OMICS

Life is an entity, which happens in different portions and stages

Understanding the whole picture requires understanding the individual
components that make the whole
Thus the need to move from genomics, transcriptomics, proteomics to
metabolomics
From the gene that is transcribed, we need to understand the
trancsriptome then the proteins produced therein and finally the
metabolites
Understanding any one of them, studying in detail then helps top get a
finer pictuire, that would be probably be missed by a wholesome study
 GENOMICS
Genomics is the study of the total or part of the genetic or epigenetic
sequence information of organisms, and attempts to understand the
structure and function of these sequences and of downstream
biological products.
Genomic technologies have been employed by researchers all over
the world to better understand the viral origin, outbreak dynamics,
transmission, and evolution.
Integration of genomics and other omics technologies played a
crucial role in the development of new diagnostics, therapeutics, and
vaccines.
Plant genomics aims to sequence, characterize, and study the genetic
compositions, structures, organizations, functions, and
interactions/networks of an entire plant genome.
Genomics relies on DNA sequencing
Whole genome sequencing entails determining the complete DNA sequence of
an organism's genome.
In order to do this, an organism's chromosomal DNA (and the DNA contained in
the mitochondria and the chloroplast for plant studies) must all be sequenced.
To sequence a genome, it must first be broken into lots of small pieces, and then
the sequence of each small piece of DNA must be determined in order to figure
out which pieces fit together.
Original DNA sequencing centered on analytical chemistry and molecule
separation techniques to determine the order of the sequence.
People analyzed the sequences, which took up a lot of time.
Evolutions in these techniques sped the process up, along with advances in machines
that allowed far more DNA strands to be read at the same, partially thanks to
automation and imaging technology.
Today, sequencing instruments are also smaller and cheaper to use.
With that sequencing comes massive amounts of genomic data -- perhaps 1 TB of
data for a human genome.
As a result, storage technology also plays a part in genomics from a practical
standpoint.
"Over the years, innovations in sequencing protocols, molecular biology and
automation increased the technological capabilities of sequencing while decreasing
the cost, allowing the reading of DNA hundreds of basepairs in length, massively
parallelized to produce gigabases of data in one run
Types of genomics

Structural genomics: Aims to determine the structure of every

protein encoded by the genome.
Functional genomics: Aims to collect and use data from sequencing
for describing gene and protein functions.
Comparative genomics: Aims to compare genomic features between
different species.
Mutation genomics: Studies the genome in terms of mutations that
occur in a person's DNA or genome.
Genomics, genetics and proteomics

The main difference is that genetics looks at how genes and their
traits are inherited, while genomics looks at all genes -- in other
words, the genome -- as well as their inter-relationships to identify
their combined influence on the growth and development of the
organism.
Proteomics is the study of the entire protein set -- the proteome --
coded by the genome of an organism or a cell type.
While the genome in an organism is constant, the proteome varies.
And while every cell in an organism has the same set of genes, the set
of proteins produced differ and are dependent on gene expression.
DNA was first isolated as early as 1869, with technological advances
happening in the 1950s, such as creating isotopes and radiolabel
biological molecules.
Also during this time, the description of the structure of the DNA helix
was made by scientists James D. Watson and Francis H.C. Crick in 1953.
But the history of modern genomics really starts in the 1970s when the
first genome was sequenced by biochemist Frederick Sanger.
He sequenced the genomes of a virus and mitochondrion in the early
1970s. Sanger and his team also created techniques for sequencing,
data storage, genome mapping and more.
Another scientist who played an important role in modern genomics is Walter
Fiers. In 1972, he and his research team from the Laboratory of Molecular
Biology of the University of Ghent in Belgium were the first to sequence a gene.
In 1990, the Human Genome Project, a publicly funded international genomics
research effort to determine the sequence of the human genome as well as
identify the genes it contains, was launched by the National Institutes of Health
and the U.S. Department of Energy. The goal of this group was to sequence and
identify all three billion chemical units in the human genome.
Genomes evolve over time, changing in sequence or size. The study of genome
evolution involves multiple fields and is constantly changing as more and more
genomes are sequenced and made available to the scientific community and the
public at large.
Transcriptomics
Transcriptomics has been used to study the differences in gene
expression in medicinal plants under abiotic stress and to identify
genes that affect the growth and development of medicinal plants
and resistance to external stress.
Transcriptomics technologies are the techniques used to study an
organism's transcriptome, the sum of all of its RNA transcripts.
The information content of an organism is recorded in the DNA of its
genome and expressed through transcription.
Currently, the two main transcriptomics techniques include DNA
microarrays and RNA-Seq.
Both techniques require RNA isolation through RNA extraction
techniques, followed by its separation from other cellular
components and enrichment of mRNA.
By studying transcriptomes, researchers hope to determine when and
where genes are turned on or off in various types of cells and tissues.
The number of transcripts can be quantified to get some idea of the
amount of gene activity or expression in a cell.
PROTEOMICS
Proteomics is the large-scale study of proteomes.
A proteome is a set of proteins produced in an organism, system, or
biological context.
We may refer to, for instance, the proteome of a species (for
example, Homo sapiens) or an organ (for example, the liver).
Proteomics studies can substantially contribute to revealing virtually
every aspect of cellular function in plant stress responses, unraveling
possible relationships between protein abundance and/or
modification and plant stress tolerance.
Functional proteomics constitutes an emerging research area in the
proteomic field focused to two major targets, the elucidation of
biological function of unknown proteins and the definition of cellular
mechanisms at the molecular level.
For toxicology the advantages of proteomics goes beyond the ability
to compare protein expression differences.
Proteomics allows a researcher to study protein modifications due to
toxic treatment and more importantly allows identification of
toxicant-protein adducts.
Recently, proteomics has been used to investigate “plant-based
bioactives” to improve the nutritional value of food crops.
Bioactives are the peptides that are released either during digestion
by the host enzymes or during food processing and ripening by
microbial enzymes
Proteomics has three main types: expression proteomics, functional
proteomics, and structural proteomics.
 Metabolomics
Metabolomics is the large-scale study of small molecules, commonly
known as metabolites, within cells, biofluids, tissues or organisms.
Collectively, these small molecules and their interactions within a
biological system are known as the metabolome.
Metabolomics is an analytical profiling technique for measuring and
comparing large numbers of metabolites present in biological
samples.
Combining high-throughput analytical chemistry and multivariate
data analysis, metabolomics offers a window on metabolic
mechanisms.
Examples of metabolites
Examples of primary metabolites are ethanol, glutamic acid, aspartic
acid, 5′ guanylic acid, acetic acid, lactic acid, glycerol, etc. Examples of
secondary metabolites are pigments, resins, terpenes, ergot,
alkaloids, antibiotics, naphthalenes, nucleosides, quinolones,
peptides, growth hormones, etc
• Assignments
• 1 explain the application of Genomic Wide Association Studies in Crop
Improvement
• 2 explain the application of monte carlo simulation model in plant
breeding
Presantations
• Application of genome editing in plant breeding (Panashe)
• The principle of Genotype by Sequencing (Malvern)
• Application of genomics in plant breeding (Liberty)
• Application of proteomics in plant breeding (Sharlyn)
• Application of metabolomics in plant breeding (Vimbai)
01/06/2023