more accurate investigation
of the genotype and its interaction with the phenotype, which is especially
crucial when dissecting complex features. Plant breeders use molecular
markers to better understand complex polygenic traits, dissect genes
responsible for desired traits, characterize plants, create a genetic linkage
map that aids in gene tagging and gene mapping, and develop new cultivars
using various marker-assisted selection (MAS) schemes, such as marker-
assisted backcross breeding (MABB), marker-assisted gene pyramiding,
and marker-assisted recurrent selection. The development of a wide range

of DNA marker technology and genetic mapping in important crops has
aided in the identification of a source of variation and acted as a reliable tool
for disease resistant individual identification and selection. Soybean is the
source of protein and oil. It’s a versatile crop that’s been utilized for human
food, protein feed ingredients, and industrial purposes. Various biotic and
abiotic stressors pose a threat to soybean production. After brown spot,
charcoal rot is the second most cost-effective soybean disease.
Macrophomina phaseolina causes soybean charcoal rot, which is an
economically significant disease all over the world. In addition to soybeans,
this virus infects a variety of crops, including sorghum and maize. The
severity of the disease grows as the temperature of the soil and air rises.
Synergistic yield losses occur owing to both environmental stress and
charcoal rot disease when soil moisture is low. Due to the confounding
effects of drought, estimating the yield loss caused by the occurrence of
charcoal rot disease is challenging. Charcoal rot disease causes 6–33 percent
output loss in vulnerable cultivars in irrigated conditions, indicating the
disease’s relevance even under irrigated conditions.
Fermentation technology is regarded as mankind’s most crucial
invention, second only to the control of fire. This viewpoint is relevant
to beer production and barley malt, a technology that has been used for
centuries around the world. The first evidence of barley beer consumption
dates from around 3350–3000 BC. Many cereal sources were domesticated
by mankind for livelihood as human settlement spread over the globe. One
of the first multipurpose cultivated grains was barley. In contrast to rice and
wheat, cultivated barley is an annual, self-pollinating temperate grass that
requires little fertilization. It blooms in both the winter and spring seasons
all over the world, with different spike morphologies. It is one of the four
primary crops produced worldwide, according to the Food and Agriculture
Organization Corporate Statistical Database, with global production of
145.96 million metric tons (Kaur et al., 2012).
Barley is currently the world’s fourth most significant cereal crop, with
large use in feed, beer production, spirit production, and the food value
chain. In both tropical and temperate settings, a surge was observed in
both usage and production of both types of barleys. Stress resistance, yield
stability, and quality traits are currently the focus of barley breeders. Due
to the integration of conventional breeding with DH production, genomic
tools, and molecular marker technologies over the decades, there has been a
favorable progress in the augmentation of lasting resistance against a variety

of relevant diseases. The use of non-traditional technologies has decreased
the time between the first cross and the introduction of disease-resistant
cultivars. The availability of genomic sequences of rice, Brachypodium,
sorghum, and wheat, high-density maps, map-based cloning, genome-wide
transcript profiling, genome editing techniques, and various bioinformatics
tools to exploit the synteny between barley and these species has boosted this
even further. Using molecular breeding procedures, more phytopathogen
resistance genes, alleles, and QTLs will be identified, isolated, mined,
transferred, and transformed into elite-susceptible cultivars in the near future
to improve disease resistance. Taking all of this information into account, all
of these advancements have improved disease resistance breeding efforts for
barley.
CHAPTER 8
SUSTAINABLE AGRICULTURE
CONTENTS
1.1 Introduction.......................................................................................... 6
8.1 INTRODUCTION
Water is vital for human health, as well as our food and farming systems’ long-
term ecological and socioeconomic resilience. Because the agricultural sector
is responsible for a major portion of water consumption and contamination,
it must take the lead in saving and safeguarding water resources. Chemical
pesticides and fertilizers are used in food production, resulting in ongoing
deterioration of water quality and increased societal expenditures. Efforts
to decrease agricultural contamination of ground and surface waterways
remain a persistent problem. Although there are many different water
treatment procedures available, not all of them are cost-effective or feasible
for small farmers, resulting in the usage of low-quality water in agricultural
fields (Reganold, Papendick, & Parr, 1990). Despite considerable progress,
bad water management practices continue to have a negative influence
on water quality. Organic farming is said to have the potential to deliver
benefits in terms of environmental protection, non-renewable resource
conservation, food quality enhancement, surplus product reduction, and
agricultural reorientation toward regions of market demand. Governments
have noticed these potential benefits and responded by providing financial
incentives or indirect assistance for research, extension, and marketing
campaigns to encourage farmers to embrace organic agricultural practices.
Farmers’ judgments about whether or not to switch from conventional to
organic farming, on the other hand, have not been thoroughly researched.
The use and release of water in both animal and plant farming is a
major source of water pollution. When water is swapped in a fish pond, for
example, effluent is discharged into the adjacent surface waterways. The
wastewater contains a variety of contaminants, as evidenced by the indicators
chosen. Chemicals, fertilizers, and feed supplied to the ponds are the source
of these contaminants. As a result, water pollution is decreased in organic
farming since the eutrophication of chemical inputs used in conventional
farming methods, such as nitrogen and phosphorus, is considerably reduced.
Organic farms also have far better soil structure, which results in less nitrate
pollution and is healthier for agricultural plants because it is chemical-free.
As previously stated, the two agricultural nutrients of significant significance
to water quality and human health are nitrate and phosphorus. Leaching
occurs when nitrate, the most frequent type of nitrogen in soils, is released.
Nitrate is negatively charged, unlike potassium, calcium, and magnesium,
which are positively charged. Because most soil particles, including organic
matter, have negative charges, positively charged nutrients are able to bond
to them. However, negatively charged nitrate is attracted to negatively
Sustainable Agriculture 169
charged soil particles. As a result, it can easily pass through the soil profile
and into the groundwater. Because phosphorus is limited in freshwater
systems, it is the nutrient of greatest concern for runoff and erosion losses.
Even a small amount of phosphorus added to lakes, rivers, or streams can
induce nutritional imbalances that promote algae growth, limiting fish
access to nutrients and oxygen. When nutrients are transferred beyond the
reach of plant roots, leaching has an impact on crop growth. When nutrients
are carried into groundwater, it is a source of problems for water quality.
The National Organic Practice Standards specifically state that
raw manure must be applied in a manner that does not contribute to the
contamination of crops, soil, or water by plant nutrients, pathogenic
organisms, heavy metals, or residues of prohibited substances to ensure
that organic production practices are implemented in a manner that protects
the environment. This criterion gives certifying authorities the authority to
prohibit problematic actions including spreading manure on the ground or
too close to water sources. The transfer of soil particles by wind or water
is known as soil erosion. Erosion takes more topsoil, reactive clays, and
organic matter than other soil components because these forces may easily
move less dense particles. As a result, it destroys the soil by eliminating
the most fertile elements. Soil erosion can also harm nearby farmland and
contaminate nearby bodies of water. Transported sediments carry nutrients,
pathogens, and other pollutants associated with them. These sediments
influence fish habitats by clouding the water, changing the temperature, and
becoming embedded in feeding and nesting regions along stream banks.
Algal blooms, fish habitat degradation, and eutrophication are all caused by
nutrients delivered by sediments. If lakes supplied by contaminated streams
are used as a source of drinking water, pathogens clinging to sediments
can decrease the quality of water for animal and human use and increase
purification expenses.
8.2 MANURES
In manure, pathogens are frequently discovered. Escherichia coli,
Cryptosporidium, and Giardia are among the pathogens that pose the
greatest threat to human health. These organisms cause gastrointestinal
issues in humans who eat or drink contaminated food or water. To kill E.
coli and ensure the safety of drinking water, municipal purification systems
chlorinate it. Cryptosporidium and Giardia, on the other hand, produce
resistant resting stages like oocysts and cysts, respectively that are not killed
by basic water treatment techniques like chlorination. To remove these

parasites from water, sand filters are required. Fresh manure applied to
growing crops or applied shortly before planting can contaminate them with
diseases. If animal production operations or septic systems upstream are not
adequately managed and enable fresh waste to flow into the water, water
from rivers or streams used for crop irrigation can contaminate plants with
diseases. Organic agriculture methods rely mostly on measures such as the
adoption of pest-resistant cultivars, cultural management approaches, and
actions that improve pest-predator balances for pest and pathogen control.
Pesticides are generally limited to biologically produced chemicals with low
mammalian toxicity and are only employed as a last option. Some botanical
pesticides, on the other hand, are poisonous to non-target organisms.
Pyrethrum kills both helpful and disease-causing insects, and rotenone is
harmful to fish. Because of its physically disrupting features, diatomaceous
earth is used to manage insect pests, but it may also be a significant irritant to
human lung tissue if not handled properly. Even low-toxicity plant fertilizers
and chemicals can become pollutants if used in large quantities, adjacent
to water sources, or during periods of high rainfall or flooding. Using
strategies that store and recycle nutrients within the farming system, organic
farmers can safeguard water from contamination. When applied as part of an
integrated, systems-based approach, such practices are most successful and
long-lasting. Maintaining nutrient balances within fields while decreasing
off-farm water flows, retaining water inside fields, and catching any water
that flows away from fields would conserve nutrients on the farm while
safeguarding the environment. The utilization of a varied range of plants
as rotation crops, cover crops, and intercrops improves soil quality, enables
nutrient capture, and aids in the recycling of nutrients that would otherwise
be lost in the soil. These crops also provide soil cover, which promotes
water infiltration while reducing the risk of nutrient runoff and erosion.
The accumulation of active organic matter and various communities of
soil organisms will improve nutrient storage in the soil while reducing the
likelihood for these nutrients to be transported to ground or surface waters.
Fresh manure should be stored on concrete slabs or soils with a low leaching
potential, with collection or treatment areas for contaminated runoff water.
Because of reduced soil erosion, increased stored soil water and organic
matter, carbon sequestration, and other ecosystem services, conservation-
tillage practices are replacing conventional-tillage practices throughout
semi-arid regions in North America and beyond. In a large portion of the US

northern Great Plains, for example, no-tillage (NT) management is currently
employed to manage over 50% of the area used for dry land crop production.
These findings have piqued the interest of farmers and academics in North
America and Europe in replacing conventional tillage with NT farming
methods in organic systems, so that the benefits of this conversion might be
realized. Although there are currently few studies on the use of biochar in
organic farming systems, there is much to be learnt from historical charcoal
use in agriculture as well as current conventional agricultural research.
Farmers have utilized biochar, the method of burying charcoal in soil to
promote fertility, from citrus fields in Japan to basket willow stands in north
Great Britain to the legendary Terra Preta soils of the Amazon Basin. Biochar
has experienced a resurgence in modern agriculture, with this carbon-rich
material now being widely employed to improve soil and encourage more
sustainable agriculture.
8.3 BIOCHAR
Biochar is a carbon-rich, stable solid material made by thermochemical
decomposition of organic material in an oxygen-limited environment under
controlled conditions. It differs from charcoal made during wildfires or
for fuel because biochar is made specifically for use as a soil amendment,
whereas charcoal is commonly used as an energy carrier. Forest or agriculture
residues, municipal solid waste, or biosolids can all be used to make biochar.
Biochar has been proposed as a technique of mitigating climate change
by sequestering carbon when applied to soils because of its C-rich nature
and unusual resistance to decomposition. Furthermore, the morphological
qualities of biochar may modify soil hydrological parameters, affecting soil
nutrient conversions. The Terra Preta soils in the Amazon River Basin were
reportedly developed by primitive tribes thousands of years ago and are still
some of the most fertile and biodiverse soils in the Amazon today. Terra
Preta’s origin is unknown, but the large amount of char found in these soils
makes it unlikely that it was created by biomass burning, but it’s unclear
whether the biochar application was done on purpose or as a means of
sanitary waste management in populated areas of the Amazon basin (Aup-
Ngoen & Noipitak, 2020).
Figure 8.1: Biochar.
Source: https://onlinelibrary.wiley.com/doi/10.1111/gcbb.12885
An old process known as formiguer, has a structure that is similar to
that of a charcoal kiln, was widely employed in the Mediterranean region
to make soil-fertilizing material with dried woody plants. Farmers in Japan
have been pioneering the use of biochar in agriculture in conjunction with
composting processes since the early twentieth century. Rice husks and
other farming residues would be used to make charcoal in traditional earthen
kilns, which would be used primarily as soil improvers or odor absorbents.

Fire is a major source of disturbance in western US forest ecosystems. Over
the last few decades, active fire suppression and a shift in forest management
have resulted in an increase in the incidence of extensively stocked second-
growth forests, which may alter wildfire behavior. In the western United
States, forest restoration and fuel reduction techniques such as selected
harvest paired with managed fire are being used to establish a more resilient
forest structure. Normally, forest leftovers from timber harvests are piled
and burned, resulting in emissions of gaseous air pollutants and volatiles,
nutrient loss, and no net environmental gain. As a result, developing a value-
added strategy for wood harvest residue management could help catalyse
restoration efforts in both private and public forest areas.
Thinning treatments have become regular practice for foresters and
landowners on the islands, as the region is mostly covered with intensively
stocked woods. The dominating timber in these forests, on the other hand,
has a poor value and significant transportation costs, resulting in the timber
being primarily piled and burned. Simultaneously, small-scale organic
farming on sandy loam soils created in glacial deposits and outwash across
the islands supports a significant portion of San Juan County’s economy. It
would be ideal to create a strategy that produces less pollution from forests
diminishing while also adding to the soil fertility of local organic farms for
food production. Biochar production from local timber harvest wastes in this
region could provide a long-term solution for reducing wildfire hazard fuel
loading while also enhancing soil health on organic farms nearby. Pests and
diseases cost fruit growers a lot of money since they reduce fruit yield by
30–100 percent. They also degrade the cosmetic look, market value, quality,
and nutritional content of fruits by sucking, gnawing, or drilling into various
reproductive regions, generating stains, cracks, and holes, as well as rotting.
For a long time, chemical pesticides have been used to manage insect
pests and fungal diseases. Pesticides used on fruit fields leave hazardous
residues in fruits that are consumed by humans, posing a health risk to
consumers. Their sustained use has a negative impact on the environment,
resulting in the development of resistance in many pests, the resurgence
and outbreak of new pests, and health risks to production workers and farm
laborers as a result of incorrect or lack of knowledge of pesticide handling
and use, as well as pesticide poisoning. Many synthetic pesticides, such as
organochlorines, organophosphates, carbamates, and organo phthalides,
have been banned or restricted from use due to their negative environmental
impact and high toxicity to non-target organisms such as beneficial insects,
amphibians, fish, and birds, as well as humans. However, for the control of
insect pests and diseases, efforts are now being made to replace chemical
pesticides with eco-friendly compounds that are safe for humans and the
environment.
Figure 8.2: Organic fruit farming.
Source: https://www.fao.org/organicag/oa-home/en/
Organic fruit farming (Figure 8.2) is a method of producing fruit that is
good for the earth, ecosystems, and people. Rather than using harmful inputs,
it relies on biological processes, biodiversity, and cycles that are tailored to
local conditions. Because it is based on low use of chemical inputs for crop
health and protection against biotic threats, it is an ecologically sustainable
fruit production method that safeguards biodiversity, physico-chemical,
and biological health of our soils. Food production has always followed an
arithmetic progression, whereas the human population has always followed
a geometrical progression. Farmers have been obliged to apply pesticides as
a result of the enormous pressure to provide food at affordable costs. These
chemicals could be growth regulators, defoliants, desiccants,
The use of pesticides to increase food production resulted in significant
environmental contamination as well as a significant reduction in food
output. Pesticides and their breakdown products are exceedingly harmful to
humans and other living organisms alike. Aldrin’s photodegradation products

are significantly more dangerous than the parent molecule, and they are
transported through numerous natural resources, contaminating them in the
process. The necessity for a significant amount of solvent, extended analysis
times, the need for professional personnel, and expensive expenditures
for executing the tests are all important drawbacks of chromatographic
procedures. As a result of these constraints, novel spectroscopy-based
pesticide detection and estimation techniques have been developed. These
strategies have the significant benefit of causing less harm to the environment
and other living things. Organic animal husbandry isn’t a one-size-fits-all
approach. It is in the process of being improved.
On production guidelines, there are distinctions between traditional,
conventional, and organic animal husbandry. Organic animal husbandry is
a significantly more sophisticated and knowledge-based method of animal
production designed to protect not only human health but also animal
welfare and the environment as a whole. Organic livestock farming has set
out to build environmentally friendly production, maintain healthy animals,
achieve high animal welfare standards, and provide high-quality goods.
Organic animal husbandry is a system that promotes the use of certified
organic and biodegradable inputs from the environment in terms of animal
nutrition, health, housing, and breeding, while avoiding drugs, feed additives,
and genetically engineered breeding inputs. When it comes to plant farming,
this may not have major effects, but when it comes to animal farming, it
can have serious consequences. The organic rule makes no mention of any
understanding of how to administer and manage an animal farm. It doesn’t
even say that the animals should live as naturally as possible.
There are a variety of diseases that commonly affect our animals.
Viruses, bacterial infections, parasitic infections, and fungal infections are all
examples of infectious disorders. Mastitis, infertility, milk fever, lameness,
metabolic abnormality, and ketosis are the most prevalent disorders in dairy
cows. Organic livestock has a lower incidence of milk fever, lameness,
infertility, and metabolic problems. Dairy cows in organic agriculture farming
systems have adequate movement, which helps to decrease lameness and
metabolic diseases. Furthermore, in the case of broilers, organic livestock
production reduces hock burn, footpad dermatitis, skin burn, blisters,
and obesity. In the case of inorganic farming, blisters and obesity are big
issues with broilers. The occurrence of blisters and obesity is reduced as a
result of proper activity, and the quality of meat is improved, resulting in a
higher dressing percentage. Organic management decreases stress, lowers
disease incidence, and improves animal comfort. Local purebred strategies

are followed in organic agriculture; synthetic breeds and GMOs are not
used. Local breeds have higher disease resistance than synthetic breeds.
Diseases are less common in indigenous breeds, and they do not suffer from
immunosuppression. Local breeds are more capable of coping with stressful
situations than synthetic types. As a result, animal health is better in organic
animal husbandry than in any other production style.
Figure 8.3: Drip irrigation.
Source: https://afko.com.tr/drip-irrigation/
8.4 DRIP IRRIGATION

Drip irrigation, (Figure 8.3) a method of providing water directly to the plant
root zone, is distinguished by water application at slow rates but increasingly
frequently throughout the crop growth season as crop water requirements.
It is best suited to vegetable crops, fruit trees, and vine crops, but because
of its water conservation potential and improved crop productivity, it is now
being used on a wide range of row crops. As a result, drip irrigation has
extended over an area of roughly 1.9 million hectares, possibly the largest
drip irrigation area in the world. Another significant benefit of drip irrigation
is the ability to use saline water. Because of the low matric stress in the
root zone caused by frequent applications, the plants are able to withstand
the high osmotic stress associated with saline water irrigation. Despite the
copious evidence accumulated over the previous three decades or so, there
has been little success in expanding the use of saline or alkali water with
drip irrigation. Furthermore, the high capital costs and knowledge necessary
to address various complicated difficulties in drip irrigation pushed
technologists to design local drip irrigation alternatives. Several of them
are not only similar to drip irrigation, but they are also very inexpensive
and need less sophistication for resource-constrained farmers to implement.
Food insecurity is linked to a decrease in household food supplies, less
frequent fruit and vegetable consumption, higher unemployment, increased
involvement in food assistance programs, and an increase in eating disorders
in the US population. Food insecurity is a spectrum with varied degrees of
severity depending on the level of hunger experienced within the home.
Food insecurity without hunger is the mildest kind of food insecurity, and
it describes families who are concerned about running out of food and will
alter their purchasing or consumption habits to affect the quality of the food
supply. In households with moderate levels of food insecurity, parents or
adults may be hungry while their children eat nutritiously enough meals. At
its most extreme, hunger affects all members of a home for long periods of
time.
According to a 2015 survey, about six million people in California,
or 15% of the population, were food insecure. Food insecurity affects
minorities disproportionately, particularly those whose members are recent
or undocumented immigrants. Food insecurity is strongly linked to a lack
of enough and consistent income. Many Mexican-American households,
for example, go through periodic cycles of food poverty due to agricultural
employment schedules. Although these advancements have had numerous
positive consequences and eliminated many risks in agriculture, they
have come at a great cost. Three key goals of sustainable agriculture are
environmental health, economic profitability, and social equality. Concerns
of animal welfare in farm enterprises that incorporate animals must also
be addressed as part of stewardship considerations. Sustainability requires
an understanding of agroecosystems and food systems. Agroecosystems are
defined in the broadest sense, encompassing everything from small fields to
farms to entire ecozones. Food systems, which comprise agroecosystems
as well as distribution and food consumption components, extend from the
farmer to the local community to the global population in a similar way.
An emphasis on a systems viewpoint provides for a holistic picture of our
agricultural production and distribution enterprises, as well as their impact

on human communities and the natural environment. A systems approach,
on the other hand, equips us with the skills we need to examine the impact of
human society and institutions on farming and environmental sustainability
(Martinez, Grandner, Nazmi, Canedo, & Ritchie, 2019).
Studies of several natural and human systems have shown that systems
that endure over time are frequently very robust, adaptive, and diverse.
Because most agroecosystems face variables such as climate, insect
populations, political situations, and others that are extremely unpredictable
and rarely constant over time, resilience is essential. Adaptability is an
important component of resilience because, while it may not always be
possible or desirable for an agroecosystem to return to its original shape and
function after a disturbance, it may be able to modify and take on a new form
in the face of changing conditions. Since the more variety that exists within
a food system, whether in terms of varieties of crops or social knowledge,
the more tools and pathways a system will have to adapt to change, diversity
typically aids in adaptation.
A multi-pronged strategy to research, teaching, and action is also part
of an agroecosystem and food system approach. Farmers, laborers, retailers,
consumers, policymakers, and others with a stake in our agricultural and
food systems all have important responsibilities to play in achieving greater
agricultural sustainability. Finally, there is no clear, well-defined ultimate aim
for sustainable agriculture. The scientific understanding of what constitutes
environmental, social, and economic sustainability is constantly growing,
and it is influenced by current concerns, viewpoints, and beliefs. Agriculture’s
ability to adapt to climate change, for example, was not considered a serious
concern 20 years ago but is now getting more attention. Furthermore, the
specifics of what makes a sustainable system might vary depending on the
circumstances, as well as from one cultural and ideological standpoint to the
next, making the term sustainable, a contentious concept. As a result, rather
than thinking of agricultural systems as either sustainable or unsustainable,
think of them as ranging along a continuum from unsustainable to very
sustainable.
When food and fiber production deplete the natural resource base,
future generations’ ability to produce and thrive is harmed. Natural resource
deterioration through non-sustainable farming and forestry methods is
thought to have influenced the fall of ancient civilizations in Mesopotamia,
Pre-Columbian southwest United States, and Central America. Sustainable
agriculture aims to use natural resources in a way that allows them to regenerate
their productive potential while minimizing negative impacts on ecosystems
beyond the field’s edge. Farmers are contemplating how to leverage existing
natural processes or how to build their agricultural systems to incorporate
critical functions of natural ecosystems as one method to achieve these aims.
It is often possible to sustain an economically viable production system with
fewer potentially hazardous interventions by constructing biologically-
integrated agroecosystems that rely more on the internal cycling of nutrients
and energy. Farmers who want to achieve a greater level of environmental
sustainability, for example, can think about how they can reduce their usage
of hazardous pesticides by relying on natural mechanisms to control insect
populations. This can be accomplished by planting hedgerows along field
margins or ground coverings between rows, which provide habitat for insects
and birds that prey on pests, or by planting more diversified crop blends
that confuse or deflect pests. Maintaining a high level of genetic variety by
preserving as many crop varieties and animal breeds as feasible can provide
additional genetic resources for breeding disease and pest resistant plants.
8.5 CONSERVATION
Conservation of resources is important for agricultural output, but it also
includes looking after soil, which is a complex and highly organized entity
made up of mineral particles, organic matter, air, water, and living beings.
Farmers that are committed to long-term sustainability place a high priority
on soil care because they understand that healthy soil encourages healthy
crops and livestock. Maintaining soil functionality frequently necessitates
a focus on preserving or even growing soil organic matter. Soil organic
matter serves as a vital source and sink for nutrients, as a microbial activity
substrate, and as a buffer against changes in acidity, water content, pollutants,
and other factors. Furthermore, the accumulation of soil organic matter can
aid in the reduction of atmospheric CO2 and, as a result, climate change.
Another key role of soil organic matter is to improve soil structure, which
leads to better water penetration, decreased runoff, improved drainage, and
higher stability, all of which reduce wind and water erosion.
The internal cycle of important plant nutrients such as nitrogen and
phosphorus has been isolated from agroecosystem functioning due to a
significant reliance on artificial fertilizers. Although phosphate minerals for
fertilizer are regularly extracted, worldwide stockpiles are only expected to
last another 50 to 100 years. As a result, unless new reserves are discovered
and new methods for recovering phosphates from waste are developed,
phosphate prices are expected to grow. Recycling nitrogen and phosphorus
at the farm and regional level, increasing fertilizer application efficiency,
and depending on organic nutrient sources like animal and green manure are
all significant aspects of sustainable agriculture. Diversified agriculture, in
which livestock and agricultural production are more spatially integrated,
facilitates nutrient recycling. As a result, broad mixed crop-livestock
systems, especially in developing countries, could make a significant
contribution to agricultural sustainability and global food security in
the future (Cordell, Drangert, & White, 2009).Water for agriculture is in
short supply in many regions of the world, and its quality is degrading.
Overdraft of surface waterways causes riparian zones to be disrupted,
while overdraft of groundwater supplies puts future irrigation capacity at
risk. Water quality problems include salinization, nutrient overloads, and
pesticide contamination. Water may be used more efficiently in sustainable
agroecosystems by selecting and breeding drought and salt tolerant crop
species and better animal breeds, using reduced volume irrigation systems,
and managing soils and crops to prevent water loss. Agriculture in the
modern era is primarily reliant on non-renewable energy sources, particularly
petroleum. Although the usage of these non-renewable resources cannot be
perpetuated indefinitely, immediately ceasing to do so would be economically
disastrous. Without the knowledge, technical competence, and trained labor
required to efficiently manage agro-ecosystems, they will not be sustainable
in the long run. Agriculture’s ever-changing and location-specific character
necessitates a diversified and adaptable knowledge base that incorporates
both formal, experimental research and farmers’ own on-the-ground local
knowledge. Agricultural production and long-term sustainability can be
increased by social institutions that support farmer and scientist education,
foster innovation, and promote farmer-researcher cooperation.
Farmers lack the economic influence to negotiate better pricing for
their inputs and crops as food manufacturers and marketers and farm input
suppliers consolidate. As a result, farmers’ profit margins are squeezed,
leaving them with little options for improving environmental and labor
conditions. Farmers can strengthen their relative economic power by banding
together in production, processing, or marketing cooperatives. Farmers
can be protected in the long run by policies that regulate consolidation.

Many rural communities have become poorer as a result of these economic
constraints on farmers, as farms and other local agricultural firms have gone
out of business. Economic development policies and tax arrangements that
encourage more diverse agricultural production on family farms can help
rural economies thrive. Consumers can also play a role within the constraints
of the market framework; through their purchases, they send strong signals
to producers, merchants, and others in the system about what they value,
such as environmental quality and social equality.
Some of the pressures that have harmed on-farm sustainability have also
harmed social equity for low-income consumers, who are frequently left
with little access to healthy food as traditional supermarkets relocate to more
lucrative neighborhoods in order to boost thin profit margins. Community
and household gardens, farmers’ markets, the utilization of fresh local farm
products in school lunch programs, and local food cooperatives are examples
of food production and marketing systems to strengthen community food
security. Furthermore, a food systems approach considers the effects of
farming techniques on the safety and nutritional quality of final food products
that reach consumers, such as reducing or eliminating harmful residues. By
2050, the world population will be over 10 billion people, and as economies
expand, the average wealth of people in emerging countries will rise, posing
new problems for agriculture and the food supply chain. One of the great
success stories of applied research to date has been the growth in food
production to meet global demand. This success is at the expense of nature;
biodiversity is rapidly dwindling, rivers, lakes, and aquifers are polluted,
soils are polluted or eroded, forests are being converted to grow crops for
food and energy, and agricultural greenhouse gas emissions are nearly equal
to those from transportation. Things cannot continue as they are; future food
security will require a focus on the long-term supply of food, as well as
technological, supply-chain, and social science or economic innovation.
Agriculture may and does benefit from ecosystem services provided by
nature, and these benefits must be factored into biodiversity management
and protection.
Figure 8.4: Ecological security.
Source: https://ars.els-cdn.com/content/image/1-s2.0-S1470160X1930086X-
ga1_lrg.jpg
8.6 ECOLOGICAL SECURITY

Ecological security (Figure 8.4) is critical for both preserving ecosystem
function and providing ecological services to human well-being. The impact
of land use change and cover on ecological security has received a lot of
attention, although cropland reclamation’s function is yet unknown. The
loss of ecological land that occurs as a result of agricultural programs has
an impact on ecological security. The land where ecological security is
expected to improve is concentrated in locations with a large number of
connected croplands. The fact that a greater number of places would worsen
rather than improve implies that agricultural modification has a detrimental
influence on ecological security that should not be overlooked. When
comparing various scenarios, croplands returning to ecological lands have
the greatest influence on ecological security, especially in the higher reaches,
where steep croplands are concentrated. According to the International
Institute for Applied Systems Analysis, ecological security refers to the state
of a natural ecosystem that can maintain its order and function while also
providing sustained ecosystem services. Due to growing urbanization and
frequent human involvement, ecological security is under unprecedented

strain today. Natural catastrophes, urbanization, and land use change/cover
or LUCC have all had an impact on ecological security in the past. The idea
of ecosystem health was first developed in the 1980s, and it was then used
to assess ecological security. To assess ecosystem health, a framework of
vigor–organization–resilience (VOR) was established, based on the stress
ecology definition of health as system organization, resilience, and vigor, as
well as the lack of indicators of ecosystem distress. Indicator assessments,
pressure–state–response (PSR) and its expanded framework driving–
pressure–state–influence–response (DPSIR), and footprint assessments
have all been established to assess ecosystem health. Because the CVOR
framework depicts ecological integrity and natural ecosystem quality at a
grid level, it is superior to the other techniques and is thus used in this study
to assess ecological security.
Despite the fact that LUCC’s impact on ecological security has been well
proven, agricultural reclamation is frequently overlooked. When croplands
are lost due to urbanization in China, farmland reclamation with the same
amount and quality is demanded in order to ensure food security. It has also
been suggested that the indirect impact on ecosystem services caused by
agricultural reclamation may be greater than the direct impact caused by
urban growth. Farmland reclamation under a strong cropland conservation
policy can result in the indirect loss of natural habitats, which is significantly
more than the direct loss caused by urban expansion. Furthermore, the loss
of carbon storage caused by agricultural reclamation between 2000 and
2010 was estimated to be 1.12 times greater than that caused by urban
expansion during the same period. As agricultural reclamation continues,
this suggests that the indirect impact of cropland reclamation on ecological
security should not be overlooked (L. Tang, Ke, Zhou, Zheng, & Wang,
2020)forest, grassland, wetland. The indirect effect of cropland reclamation
on ecological security, however, is unknown.
The amount of arable land available is unlikely to change, and as the
world’s population expands, producing more crops from limited resources
will become a requirement. By 2050, the world’s population will have grown
to 9 billion people, up from 7.7 billion today, and food production would
need to expand by at least 70% to feed the growing population. Without
a shift away from traditional agricultural techniques, future generations’
ability to produce and exploit our arable land would dwindle. Previously,
the emphasis was on making the most of available land and producing as
many crops as possible. There was little emphasis on sustainable agricultural
production or land preservation, and there was a comparable lack of emphasis

on profitability and land and resource conservation from a financial aspect.
These issues are intertwined, and the answers will help to modernize
agriculture. Farmers’ decisions to adopt more sustainable practices, such
as organic farming, hedgerow restoration, or cover crop planting, have
their own risks. Farmers’ decisions to adopt more sustainable practices are
primarily business decisions, occur less frequently, often have long-term
personal and economic consequences, may entail large investments and
long-term commitments like participating in voluntary land conservation
programs, and entail the provision of public goods.
Farmers’ decisions to adopt more sustainable techniques can likewise
be expected to be more controlled and well-thought-out as compared to the
above-mentioned examples of consumer or citizen decision-making. This
does not, however, imply that these choices are free of heuristics and biases,
or that the result will be sensible. Although the assumption of rationality
provides a broad, often statistically valid account of producer choices, it
precludes a more nuanced understanding of facts, which is especially
inappropriate when studying farmer-environment interactions. Because of
the fundamental distinctions between the intended goals of a behavioral
approach and farmers, not all behaviorally informed interventions designed
for consumers and citizens will be relevant or effective in the context of
farmers’ decisions to embrace more sustainable farming techniques.
Individual variances in thinking, feeling, and acting patterns are
known as personality traits. Personality traits are far removed from specific
decision-making tasks because they consist of regular patterns of behavior.
Extraversion, openness to new experiences, agreeableness, neuroticism, and
conscientiousness are the personality traits that are commonly regarded.
Farmers’ aversion to change has been mentioned as a possible cause for
their failure to adopt more sustainable practices. To address the social
issues impacting farmers’ adoption of sustainable practices, several policy
recommendations can be made. In terms of descriptive norms, the approach
to take is largely determined by the amount of adoption of sustainable
practices in a given area. If the level is high, one useful policy option is
to inform farmers that the majority of their neighbors have embraced
sustainable farming practices.
Consumers have been successfully motivated to conserve energy using
a similar strategy. This approach is especially essential in the context of
the CAP for voluntary schemes. When participants were told that 80%
of other farmers planned to continue using sustainable farming practices

even if their contract was not renewed, their chances of doing so more than
doubled. Farmers would produce perennial crops for bioenergy against a
reduced compensation premium if their neighbors did as well. However, a
study conducted in the United States found that disclosing the popularity of
a volunteer program had no effect on new or renewal sign-ups. On the other
hand, if adoption is poor, articulating this descriptive norm could backfire.
If the majority of farmers in a given area continue to utilize conventional
procedures, presenting them with information on this descriptive norm is
likely to dissuade, rather than encourage, them to convert to more sustainable
practices. Farmers, for example, who are advised that they use less water
than the majority of their peers, are more likely to increase their water usage.
Economic incentives may be more appropriate in places where the adoption
of sustainable practices is very low, in order to reverse this self-feeding
low descriptive norm. Using collective compensation for enrolling in agri-
environmental programs is one known approach of enhancing farmers’
perceptions that adoption is the descriptive norm. Farmers’ expectations of
others’ participation are raised by this monetary bonus, which is provided in
addition to the agri-environmental scheme premium if a specified adoption
level is met. As a result, farmers are more likely to sign up for a lower
subsidy amount, resulting in improved budget efficiency. Farmers, on the
other hand, do not value communal participation in agri-environmental
projects, according to studies.
CHAPTER 9
CLIMATE RESILIENT AGRICULTURE
CONTENTS
1.1 Introduction.......................................................................................... 6
9.1 INTRODUCTION
Temperature, precipitation, soil quality, insect regimes, and seasonal growth
patterns are all projected to change as a result of rapid global climate change.
It will be difficult to foresee the exact kind and degree of these changes for
any given place. While the agricultural industry is being affected by climate
change, research shows that existing agricultural activities are a significant
source of greenhouse emissions that exacerbate climate disruption. The
amount of GHGs emitted by an agricultural operation is determined by
the system and management of the operation. Agricultural systems must
be resilient and adaptable to change in order to cope with climate change,
which is anticipated to be both rapid and unpredictable. In the face of
major exogenous shifts such as climate change and price volatility, resilient
agriculture systems are more likely to preserve economic, ecological, and
social benefits. In the face of unpredictability, food production systems that
are diversified and relatively flexible, with livestock and crop production
integration and coordination, should be built (Kashyap, Rai, Srivastava, &
Kumar, 2017).
Through energy conservation, lower levels of carbon-based inputs,
lower usage of synthetic fertilizers, and other aspects that limit GHG
emissions and trap carbon in the soil, sustainable and organic agriculture
systems can help reduce agricultural GHG emissions. Agricultural
land, particularly through soil carbon sequestration, can act as a sink for
greenhouse gas emissions, potentially assisting in the mitigation of climate
change. However, agricultural land can only act as a long-term GHG sink if
agricultural systems are implemented that improve general soil quality and
enable reasonably consistent GHG reduction or sequestration. Fertilizer use
and efficiency, nitrogen sequestration, and overall GHG emissions of linked
animal production systems are all characteristics of agricultural crop and
forage production systems (Li et al., 2004).
Climate Resilient Agriculture 189
Figure 9.1: Green House Gases.
Source: https://www.epa.gov/sites/default/files/2021-04/gases-by-source-z021-
caption.png
9.2 GREEN HOUSE GASES (GHG)

GHGs (Figure 9.1) are released into the atmosphere due to burning fossil
fuels, clearing forests, manufacturing cement, and a variety of other industrial
and agricultural operations, increasing the quantity of radiation trapped near
the earth’s surface and accelerating warming. This process, known as the
enhanced greenhouse effect, is triggered by a forced release of GHGs from
their terrestrial storage into the atmosphere. Global temperatures are rising,
which is altering core climatic processes. Some of the modifications may be
beneficial in some regions, but the majority is projected to cause more harm
than good. Following the agricultural and industrial revolutions, the majority
of these human impacts to climate change happened in the previous 200–
300 years. Many countries around the world are experiencing food crises as
a result of conflict and natural disasters, while food security is being harmed
by unprecedented price increases for basic foods, fueled by historically
low food stocks, high oil prices, and rising demand for agrofuels, as well
as droughts and floods linked to climate change. Food riots have already
erupted in some nations as a result of rising international cereal prices.
Figure 9.2: Climate change.
Source: https://www.iberdrola.com/environment/impacts-of-climate-change
9.3 CLIMATE CHANGE

Climate change (Figure 9.2) will exacerbate food insecurity, especially
among the resource poor in developing nations who are unable to achieve
their nutritional needs through market access. Communities must prepare
for the likelihood of a food crisis by making effective use of resources in
order to protect livelihoods, as well as lives and property. It is critical to find
and institutionalize measures that help the most vulnerable people cope with
the effects of climate change. This necessitates collaborative thinking and
responses to concerns arising from the intersection of food security, climate
change, and sustainable development. Agriculture and food systems must
adapt to climate change and natural resource demands in order to improve
and ensure food security, and they must also contribute to climate change
mitigation. Because these issues are intertwined, they must be addressed
at the same time. Climate change offers complex concerns such as various
abiotic pressures on crops and animals, water scarcity, land degradation,
and biodiversity loss, necessitating concentrated and long-term study to find

solutions. It is vital to put in place the required infrastructure to conduct
basic and strategic research. Simultaneously, there is potential to improve
agriculture’s resilience by applying existing knowledge and technology
to farmers’ fields as a whole. As a result, improved technologies must
be developed through short- and long-term research, as well as existing
technologies must be shown on farmers’ fields to improve resilience.
Figure 9.3: Sustainable agriculture.
Source: https://www.pmfias.com/sustainable-agriculture-organic-farming-bio-
fertilizers/
9.4 SUSTAINABLE AGRICULTURE

Sustainable agriculture (Figure 9.3) aims to transform agriculture into a
climate-resilient, ecologically sustainable production system while also
maximizing its full potential, ensuring food security and equitable access
to food resources, improving livelihood opportunities, and contributing to
economic stability. Climate resilient agriculture (CRA) aids in the attainment
of long-term development objectives. By jointly tackling food security and
climate concerns, it unifies the three elements of sustainable development

like economic, social, and environmental. Land usage and changes in land
use can have a significant impact on overall climate change. In most cases,
vegetation and soils operate as carbon sinks, storing carbon dioxide ingested
during photosynthesis. When the land is disturbed, the carbon dioxide,
methane, and nitrous oxide trapped in the soil are released, re-entering the
atmosphere. Clearing land can lead to soil degradation, erosion, and nutrient
leaching, all of which can diminish the land's ability to operate as a carbon
sink. As a result of the reduced ability to store carbon, more carbon dioxide
may pump into the atmosphere, increasing the total amount of greenhouse
gases.
Direct anthropogenic alterations and indirect changes are the two
categories of land-use change. Deforestation, reforestation, and afforestation,
as well as agriculture, are examples of anthropogenic alterations. Climate
or carbon dioxide concentration changes that force vegetation changes are
examples of indirect alterations. On a global basis, carbon dioxide emissions
from land-use changes account for about 18 percent of total annual
emissions, with one-third of that coming from emerging countries and more
than 60% coming from less developed countries. These factors determine
the biosphere's carrying capacity for producing enough food for humans
and domesticated animals. The balance of these effects will determine the
overall impact of climate change on agriculture. Assessing the effects of
global climate change on agriculture could aid in correctly anticipating and
adapting farming to maximize agricultural output.
Carbon dioxide enrichment would probably be beneficial to agriculture
if there were no accompanying climatic changes. More severe warming,
flooding, and drought, on the other hand, may diminish yields. Higher
temperatures, on the other hand, may hasten the microbial breakdown of
organic materials, reducing soil fertility over time. Higher temperatures
speed plant maturity in annual species, decreasing the growth stages of crop
plants, according to a study on the biophysical impact of climate change
linked to global warming. In addition, research of the effects on pests and
diseases reveals that rising temperatures may expand the geographic range
of several insect pests that are currently restricted by temperature. Increased
ultraviolet-B radiation has a negative impact on the productivity of some
agricultural crops. Heat stress may put livestock at risk, as well as a reduction
in the quality of their food source. Changes in water temperature will affect
fisheries by shifting species ranges, making environments more conducive
to invading species, and altering life cycle timing.
The world climate is being influenced by rising CO2 levels in the

atmosphere and accompanying temperature rises, which will affect plant
growth, development, and function. Higher photosynthetic rate, enhanced
light-use efficiency, reduced transpiration and stomatal conductance, and
improved water-use efficiency are the principal impacts of increased CO2
concentration. Since the year 2000, these levels have been continuously
increasing by 1.9 ppm each year, owing mostly to the burning of fossil
fuels. Photosynthesis requires carbon dioxide. Even small increases in
carbon dioxide cause higher plant growth, according to scientists. Increased
CO2 levels are anticipated to result in higher harvestable crop yields. This,
however, is highly dependent on the availability of sufficient water and
nutrients for plant growth. Crops with reduced nutritional and protein levels,
according to some scientists, will be one of the drawbacks of greater output.
If extra fertilizers are not introduced into food production, this could have a
significant and broad influence on long-term human health.
Climate change has a favorable impact on agriculture and forestry
because plants respond favorably to rising CO2 levels in the atmosphere.
Higher CO2 levels stimulate plant development by increasing the rate of
photosynthesis and improving the efficiency of water consumption in
plants known as CO2 fertilization. Experiments showed that when CO2
concentrations increased by nearly 50%, they resulted in 15 percent growth
increases in crops and 10–50 percent growth increases in tropical savanna
grasses. Wheat yields increased by 10–50 percent, cotton biomass grew by
35 percent, whole boll yields climbed by 40 percent, and lint yields increased
by 60 percent in tests where CO2 levels were increased up to 700 ppm.
Increased evaporative demand, fluctuations in rainfall, and variations in
river runoff and groundwater recharge, the two sources of irrigation water,
will all have an impact on agriculture (Bond & Midgley, 2012).
Because water is so important to plant growth, changing precipitation
patterns have a big impact on agriculture. Because rain-fed agriculture
accounts for more than 80% of overall agricultural production, estimates of
future precipitation variations frequently influence the degree and direction
of climate impacts on crop production. Due to strong dependencies on
changes in atmospheric circulation, the impact of global warming on regional
precipitation is difficult to predict. Even if there is an agreement in the sign
of change in some places, these uncertainties imply distinct indications of
precipitation change averaged over all croplands. One scenario that forecasts
a rise in precipitation overall shows significant increases in the southern
United States and India, but significant losses in the tropics and subtropics.
The opposite scenario depicts decreases in low latitudes, but no significant

rises in India. Seasonal precipitation changes could be more important to
agriculture than annual mean variations.
9.5 WATER AVAILABILITY

Water availability is influenced by more than just precipitation. Increasing
evaporative demand as a result of rising temperatures and longer growing
seasons might raise crop irrigation requirements globally by 5 to 20%, or
possibly more, by the 2070s or 2080s, but with significant regional variations
Southeast Asian irrigation requirements could rise by 15%. Irrigation
demand is expected to rise throughout the Middle East and North Africa,
according to regional assessments. Clearly, these estimates are also reliant
on unknown precipitation changes. Precipitation is the most important
element determining crop productivity because it is the principal source of
soil moisture. While global climate models indicate an overall rise in mean
global precipitation, their findings also point to the possibility of altered
hydrological regimes in most regions. Total seasonal precipitation, its
within-season pattern, and the between-season variability can all be affected
by climate change. A change in the pattern of precipitation events may be
more important than a change in the yearly total for agricultural productivity.
Warmer temperatures, drier air, or windier circumstances may cause a spike
in the daily rate of evapotranspiration and a shift in the seasonal pattern of
evapotranspiration, putting crops’ water regime at risk.
Drought conditions can also be exacerbated by less precipitation falling
as snow and early snow melt. These effects may affect subsequent river
discharge and irrigation water supplies during the growing season in arid
locations, such as the Sacramento River Basin in California. High relative
humidity, frost, and hail can all damage maize and other grains, as well
as the quality of fruits and vegetables. Crop yields and yield quality are
variable due to interannual precipitation variations. Droughts in the United
States’ Great Plains lowered wheat and corn production by up to 50% in the
1930s. Droughts worsen wind and water erosion by reducing plant cover,
lowering crop output in the future. If dry spells occur during important
developmental stages such as reproduction, crop yields are most likely to
decrease. Flowering, pollination, and grain filling are all very vulnerable
to water stress in most grain crops. Because of climate change, the soil
system responds to short-term events like rainfall as well as long-term
changes like physical and chemical degradation (Otkin et al., 2018). The
organic matter supply, temperature regimes, hydrology, and salinity are all
potential implications of climate change on soil health. Because of lower net
primary production, soil carbon levels are predicted to fall. Higher carbon
mineralization following episodic rainfall and reduced yearly and growing
season rainfall is anticipated to exceed any gains from increased plant
water-use efficiency due to elevated CO2. Where the more inert components
of the carbon pool predominate, the quality of soil organic matter may
likewise vary. N mineralization increases when soil temperature rises, but
availability may decrease due to increased gaseous losses from processes
like volatilization and denitrification.
There is yet to be a full examination of the influence of possible climate
changes on soils. Higher temperatures may hasten the decomposition of
organic materials by microbes, reducing soil fertility in the long run. However,
higher rates of photosynthesis could offset these impacts by increasing root
biomass. Higher temperatures could speed up nutrient cycling in the soil,
and faster root growth could lead to higher nitrogen fixation. However, these
benefits may be insignificant in comparison to the negative consequences
of changing rainfall patterns. Greater rainfall, for example, in existing
damp places could contribute to increased mineral leaching, particularly
nitrates. The effects of GHG accumulation in the atmosphere and water
are linked to a variety of physical phenomena, including slow temperature
changes, acidification of water bodies, changes in ocean currents, and rising
sea levels. These physical changes have an impact on aquatic ecological
functions as well as the frequency, intensity, and location of extreme weather
events. There will be a variety of direct and indirect effects on fisheries and
aquaculture.
In most tropical and subtropical oceans, seas, and lakes, ecosystem
productivity is anticipated to decline. Productivity is expected to rise in
high-latitude environments. Climate change has an impact on agricultural
crops as well as their pests like weeds, insects, and infections. Climate
has a big influence on the distribution and proliferation of weeds, fungus,
and insects. Organisms become pests when they compete with, prey on, or
induce disease in crop plants to the point where productivity is reduced.
Climate influences not just the types of crops farmed and the severity of
pest problems, but also the insecticides commonly employed to control or
prevent outbreaks. Pesticide effectiveness, persistence, and transport are all
influenced by rainfall intensity and timing in relation to pesticide application.
Pests will become more prevalent as temperatures rise due to a number of
interconnected mechanisms, including range extensions and phenological
shifts, as well as faster population growth and migration. The equilibrium

between pests, their natural enemies, and their hosts is anticipated to shift
as a result of climate change. The increase in temperature will help pests
develop and survive the winter. As a result of lower foliar nitrogen levels,
rising atmospheric carbon dioxide concentrations may result in a drop in food
quality for plant-feeding insects. Plant disease epidemiology will change
as a result. In times of rapidly changing climate and inclement weather,
forecasting disease outbreaks will be more difficult.
Increased prevalence of harsh weather and environmental instability
may impair the effectiveness of insecticides on targeted pests or result in
more harm to non-target organisms. The photodegradation products of
one class of atmospheric trace gases, chlorofluorocarbons (CFCs), have a
significant extra influence on the atmosphere, destroying ozone (O3) in the
stratosphere(Plummer & Busenberg, 2000)synthetic, halogenated alkanes,
developed in the early 1930s as safe alternatives to ammonia and sulphur
dioxide in refrigeration. Production of CFC-12 (dichlorodifluoromethane,
CF2C12 (Figure 9.4). The stratospheric ozone layer acts to filter out much
of the ultraviolet component of the solar spectrum before it reaches the
earth’s surface, as ozone is a significant absorber of solar ultraviolet light.
As a result of the decrease in stratospheric O3, more solar UV can reach the
earth’s surface. Changes in precipitation and rising temperatures between
1981 and 2001 resulted in yearly cumulative losses of wheat, maize, and
barley of around 40 million tonnes per year. While the scientists believe
these losses are minor in comparison to technical yield advances over the
same time period, the findings show that climate change is already having a
negative influence on agricultural yields on a worldwide scale.
The data show that food yields in developing countries are falling
while yields in developed countries are rising. The production of the four
crops would be insufficient to feed the world in all scenarios. However,
this is only possible if food is transferred from wealthy northern countries
to impoverished southern countries. Individual crops, on the other hand,
respond differently to climate change, making generalizations difficult. It
is necessary to do a crop-by-crop and region-by-region analysis. Moisture,
on the other hand, is critical in all crop production, and a lack of it will
undoubtedly be a key limiting issue in North America.
Figure 9.4: Destroying ozone (O3).
Source: https://biophysics.sbg.ac.at/atmo/o3-scans/chapman.jpg
Heat stress might also be a problem for crops like corn and potatoes.
Due to expected increased rainfall in eastern and central Africa, the picture
is different. More yields of 10–30% are conceivable with increased rainfall
and improved farming methods. Even these expected improvements,
however, will not be enough to feed Africa’s rapidly rising population.
Long-term significant changes in the projected patterns of average
weather in a specific region due to global warming are known as regional
consequences of global warming. The greenhouse effect, which is produced
by rising amounts of greenhouse gases, particularly carbon dioxide, is
causing global average temperatures to rise. When the global temperature
changes, climatic changes are not likely to be uniform around the globe.
Land areas, in particular, change quicker than oceans, northern high latitudes
change faster than the tropics, and biome region edges change faster than
their cores. The nature of global warming’s regional effects varies. Some
are the result of a more widespread global shift, such as rising temperatures,
which have local consequences, such as ice melting. A change could also
be linked to a shift in a certain ocean current or weather system. In such
circumstances, the regional impact may be exaggerated, and the global trend
may not necessarily be followed.
Figure 9.5: Hydrological cycle.
Source: https://www.noaa.gov/education/resource-collections/freshwater/wa-
ter-cycle
Melting, modifying the hydrological cycle of evaporation and
precipitation (Figure 9.5), and changing currents in the oceans and air flows
in the atmosphere are three primary ways that global warming will affect
regional climate. The fast-rising gap between limited water availability and
escalating demand for water from diverse economic sectors is a big concern.
Egypt’s rate of water use has already hit its peak, and climate change will
worsen this vulnerability. Reduced crop yields in several locations will
put many millions of Asians at risk of starvation. Decreased freshwater
availability will affect more than 100 million people in Central, South, East,
and Southeast Asia, notably in large river basins like Changjiang. With a
temperature increase of 2–3 °C combined with decreasing precipitation in
the semiarid and arid zones, grassland production is anticipated to drop by
as much as 40%–90%.
9.6 AGRICULTURAL PRODUCTIVITY

Agriculture productivity in northern areas may increase. Boreal forest in
North Asia may expand northward, while forest fires are anticipated to
increase in frequency and size, limiting forest extension. In Asian countries,
there are a variety of contemporary water vulnerabilities. Some countries
that are not currently at high risk of water stress are likely to encounter water
stress in the future, with varying capacity for response. Increased river and
coastal flooding are projected to be most severe in coastal areas, particularly
heavily inhabited mega delta regions in South, East, and Southeast Asia.
The interplay of climate change consequences with rapid economic and
population expansion, as well as migration from rural to urban regions, is
projected to have an impact on development across southern and eastern
Asia. The development path, physical exposures, resource distribution,
antecedent stresses, and social and government institutions all influence a
society’s vulnerability. Adaptive capacities are unevenly distributed among
countries and within cultures, despite the fact that all societies have the
innate capacity to deal with certain variations in the environment.
Historically, the poor and underprivileged have been the most
vulnerable to the effects of climate change. Recent Asian studies suggest
that marginalized, primary-resource-dependent livelihood groups are more
vulnerable to climate change impacts if their natural resource base is severely
strained and deteriorated by overuse, or if their governance structures are
incapable of responding effectively. Water security issues in southern and
eastern Australia, New Zealand’s Northland, and other eastern regions are
expected to worsen by 2030. Land degradation issues including erosion and
salinization are anticipated to worsen. Drought and fire are expected to reduce
agricultural productivity across much of southern and eastern Australia, as
well as sections of eastern New Zealand, by 2030. Due to a longer growing
season, reduced frost, and more rainfall in north-eastern Australia and the
main portions of New Zealand, substantial yield increases are possible. Heat
stress, decreased pasture productivity, lower fodder quality, and the spread
of animal diseases such as cattle ticks are all expected to affect livestock
productivity in Australia.
CO2 fertilization, more rainfall, and a longer growing season will benefit
forests, but increased water stress, pests, fires, and erosion will have negative
consequences. Despite their hydrological and geological differences, both
Australia and New Zealand are already suffering water supply consequences
as a result of recent climate change, both due to natural variability and human
activities. The El Nino Southern Oscillation cycle is the most powerful

regional driver of natural climate variability. Almost all of Australia’s
eastern states and the southwest region have been in drought since 2002.
This drought is on par with the so-called Federation droughts of 1895 and
1902, and it has sparked heated debate over climate change’s impact on
water resources and long-term water management (Graham, Michaelsen,
& Barnett, 1987)a new approach in geophysical modeling. Our results are
of interest both as they show the dominant modes of evolution in the SLP
and wind fields through the El Niño-Southern Oscillation cycle and with
respect to the problem of predicting equatorial SSTs. This paper deals with
the first issue above and describes some statistical composites that typify the
development of features in the predictor fields over periods of years. The
results of the EEOF analyses clearly show slowly propagating anomalies in
both the near-global SLP and trade wind fields. The CCA analysis, which
highlights the co-evolution of the two fields, suggests a strong coupling
between the two and depicts the anomalous features as migrating centers of
divergence and convergence that first appear over the eastern Indian Ocean.
These features propagate slowly eastward, amplify as they expand into the
western Pacific, decline as they cross the central ocean, then reamplify over
the eastern Pacific. As reamplification takes place, new opposing anomalies
appear in the Indo-Pacific. Descriptions of the predictor data sets and details
of the statistical techniques used may also be found in this paper. The SST
data, model validation techniques, and forecast model results are presented
in a companion paper (Graham et al., this issue.
Due to water constraints, increasing biosecurity threats, environmental
deterioration, and social instability, farming of marginal land in drier
locations are projected to become unsustainable. When irrigation water
availability is restricted, cropping and other agricultural businesses that rely
on irrigation are likely to be threatened. Reduced growth length for maize
in New Zealand reduces crop water requirements, allowing development
to be more closely synchronized with seasonal climatic conditions. Crop
productivity will grow slightly, but this may be considerably overshadowed
by technological advancement. Crops from southern Europe, such as maize,
sunflower, and soybeans, will expand northward. Droughts and dry spells
will impact Mediterranean crop productivity, resulting in lower yields,
scrublands and deciduous forests, increased water demand for irrigation,
fire danger, and diminished biodiversity.
The risk of livestock diseases such as bluetongue and African

horse sickness will rise. Northern Europe’s Forest productivity will rise
dramatically. In boreal forests, there will be soil carbon losses and seasonal
variations in frost damage. The most popular and planned techniques to
adapt to increasing water stress are measures such as damming rivers to
create instream reservoirs. However, environmental constraints and hefty
investment costs are limiting the construction of new reservoirs throughout
Europe. Other options, such as wastewater reuse and desalination, are
becoming increasingly popular, although their popularity is hampered by
health issues with wastewater reuse and high energy costs with desalination,
respectively. Household, industrial, and agricultural water conservation, as
well as the reduction of leaky municipal and irrigation water systems and
water pricing, are all potential. Introduce crops that are more suitable to a
changing climate to reduce irrigation water use. Regional and watershed-
level climate change adaptation strategies are being incorporated into
plans for integrated water management, while national strategies are being
constructed to fit into current governance institutions, as an example of a
unique European strategy to adjusting to water stress.
Some countries and regions like the Netherlands, the United Kingdom,
and Germany are developing water sector adaptation procedures and
risk management techniques that reflect the unpredictability of expected
hydrological changes. Food security will be harmed in dry areas due to
salinization and erosion of agricultural land, which will reduce crop yields
and livestock output. By the 2050s, agricultural lands are extremely likely
to be desertified and salinized to the tune of 50% in some locations. Crop
yields may be lowered in certain locations, while they may increase in
others. Increased temperatures and groundwater loss have resulted in habitat
loss and species extinction in many locations, including tropical forests,
affecting indigenous tribes in particular. Population expansion is expected to
continue, resulting in increased food demand. Because most Latin American
countries’ economies are based on agricultural output, regional diversity in
crop yields is a critical concern. As a result of its geographical configuration,
Latin America offers a wide range of climates. There are also extensive dry
and semiarid areas in the region. From snow mountains to moderate and
warm climates, the climatic spectrum is vast (Kang & Banga, 2013)caused
by anthropogenic activities, is a universal phenomenon across the globe.
There is general consensus that combating climate change will require a set
of internationally coordinated policy interventions for reducing greenhouse
gas (GHG.
Figure 9.6: Receding glaciers.
Source: https://www.dailymail.co.uk/sciencetech/article-4369402/Timelapse-
images-reveal-Earth-s-receding-glaciers.html
In recent decades, glaciers have typically receded, (Figure 9.6) and
some very minor glaciers have already vanished. The Amazon, Parana, and
Orinoco rivers collectively convey more than 30% of the world’s renewable
fresh water into the Atlantic Ocean. These water resources, on the other
hand, are inequitably distributed, and broad zones have a very low water
supply. When there is a lack of precipitation or greater temperatures, it puts
a strain on water availability and quality. Droughts in many parts of Latin
America are statistically linked to ENSO episodes, resulting in severe limits
on water resources. Rainfed agriculture is expected to boost yields by 5–20
percent in the early decades of the century, with significant regional variation.
Warming in the western mountains will alter water resources, resulting in
decreasing snowpack, greater winter flooding, and reduced summer flows,
aggravating competition for over-allocated water resources. Crops that rely
on heavily consumed water resources, such as wine grapes, or those that
are near the warm end of their acceptable range may encounter significant
issues. Forest growth is expected to increase by 10–20 percent in the twenty-
first century as a result of longer growing seasons and increased CO2 levels,
though there will be significant spatiotemporal variance. Depending on the
emission scenario, increases in insect, disease, and wildfire disturbances, as
well as associated losses, are predicted to influence forests.
Figure 9.7: Cold-water fisheries.
Source: https://www.thesprucepets.com/what-fish-species-are-coldwa-
ter-1380965
Cold-water fisheries (Figure 9.7) are expected to suffer, while warm-
water fisheries are expected to benefit, with mixed effects for cool-water
fisheries. Higher temperatures will cause species distribution to shift
northward. Most regions of North America should expect changes in the
time, volume, quality, and spatial distribution of freshwater accessible for
human settlements, agricultural, and industrial uses as the rate of warming
accelerates in the next decades. While some of the above water resource
changes are true for all of North America, twentieth-century trends show
that climate change impacts on runoff, stream flow, and groundwater
recharge vary greatly by location. In both Canada and the United States,
differences in wealth and geography lead to an uneven distribution of
likely consequences, vulnerabilities, and adaptability. As animals migrate
northward in response to warmer temperatures and a longer growing season,
opportunities for agricultural and pastoral operations expand, but there are
risks of invasive species, biodiversity loss, and the development of animal-
transmitted diseases. Scrubland and woods might potentially replace 10–
50 percent of the tundra. Increased warmth, decreased sea-ice cover, and
shifts in hydrological regimes would impact ecosystems, causing harm
to numerous creatures, including migratory birds, mammals, and higher
predators. Changes in ecosystems, decreased transportation and market
access, and lower-quality drinking water will jeopardize the food security of
some subsistence systems.
They found, with moderate confidence, that the benefits of a milder
climate were contingent on local factors. Increased agricultural and forestry
potential were deemed to be one of these benefits. The broad seeding of
barley, which had been impossible 20 years earlier, was now conceivable
due to rising temperatures. Some of the warming was caused by a local
transient effect caused by Caribbean Ocean currents, which had also
harmed fish stocks. Sea-level rise, soil salinization, seawater intrusion into
freshwater areas, and a loss in freshwater availability will all have an impact
on agricultural land and, as a result, food security. Extreme occurrences
will have an overall impact on agricultural productivity. Increasing sea
surface temperatures, rising sea levels, and damage from tropical cyclones
will have an impact on fisheries. Fishing incomes will be impacted by coral
reef degradation and bleaching. Forests that have been damaged by harsh
events will take a long time to recover. On some high-latitude islands, forest
cover may increase. Because of the reduction in island size or complete
inundation, the viability and thus sovereignty of some governments would
be jeopardized.
Figure 9.8: Climate Smart Agriculture.
Source: https://www.researchgate.net/publication/326847389_Assessment_of_
Climate-Smart_Agriculture_CSA_Options_in_Nepal/figures?lo=1
Climate Smart Agriculture (CSA) (Figure 9.8) is a method for guiding

agricultural management in the face of climate change. The concept was
first introduced in 2009, and it has since evolved based on the inputs
and interactions of numerous parties involved in its development and
implementation. The CSA intends to develop globally applicable principles
for managing agriculture for food security in the face of climate change,
which might serve as a foundation for policy support and recommendations
from multilateral agencies such as the United Nations’ FAO. The key
aspects of the CSA approach were established in response to discussions and
conflicts surrounding climate change and agriculture policy for long-term
sustainability. It’s vital to understand the trajectory of global climate change
policies in recent years in order to place CSA and its debates in context. He
categorizes evolution into five distinct stages (Lipper et al., 2014).
During this time, the main focus of global climate change policy was
the need for global action to stabilize greenhouse gas (GHG) emissions,
which would be supported and guided by the IPCC, a globally cooperative
framework for scientific research, and with the understanding that developed
and developing countries would bear different responsibilities for mitigating
climate change. This necessitates taking preventive action even before full
knowledge regarding human-induced climate change is established, as well
as emphasizing acts that would be beneficial even if climate change did
not exist. The Brundtland Commission Report on Sustainable Development
was also significant in recognizing the links between climate change and
sustainable development, as well as the benefits of studying them together.
The CSA concept arose at a period when there was a lot of debate about
the concept of sustainable agricultural development and how to approach
it. Agriculture’s critical role in food security was not well articulated in
the global climate change policy arena, and the discussion of adaptation
and mitigation in two separate negotiation streams hindered the ability to
establish synergies between them. The agricultural sector, according to
these early formulations of the climate smart agriculture concept, is critical
to climate change response not just because of its high vulnerability to
climate change consequences, but also because it is a major contributor to
the problem. It also stated that ensuring food security requires a long-term
restructuring of the agricultural sector, and that climate change measures
must be framed in this context. Recognition of potential trade-offs between
the three aims, as well as the possibility to create synergy between them
through policies, institutions, and finance, has been a significant component
of the CSA idea since its conception. A requirement for locally specialized
solutions was also a significant factor.
FAO gave a broad framework for examining trade-offs and synergies,
as well as various instances of sustainable land management methods
and modern inputs. However, there was no particular direction on how
to design a CSA practice or prioritize objectives in order to develop site-
specific solutions. The intricacy of linking together the three primary aims
also prevented a clear conceptual conceptualization of the link between
sustainable agriculture and CSA. The lack of a clear methodology, combined
with the concept’s quick adoption, resulted in a great deal of variation.
Climate change has many effects on agriculture, both in terms of space
and time. The outcomes are unpredictable and varied. Agriculture innovation
is certainly a critical answer for successful and equitable adaptation and
mitigation, and we need to reconsider how we foster innovation to handle
the variability and uncertainty of climate change consequences. In both
developing and developed countries, innovation will be critical in advancing
toward climate smart agricultural (CSA) systems. For both adaptation and
mitigation, we will require more resilient agricultural systems as well as
higher resource efficiency. Technological innovation will be critical, but it
will not be sufficient. In dealing with the varied and unknown implications
of climate change, managerial and institutional innovations are going to be
even more critical. To build CSA practices, innovation can be combined
with various forms of climate change adaptation. In particular, innovation
can improve technology adoption, avoid or assist production/population
movement, improve trade and aid, and improve insurance efficiency and
inventory feasibility. Climate change is projected to raise global temperatures
by 1–3 °C, which is equal to a shift of 300–500 km of weather patterns away
from the equator and towards the poles, depending on the range of mitigation
activities done in the next decades. Similarly, temperature variability will
rise in higher-altitude places. While climate change may have a negative
overall effect on agricultural production, the distributional effects are
significantly more significant. As a result, crop production in some warm
agricultural areas in Texas, Oklahoma, Mexico, and Western Africa will
become unviable. At the same time, agricultural production will be possible
in parts of Russia, Canada, and even the Arctic.
In many parts of the world, the sea level rise may result in the loss of
high-value agricultural land as well as critical infrastructure for exporting
and importing food. Coastal zones i.e., at less than 10 m altitudes are home
to an estimated 10% of the world’s population, with considerable variations
in population share by country, accounting for 14% of worldwide GDP
Most notably, about half of the populations of Vietnam, Bangladesh, and
Egypt live in these zones, while China and India, despite having a much
lower overall population, have over 200 million people residing in these
zones. The population affected by SLR will vary greatly depending on the
actual rise in sea level, ranging from 56 million people with a 1-m rise to
245 million people or 5.57 percent with a 5-m rise (Dasgupta, Laplante,
Meisner, Wheeler, & Yan, 2009)and unexpectedly rapid breakup of the
Greenland and West Antarctic ice sheets might produce a 3–5 m SLR. In
this paper, we assess the consequences of continued SLR for 84 coastal
developing countries. Geographic Information System (GIS. Furthermore,
rising sea levels will endanger significant swaths of prime agricultural land,
particularly in tropical areas. Given the diversity of locations, developing
location-specific solutions is critical. Transformational innovation, rather
than incremental measures, may be necessary in areas most vulnerable to
SLR in order to stimulate adaptation and preserve vulnerable populations.
Fragile coastal districts may be saved in some situations by investments
in protective infrastructure such as dikes and dams, but in many others,
vulnerable areas will have to be abandoned, generating displacement issues.
Different methods of agricultural production may be possible in some
locations, but this will necessitate innovation.
Increased temperatures, in addition to changing precipitation patterns,
will increase melting, reducing the feasibility of using water stored in snow
accumulated during the rainy season for irrigation during the dry season.
Additionally, floods may become more likely. Given the importance of
irrigated agriculture during dry seasons in many regions of the world, this
change could have a large impact on food supply unless certain actions are
done to mitigate it. The conditions at each site determine these solutions.
Investment in new forms of water inventories and storage, such as flood
control and storage dams and water diversion to subterranean reservoirs,
could be one solution. Variations in crop timing and selection may be
required as a result of these changes in water availability. Changes in water
availability may also have an impact on the availability of hydroelectric
power for irrigation, affecting agricultural supplies. As a result of climate

change, agricultural water resources will need to be rearranged and managed
differently.
As previously stated, the form of innovative climate change responses
must adapt to two aspects of these consequences. The first is the concept
of heterogeneity. Climate change affects different locations differently:
for certain desert or low-lying coastal regions, climate change may be
disastrous, while for others, it may be seen as “climate betterment.” These
disparities in consequences, as well as disparities in benefits and losses
from mitigation initiatives, may explain the varied responses and desire
to participate in and contribute to coordinated efforts to avert or reduce
climate change. Uncertainty is the second factor that influences taking
action to solve climate change concerns. The exact dates, magnitudes, and
locations of certain climate change impacts remain unknown. On the same
hand, there is a large body of evidence suggesting that farmers and other
agricultural operators operate in a risk-averse manner. Risk aversion limits
the magnitude of activities made by risk averse firms as the dangers they
confront an increase in a static framework.
Heterogeneity and uncertainty will thus make identifying the full range of
responses to climate change from observable data more difficult, especially
now, when some of the impacts of climate change like migration of warm
weather toward the pole and a significant rise in sea level, triggering of tipping
points leading to irreversible changes are more likely to occur in the long
run. Others, such as those that enhance the likelihood of extreme occurrences
such as floods and droughts, may have already occurred or will do so in the
near future. As understanding about the concerns of climate change grows,
so will investment in new initiatives to address them. New technology and
institutional choices, as well as changes in behavioral responses to climate
change and related solutions over time, must be considered in the inventive
approach. We can learn about some activities from the responses thus far, as
well as the future potential to adapt to climate change and the elements that
influence responses.
Figure 9.9: Economic growth theory.
Source: https://www.doorsteptutor.com/Exams/IEcoS/Paper-2/Questions/
Topic-Economic-Growth-and-Development-4/Subtopic-Theories-of-Economic-
Development-3/Part-1.html
Innovations can be classified in a variety of ways. According to
economic growth theory, (Figure 9.9) technologies are classified based
on their impact on inputs and outputs. For example, capital-saving, labor-
saving, quality-improvement, and risk-reduction innovations can all be
distinguished. Another method to categories innovations is by their form,
such as technological, managerial, or institutional innovations. New
machinery embodies technological innovations, which are further split
into mechanical like tractors, biological, and chemical categories. Better
procedures like Integrated Pest Management, enhanced pruning techniques,
and crop rotation are examples of managerial advances that are not reflected
in physical capital. New organizational structures such as cooperatives and
trading arrangements are examples of institutional innovations. Because of
the variability and randomness of climate change impacts, numerous types
of innovation will be particularly helpful.
Throughout history, practitioners have been a primary source of
innovation. Practitioners identified and improved the cultivation of crops,
and early farming procedures. In the present period, however, science and
research are becoming key sources of new breakthroughs. Furthermore, in
the case of climate change, it is critical to speed up the innovation process

so that new solutions are available when and where climate change occurs.
Scientific research has aided in the invention of new types of engines, electric
appliances, new medications, fertilizers, and crop kinds. There are several
stages to the innovation process. The process of technical innovation starts
with research efforts that lead to the discovery of ideas, which are at the heart
of new developments. Following that, concepts are polished, tested, and
scaled up through more experimentation as part of the development process.
The development process for many biological and chemical discoveries
also entails government permission for usage prior to commercialization.
Production and marketing operations are used to commercialize the product
after it has been approved for feasibility. Consumers begin to use and
evaluate the product, and their feedback leads to product improvement and
additional developments. This linear characterization ignores feedback and
interactions, but it does provide a useful foundation for thinking about some
of the major obstacles that new technologies face. The innovation process in
managerial and institutional innovation may also begin with research efforts
that identify alternate solutions to a problem, such as economic research or
decision theory.
CHAPTER 10
PLANT BREEDING
CONTENTS
1.1 Introduction.......................................................................................... 6
10.1 INTRODUCTION
Plant breeding is an attempt by people to manipulate nature in order
to benefit plants’ heredity. Plant modifications are both permanent and
heritable. The desire of humans to improve specific qualities of plants in
order for them to perform new tasks or enhance existing ones is driving
this attempt to change the status quo. As a result, in modern society, the
terms plant breeding and plant improvement are frequently interchanged.
Plant traits, structure, and composition are thus manipulated in breeding to
make them more beneficial to humans. It’s significant to note that not every
plant attribute or characteristic is easily manipulated by breeders (Hayes,
Immer, & Smith, 1955). Plant breeders are increasingly able to achieve
amazing plant manipulations as technology improves, though not without
controversy, as is the case with the invention and use of biotechnology to
plant genetic manipulation. Transgenesis, the technology for transferring
genes over natural biological boundaries, is one of the most contentious of
these modern technologies.
Plant breeding is required to increase the value of food crops by
increasing the production and nutritional quality of their products for human
health. Key plant foods are low in certain important elements to the point
where disorders related to nutritional deficiencies are widespread when
these foods make up the majority of a regular diet. Cereals have low levels
of lysine and threonine, whereas legumes have low levels of cysteine and
methionine. To advance the nutritional quality of food crops, breeding is
required. Rice, a staple of the world’s diet, is deficient in pro-vitamin A. The
Golden Rice project, which is currently being carried out at the International
Rice Research Institute (IRRI) in the Philippines and parts of the world,
aims to develop, for the first time, a rice cultivar capable of producing pro-
vitamin A or Golden rice, which has a 20-fold increase in pro-vitamin A,
was developed by Syngenta’s Jealott’s Hill International Research Centre in
Berkshire, UK.
Plant Breeding 213
Figure 10.1: Malnutrition.
Source: https://www.fao.org/news/story/en/item/1199760/icode/
Around 800 million people worldwide, including 200 million children,
suffer from chronic malnutrition, which causes a slew of health problems.
Malnutrition (Figure 10.1) is particularly common in underdeveloped
nations. By lowering harmful components and increasing texture and other
features, breeding can also make some plant products more digestible
and safer to eat. The value of plant material for animal feed is reduced
by its high lignin content. Alkaloids in yam, cyanogenic glycosides in
cassava, trypsin inhibitors in pulses, and steroidal alkaloids in potatoes are
examples of toxic compounds found in key food crops. Forage breeders are
interested in enhancing feed quality i.e., high digestibility, high nutritional
profile for cattle, among other reasons. The current phenomenon of global
climatic change is partly to blame for changing the crop production
environment. This necessitates the development of new crop cultivars for
new production settings. While affluent economies may be able to mitigate
the consequences of unseasonably warm weather by supplementing the
production environment, poorer countries are easily destroyed by even
brief bouts of bad weather. Drought resistant cultivars, for example, are
useful to agricultural productivity in places with marginal or irregular
rainfall regimes. Breeders must also create novel plant varieties that can
withstand biotic and abiotic challenges in the producing environment.
Crop distribution can be broadened by adapting crops to new production
settings. The development of photoperiod-insensitive crop cultivars might
allow previously photoperiod-sensitive species to be produced in greater
quantities. Processed foods account for an important portion of the global
food supply (Hussain, 2015). Fresh produce for the table has different
quality criteria than fresh produce for the food processing business. One of
the reasons why the “FlavrSavrTM” tomato, the first genetically modified
(GM) crop approved for, failed was that the product was marketed as a table
or fresh tomato when, in fact, the gene of interest was placed in a genetic
background for developing a processing tomato variety. Plant breeders can
address a variety of commercial needs in their endeavors.
Figure 10.2: Potatoes (GM).
Source: https://www.bbc.com/news/science-environment-26189722
10.2 POTATOES
Potatoes (Figure 10.2) are a versatile crop that may be utilized for both food
and industrial purposes. Breeders are working on several kinds for baking,
cooking, frozen fries, chipping, and starch. The size, specific gravity, and
sugar content of these cultivars vary, among other things. Because sugar
caramelizes under high heat, causing unwanted browning of fries and chips,
high sugar content is undesirable for frying or chipping. This is a traditional
strategy. Traditional or classical breeding is another term for conventional
breeding. The major method for creating variety in flowering species is to
Plant Breeding 215
cross two plants. The most desired recombinant is subsequently identified

using a variety of breeding strategies to discriminate among the diversity.
Before being released to producers, the genotype is raised and checked for
performance. Plant features that are controlled by a large number of genes
are more challenging to breed. Despite its age, the traditional technique
to plant breeding remains the industry’s workhorse. It is accessible to the
average breeder and reasonably simple to implement when compared to the
unconventional method. The unorthodox approach to breeding comprises
the application of cutting-edge technologies to generate novel variety
that is sometimes impossible to obtain using traditional approaches. This
method, on the other hand, is more involved and necessitates specialized
technical abilities and understanding. It is also costly to carry out. Breeders
gained a new set of strong tools for genetic study and manipulation with
the introduction of recombinant DNA (rDNA) technology. Gene transfer
can now occur across natural biological barriers, bypassing the sexual
process, for example, Bt. products, which are made up of bacterial genes
that are introduced into crops to give resistance to the European corn borer.
Molecular markers can be used to help with the selection process, making it
more efficient and effective.
Figure 10.3: Tomato (GM).
Source: https://www.deccanherald.com/content/343645/gm-tomato-gets-pur-
ple-hue.html
10.3 TOMATO
The tomato can be used to demonstrate how different breeding objectives
for a single crop may be developed. Tomatoes are a widely used fruit with
a variety of applications, each requiring different attributes. Tomatoes are
used whole in salads, so tiny sizes are desirable; tomatoes are sliced in
hamburgers, thus round huge fruits are preferred. Tomato pulp for canning
must meet certain specifications. Gardeners want a tomato cultivar that
ripens over time so harvesting can be spaced because tomatoes are a popular
garden plant. However, for industrial applications, like canning, the fruits
on the commercial cultivar must ripen at the same time so that the field may
be collected mechanically. Furthermore, while the look of the fruit is not a
top priority for a tomato juice processor, the appearance of fruits is crucial
in marketing the fruit for table usage. A breeding system has been developed
into every successful breeding program. The breeding system regulates how
breeding lines progress through the selection process and how much planting
material is available for cultivar release. The selection procedure will take
place over several years and under various environmental circumstances.
Many thousands of distinct genotypes will be screened in the early stages of
breeding programs. As a result, early screening is typically unsophisticated,
including merely visual selection in many cases. The disease-resistant
genotypes will be kept for further study after each round of selection,
whereas the least adapted lines will be removed. This procedure will be
repeated over a number of years, with the number of individual genotypes
or populations being reduced at each stage and the value of each input being
estimated with higher precision.
The breeding strategy will be heavily influenced by the crop species
and cultivar being developed. As a result, the overall idea for generating a
clonal cultivar such as potato differs from that of a pure-line grain cultivar
such as barley. Breeding selections are genetically fixed through vegetative
propagation in the former, while there will be a low rate of planting material
multiplication in the latter. Although the segregating character of the early-
generation breeding lines may complicate the selection process, there will
be a faster increase in planting material in the future. The most efficient
breeding strategies will make use of a crop species’ beneficial characteristics
while reducing problems that may develop during the selecting process.
Barley, chickpea, flax, lentil, millet, peas, soybean, tobacco, tomato, and
wheat are among the crops grown as pure-line varieties. Most inbred crop
species were farmed as ‘landraces’ in agriculture one and a half centuries ago.
Plant Breeding 217
Landraces were locally developed populations that consisted of a mixture of

several different genotypes that were genetically and phenotypically varied.
Farmers first developed pure-line or inbred cultivars from these landraces by
selecting specific plants from mixed populations and keeping them isolated,
encouraging selfed progenies, and eventually developing homozygous, or
near-homozygous, lines. Because landraces had almost totally vanished
in countries with advanced agricultural systems by the end of the 19th
century, it is safe to believe that these homozygous lines were actually more
productive than the original landraces (Newton et al., 2011). These early
pure-line breeders took advantage of naturally occurring genetic variety
within the landraces they were propagating, as well as inherent inclination
to self-pollinate. However, because this strategy has limited potential for
generating new variation, modern plant breeders must constantly generate
genetic variation, which is why three-phase breeding schemes were
developed to generate genetic variation, identify desirable recombinant lines
within progenies, and stabilize and increase the desired genotype. It’s worth
noting, however, that a number of plant breeders have recently returned to
old wheat and barley landraces to explore their genetic diversity, as well as
to testing line combinations in modern landrace combinations (Figure 10.4).
Figure 10.4: Modern landrace combinations.
Source: https://www.flickr.com/photos/cimmyt/5755175171
Unfortunately, most landraces that existed even 100 years ago are no
longer available, resulting in the loss of potentially valuable germplasm and
adapted pairings. To shorten seed-to-seed time, single seed descent entails
periodically growing a large number of individuals from a segregating
population, usually under high-density, low-fertility circumstances. Every
plant is replanted with a single seed from its natural self when it reaches
maturity. To generate homozygous plants, this procedure is performed
several times. In a greenhouse, where a number of growth cycles may be
possible each year, single seed descent is most suited for rapid generation
expansion. Growing plants under stress conditions of high density, high
light, restricted root growth, and low nutrient levels can speed up single
seed descent in canola, wheat, and barley, resulting in stunted plants with
only one or two seeds per plant, but in a shorter growing period than growth
under normal conditions. When employing single seed descent, it is critical
to ensure that no unintended selection for unfavorable characters takes
place. Vernalization needs may be artificially overcome in a cold chamber
in a single seed descent system in winter wheat where plants will require a
vernalization time prior to commencing a reproductive phase.
Figure 10.5: Modern genetics.
Source: https://en.wikipedia.org/wiki/Genetics#/media/File:DNA_sequence,_
sequences.gif
Plant Breeding 219
10.4 MODERN GENETICS

Modern genetics (Serra, 1966)(Figure 10.5) has one of the most well-defined
beginnings of any science. As previously stated, early plant breeders were
aware of some relationships between parent and offspring, and researchers
had conducted experiments to investigate these relationships at various
times throughout history. However, true experimental genetics began in the
middle of the nineteenth century with Gregor Johann Mendel’s work, and
was only truly acknowledged until the turn of the twentieth century. Because
the blooms of pea plants are designed to encourage self-pollination, the
bulk of Mendel’s lines were homozygous or near-homozygous genotypes.
Mendel’s selection of peas as an experimental plant species provided a
significant advantage over many other plant species he may have used. The
characters he chose were also serendipitous in their differences. As a result,
many modern scientists say that Mendel’s discoveries are based on a lot
of luck because of the decisions he made about what to examine. Many
have concluded that he must have already foreseen the results he expected
to attain when this is combined with segregation ratios that are better than
would be expected by chance. There are a few general remarks to make
about Mendel’s experiments before we look at an example of one of his
studies. Others had made intentional hybridizations or crosses within various
animals before Mendel.
Figure 10.6: Mendel.
Source: https://www.britannica.com/biography/Gregor-Mendel
To begin with, Mendel (Figure 10.6) possessed a bright analytical mind

that enabled him to interpret his findings in ways that outlined heredity
principles. Second, Mendel was an accomplished experimenter. He knew
how to design trials in such a way that the chances of getting useful results
were increased. He knows how to make data more understandable. He
chose individuals with radically differing traits as parents in his crosses.
Finally, in the crosses he analyzed, he used true breeding lines as parents
(Figure 10.7). Plant breeders try to make a wide range of predictions that
will allow them to create genetic variation and select attractive genotypes
in the most efficient way possible. Plant breeders need to be able to make
accurate forecasts since they can foresee conditions that may not be realized
or noticed in field evaluations for several years. The questions answered and
the trust in the predictions generated will determine whether those forecasts
lead to substantial genetic progress and the production of improved breeding
lines. With that due to the environment, progress can be made but only
slowly unless very large numbers are handled. In other words, the breeder
will be selecting phenotypes that are superior much of the time, but because
this is mostly due to the environment, it will not give a reliable indication
of a superior genotype. The phenotype is a good reflection of the genotype,
meaning that the majority of variation is genetic, then progress will be rapid
because when a breeder selects a good phenotype and uses it as a parent, it
will pass on the superior attributes via its genes to its offspring.
Figure 10.7: Mendel Experiments.
Source: https://www.britannica.com/biography/Gregor-Mendel
Plant Breeding 221
Controlled cross-pollinations between two or more chosen parents are

by far the most prevalent process for creating genetic varieties in plant
breeding. Induced mutation, interspecific species hybridization, protoplast
fusion, and plant genetic transformation are just a few of the techniques
that have been employed to increase the genetic variability accessible to
breeders and thus their chances of success. All living plants and animals,
including all crop species, show variety as a result of natural mutations at the
DNA level, with subsequent recombination and selection taking place over
millions of years. However, this has been followed by structural alterations
in the genetic material, such as chromosome rearrangement within and
between them. Within plant species, mutations occur in the development
of extra genetic variety. Mutations occur at a frequency of 1 in 1,000,000
each generation per locus in nature (Haldane, 2004). Because the majority
of these mutations are recessive and detrimental, these new alleles only
survive at a very low frequency in nature. As a result, the frequency of the
novel allele within the population increases over generations. During the
last 90 years or so, mutations have been openly employed as an additional
source of genetic variation.
It was discovered in the mid-1920s that X-rays could be used to cause
high mutation rates, which was first demonstrated in the fruit fly and then
in barley. Plant breeders were quick to recognize the promise of induced
mutation, and mutation breeding became routine practice in practically all
crop species and many ornamental flower breeding programs. In general,
two strategies have been employed to increase the frequency of mutations
in plant species: radiation and chemical induction, with radiation-induced
mutants having the highest frequency of mutation-derived cultivars.
Radiation-induced mutations are caused by a range of factors, ranging from
physical damage to the disruption of chemical interactions. In crop breeding
plans, two forms of radiation have been used to cause mutation. The most
commonly employed radiation source in plant breeding is gamma rays, which
have been used to create 64 percent of radiation-induced mutant derived
cultivars. The disintegration of radioisotopes produces gamma rays, which
are high-energy electromagnetic radiation. Cobalt-60 and caesium-137
are the two main sources of gamma radiation for induced mutation. Plant
breeding programs have used single-dose gamma-ray radiation treatments
or have treated entire plants with long-term gamma radiation exposure.
10.5 X-RAYS
X-rays (Figure 10.8) were the first radiation mutagen, yet 22% of the
cultivars released worldwide are as a result of mutation-induced breeding
programs. When high-speed electrons collide with a metallic target, X-rays
are created. High-energy ionizing radiation with wavelengths spanning from
ultraviolet to gamma radiation is known as X-rays (Oladosu et al., 2016).
Mutations are caused by exposing seeds, complete plants, plant organs, or
plant parts to a certain frequency of X-ray radiation for a set amount of time.
Because X-rays require the expertise of professional radiologists, they are
not always readily available to plant breeders, who must frequently rely on
medical facilities for mutagenic plant therapy. Neutrons, beta radiation, and
ultraviolet radiation used primarily for inducing mutations in pollen grains
are other types of radiation that have been used to induce mutations.
Figure 10.8: X-rays.
Source: https://en.wikipedia.org/wiki/X-ray_generator#/media/File:X-ray_ta-
ble.JPG
Sulphur mustards, nitrogen mustards, epoxides, ethylene-imines,
sulphates and sulphites, diazoalkanes, and nitroso compounds are all
alkylating agents that bond to cellular DNA and interfere with chromosome
Plant Breeding 223
division. Ethyl-methane-sulphonate (EMS) and ethylene-imine (EI) have

been the most widely employed chemical mutagens (EI). It should be
mentioned that all mutagenic compounds are extremely poisonous and
carcinogenic, hence they must only be handled by qualified individuals
in appropriate facilities at all times. The oxygen level in plant material,
water content, and temperature can all influence the frequency of mutation.
Translocation is a chromosomal aberration involving the interchange of
different non-homologous chromosomes. Inversions are the changes in
the arrangement of the loci but not in their number, deficiencies, deletions,
duplications, and fusions are all structural changes in the chromosomes.
Gene mutations, also known as point mutations, are changes in a single
gene that are caused by a single base-pair change in the DNA. Some point
mutations have no effect on the amino acid represented by the triplet of
nucleotides where the mutation occurred due to the repetitive nature of the
genetic code.
Figure 10.9: Extranuclear mutations.
Source: https://slidetodoc.com/chapter-16-mitochondrial-dna-and-extranucle-
ar-inheritance-jones/
Extranuclear mutations (Figure 10.9) involve one of the cytoplasmic
organelles. Because the DNA involved comprises plastids and mitochondria,
the mutation is normally passed down through only one sex, usually the egg
cells, from one generation to the next. Cytoplasmic male sterility, which
is frequent in many crop species, is an example of this type of mutation.
Because they modify the genetic makeup of plants and promote variety,
mutagenic agents and radiation are effective. They will, of course, have a
similar effect on DNA if they are exposed to them. As a result, the importance
of following proper safety precautions when handling any mutagen cannot be
overstated. As previously stated, the facilities for administering mutagenic
treatments are not always readily available to the average plant breeder; in
most cases, specialized operators or personnel are responsible for the actual
radiation exposure. To utilize chemical mutagenic agents safely, a variety
of safety features are required, as spelled out by particular safety protocols
in many countries. Employees who work with these compounds should be
informed of the dangers and safety precautions that have been recommended.
Minimum safety will almost certainly necessitate the use of appropriate
gloves, protective clothes, and safety glasses, as well as mandatory Good
Laboratory Management Practice’ Procedures and equipment must also be
in place to cope with proper chemical disposal and to contain and clean up
any unintentional leaks of mutagenic chemicals.
Plant breeders have traditionally used inbreeding, or the practice of
selfing or mating between close relatives, to attain homozygosity, which
is a time-consuming process. Many plant breeders have aspired to be able
to generate plants from gametic, haploid cells because this technique can
produce ‘immediate’ inbred lines once the haploids’ chromosomes are
doubled. The time it takes to create completely homozygous lines can be cut
in half, allowing for the faster development of novel cultivars. The higher
expenses and complexity of developing double haploid lines are frequently
justified by the faster breeding cycle they provide. The creation of haploid
gametes by meiosis is a genetic event crucial for obtaining homozygous lines.
The number of chromosomes is halved during this form of cell division, and
each chromosome is only represented once in each cell. If such gametic,
haploid cells can be induced to develop into plantlets, a haploid plant can
emerge, which can then be treated to encourage the chromosomes to double,
resulting in a completely homozygous genotype.
Running a plant breeding program is no different than organizing a
series of scientific tests, thus all components of the operation should be
planned and handled with the same care and attention to detail as individual
studies. Good experimental design leads to knowledge of accuracy, which
is used to evaluate and select candidates. Whether a plant breeding effort
Plant Breeding 225
is based primarily on traditional procedures or includes molecular-based

technologies, the quality of information obtained is the most important
aspect determining its success. The right application of statistically valid
designs can improve the heritability of the trait under selection, i.e., the
ratio of genetic signal to experimental noise, and hence the rates of genetic
gain, response to selection, and the likelihood of success. Unfortunately,
this is frequently neglected. Multiple environment testing refers to a set of
trials used by a breeding program to acquire insight into the performance
of advanced breeding lines in a target Population of Environments. Within
the same trial, it is typical to compare breeding lines to existing cultivars.
In some circumstances, only one cultivar is employed, but in most cases,
multiple cultivars are used in the evaluation trials. The range and number of
cultivars already being grown in the target region for new cultivars, the style
of trial, and the number of evaluations to be made all influence the choice
and number of control entries. An evaluation trial can include the highest
yielding cultivar available to compare yielding performance, the best quality
cultivar to provide a quality baseline, a disease-resistant cultivar to assess
response under disease pressure, and so on.
Several USDA breeding groups, as well as similar public breeding
efforts elsewhere, offer the cultivars they develop to the farming community
royalty-free, and thus they do not hold any rights to the new varieties. In
other words, the cultivar can be multiplied and sold by others. However,
obtaining some kind of exclusive protection of ownership of newly released
cultivars is now fairly frequent. All commercial firms require proprietary
ownership of the cultivars they generate in order to control the supply of
seed, determine who can grow the crop, and benefit from seed sales or
royalties from seed sales to fund further research and breeding. It is possible
to have automatic proprietary ownership when the cultivar generated is
a synthetic or a hybrid by simply keeping the parents that were used to
develop the synthetic population or hybrid seed and not giving access to the
parents. Finally, if a cultivar is not a hybrid, the most frequent method of
preserving cultivars propagated by seeds is to file a Plant Variety Protection
application in the United States or a Plant Variety Rights (PVR) application
in other countries.
10.6 TRANSGENICS
Transgenic crop development is a time-consuming and expensive process,
and biotechnology-based seed firms are no different from traditional
breeding enterprises in that they must recoup their expenses. There are
currently an increasing number of academic and publicly supported efforts
focused on generating commercial transgenic crops, both in developed and
developing nations, which will face similar hurdles in terms of acceptance
and deregulation as GM cultivars. It’s yet unclear whether the benefits
of transgenic lines will be adequate to cover the expenses and whether
investments will be repaid. The regulatory studies required to comply with
the risk assessment procedure account for a significant portion of such costs.
This circumstance has caused problems since it may delay access to the
benefits of transgenic crops created by academic institutions to meet the
demands of small farmers or crops with a little acreage. Many of the first
transgenic plants in species like potatoes were created by genetic engineering
of cultivars that were not protected by plant variety laws. To compete
successfully in commercial contexts, genetic engineering companies must
develop cultivars transformed for specific traits that cannot be readily
produced by more traditional means, and collaborate with traditional
breeding programs or companies to keep the development of the myriad of
other characteristics increasing in performance.
Plant transformation technologies supplement traditional plant breeding
by increasing the range of genes and germplasm available for inclusion into
crops and reducing the time necessary for cultivar production. Plant genetic
engineering also provides an intriguing potential for the agrochemical,
food processing, chemical, and pharmaceutical industries to develop novel
products and production methods within crop species. However, it is
exceedingly doubtful that these procedures will ever completely replace the
traditional methods utilized in the past. Recombinant DNA technology, on
the other hand, will expand the array of options available to plant breeders
in the production of future cultivars. Projects that combine gene discovery,
genetic engineering, the routine use of molecular markers, and effective
breeding programs are successful biotechnology efforts. A well-run breeding
program is uniquely positioned to play a critical role in assembling a cultivar
desired by farmers, which requires tolerance to biotic and abiotic stress, and
adaptation to the farming environment. Transgenic crops are no exception.
No single technique can realistically provide a solution to all agricultural
concerns. Nonetheless, they are yet another weapon in inventory for dealing
with important concerns such as feeding a fast-growing population, reducing
environmental impact, limited availability of new farming regions, and the
growing demand for accessible food, fiber, and fuel.
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INDEX
A Arabidopsis 53, 54, 59, 60, 61, 70,

80, 110, 113, 121
ABA-responsive proteins 122 Arabidopsis genome 53
Abiotic stress 146 Artemisia sphaerocephala 131
abscisic acid (ABA) 128 Artificial intelligence 7
Acidovorax avenae 149 artificial intelligence–based denoiz-
Acinetobacter 90 ing 31
Agribusiness 4 atmospheric trace gases 196
agricultural contamination 168 aubergine 85
agricultural reorientation 168 automated mechanical oscillatory
Agriculture 4, 5, 7, 9, 13, 15, 27 shaking (AMOS) 41
Agriculture productivity 199
Agriculture technology 5 B
Agriophyllum squarrosum 131
Bacillus thuringiensis (Bt) 85, 93
Agrobacterium 30
bacteria 150, 157, 159, 161, 162
Agrobacterium-mediated plant
bacterial infections 175
transformation 97
bactofection-mediated gene transfer
Agrobacterium tumefaciens 54, 91
100
agronomy 38
barely any meristem (BAM) 130
Alkaloids 213
barley 60, 61
Allergies 80
Barley 216
allyl 17
beta radiation 222
alternative energy 33
Biochar 171, 172, 173
Amborella trichopoda 59, 65
biochemistry 38
Animal feeds 11
biolistics 54
antifeedants 34
Biological indexing 116
applied biosystems (ABI) 20
biological systems 30 clustered regularly interspaced short

biomedical research 116 palindromic repeats (CRIS-
Bioreactors 40 PR) 75
biosafety frameworks 86, 87 Cochliobolus carbonum 161
Biotechnology 101, 104 Co-expression analysis 110
Brachypodium 61 Cold-water fisheries 203
Brassicaceae 111 Conservation 179
Brassinosteroid (BR) 128 Cooperative Research Centre (CRC)
Burkholderia glumae 149 101
copy number variants (CNVs) 71
C
Corispermum mongolicum 131
Caenorhabditis elegans 54 Cotton 30
callose deposition 153 Cotton fibers 119
cancer 116 C-repeat binding factors (CBFs)
Caragana korshinskii 131 126
Carbon dioxide enrichment 192 Crop plants 43
carbon sequestration 170 Crop protection 44
Carotenoids 17 crop yields 128, 138
Cartagena Protocol on Biosafety Cryptosporidium 169
(CPB) 87 crystal protein gene 85
cell-wall biosynthesis 111
D
centiMorgans (cM) 55
Chemical pesticides 168 dehydration 128
Chemical weed management 76 dehydration avoidance (DA) 128
chemistry 17 diallyl sulphides 17
Chemistry-enabled imaging 32 diazoalkanes 222
chickpea 216 DNA fragments 57
chlorofluorocarbons (CFCs) 196 DNA polymerization 57
chromosomal engineering 30 double-strand breaks (DSBs) 157
Cicer arietinum 147 Drip irrigation 176
circadian rhythms 120 driving–pressure–state–influence–
citationID 11 response (DPSIR) 183
Climate change 141, 142 drones 4, 5, 8
climate changes 146 Drosophila melanogaster 53, 54
Climate resilient agriculture (CRA) Drought 127, 128, 132, 133, 134,
191 135, 136, 137, 138, 140, 142,
climate smart agricultural (CSA) 144
206 drought escape (DE) 128
Climate Smart Agriculture (CSA) drought-resistant crop plants 133
205
Index 243
drought tolerance 120 forestry 38

Drought tolerance 137 fungal infections 175
fungi 150, 158, 162
E
Fusarium solani 151
Ecological security 182
G
ecosystem services 170, 181, 182,
183 gene targeting 30
effector-triggered immunity (ETI) genetically modified (GM) 72
153 genetically modified (GM) crop
eggplant 85 plants 86
endogenous genes 88 genetically modified organisms
environmental protection 168 (GMOs) 86, 104
epoxides 222 genetic code 37
ethylene-imine (EI) 223 Genetic crop enhancement 91
ethylene-imines 222 Genetic engineering 84, 95
Ethyl-methane-sulphonate (EMS) Genetic Manipulation Advisory
223 Committee (GMAC) 103
Euphorbiaceae 81 genetic networks 52, 70
Exome sequencing 58 genetics 38, 50
expressed sequence tags (ESTs) 28, Genetic use restriction technology
39, 48 (GURT) 94
Expressed Sequence Tags (ESTs) 54 Gene transfer 90, 215
Extranuclear mutations 223 Genlisea aurea 59
genome-wide association studies
F
(GWAS) 154
Farming technology 5 Genomic Criteria Consortium
fatty acid-amino acid conjugate (GSC) 64
(FAC) 46 genomic organization 52
fertilizers 168, 170, 179 genomics 33, 37, 38, 39, 42, 45, 48
flavonoids 17 Genomic science 52
flax 216 genotype 52, 59, 71, 72
food allergenicity 17 genotyping by sequencing (GBS)
Food processing 4 155
food quality enhancement 168 Giardia 169
Food riots 190 global warming 146
Food safety 13 glucosinolate biosynthesis 111
food security 180, 181, 183 Glucosinolates 111
Forage breeders 213 greenhouse gas (GHG) 205
greenhouse gas (GHG) emissions L

205
late-embryogenesis-abundant (LEA)
GreenPhylDB 61, 68
122
H lentil 216
leucine rich repeat (LRR) 48
Haloxylon ammodendron 131
lipid metabolism 120
health impacts 17
Heat shock factors (HSFs) 40 M
heat shock proteins (HSPs) 40
machine learning 4
Heat stress 149
Macrophomina phaseolina 147, 165
herbicide-resistant (HR) 72
maize 53, 59, 60, 61, 69, 77
Herbicides 74, 77
Malnutrition 213
herbicides tolerant (HT) crops 78
Manihot esculenta 81
hormone signals 43
marker-assisted breeding (MAB)
horticulture 38
152, 160, 162
hypersensitive response (HR) 153
marker-assisted selection (MAS)
hypoxanthine guanine phosphoribo-
19, 158, 164
syl transferase (HPRT) 101
Marker-assisted selection (MAS) 20
I marker-free transgenics 30
Massive datasets 12
Imidazole Glycerol Phosphate De-
mass spectrometry (MS) 43
hydratase (IGPD) 76
Medicago 61
immunological techniques 116
messenger RNA (mRNA) 24, 109
indole-3-acetic acid (IAA) 125
metabolism 17
indoles 17
metabolomics 33, 46
insecticides 34
Microarrays 108, 109, 110, 112,
insect regimes 188
117, 118, 125, 126
Integrated Pest Management 209
Microbial interactions 33, 34
integrated weed management (IWM)
microRNAs (miRNAs) 25
72
microstructured channel 57
Integrin receptors 100
millet 216
International Rice Research Institute
mitogen-activated protein kinases
(IRRI) 212
(MAPKs) 153
J Modern automation 6
molecular hybridization 116
Jasmonate-responsive 122
Molecular plant breeding 26, 27
Jatropha curcas 81
molluscicides 34
Mutation breeding 78
Mutations 221, 222
Index 245
N Pathogen associated molecular pat-

tern (PAMP) 153
Natural catastrophes 183
pathogen associated molecular pat-
NCBI (National Center for Biotech-
terns (PAMPs) 156
nology Information) 64
pathogenesis-related (PR) genes
nested association mapping (NAM)
153
154
pathogen stress 149, 150, 151, 152
Neutrons 222
pathology 38
next-generation sequencing (NGS)
pattern recognition receptors (PRRs)
20
156
Next-generation sequencing (NGS)
peas 216, 219
50
Personality traits 184
nitrogen mustards 222
Pesticide 34
nitroso compounds 222
pharmacology 116
nonhomologous end-joining (NHEJ)
Phaseolus vulgaris 151
157
phenolic acids 17
non-renewable resource conserva-
Phenology 138
tion 168
phenotype 52, 55, 71
no-tillage (NT) management 171
Phylogenomics 62, 63
novel genetic modification tech-
Phytochrome 40
niques 86
Phytozome 60, 67
novel plant products (NPPs) 79
Pilose mutant 119, 120
nucleotide-binding site and leucine-
plant biology 52, 55, 69
rich repeats (NBS-LRRs) 153
Plant biology 37
O plant biopesticides 34
Plant biotechnology 33
omega-3 fatty acids 17
Plant breeding 212, 221
organic agriculture 5
Plant genomics 20, 52, 68, 70
Organic animal husbandry 175
Plant growth-promoting bacteria
Organic farming 5
(PGPB) 35
Organic fruit farming 174
Plant Kingdom 69
organic matter 168, 169, 170, 179
Plant modifications 212
osmolyte synthesis 43
plant molecular analysis 52
oxophytodienoic acid (OPDA) 48
Plants 30, 39, 41, 42, 46, 49, 50
Oxygen sensors 32
Plant sensitivity 40
P plant sterols 17
plant symbionts 35
PAMP-triggered immunity (PTI) plant tissue and cell culture (PTCC)
156 40
parasitic infections 175
Plant transformation 226 Robots 4

pollen development 111 root length density (RLD) 150
polyethylene glycol (PEG) 144
S
polymerase chain reaction (PCR)
116 Saccharomyces cerevisiae 54
post-translational modification Salicylic acid (SA) 47
(PTM) 42 Selaginella moellendorffii 59
Potatoes 214 sequence-specific nucleases (SSNs)
precipitation 188, 193, 194, 196, 157
198, 202, 207 sequencing-by-synthesis (SBS) 56
Precision agriculture 8, 14 site-specific crop management 8
pressure–state–response (PSR) 183 Small interfering RNAs (siRNAs)
proteomics 33, 42, 43, 44 25
Proteomics 43, 45 Soil erosion 169
Pyrosequencing 23, 24 soil microfauna 36
Pythium debaryanum 150 soil quality 188
Pythium ultimum 150 soil water 170
Sorghum 61
Q
Soybean 136, 137, 138
quantitative disease resistance Spirodela polyrhiza 59
(QDR) 152 Stomata 130
quantitative trait loci (QTLs) 121 sulphates 222
sulphites 222
R
Sulphur mustards 222
Rainfall 139 surplus product reduction 168
Rainfed agriculture 202 Sustainable agriculture 191
Ralstonia solanacearum 90, 149, Synthetic chemicals 96
150 systematics 38
reactive oxygen species (ROS) 43, systemic acquired resistance (SAR)
48, 129, 153 40, 48
Recombinant DNA technology 84, systems biology 33, 46
89
T
Resilience 140
resistance (R) genes 152, 153 Temperature 188
reverse transcription (RT) 116 thermal tolerance acquisition (TAT)
Rhizoctonia solani 150 40
rice 53, 54, 60, 61, 80 Thermosensors 40
Ricinus communis 81 tobacco 216
RNA interference (RNAi) 156 Tomato 59, 61
Index 247
Tomatoes 216 Vitis vinifera 147

transcription activator-like effector
W
nucleases (TALENS) 75
transcription factors 40, 43 Water 131, 134, 137, 139, 141, 144
transcription factors (TFs) 136 water resources 146
Transcript profiling 121, 122 water scarcity 128, 134, 135, 141
Transgenic crop development 225 Weeds 72, 73, 146
wheat 53, 60, 62, 76, 78
U
wild-type (WT) plants 133
ultraviolet-B radiation 192
X
ultraviolet radiation 222
unmanned aerial vehicles (UAVs) 7 X-rays 221, 222
Utricularia gibba 59
Z
V
zinc-finger nucleases (ZFNs) 155
Vertical farming 5 zinc finger nucleases (ZFNS) 75
vigor–organization–resilience Zygophyllum xanthoxylum 131
(VOR) 183
Viruses 175

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INTRODUCTION

Agriculture is an integrated field that allows us to experiment in any area. It

technology improves the quality of life, it is essential to follow sustainable

Figure 1.1: Agriculture.

avoids the use of artificial fertilizers and pesticides to a considerable extent

1.3 ARTIFICIAL INTELLIGENCE

Figure 1.2: Drones.

Changes in the global economy are converting American agriculture into

marrow or organ transplants, as well as patients receiving chemotherapy or

Figure 1.3: Genomic technologies.

expected to yield significant insights into the determinants of environmental

1.6 PRECISION AGRICULTURE

Figure 1.4: Precision Agriculture.

Figure 1.5: Bioactive compounds.

The development of an animal model of food allergenicity in humans, for

1.7 BIOACTIVE COMPOUNDS

Improved knowledge of how genes influence individual dietary status

Plant genomics encompasses both scientific and applied aspects, and

Figure 1.6: Molecular markers.

allows for the detection of higher amounts of polymorphisms. AFLPs are

Figure 1.7: Pyrosequencing.

Figure 1.8: Small interfering RNAs.

complementary base pairs. To count the relative abundance of nucleic acid

1.10 PLANT BREEDING

Figure 1.9: Molecular plant breeding.

There has been a great increase in genomic resources available,

2.2 IMAGING TECHNOLOGY

Figure 2.1: Imaging technology.

derivatives, also known as the Kakshine series, are super, cell-permeable

2.3 MICROBIAL INTERACTIONS

Figure 2.2: Microbial interactions with plants.

Figure 2.3: Plant growth-promoting bacteria.

2.4 PLANT GROWTH- PROMOTING BACTERIA

solid, liquid, or gel employed in the formulation process is referred to as the

2.5 GENETIC CODE

Figure 2.4: Genetic code.

Challenges in genomics, particularly for plants, are presented in order

2.6 PESTS AND DISEASES

approach for revealing major signaling and biochemical pathways of plant

various tissues. Organ-specific proteomics, in combination with subcellular

2.9 TRANSGENIC CROPS

already revealing new genes, gene families, and mechanisms involved in

integration of transcriptomics, metabolomics, and other large-scale “omics”

of a host plant, as well as attributes relevant for induction or repression of

to biotrophic diseases or insects that cause little damage, such as phloem-

wounded and stimulated with caterpillar regurgitation, corn seedlings

Figure 3.1: Reterotransposons.

for the substantial size disparity between collinear genome segments in

Figure 3.2: Drosophila melanogaster.

3.2 MODEL ORGANISMS

3.3 MOLECULAR MARKERS

3.4 DNA SEQUENCING TECHNOLOGY

Figure 3.3: DNA sequencing technology.

Figure 3.4: Exome sequencing.

3.5 EXOME SEQUENCING

abundance of short RNA targets. Genotyping by sequencing or GBS, a high-

approaches to fully validate the development of high-quality sequences

families, phylogenetic trees, and genomic collinearity between species are

Figure 3.5: GreenPhylDB.

wheat have database instances in PlantsDB. Individual plant genomes are