s40659-024-00562-6

Kumar et al.
Biological Research (2024) 57:80 Biological Research

https://doi.org/10.1186/s40659-024-00562-6
REVIEW Open Access
Advances in genomic tools for plant

breeding: harnessing DNA molecular markers,
genomic selection, and genome editing
Rahul Kumar1* , Sankar Prasad Das2, Burhan Uddin Choudhury1, Amit Kumar3, Nitish Ranjan Prakash4,
Ramlakhan Verma5, Mridul Chakraborti5, Ayam Gangarani Devi1, Bijoya Bhattacharjee1, Rekha Das1, Bapi Das1,
H. Lembisana Devi6, Biswajit Das1, Santoshi Rawat7 and Vinay Kumar Mishra3
Abstract
Conventional pre-genomics breeding methodologies have significantly improved crop yields since the mid-twentieth
century. Genomics provides breeders with advanced tools for whole-genome study, enabling a direct genotype–phe-
notype analysis. This shift has led to precise and efficient crop development through genomics-based approaches,
including molecular markers, genomic selection, and genome editing. Molecular markers, such as SNPs, are crucial
for identifying genomic regions linked to important traits, enhancing breeding accuracy and efficiency. Genomic
resources viz. genetic markers, reference genomes, sequence and protein databases, transcriptomes, and gene
expression profiles, are vital in plant breeding and aid in the identification of key traits, understanding genetic diver-
sity, assist in genomic mapping, support marker-assisted selection and speeding up breeding programs. Advanced
techniques like CRISPR/Cas9 allow precise gene modification, accelerating breeding processes. Key techniques
like Genome-Wide Association study (GWAS), Marker-Assisted Selection (MAS), and Genomic Selection (GS) enable
precise trait selection and prediction of breeding outcomes, improving crop yield, disease resistance, and stress toler-
ance. These tools are handy for complex traits influenced by multiple genes and environmental factors. This paper
explores new genomic technologies like molecular markers, genomic selection, and genome editing for plant breed-
ing showcasing their impact on developing new plant varieties.
Keywords Molecular markers, Genomic selection, CRISPR-Cas9, Genomic tools, Genomic resources, Plant breeding
Background
Since plant domestication around 10,000 years ago, plant
breeding has successfully developed crops and varieties
*Correspondence:
Rahul Kumar essential to modern society, consistently defying Malthu-
[email protected] sian predictions [44]. Traditional pre-genomics breeding
1
ICAR Research Complex for NEH Region, Tripura Centre, Lembucherra, methods have resulted in modern cultivars, significantly
Agartala 799210, Tripura, India
2
ICAR-National Research Centre for Orchids, Pakyong, Sikkim, India increasing the yields of major crops since the mid-twen-
3
ICAR Research Complex for NEH Region, Umiam 793103, Meghalaya, tieth century. Today, genomics offers breeders advanced
India tools and techniques for whole-genome analysis, rep-
4
ICAR-Central Soil Salinity Research Institute, Karnal, India
5
ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India resenting a significant shift by enabling direct examina-
6
ICAR –Krishi Vigyan Kendra, Tamenglong District, Manipur, India tion of the genotype and its connection to the phenotype
7
Department of Food Science and Technology, College of Agriculture, [166, 167]. This new era of crop development leverages
G.B.P.U.A.&T., Pantnagar, India
genomics-based approaches, such as molecular markers,
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Kumar et al. Biological Research (2024) 57:80 Page 2 of 23
genomic selection, and genome editing tools, for pre- The existing variability among crop species is utilized
cise and efficient improvements [166, 167]. Gene posi- for plant breeding activities, which can also be generated
tion or genomic regions that regulate important traits in through crossing or induced mutagenesis. In addition to
plants are discovered using molecular markers. Markers the identification of genetic markers and the availability
are typically categorized into two main groups: classical of published genomes, clustered regularly interspaced
and molecular markers. The limitations associated with short palindromic repeats-associated protein 9 (CRISPR/
phenotype-based markers prompted the development Cas9) is promising for application to modern breeding
of direct DNA-based markers, often known as molecu- and is a novel technology for genome editing in major
lar markers, which exhibit greater versatility. Classical crops [132]. CRISPR/Cas9-based directional breeding is
markers encompass morphological, cytological, and bio- highly efficient and saves more time than other breeding
chemical markers, while DNA markers include a variety techniques that use genome editing. It further enables
of types such as Restriction Fragment Length Polymor- targeted genetic modifications, opening new avenues for
phism (RFLP), Random Amplified Polymorphic DNA crop improvement.Genomics approaches are beneficial
(RAPD), Amplified Fragment Length Polymorphism when dealing with complex traits, as these traits usu-
(AFLP), Simple Sequence Repeats (SSRs), Single Nucleo- ally have a multi-genic nature and a significant environ-
tide Polymorphism (SNP) markers etc. [60]. In modern mental influence [102]. Genomic tools provide genomic
plant breeding, SNPs are extensively utilized as DNA information and facilitate the detection of QTLs and the
markers to pinpoint genomic regions associated with key identification of existing favorable alleles of small effect,
traits, thereby accelerating the breeding process. Rec- which have frequently remained unnoticed and have not
ognized as the most prevalent variations within plant been included in the gene pool used for breeding [102].
genomes, SNPs are invaluable for high-resolution geno- Genomic tools have revolutionized plant breeding by
typing, offering the highest map precision. enabling more precise, efficient, and targeted approaches
Moreover, SNPs are both more efficient and cost-effec- to developing new plant varieties through genome-wide
tive compared to other markers. Their popularity surged association study, marker-assisted selection, genomic
in the twenty-first century, largely due to genotyping by selection, and gene editing. In this review, we present and
sequencing (GBS) technique advancements. Some other discuss the most relevant advances in the development
novel marker techniques, such as Intron Length Poly- of genomic tools and provide examples of applying these
morphism (ILP), Diversity Array Technology (DArT), tools to plant breeding.
Penta-Primer Amplification Refractory Mutation System
(PARMS), Inter small RNA polymorphism (iSNAP), etc., Molecular markers: tool for the genetic analysis
have been employed in plant breeding, which has ena- Based on nucleotide sequence polymorphisms, molecu-
bled precise selection of desirable traits in plants, genetic lar markers include insertions, deletions, point muta-
diversity analysis, and accelerated breeding (Amiteye, tions, duplications, and translocations. They are ideal
2021). They pinpoint the precise genetic differences con- when codominant, evenly distributed, highly repro-
nected to desirable qualities, making it possible to pick ducible, and detect significant polymorphism. The first
individuals with the best genomic profiles for breeding molecular marker technique, RFLP, was introduced by
with accuracy and efficiency. Recent advances in genom- Botstein et al. [15]. RFLP, RAPD, AFLP, and Isozyme
ics are producing new plant breeding methodologies and markers are first-generation molecular markers that have
ways (e.g., association mapping, marker-assisted selec- been developed and used in genetic analysis and plant
tion, genomic selection, genome editing, etc.). breeding (Table 1). Advancements in molecular markers
Genomic resources for plant breeding encompass have significantly enhanced their efficiency, resolution,
genetic markers, reference genomes, genomic and pro- and application scope in genetic analysis and plant breed-
tein databases, transcriptomes, and gene expression ing (Table 2) [156]. These advancements can be broadly
profiles. These resources facilitate the identification of categorized into the development of new types of mark-
genes associated with desirable traits, understanding ers, improvements in marker technologies, and the inte-
genetic diversity, and acceleration of breeding programs gration of molecular markers with other genomic tools.
[112]. Key techniques include genome-wide associa- Here are some key advancements:
tion studies (GWAS), marker-assisted selection (MAS),
and genomic selection (GS), which allow for precise trait SSRs or microsatellites
selection and prediction of breeding outcomes. By inte- Microsatellites, alternatively known as short tandem
grating these genomic tools, plant breeders can improve repeats (STRs) or simple sequence repeats (SSRs), are
crop yield, disease resistance, and stress tolerance, short DNA sequences with lengths typically ranging
enhancing agricultural productivity and sustainability. from one to six base pairs in contrast to minisatellites
Table 1 Salient features of major molecular marker

Characteristics RFLP RAPD AFLP SSR SNP DArT
Genome abundance High Very High Very High Medium Very High Very High
DNA Quantity 10,000 20 500–1000 50 50 50–100
Needed (ng)
DNA Quality Prereq- High High High Low High High
uisites
Type of probes/ Genomic DNA Usually, ten bp ran- Specific sequence Specific sequence Allele specific-PCR Microarray chip
primers or cDNA clones dom nucleotide primers
with short, single/
low copy sequences
Locus specificity Yes No No Yes Yes Yes
Type of polymor- Single nucleotide Single nucleotide Single nucleotide Variations Single nucleotide Single nucleotide
phism changes, InDels changes, InDels changes, InDels in the length changes, InDels polymorphisms
of repeats at restriction sites
Level of Polymor- Medium High High High High High
phism
Inheritance Codominant Dominant dominant Codominant Codominant Dominant
PCR requirement No Yes Yes Yes Yes No
Radioactive detec- Usually yes No Usually yes No No No
tion
Visualization Radioactive Agarose gel Agarose gel Agarose gel SNP-VISTA Microarray
Reproducibility High Low Intermediate High High High
Cost High Less High High Variable Cheapest
(VNTRs), which feature longer repeat sequences span- association, and breeding. SSR markers, are used in plant
ning from 11 to 60 base pairs [115]. Microsatellites are genetics for various applications. For example, in rice,
found throughout the genome, including in chloroplasts SSR markers have been used to map QTLs related to
and mitochondria [125, 127]. Due to the different num- drought resistance and yield enhancement [65]. In wheat,
bers of repeats present in these locations, SSRs exhibit SSR markers help identify genetic diversity and select for
high polymorphism that is simple to detect using poly- traits like disease resistance and stress tolerance [174,
merase chain reaction (PCR). Mismatches, recombina- 175]. A 2023 study on Brassica napus utilized 304 SSR
tion, mobile element transfer (retrotransposons), and markers to evaluate genetic diversity, uncovering a 76%
DNA strand slippage are some of the mechanisms that polymorphism rate and pinpointing loci associated with
contribute to the occurrence of SSRs. Common SSR oil content and disease resistance [173]. The research
motifs encompass mononucleotide (A, T), dinucleo- emphasized SSR markers’ effectiveness in detecting
tide (AT, GA), trinucleotide (AGG), and tetranucleo- allelic variation and mapping important agricultural
tide (AAAC) repeats. The creation of primers often uses traits. Additionally, SSR markers showed cross-species
flanking sequences that are conserved around SSRs. transferability, proving valuable for identifying traits
Developing SSR markers involves creating an SSR library, beneficial for breeding programs and conserving genetic
identifying specific microsatellites, designing primers in diversity. SSR markers are crucial for crop improvement
favorable regions, and conducting PCR. Banding patterns and understanding genetic variation [83].
are then interpreted and evaluated for polymorphism.
SSR markers are highly favored due to their codomi- Inter small RNA polymorphism (iSNAP)
nant inheritance, abundance, allelic diversity, and ease Endogenous noncoding small RNAs, typically 20–24
of assessment via PCR with flanking primers. McCouch nucleotides long and have important regulatory roles,
et al. [107] conducted a pivotal study on Simple Sequence are widely distributed in eukaryotic genomes [54].
Repeat (SSR) markers in rice, focusing on developing These small RNAs offer a valuable resource for molecu-
and mapping these markers to enhance genetic research. lar marker development due to their conserved flanking
They identified numerous SSR loci across rice chromo- sequences, enabling primer design for PCR-based finger-
somes and designed primers for their use. This compre- printing. The Inter small RNA polymorphism (iSNAP)
hensive set of SSR markers has become instrumental in technique, pioneered by Gui et al. [54], capitalizes on this
rice genetic studies, including linkage mapping, trait characteristic. To detect length polymorphisms brought
Table 2 Principle of advance molecular markers and their use in crop improvement
Kumar et al. Biological Research
Marker type Principle Pros Cons Suitability in Breeding Contexts Reference
SSRs (Simple Sequence Repeats) SSRs are short tandem repeat - High polymorphism -Labor-intensive Best suited for MAS, genetic Gupta et al. [55]
sequences in the genome. - Co-dominant inheritance - Requires high-quality DNA diversity studies, population struc-
Variation in the number of repeats - Cost-effective - Limited genome coverage ture analysis, and evolutionary
is detected through PCR and gel - High reproducibility studies in low-resource breeding
(2024) 57:80
electrophoresis programs
SNPs (Single Nucleotide Polymor- SNPs are single-base variations - Abundant across genomes - High cost of initial setup Ideal for high-resolution GWAS, Kumar et al. [86]
phisms) at specific genomic positions. They - Co-dominant inheritance - Low polymorphism in some genomic selection, QTL mapping,
are identified through sequencing - High throughput species and fine-mapping in advanced
or microarray-based techniques - Automation-friendly - Requires sequence information breeding programs
DArT (Diversity Arrays Technology) DArT identifies polymorphisms - No prior sequence knowledge - Dominant markers (less useful Useful for genome-wide diversity Cruz et al. [32]
based on the hybridization required for co-dominant traits) assessment, QTL mapping, MAS
of genome-wide fragments - Cost-effective - Lower resolution than SNPs in under-researched or non-model
to a microarray. It does not require - High-throughput - Requires specialized equipment crops where genome sequences
prior sequence knowledge - Detects both known are unavailable
and unknown polymorphisms
PARMS (Penta-Primer Amplifica- PARMS detects SNPs or other - High specificity - Requires real-time PCR equip- Suitable for SNP validation, MAS, Xu et al. [179]
tion Refractory Mutation System) mutations via allele-specific prim- - Cost-effective ment and high-throughput genotyping
ers and real-time PCR, distin- - Scalable for large populations - Lower multiplexing capability in breeding programs, especially
guishing alleles by melting curve - Fast and real-time detection than sequencing for traits with known SNPs
analysis - Moderate technical difficulty
iSNAP (Inter Small RNA Polymor- iSNAP detects polymorphisms - Targets regulatory regions - Limited technology and avail- Applicable for studying gene Pant et al. [121]
phism) in small regulatory RNAs (sRNAs) - Detects functional variations ability regulation in stress tolerance,
that impact gene expression. - Useful for traits controlled - Requires bioinformatics expertise metabolic traits, and developing
These are amplified and analyzed by gene regulation - Lower throughput regulatory SNP markers in breed-
using PCR-based methods - Emerging tool ing programs
ILP (Intron Length Polymorphism) ILP detects length variations - Genome-specific - Low polymorphism frequency Useful for comparative genomics, [97, 98]
in intronic regions between exons - Detects rare variants - Limited to non-coding regions phylogenetic analysis, and spe-
using PCR amplification, revealing - High specificity - Lower throughput than SNPs cific MAS for traits associated
intron-based polymorphisms - Low cost with intron polymorphisms affect-
ing gene expression in crops
Page 4 of 23
on by insertions and deletions (InDels) within the small The amplification of introns via PCR involves designing
RNA pool, primer pairs flanking small RNAs are used to primers in flanking exons, a method known as exon-
start PCR reactions. It is a noncoding, sequence-based primed intron-crossing PCR (EPIC-PCR). Notably, exon
marker system and is suitable for genotyping and genome sequences tend to be more evolutionarily conserved,
mapping [3]. Unlike traditional markers that focus on enhancing the versatility of primers designed within
coding sequences or microsatellites, iSNAP markers exons compared to noncoding sequences. ILP markers
explore variations in non-coding regulatory regions. are particularly advantageous when they target multiple
This opens up new possibilities for studying gene expres- insertions and deletions (InDels) within a single intron
sion and complex traits influenced by small RNA path- during amplification. This strategy significantly increases
ways, including plant stress responses, development, and the likelihood of identifying genetic polymorphism. ILP
epigenetic regulation. iSNAP markers have functional markers are highly transferable across related species,
relevance, as they are closely associated with gene regu- allowing for comparative genomics and evolutionary
latory mechanisms. This makes them particularly use- studies [27]. For example, in cereals such as rice, maize,
ful for marker-assisted selection (MAS), enabling the and wheat, ILPs have shown consistent results, mak-
identification of traits governed by post-transcriptional ing them invaluable for research across different species
gene regulation, such as disease resistance and stress without needing species-specific markers. Liu et al. [99]
tolerance. A recent case study by Zhang et al. [196] illus- developed intron length polymorphism (ILP) markers
trates the application of iSNAP markers in identifying for plants, identifying 1507 ILP markers in Oryza sativa
disease-resistant genes in tomatoes (Solanum lycoper- (rice). These markers were highly transferable across
sicum). In this study, researchers focused on identifying species and showed polymorphism rates of 85.3%. ILP
polymorphisms in intergenic regions flanked by micro- markers proved useful for genetic diversity analysis and
RNAs (miRNAs) associated with defense responses. breeding applications in various crops. A recent study
They developed a set of iSNAP markers and used them by Chen et al. [27] demonstrated the effectiveness of ILP
to screen tomato varieties for resistance to Phytophthora markers in mapping drought tolerance in rice (Oryza
infestans, the pathogen responsible for late blight dis- sativa). The researchers used ILP markers derived from
ease. In maize, iSNAP markers have been used to identify conserved intron regions of the Dehydration-Responsive
genetic loci associated with disease resistance and yield Element-Binding (DREB) gene family. These markers
traits, enabling more efficient breeding [97, 98]. In wheat, were employed to screen a diverse set of rice germplasm,
they assist in mapping quantitative trait loci (QTLs) for leading to the identification of several drought-tolerant
drought tolerance, enhancing the development of resil- varieties. The study showcased how ILP markers could
ient varieties [26]. be used to identify quantitative trait loci (QTLs) associ-
ated with drought tolerance. The QTLs identified were
Intron length polymorphism (ILP) then validated across multiple rice populations, proving
In eukaryotic genomes, introns are prevalent and found the reliability of ILPs in marker-assisted selection (MAS)
throughout various gene components. Due to their lower for complex traits like drought resistance. These develop-
selective pressure, Introns exhibit greater variability ments underscore the importance of introns and their
compared to coding sequences, rendering them valu- applications in molecular genetics, enabling more effec-
able as highly polymorphic genetic markers. Recently, tive crop breeding and resource management.
researchers have focused on annotating and leveraging
gene introns to create intron-length polymorphism (ILP) Single nucleotide polymorphism (SNP)
markers on a genome-wide scale. An Intron Length Poly- Single Nucleotide Polymorphisms are single nucleotide
morphism marker (ILP marker) is a genetic marker used differences seen in the genomic sequences of individu-
in plant and animal breeding to identify variations in the als within a population. These are the most prevalent
length of introns—non-coding regions of a gene that are molecular markers, and their distribution varies between
transcribed but not translated into proteins. These mark- species. Contrastingly, while humans exhibit an average
ers exploit natural differences in intron lengths among of one Single Nucleotide Polymorphism (SNP) per every
individuals or populations, aiding in genetic mapping, 1000 base pairs [137], rice displays a higher frequency,
diversity studies, and breeding programs by distinguish- with approximately one SNP occurring within every 130–
ing between different genotypes or assessing genetic 140 base pairs [51]. SNPs are frequently discovered in
diversity [7]. These markers have proven invaluable for noncoding areas. According to Sunyaev et al. [158], SNPs
large-scale genotyping in major food crop plants, such in coding areas can be synonymous or nonsynonymous,
as rice [7, 170], wheat [147], and maize [94]. PCR, a changing phenotypic features and amino acid composi-
widely used technique, conveniently detects ILP markers. tion. SNPs are the smallest units of genetic variation,
providing a simple and abundant source of markers cru- genetic variability within a species. There are three main
cial for genetic mapping, marker-assisted breeding, and types of SNP genotyping platforms: single SNP genotyp-
map-based cloning. [188]. Significant techniques for SNP ing (using PCR with Taqman from Life Technologies or
genotyping include primer extension, invasive cleavage, KASP genotyping from LGC Genomics), multiple SNP
oligonucleotide ligation, and allele-specific hybridization genotyping (using SNP chips from Illumina and multi-
[154]. SNP markers discovered by two methods, includ- plexing from Sequenom), and SNP genotyping by next-
ing SNP discovery from PCR and SNP discovery from generation sequencing methods such as Genotyping by
High Throughput-Next generation sequencing (NGS) – Sequencing (GBS) and Restriction site Associated DNA
RNA-Seq, RAD-Seq, Genotyping by Sequencing (Fig. 1), sequencing (RADSeq). For large-scale genotyping, high-
WGS (Whole-Genome Sequencing), WGR (Whole- throughput methods such as Genotyping by Sequenc-
Genome Regression), etc. ing (GBS), Restriction site- associated DNA sequencing
Next-Generation Sequencing (NGS) is a high-through- (RADSeq), and allele-specific PCR are used [37]. These
put DNA sequencing technology that enables rapid, technologies have been extensively used to discover and
parallel sequencing of millions of DNA fragments for genotype SNPs in food crops, including cereals [barley
comprehensive genomic analysis. In recent years, NGS [31, 48, 134, 162], rice [28, 185], and wheat [20]], oil crops
technologies have identified thousands to millions of [oilseed rape [29] and sunflower [100]], horticultural
SNPs in various crops, facilitating genetic diversity stud- crops [cowpea [30], potato [59], tomato [149]], soybean
ies, trait mapping, and breeding improvements. Numer- [155], and among others. SNP markers are crucial in
ous tools are available for SNP discovery, including genetics and agriculture, aiding genetic mapping, identi-
BioEdit, DNASTAR Lasergene Genomics Suite, SAM- fying disease associations, and improving crops through
tools, SOAPsnp, Stacks, Ddocent, PyRAD, and GATK. selective breeding. In their 2011 study, Kump et al. used
Typically, biallelic SNPs are straightforward to assay. SNP SNPs to pinpoint disease resistance genes in maize, spe-
is detected when a nucleotide from an accession read cifically targeting Southern Leaf Blight (SLB), caused by
differs from the reference genome at the corresponding Cochliobolus heterostrophus. They identified 32 quanti-
position. Without a reference genome, this comparison is tative trait loci (QTLs) significantly associated with SLB
made by examining reads from different genotypes using resistance. The identified SNPs and associated QTLs can
de novo assembly methods. SNP calling is performed be used in marker-assisted selection (MAS) and genomic
using read assembly files generated by mapping pro- selection (GS) programs to develop SLB-resistant maize
grams. Various empirical and statistical criteria, such as varieties. SNPs also play a pivotal role in integrating
read depth, quality scores, and consensus base ratios, are multi-omics data for crop improvement by acting as key
employed in the SNP calling process. SNP discovery is genetic markers that link DNA variations to other molec-
more effective when multiple and diverse genotypes are ular levels, such as gene expression (transcriptomics),
analyzed simultaneously, as this approach captures the protein abundance (proteomics), and metabolite profiles
Fig. 1 SNP discovery in plants through genotyping by sequencing (GBS) system and its application in crop improvement
(metabolomics). These connections help to unravel the locus [159]. PARMS involves the use of five primers to
complex genetic architecture of important agronomic achieve high specificity and efficiency in identifying spe-
traits, including yield, stress tolerance, and disease cific alleles. Two universal primers bind to conserved
resistance. By mapping SNPs to different omics layers, regions of DNA surrounding the SNP or mutation of
researchers can identify critical genes, pathways, and interest. Two allele-specific forward primers and a
molecular interactions responsible for these traits [90]. reverse shared primer are designed to match perfectly
This comprehensive approach enhances breeding accu- with either the wild-type allele, mutant allele, or a third
racy, enabling the development of superior crop varieties variant allele, with mismatches at critical positions near
with enhanced performance through more informed and the SNP or mutation. This allows for selective amplifi-
precise selection methods. cation of only the specific alleles in question. It employs
competitive allele-specific polymerase chain reaction
Diversity array technology (DArT) (AS-PCR) and a fluorescence-based reporting system to
The DArT sequencing technique is a highly reproduc- detect genetic variations, specifically single-nucleotide
ible microarray-based method for discovering polymor- polymorphisms (SNPs) [159]. It can efficiently handle dif-
phic markers [177]. DArT is a genomic analysis method ferent numbers of SNPs and samples to be analyzed. The
designed to enhance the detection of SNPs (Single process requires only standard liquid handling, thermal
Nucleotide Polymorphisms) across the genome, par- cycling instruments, and plate reading instruments.
ticularly insertions and deletions. It begins with creat- Furthermore, it is compatible with DNA samples from
ing a purposefully randomized fragment library, which various sources and extraction methods, including alka-
serves as a genomic representation. DArT libraries are line lysis. This makes it ideal for a direct PCR-based SNP
tailored for specific research purposes, utilizing suitable marker-assisted selection system (D-MAS), known for
individuals, whether individual or pooled samples. The its simplicity, cost-effectiveness, and labor efficiency in
subsequent steps involve identifying the genetic repre- SNP genotyping. In a practical application, Gao et al. [49]
sentations, hybridizing them onto the chips, and printing developed a PARMS marker for the TAC1 gene, illus-
the genomic library onto microarray chips. DArT sim- trating its usefulness in rice plant architecture breeding.
plifies the genome by initially subjecting it to restriction Having outlined the significance of molecular markers,
digestion and then hybridizing the resulting DNA frag- we now delve into the applications of genomic resources
ments onto microarray chips. Data analysis is done after in crop improvement.
scanning. This method allows thousands of genomic loci
to be simultaneously genotyped in a single reaction test,
requiring as little as 50–100 ng of genomic DNA. Once Genomic resources for plant breeding
markers are identified, the need for specific assays for The availability of whole genome sequences is invalu-
genotyping is eliminated, except for consolidating poly- able for plant breeding. Arabidopsis (125 Mb) and rice
morphic markers into an array for a particular genotype. (466 Mb) were early models for plant genetics due to
These genotyping arrays are equipped with these poly- their small genomes among dicots and monocots. Their
morphic markers and are commonly employed in geno- genome sequences, announced in 2000 and 2005, have
typing tasks [66]. DArT markers are primarily dominant been pivotal in understanding key genes and biologi-
and require specialized software, laboratory facilities, cal functions. The advent of next-generation sequenc-
a substantial investment, and skilled personnel (Sinha ing (NGS) technologies has revolutionized genomics.
et al., 2023). Among these, the 454 (Roche) and Illumina platforms are
widely used for crop sequencing. NGS technologies have
Penta‑primer amplification refractory mutation system significantly increased sequencing capacity; for instance,
(PARMS) the Illumina HiSeq 2000 can generate 55 Gb per day, far
The Penta-Primer Amplification Refractory Mutation exceeding the human genome size. The development of
System (PARMS) is a specialized genotyping technique third-generation sequencing platforms like PacBio RS
used for identifying specific single nucleotide polymor- (Pacific Biosciences, https://www.pacb.com/), Helicos
phisms (SNPs) or mutations in DNA sequences. It is (Helicos, https://seqll.com/), and Ion Torrent has further
particularly useful in plant and animal genetics, as well advanced the field. These platforms enable the produc-
as in medical research, for detecting alleles associated tion of long reads, resulting in more accurate and con-
with certain traits or diseases. It is an extension of the tiguous genome assemblies. Third-generation sequencing
traditional Amplification Refractory Mutation System is particularly effective for assembling genomes de novo,
(ARMS), which relies on the specificity of DNA primers especially in regions with highly repetitive sequences and
to distinguish between different alleles at a given genetic clarifying structural variants.
Additionally, isoform sequencing from these platforms New genomic tools are crucial for advancing and
facilitates detailed studies of exons, splice sites, and alter- speeding up gene expression studies. Gene expres-
natively spliced regions, improving genome annotation. sion analysis provides breeders with valuable biological
NGS-generated sequences are typically deposited in the insights, helping them understand the molecular basis
NCBI Sequence Read Archive, making them accessible of complex plant processes and identify new targets for
for further research. The emergence of third-generation manipulation. While QRTPCR is an affordable, quan-
sequencing has enabled the generation of long reads and titative technique, it can only analyze a limited number
allowed the production of more accurate and contiguous of genes per experiment. Other methods, such as dif-
genome assemblies [25]. Third-generation sequencing ferential display and cDNA-AFLPs, allow the study of
enhances the creation of high-quality whole genome de thousands of genes but lack quantitative precision and
novo assemblies by providing long reads that cover com- struggle with low-abundance transcripts (M Perez-de-
plex regions with highly repetitive sequences. This tech- Castro et al. 2012). More advanced techniques like serial
nology also elucidates other complex repeat sequences analysis of gene expression (SAGE) and massively parallel
and structural variants. Third-generation sequencing signature sequencing (MPSS) address some of these limi-
techniques, such as isoform sequencing, produce full- tations. However, the most popular methods today for
length transcripts, enabling detailed analysis of exons, transcript profiling are hybridization-based platforms or
splice sites, and alternatively spliced regions, which microarrays. Expression arrays offer several advantages,
aids in refining genome annotations. Sequences gener- including measuring tens of thousands of transcripts
ated through NGS are typically archived in the NCBI simultaneously, semi-quantitative results, and sensitiv-
Sequence Read Archive (https://www.ncbi.nlm.nih.gov/ ity to low-abundance transcripts. Several web resources
sra) for public access. facilitate microarray data analysis, such as Babelomics
Two standard analyses performed on NGS reads are (http://babelomics.bioinfo.cipf.es/), and software pack-
genome assembly and mapping. Assemblers like Roche’s ages like Bioconductor (http://www.bioconductor.org/
454 Gsassembler, Celera Assembler, and Mira are fre- help/workfl ows/oligo-arrays/) and MeV (http://www.
quently used for genome assembly. Once a reference tm4.org/mev/) specialize in microarray analysis. Babe-
genome is available, variation studies are typically con- lomics was used to analyze transcriptomic data in Arabi-
ducted using mapping software such as Bowtie, BWA, dopsis thaliana to identify genes differentially expressed
and TopHat, which align reads to the reference genome. under drought stress. The tool facilitated functional
SNPs can then be detected with tools like SAMtools or annotation and identified key genes involved in stress
GigaBayes. The algorithms for processing raw genomic responses [108] In Solanum tuberosum (potato), Biocon-
data vary based on the data type and desired results. Bio- ductor was utilized to analyze gene expression profiles
informaticians must present their findings to breeders under biotic stress conditions, identifying genes linked to
via user-friendly interfaces, often through easily naviga- pathogen resistance [194]. Genevestigator (https://www.
ble websites. General-purpose web databases like Gen- genevestigator.com/gv/doc/plant_biotech.jsp) is a handy
Bank (http://www.ncbi.nlm.nih.gov/genbank/), EMBL database containing extensive microarray data from
(http://www.ebi.ac.uk/embl/), DDBJ (http://www.ddbj. various species, with the most comprehensive data from
nig.ac.jp/), UniProt (http://www.uniprot.org), and Swiss- Arabidopsis thaliana. Data from crops like maize, wheat,
Prot (http://expasy.org/sprot/) provide researchers and rice, barley, and soybean are increasingly becoming avail-
breeders with essential biological information. Genomic able. Published expression data are publicly accessible in
sequence databases GenBank, EMBL, DDBJ, Ensembl, databases such as GEO (http://www.ncbi.nlm.nih.gov/
UCSC Genome Browser, and dbSNP offer extensive geo/), ArrayExpress (http://www.ebi.ac.uk/arrayexpre
genomic data, analysis tools, and resources. Protein ss/), and species-specific repositories, providing valu-
function databases, integrating sequence data, struc- able resources for analyzing gene expression in these and
tural information, and functional annotations, include other crops. A summary of genomic resources related to
UniProt, Swiss-Prot, Gene Ontology, Protein Data Bank, genome sequence and functional analysis is presented in
InterPro, KEGG, Pfam, STRING, BioGRID, and Phos- Table 3.
phoSitePlus (Table 3). Additionally, specialized data-
bases for specific species useful to breeders, such as SGN, Genomic tools for plant breeding
Phytozome, Gramene, and CropNet, provide targeted Traditional plant breeding involves selection and cross-
information for breeding programs. These resources col- ing of plants with desirable traits over several gen-
lectively support the plant breeding process by enabling erations. Techniques include selection of superior
detailed genetic and protein analyses, aiding in develop- individuals, hybridization, and backcrossing. Breeders
ing improved crop varieties. aim to enhance traits like yield, disease resistance, and
Table 3 Important Databases and Repositories of Genomic Information

Database Description URL
Genbank General public sequence repository http://www.ncbi.nlm.nih.gov/genbank/

EMBL General public sequence repository http://www.ebi.ac.uk/embl/
DDBJ General public sequence repository http://www.ddbj.nig.ac.jp
NCBI Biomedical and genomic information http://www.ncbi.nlm.nih.gov/
GOLD Repository of genome databases http://genomesonline.org/cgi-bin/GOLD/bin/gold.cgi
Phytozome Genomic plant database http://www.phytozome.net/
Plantgdb Genomic plant database http://www.plantgdb.org
CropNet Genomic plant database http://ukcrop.net/
CPGR Phytopathogen genomic resource http://cpgr.plantbiology.msu.edu/
Gramene Cereals information resource http://www.gramene.org/
R-PAN Rice pan-genome browser for ~ 3000 rice genomes http://cgm.sjtu.edu.cn/3kricedb/
Rice SNP-seek A new SNP-calling pipeline http://snp-seek.irri.org/
CerealsDB Genotyping information for over 6000 wheat accessions https://www.cerealsdb.uk.net/cerealgenomics/Cerea
lsDB/indexNEW.php
SoyBase Soybean information resource http://soybase.org/
MaizeGDB Maize information resource http://www.maizegdb.org/
Tair Arabidopsis information resource http://www.arabidopsis.org/
SGN Solanaceae information resource http://solgenomics.net/
Gene Index Project Transcriptome repository http://compbio.dfci.harvard.edu/tgi/
UniProt Protein sequences and functional information http://www.uniprot.org/
Swiss-Prot Protein Sequence database https://www.expasy.org/resources/uniprotkb-swiss-prot
Protein Data Bank (PDB) Repository for the 3D structural data of proteins and other biologi- https://www.rcsb.org/
cal macromolecules
Gene Ontology (GO) Describe gene and protein functions across species and databases https://geneontology.org/
InterPro Integrates predictive models (known as signatures) from multiple https://www.ebi.ac.uk/interpro/
databases into a single resource for protein classification
KEGG Annotations for genes and proteins, including their roles in path- https://www.genome.jp/kegg/
ways
Pfam Information on protein families and domains http://pfam.xfam.org/
STRING Database of known and predicted protein–protein interactions https://string-db.org/
BioGRID Database of protein and genetic interactions, chemical interactions, https://thebiogrid.org/
and post-translational modifications
PhosphoSitePlus Comprehensive resource for the study of protein post-translational https://www.phosphosite.org/homeAction.action
modifications
quality. The process relies on natural genetic variation Quantitative trait Loci (QTL) mapping
and careful observation to achieve desired improve- QTL mapping is a statistical technique that combines
ments in crops over time. Genomic tools enhance tra- phenotypic data (traits) with genotypic data (molecu-
ditional plant breeding by providing precise insights lar markers) in a specific population to identify genetic
into genetic variations, speeding up trait identification, regions (QTLs) associated with complex traits. Vari-
and enabling targeted modifications. They use DNA ous QTL mapping models have been developed, such
sequencing and markers to identify desirable traits as standard interval mapping (SIM) and multiple impu-
more accurately and rapidly, reducing the time and tation (IMP) for unlinked QTLs and composite inter-
cost of developing improved plant varieties compared val mapping (CIM) for both linked and unlinked QTLs/
to traditional methods that rely on broader, less precise genes on chromosomes. The effectiveness of these meth-
selection processes [87]. These tools help identify desir- ods is evaluated using LOD (logarithms-of-odds) scores,
able traits, speed up the breeding process, and improve with QTLs considered significant above a threshold LOD
the overall outcomes of breeding programs. Some key score of 3.0. Access to reference genomes provides valua-
genomic tools in plant breeding include: ble genetic information on QTLs, aiding marker-assisted
selection (MAS). Traditional QTL mapping requires a associations in diverse populations, although it faces
balanced population with known recombination data, challenges with false positives due to population struc-
enabling statistical associations between phenotypic and ture and kinship (Huang et al. 2014). To mitigate this,
genotypic data through linkage mapping (Lander et al. covariates for structure and kinship are incorporated into
1989). Identifying QTL locations helps pinpoint genes mixed linear models (MLMs). Various statistical tools are
responsible for specific traits and understand genetic used for association mapping, including MLM, CMLM,
variation mechanisms [84, 105]. Several software tools ECMLM, MLMM, GLM, and FarmCPU. Among these,
facilitate efficient QTL mapping, including QTL Car- the FarmCPU model is particularly effective at control-
tographer, QTL IciMapping, MapQTL, R/qtl, TASSEL, ling false positives [77]. With advancements in sequenc-
PLABQTL, and JoinMap. In the 2017 study by Duhnen ing technologies, GWAS has become a prominent tool
et al., the accuracy of traditional QTL mapping was com- for identifying loci linked to natural trait variations in
pared with newer genomic prediction models, such as crops. A population needs to be genotyped once and can
GBLUP and Bayesian methods, in soybean. The results be repeatedly used to map different traits with new phe-
showed that genomic prediction models outperformed notypic data. Despite its high false positive rate due to
QTL mapping by utilizing genome-wide markers, captur- population structures and genetic relationships, GWAS
ing both major and minor effect loci. This led to higher is favored for exploratory analyses to identify a wide
predictive accuracy for complex traits like yield and seed range of genomic leads. Unlike QTL mapping, GWAS
protein content, making genomic selection more effective is more likely to pinpoint specific candidate genes for
for breeding. QTL mapping bridges genomics and field crop improvement. It has been applied to various crops,
studies by linking genetic regions to quantitative traits. including rice, soybean, maize, wheat, and canola. [24,
However, integrating data from multiple QTL studies 33]. For example, in Oryza sativa indica, sequencing of
to identify high-quality candidate loci for crop breed- 517 landraces identified approximately 3.6 million SNPs,
ing remains challenging. Meta-analysis, which combines with GWAS of 14 agronomic traits explaining over 36%
results from various studies, is crucial in accurate QTL of phenotypic variance [64]. Myles et al. [112] used
prediction. Tools like MetaQTL reduce the confidence genomic resources to conduct a genome-wide associa-
interval of QTL, improving location and effect estimation study (GWAS) in grapevine, identifying 3,600 SNP
tion. Other tools, such as solQTL and RASQUAL, offer markers. They discovered loci linked to key traits like
low-bias QTL analysis and data visualization. Meta-QTL berry color (VvmybA1) and powdery mildew resistance,
analyses have been applied to crops such as rice, wheat, showcasing the utility of GWAS in identifying agricultur-
maize, cotton, and soybean, identifying significant traits ally significant genes in crops. In maize, GWAS revealed
like yield-related genes in wheat [182] and nitrogen use the genetic architecture of leaf traits, linking variation in
efficiency QTLs in rice [82]. Van and McHale (2017) per- liguleless genes to upright leaves [160]. He et al. [61] inte-
formed a meta-QTL analysis with genetic information grated GWAS with transcriptomic data and identified
comprised of 175 QTLs for protein, 205 QTLs for oil, 156 candidate genes involved in yield-related traits. This inte-
QTLs for amino acids, and 113 QTLs for fatty acids. They grative approach facilitates the functional validation of
detected 55 meta-QTL for seed composition on 6 out of the candidate genes. Bioinformatics tools such as PLINK,
20 chromosomes. They also identified candidate genes which uses standard regression for genotype–pheno-
within each meta-QTL aiding in crop improvement type associations [126], and TASSEL, which incorporates
program. While QTL mapping effectively links traits to mixed linear models to account for population structure,
genomic regions and detects rare alleles, its resolution is enhance GWAS studies [16]. GAPIT, another advanced
limited by parental allelic diversity. Genome-wide asso- tool, efficiently handles large datasets with over 1 mil-
ciation studies (GWAS) can address these limitations lion SNPs in 10,000 individuals using compressed mixed
by identifying trait-associated genomic areas of diverse linear models and model-based prediction and selection
populations. methods [93].
Genome‑wide association study (GWAS) Genome‑based molecular breeding

Like QTL mapping, genome-wide association stud- Advancements in genomics and the availability of pub-
ies (GWAS) employ statistical association mapping to lic genomic databases have significantly improved tradi-
link molecular markers with traits of interest. GWAS tional breeding methods and facilitated the development
leverages diverse populations and historical recombi- of innovative crop breeding approaches (Fig. 2). Modern
nation, addressing linkage disequilibrium (LD) caused plant breeding focuses on evaluating the genetic gain of
by physical linkage, genetic drift, selection, and popula- new genotypes by isolating genetic effects from environ-
tion structure [71]. This method assesses marker-trait mental and noise components [12]. Different strategies,
Fig. 2 Trait discovery and genome based molecular breeding
such as traditional phenotypic selection, marker-assisted Sub1, using marker-assisted breeding techniques [144].
selection (MAS), and genomic selection (GS), are In wheat, Lr34 and Sr2 are two crucial genes that confer
employed. Traditional selection relies on phenotypic data durable resistance to leaf rust and stem rust, respectively.
for genetic evaluation. MAS, on the other hand, uses spe- These genes have been incorporated into wheat varie-
cific genetic markers linked to traits of interest, selecting ties using Marker-Assisted Selection (MAS) to develop
individuals based on their marker scores [23]. Genomic improved cultivars viz. Avocet S (Lr34) and Thatcher
selection is a more advanced method that considers (Sr2) that are resistant to rust diseases [184].
markers with small effects on phenotypic variation. The Similarly, the enhancement of oleic acid content in
process of genome-based molecular breeding involves soybean oil using Marker-Assisted Selection (MAS) has
several steps (Fig. 2). MAS, known for its efficiency, been a significant achievement in soybean breeding. This
reduces both time and costs. MAS is faster as it doesn’t improvement is primarily focused on selecting specific
require extensive phenotype testing of large progeny sets alleles at the FAD2-1A and FAD2-1B loci, which are criti-
and allows for the pyramiding of multiple alleles. cal in regulating the fatty acid composition of soybean
Additionally, it reduces linkage drag and increases oil [122]. The FAD2-1A and FAD2-1B genes encode the
genetic gain compared to phenotypic selection [63]. enzyme omega-6 desaturase, which is responsible for
Genetic merit can be evaluated in larger populations converting oleic acid (a monounsaturated fatty acid) into
without losing genetic diversity. MAS-based breeding linoleic acid (a polyunsaturated fatty acid). By modifying
programs have been widely implemented in crops such or silencing these genes, the conversion of oleic acid to
as wheat, rice, maize, and tomato. For instance, MAS linoleic acid is reduced, leading to a higher proportion
has been used to incorporate the Pi-ta gene into vari- of oleic acid in the oil. Oleic acid is a healthier monoun-
ous rice varieties, enhancing resistance to rice blast dis- saturated fatty acid that is more stable and resistant to
ease caused by the fungus Magnaporthe oryzae [72]. oxidation than linoleic acid, which is more prone to ran-
Researchers identified the Sub1 gene in a flood-tolerant cidity. Through MAS, breeders have been able to select
traditional rice variety called FR13A. The gene, located soybean plants carrying specific alleles at the FAD2-1A
on chromosome 9 of the rice genome, was found to play and FAD2-1B loci that reduce the activity of the FAD2
a critical role in enhancing a plant’s ability to survive enzyme. Several high-oleic soybean varieties have been
under submerged conditions. The Sub1 gene is part of a developed through this approach. These varieties contain
regulatory mechanism that involves three key ethylene over 70% oleic acid compared to traditional soybeans,
improved varieties include: Plenish®, Vistive Gold®, and

response factors (ERFs)—Sub1A, Sub1B, and Sub1C. Of which contain around 20–30%. Some of the notable
Monola® [57]. MAS has been used in barley for yield-

these, Sub1A is the primary gene responsible for sub-
mergence tolerance and enables rice plants to enter a
state of metabolic dormancy, where growth and energy related and stress tolerance traits, resulting in elite lines
consumption are slowed, allowing the plant to conserve with improved malting quality by transferring the ther-
energy and survive for up to two weeks underwater. In mostable α-amylase from wild barley into a commercial
2009, researchers successfully integrated the Sub1 gene variety [178]. Next-generation sequencing (NGS) tech-
into several high-yielding, widely cultivated rice varieties, nologies have increased the number of available markers,
such as Swarna Sub1, IR64 Sub1, and Samba Mahsuri significantly boosting breeding efficiency. Markers such
as SSRs, SNPs, InDels, and haplotypes are now crucial for A selection of significant markers is used in modified
efficient genotyping and constructing genetic maps. For least-squares regression. This log-likelihood model may
example, SSR markers were used to map the Als gene on lead to the loss of important data when choosing markers
the 3H chromosome of barley, which is associated with with significant effects.
a low number of tillers [34]. In a study on barley, 83 sig- Ridge regression (RR) is a penalized regression tech-
nificant marker-trait associations were identified for six nique that solves overparameterization and multicollin-
yield-related traits under drought conditions [1]. Various earity [109]. The least absolute shrinkage and selection
strategies have been applied to identify QTLs for relevant operator (LASSO) is another variant, that may have dif-
traits in these crops, greatly enhancing genomic-based ficulties with strongly correlated predictors [118]. Elas-
molecular breeding through MAS. tic net (ENET) is a modification of LASSO that balances
Genomic Selection (GS), developed by Meuwissen et al. the ℓ1 and ℓ2 penalties in LASSO and RR, respectively,
in 2001, represents a significant advancement beyond and is robust to extreme correlations among the predic-
conventional Marker-Assisted Selection (MAS). While tors [46]. A Bayesian method to estimate marker effects is
MAS suits traits influenced by a limited number of major provided by Bayesian models like Bayes A, Bayes B, Bayes
genes, it falters with quantitative traits, often governed C, and Bayes D [56]. Genomic BLUP (GBLUP), one of the
by numerous minor genes, as seen in yield and stress best linear unbiased prediction (BLUP) techniques, uses
tolerance traits. GS tackles this challenge by harnessing genomic relationships to estimate genetic values [131].
an array of genetic markers spread across the genome to Ridge regression (RR), best linear unbiased prediction
compute Genomic Estimated Breeding Values (GEBV) (BLUP), least absolute shrinkage and selection operator
for each individual. GEBV integrates phenotypic data (LASSO), support vector machine (SVM), artificial neu-
with marker and pedigree data, yielding superior predic- ral network (ANN), and random forest (RF) are examples
tion accuracy compared to MAS [18, 62]. GS strategically of approaches based on single trait genomic selection
selects genome-spanning genetic markers, ensuring that (STGS). The multi-trait genomic selection technique
all Quantitative Trait Loci (QTLs) align with at least one (MTGS), which increases prediction accuracy for numer-
marker [52]. The first step in the genomic selection pro- ous characteristics, uses multivariate regression with
cess is creating a training population of individuals with covariance estimation (MRCE) and multivariate LASSO
genotypic and phenotypic data (Fig. 2). This data is used (MLASSO). A number of software tools and packages
to construct a predictive model, employing phenotypes have been created to evaluate genomic prediction accu-
as responses and genotypes as predictors. racy and make genomic selection (GS) usable. Some nota-
Insights derived from this model then enable the esti- ble tools and approaches are rrBLUP, solGS, GMStool,
mation of GEBV for the breeding population, consisting BWGS, BGLR, GenSel, GSelection and lme4GS [18].
solely of individuals with genotypic data. Genomic Selec- Genomic Selection (GS) revolutionizes crop improve-
tion seems a viable approach to advance genetic development, streamlining breeding for precision and effi-
ment within breeding programs in climate change. Grain ciency. Utilizing genetic markers, GS predicts crop yields
yield, qualitative characteristics, and abiotic stress resist- (Table 4). For example, Cerioli et al. [21] used the LSU500
ance have all benefited from using genomic selection. marker set to achieve predictive abilities of 0.13 to 0.78
This rapid improvement results from the selection of in various rice trials. GS is equally potent in disease
desired phenotypes across generations. Genomic selec- resistance breeding, as seen in Zhang et al.’s [189] study
tion offers a significant advantage by reducing breeding on Fusarium head blight (FHB) traits in wheat, yielding
cycle duration and lowering phenotyping costs, thereby prediction accuracies of up to 0.59 for FHB disease index
accelerating genetic improvements for food security. Fac- and 0.54 for Fusarium damaged Kernels (FDK). Further-
tors influencing prediction accuracy include training and more, GS enhances abiotic stress tolerance. Zhang et al.
breeding population sizes, genetic diversity, heritability, [190] assessed maize drought tolerance with prediction
genotype-environment interactions, marker density, and accuracies ranging from 0.19 to 0.33 for traits like seed-
genetic relationships [96]. Several methods have evolved ling emergence rate, plant height, and grain yield. Rut-
for genomic selection over time. An easy linear model, koski et al. [136] reported that genomic selection (GS)
such as ordinary least-squares regression, is frequently improved wheat grain yield by 15% compared to con-
used as the first step in the genomic selection process. ventional breeding methods. In their study, GS utilized
An issue that frequently arises in linear models with a 1,056 single nucleotide polymorphism (SNP) markers to
large number of genome-wide markers is that the num- predict breeding values, enabling more accurate selection
ber of markers (p) might significantly exceed the number and accelerating yield gains from 0.5% to 1.5% per year,
ment. In Maize two hybrids viz. Pioneer® P1197AM and

of observations (n), leading to overparameterization. An demonstrating the effectiveness of GS in wheat improve-
alternative strategy is adapted to deal with this problem.
Table 4 Genomic prediction of traits in different crops

Crop Model Population Type Trait Prediction Accuracy Reference
Rice GBLUP 128 Japanese rice cultivars Field grain weight 0.28 Yabe et al. [180]
Variance of field grain 0.53 Yabe et al. [180]
GBLUP, RKHS Germplasm Drought-resistance 0.23–0.80 Bhandari et al. [14]
MT-RRM 357 Accessions Daily water usage 0.29–0.87 Baba et al. [6]
Projected shoot area 0.38–0.80 Baba et al. [6]
Wheat GBLUP F4:6 population Grain Yield 0.75 Michel et al. [110]
RRBLUP Winter wheat breeding lines Powdery mildew resistance 0.6 Sarinelli et al. [141]
MLM Winter wheat breeding lines Stripe rust resistance 0.13–0.46 Shahinnia et al. [146]
Maize GBLUP and multigroup TC Grain Yield 0.78 Rio et al. [133]
GBLUP
RRBLUP and GBLUP Inbred lines and half diallel Water-logging tolerance 0.53–0.84 [35]
population
GBLUP Adapted and an exotic- Tocochromanols (vitamin E) 0.79 [161]
derived maize population
Soybean RRBLUP RILs from interspecific cross Yield 0.68 Beche et al. [10]
Extended Genomic BLUP 702 advanced breeding lines Optimal cross combinations 0.56 Miller et al. [111]
Groundnut Bayesian generalized linear Breeding lines Yield 0.49–0.60 Pandey et al. [120]
regression
Protein 0.41–0.46 Pandey et al. [120]
Rust resistance 0.74–0.75 Pandey et al. [120]
Chickpea RRBLUP 315 advanced breeding lines Yield 0.33 Li et al. [90]
Lentil RRBLUP Diversity panel, RIL Maturity duration 0.58–0.84 Haile et al. [58]
ioneer® P1329AM have been developed using genomic

P origins date back to successful gene insertions in mam-
selection to enhance traits like yield and disease resist- malian genomes in 1985–1986 [152]. Three main genome
ance [153]. GS facilitated the development of soybeans editing technologies are Zinc finger nucleases (ZFNs),
sgrow®® variety of
with enhanced resistance to diseases and pests, improv- transcription activator-like effector nucleases (TALENs),
ing overall crop resilience and yield. A and CRISPR/Cas systems. CRISPR/Cas stands out for its
soybean has been developed through GS with improved simplicity, efficiency, and versatility [148]. Genome edit-
disease resistance and enhanced yield potential [135]. ing in agriculture enhances crop traits, like increased
These findings underscore Genomic Selection’s potential yield, disease and pest resistance, accelerating breeding
to boost crop productivity and resilience to adverse envi- programs, ensuring food security, and promoting sus-
ronmental conditions and accelerates the development tainable farming practices in a rapidly changing world
of new varieties with desirable traits. Recent advance- (Table 6). Clustered Regularly Interspaced Short Palin-
ments in plant breeding have prominently featured dromic Repeats (CRISPR) system is an amazing bacterial
genome editing technologies which allows precise altera- defense mechanism against plasmid and virus invasion
tions to specific genes, enabling targeted modifications [75]. The sequences were first discovered in E. coli in
for traits like disease resistance or yield improvements. 1987 when researchers found conserved direct-repeat
This approach provides exact changes at the genetic level. sequences [69]. A crucial CRISPR/Cas9 development
In contrast, genomic selection involves evaluating the occurred in 2012 when Jinek et al. demonstrated SpCas9,
genetic potential of plants using DNA markers linked derived from Streptococcus pyogenes, to be successful as
to multiple traits. It assesses overall genetic merit and an RNA-guided DNA endonuclease in vitro. This system
guides breeding decisions by predicting future perfor- inserts invading DNA pieces between crRNA repetitions
mance. While editing is precise, selection offers a broader in the host CRISPR locus. Mature crRNAs are produced
assessment for enhancing complex traits [114]. through active transcription and pre-processing of these
pre-crRNAs by Cas9 and host factors. Cas9 is directed
Genome editing to the appropriate target locus inside the invading DNA
Genome editing, a powerful genetic modification by the mature crRNA-Cas9 complex. The PAM motif
method, enables precise alterations in DNA sequences (Protospacer adjacent motif ) is often ahead of the site-
using molecular scissors and artificial nucleases. Its specific cleavage that the Cas9 nuclease produces. The
conventional PAM sequence 5’ NGG 3’ at the 3′ end property [5]. Cas9 undergoes conformational changes,
of the target site is principally needed for the SpCas9. activating its nuclease domains during R-loop formation.
CrRNA and tracrRNA are combined to create chimeric After activation, Cas9 hydrolyses DNA’s phosphodies-
single guide RNA (sgRNA), which directs Cas9 to the tar- ter backbone via the HNH nuclease, cleaving the target
get region and introduces double-stranded breaks. Both DNA strand linked to the guide RNA and the RuvC-like
homology-directed repair (HDR) and non-homologous nuclease, cleaving the non-target DNA strand contain-
end-joining (NHEJ) techniques can be used to fix these ing PAM. Cas9 nickases, produced by mutations in either
breaks. Customized gRNA-Cas9 complexes have been nuclease domain, are valuable for base and prime editing
used to target economically significant traits in plants, as they cleave a single DNA strand [130]. Both domains
highlighting the promise of CRISPR/Cas9 in agricultural can be inactivated to create catalytically dead Cas9
applications [164]. (dCas9), retaining DNA binding abilities for applications
In nature, there are two main types of CRISPR-Cas like transcriptional regulation and epigenetic modifica-
immune systems: class 1, which uses multiprotein com- tions. Many Cas9 variants have evolved since the discov-
plexes for nucleic acid cleavage, and class 2, which uses ery of Streptococcus pyogenes (SpCas9) Cas9 nuclease,
single-protein effector domains (Makarova et al., 2020). varying in size, PAM recognition, guide RNA architec-
Because they benefit from a single protein effector, class ture, spacer length, editing efficiency, and specificity.
2 systems, especially types II, V, and VI, are preferred SpCas9, the most popular, contains 1,368 amino acids,
in biological research and translational applications. recognizes NGG PAMs, and supports both sgRNAs and
Regarding the class 2 Cas proteins, type-II Cas9 and type- crRNA/tracrRNA pairings with 20-nt spacers. However,
V Cas12 are RNA-guided DNA endonucleases, whereas it exhibits a higher off-target editing rate. Specialized
type-VI Cas13 mainly targets and cleaves RNA. Com- Cas9 variants like SaCas9 (smaller, 1053 amino acids) and
pared to type II CRISPR-Cas9, type V CRISPR-Cas12a Nme2Cas9 (recognizing pyrimidine-rich PAMs) offer
(formerly CRISPR-Cpf1, a CRISPR from Prevotella and unique advantages, enabling researchers to tailor their
Francisella 1) and CRISPR-Cas12b are significantly dif- choice of Cas9 effector for specific genome editing needs
ferent (Wang et al. 2020). SpCas9 requires a 5′-NGG-3′ [42, 128]. This diversity advances the study of molecular
PAM, whereas Cpf1 uses a 5′-TTTN-3′ or 5′-TTN-3′ biology and biotechnology by enabling researchers to
PAM, hence extending the range of target sites in the choose the best Cas9 effector for their particular needs
genome. Additionally, Cas12a permits gene targeting in genome editing. Wang et al. [169] reported a new gain-
with shorter crRNAs, possibly lowering genome edit- of-function OsGS2/GRF4 allele generated by CRISPR/
ing costs [8]. The RNA-guided endonucleases known Cas9 genome editing increases rice grain size and yield.
as Cas9 from type-II CRISPR systems have revolution- Errum et al. [43] found that CRISPR/Cas9 editing of
ized genome editing. In the target DNA sequences, wheat Ppd-1 gene homoeologs alters spike architecture
they cause double-strand breaks (DSBs) [73]. To create and grain morphometric traits and increases 1000-grain
ribonucleoprotein complexes in their natural environ- weight, grain width, grain length, plant height, and spike-
ment, Cas9 nucleases rely on CRISPR RNAs (crRNAs) lets per spike. Genome editing has led to the development
linked with trans-activating crRNAs (tracrRNAs) [36]. of several crop varieties with improved traits, showcas-
However, single guide RNAs (sgRNAs), which combine ing the potential of this technology in agriculture. In
crRNA and tracrRNA into one molecule, are used in the rice, CRISPR-edited varieties such as Sasakure and Nip-
majority of genome editing applications [75]. An impor- ponbare have been developed to enhance yield and boost
tant sequence is the protospacer adjacent motif (PAM), resistance to diseases, addressing key agricultural chal-
which is located 3’ of the target DNA strand in opposi- lenges [91]. In wheat, CRISPR-edited lines resistant to
tion to the guide RNA. Cas9 nuclease typically generates wheat blast provide protection against this devastating
blunt-ended DSBs 3 base pairs upstream of the PAM, fungal pathogen, improving crop resilience and produc-
although some Cas9 nucleases exhibit alternative cut- tivity [174, 175]. Wheat variety developed for drought
ting patterns [142]. After the Cas9-guide RNA complex tolerance through genome editing is the CRISPR/Cas9-
binds to the corresponding PAM, the DNA is unwound edited wheat targeting the TaDREB2 gene, which is asso-
to create an RNA•DNA heteroduplex with the target ciated with drought stress response. By modifying this
DNA strand [73]. From the PAM-proximal region of the gene, researchers improved the plant’s drought tolerance
protospacer to the PAM-distal end, the process moves in without negatively impacting yield. For instance, Kim
one direction. ’R-loop’ formed by the non-target DNA et al. [79] reported enhanced drought tolerance in wheat
strand is a single-stranded DNA structure that is exposed through CRISPR/Cas9 by targeting transcription factors
and accessible. Base editing and prime editing, two more like TaDREB2, aiding in the development of more resil-
recent genome editing techniques, take advantage of this ient wheat varieties in drought-prone regions. Similarly,
Kumar et al. Biological Research
Table 5 Alternative genome editing systems

(2024) 57:80
Genome editing Concept Application Reference
Base editors It is created by combining the single-stranded DNA deaminase A novel selectable marker for wheat and the development of herbicide Zhang et al. [192]; Kuang et al. [80]
enzyme with dormant SpCas9 (dSpCas9), which cannot create tolerance traits; Development of herbicide-tolerant rice germplasm
DSBs. Base editors precisely install targeted point mutations with-
out the need for donor DNA templates, DSBs, or HDR. Adenine base
editors (ABEs) and cytosine base editors (CBEs), which transform A•T
to G•C pairings and C•G to T•A pairs, respectively, are the two main
subcategories of base editors
CRISPR-associ- It is an engineered Cas-transposon system that combines transposase Type V-K CRISPR-associated transposases that are specifically designed Tou et al. [163]
ated transposases with dCas9 for programmable DNA transposition. It efficiently inserts to allow for precise cut-and-paste DNA insertion
large genomic cargos into TA motifs in the genome. However, it
has limitations, including off-target cargo integration and applicability
only to bacterial cells
Prime editors It utilizes a specialized protein called Prime Editing Protein (PEP) Correction of phenotypes and mutations in adult mice with hepatic Jang et al. [70]; Jiang et al. [74]
and a prime editing guide RNA (pegRNA) with an extension con- and ocular disorders; Deletion and replacement of long genomic
taining the desired genetic edit. PEP introduces single-strand sequences
breaks in the DNA and copies the edit from the RNA extension
into the genome, offering greater accuracy and versatility compared
to traditional methods like CRISPR-Cas9
Page 15 of 23
in soybeans, genome editing has led to the creation of frameworks and foster open, transparent public discus-
high oleic acid varieties, which improve the nutritional sions on the use of genome editing technologies [140].
quality and stability of soybean oil, offering health and Regulations for genome-edited crops vary globally [157].
market benefits (Zhai et al., 2020). Alternative genome In the USA, the regulatory framework for genome-edited
manipulation techniques such as base editing and prime crops is managed by three agencies. In the United States,
editing offer distinct approaches for precise DNA modi- the regulatory framework for genome-edited crops is
fications without causing double-strand breaks, beyond relatively permissive. The U.S. Department of Agricul-
traditional methods like CRISPR-Cas9, making them ture (USDA) oversees genetically engineered (GE) plants
ideal for crop improvement (Table 5). Base editing ena- under the Plant Protection Act. In 2020, the USDA
bles direct base conversion, such as converting cyto- announced that crops developed through genome edit-
sine to thymine. For example, it has been used to create ing, such as those edited with CRISPR/Cas9, would not
herbicide-resistant rice by modifying the ALS gene [191, be regulated if they do not contain DNA from other
195]. Prime editing is more versatile, allowing targeted species. This approach is exemplified by the CRISPR-
insertions, deletions, and base substitutions. It has been edited mushroom developed by Penn State researchers,
applied to improve disease resistance in crops like rice which resists browning and was not subjected to USDA
by precisely altering genes like OsSWEET for bacterial regulations because it does not introduce foreign genes
blight resistance [191, 195]. Beyond simply modifying [13]. However, genome-edited crops may still be subject
DNA sequences, CRISPR-Cas9 has also been adapted to regulation by the Environmental Protection Agency
to control gene expression. Cas9 variants that lack cut- (EPA) and the Food and Drug Administration (FDA),
ting activity, such as dCas9 (dead Cas9), can be fused depending on their traits. The FDA reviews crops for food
with transcriptional activators or repressors to modu- safety, while the EPA regulates plants engineered to pro-
late gene expression, opening new doors for research duce pesticides. The European Union (EU) adopts a more
into gene regulation, epigenetics, and functional genom- stringent regulatory approach. Genome-edited crops
ics. CRISPR-dCas9 offers a non-invasive way to control are treated similarly to genetically modified organisms
gene expression without introducing mutations. This (GMOs) under EU regulations. This requires extensive
is particularly advantageous in crops where regulatory safety assessments, risk evaluations, and labeling before
and public concerns over genetically modified organ- they can be marketed. In 2018, the European Court of
isms (GMOs) are prevalent. By modulating gene activ- Justice (ECJ) ruled that genome-edited crops should be
ity instead of editing the genome, CRISPR-dCas9 allows regulated under the same laws as GMOs, meaning they
for crop improvement while potentially avoiding some must undergo rigorous assessments [41]. For exam-
regulatory hurdles associated with traditional genetic ple, CRISPR-edited wheat developed by Rothamsted
modification. In a significant study by Lowder et al. [101], Research, aimed at improving disease resistance, faced
researchers used CRISPR-dCas9 technology to enhance substantial regulatory hurdles due to the EU’s stringent
yield and drought tolerance in tomato (Solanum lyco- GMO regulations [11]. The wheat’s developers had to
persicum). The researchers designed a CRISPR-dCas9 navigate a complex approval process, reflecting the EU’s
system where dCas9 was fused with transcriptional acti- cautious stance on genome editing. Canada’s regulatory
vators to upregulate genes involved in auxin biosynthesis framework is focused on the end product rather than the
and drought stress response. This enabled precise modu- method of development. The Canadian Food Inspection
lation of key genes without altering the tomato genome. Agency (CFIA) evaluates whether genome-edited crops
A detailed study of genome editing has been presented require regulation based on their traits. If the modifica-
in Table 6. tions do not result in novel traits or substances, the crop
may not require extensive oversight [22]. For example,
Regulatory framework for genome‑edited crops CRISPR-edited canola with improved oil composition
Genome editing raises several ethical issues, including has been developed, and the CFIA determined that it did
the possibility of unintended genetic changes, long-term not necessitate extensive regulatory scrutiny as long as it
effects on ecosystems, and disparities in access to tech- did not introduce novel traits [151].
nology. Potential risks involve off-target mutations and Australia’s approach is also product-based, with a
unforeseen consequences that could impact environmen- focus on the characteristics of the final crop. The Gene
tal stability or human health. Ethical discussions focus Technology Regulator (GTR) assesses whether genome-
on maintaining responsible research practices, obtaining edited crops contain new traits or genes that would war-
informed consent, and considering the broader societal rant regulation. If the modifications do not introduce
impacts of genetic alterations. To manage these con- new genetic material or traits associated with GMOs, the
cerns effectively, it is vital to establish strong regulatory crop may not face stringent controls [53]. An example is
Table 6 The application of genome editing techniques for the improvement of agronomic traits in crops
Crop Technology Target genes Result/Trait improvement Reference
Rice CRISPR-Cas9 GS2 Increased grain size and yield and bigger grain Wang et al. [169]
length/width ratio
Rice CRISPR-Cas9 RBL1 Broad-spectrum disease resistance Sha et al. [145]
Rice CRISPR-Cas9 OsCul3a Xanthomonas oryzae/Magnaportheoryzae Gao et al. [50]
resistance
Rice CRISPR-Cas9 OsPi21, OsXa13 Magnaportheoryzae/Xanthomonas oryzae Li et al. [89]
resistance
Rice CRISPR-Cas9 SWEET11, SWEET13 and SWEET14/promoter Xanthomonas oryzae pv. Oryzae resistance Oliva et al. [119]
Rice CRISPR-Cas9 EBEs of OsSWEET14 Resistance to Xanthomonas oryzaepv. oryzae Zafar et al. [187]
Rice CRISPR-Cas9 ERA1 Drought tolerance Ogata et al. [117]
Rice CRISPR-Cas9 bHLH024 Salinity tolerance Alam et al. [2]
Rice CRISPR-Cas9 miR535 Tolerance to drought and salinity Yue et al. [186]
Wheat CRISPR-Cas9 Ppd-1 Increase in 1000-grain weight, grain width, grain Errum et al. [43]
length, plant height, and spikelets per spike
Wheat TALEN TaMLO Powdery mildew resistance Wang et al. [172]
Wheat CRISPR-Cas9 TaNFXL1 Fusarium graminearum resistance Brauer et al. [17]
Wheat CRISPR-Cas9 NAC071-A Drought sensitive Mao et al. [106]
Wheat CRISPR-Cas9 MYBL1 Drought sensitive Mao et al. [106]
Maize ZFN PAT Herbicide resistance Schornack et al. [143]
Maize CRISPR-Cas9 ZmPLA1 Haploid induction in tropical maize line Rangari et al. [129]
Maize CRISPR-Cas9 abh2 Drought tolerance [95]
Maize CRISPR-Cas9 STL1 Salinity tolerance Wang et al. [171]
Barley CRISPR-Cas9 HvMorc1 Resistance against Blumeriagraminis and Fusar- Kumar et al. [81]
ium graminearum
Barley CRISPR-Cas9 HVP10 Salinity sensitive Fu et al. [47]
Barley CRISPR-Cas9 ß-1-3glucanase Reduction of callose deposition in maize sieve Kim et al. [78]
tubes
Arabidopsis CRISPR-Cas9 eIF4E Transgene free resistant against Clover yellow Bastet et al. [9]
vein virus
Arabidopsis CRISPR-Cas9 TRE1 Drought tolerance Nunez-Munoz et al. [116]
Arabidopsis CRISPR-Cas9 C/VIF1 Salinity tolerance Yang et al. [181]
Soybean CRISPR-Cas9 FAD2 Increase in oleic acid content Zhou et al. [197]
Soybean CRISPR-Cas9 GmF3H1/2, FNSII-1 Soybean mosaic virus [191, 195]
Soybean CRISPR-Cas9 MYB118 Sensitive to drought, salinity Du et al. [39]
Cotton CRISPR-Cas9 GhDIR5 and GhDIR6 Toxicity-depleted cotton seed Lin et al. [92]
Cotton CRISPR-Cas9 Gh14-3-3d Verticillium dahlia resistance Zhang et al. [193]
Cotton CRISPR-Cas9 ALARP Cotton fiber development Sander and Joung [139]
Tobacco CRISPR-Cas9 IR, C1 Cotton leaf curl multan virus resistance Yin et al. [183]
Tomato CRISPR-Cas9 Solyc08g075770 Fusarium oxysporum f. sp. lycopersici Prihatna et al. [123]
Tomato CRISPR-Cas9 GID1a Drought tolerance Illouz-Eliaz et al. [68]
Tomato CRISPR-Cas9 ABIG1 Salinity tolerance Ding et al. [38]
Tomato CRISPR-Cas9 GRXS14, GRXS15, GRXS16, GRXS17 Sensitive to heat, chilling, drought, heavy metal Kakeshpour et al. [76]
toxicity, nutrient deficiency
Brassica napus CRISPR-Cas9 BnCRT1a Verticillium longisporum resistance Probsting et al. [124]
Potato TALEN ALS Herbicide resistance Butler et al. [19]
Capsicum CRISPR-Cas9 CaERF28 Anthracnose disease resistance Mishra et al. [113]
CRISPR-edited barley with enhanced disease resistance. is evolving as the country seeks to balance safety with
The GTR decided that the crop did not require additional innovation. Initially, genome-edited crops were assessed
regulatory measures as long as the edits did not involve under the existing GMO framework, which involves
new genetic material [45]. Japan’s regulatory framework rigorous safety evaluations. However, Japan is working
towards creating a more tailored approach to genome simplicity. These technologies facilitate highly accurate
editing [103]. For example, CRISPR-edited soybeans modifications of nuclear genomes. However, a significant
with improved nutritional properties are currently under challenge is the potential for off-target mutations, which
review. Recent discussions in Japan are focused on devel- can lead to harmful phenotypes and limit the broader
oping regulations that distinguish between genome application of genome editing. To address this issue, new
editing and traditional GMOs, potentially streamlin- CRISPR/Cas variants are being developed, and existing
ing the approval process [138]. The government of India systems are being enhanced to minimize off-target effects
issued an Office Memorandum on 30th March 2022 by selecting specific single guide RNAs (sgRNAs) with
and exempted SDN-1 and SDN-2 genome-edited plants fewer predicted off-target sites based on a comprehen-
without foreign DNA from Rules 7 to 11 of the EPA, sive reference genome sequence. Genome editing holds
1986. This streamlines approval, bypassing the Genetic immense potential for creating crops with improved
Engineering Appraisal Committee (GEAC) for genome- nutritional content, reduced susceptibility to pests and
edited crops in India. The global regulatory landscape diseases, and increased environmental resilience. Col-
for genome-edited crops varies widely, reflecting diverse lectively, these tools are instrumental in developing crop
national priorities and approaches to biotechnology. At varieties that meet the challenges of a growing global
present, the United States and India employs a permis- population, changing climates, and sustainable agricul-
sive approach focused on the end product, while the ture practices. However, ethical, regulatory, and safety
European Union maintains strict GMO-like regulations. considerations will shape their future deployment.
Canada and Australia use a product-based perspective,
Abbreviations
assessing crops based on their traits rather than their SNP Single Nucleotide Polymorphism
development method. Japan is evolving towards a more CRISPR/Cas9 Clustered Regularly Interspaced Short Palindromic Repeats-
nuanced regulatory framework. These differences high- Associated Protein 9
QTL Quantitative Trait Loci
light the ongoing debate over balancing innovation with RFLP Restriction Fragment Length Polymorphism
safety and environmental considerations in the era of RAPD Random Amplified Polymorphic DNA
advanced genetic engineering [138]. AFLP Amplified Fragment Length Polymorphism
SSR Simple Sequence Repeats
STR Short Tandem Repeats
Conclusion and perspectives VNTR Variable Number of Tandem Repeats
The future of plant breeding promises advancements PCR Polymerase Chain Reaction
NGS Next Generation Sequencing
through genetic tools, precision breeding techniques, NCBI National Center for Biotechnology Information
and climate-resilient crops to address global food secu- EMBL European Molecular Biology Laboratory
rity. Key genomic resources include genetic markers, DDBJ DNA Data Bank of Japan
UniProt Universal Protein Resource
reference genomes, databases, transcriptomes, and gene UCSC University of California Santa Cruz
expression profiles. These tools are crucial for identify- KEGG Kyoto Encyclopedia of Genes and Genomes
ing genes linked to desirable traits, understanding genetic STRING Search Tool for the Retrieval of Interacting Genes/Proteins
BioGRID Biological General Repository for Interaction Datasets
diversity, and accelerating breeding programs. Molecular SGN Sol Genomics Network
markers will continue to enhance traditional breeding by QRTPCR Quantitative Real-Time PCR
enabling the selection of disease-resistant, drought-tol-
Acknowledgements
erant, and high-yield plants, leading to faster and more Not applicable.
precise crop development. Genomic selection is poised
to revolutionize plant breeding. It harnesses big data and Author contributions
All authors contributed to the study conception and design. RK and NRP
advanced analytics to predict an individual plant’s per- conceptualized the manuscript topic. RK, AK, RLV, MC, NRP, SR, AGD, RD, BD,
formance based on its genetic makeup [18]. This enables and HLD wrote the initial draft of the manuscript. RK, SPD, BUC, BB and VKM
breeders to select and propagate plants with the high- revised the manuscript. All authors read and approved the final manuscript.
est genetic potential, significantly shortening breeding Funding
cycles and increasing the efficiency of trait improvement. Not Applicable.
Genome editing technologies, like CRISPR-Cas9, offer
Availability of data and materials
unprecedented precision in crop enhancement. They Not applicable.
allow for the targeted modification of specific genes to
introduce or enhance desirable traits while minimizing Declarations
unintended changes [4]. CRISPR/Cas-9 and related sys-
tems (such as CRISPR/Cas-12 and CRISPR/Cas-13) are Ethics approval and consent to participate
This submitted work has not been published before. It is not under consid-
recognized as groundbreaking tools for genome edit- eration for publication elsewhere. Its publication has the consent of all the
ing due to their precision, efficiency, affordability, and authors and the responsible authorities where the work was carried out. If
accepted, it will not be published elsewhere in the same form, in English, or in 18. Budhlakoti N, Kushwaha AK, Rai A, Chaturvedi KK, Kumar A, Pradhan AK,
any other language without the written consent of the copyright holder. Kumar U, Kumar RR, Juliana P, Mishra DC, Kumar S. Genomic selection: a
tool for accelerating the efficiency of molecular breeding for develop-
Consent for publication ment of climate-resilient crops. Front Genet. 2022;13: 832153.
The authors approved this version of the manuscript to publish. 19. Butler NM, Baltes NJ, Voytas DF, Douches DS. Geminivirus-mediated
genome editing in potato (Solanum tuberosum L.) using sequence-
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Kumar et al.

Biological Research (2024) 57:80 Biological Research

REVIEW Open Access

Advances in genomic tools for plant

Table 1 Salient features of major molecular marker

Marker type Principle Pros Cons Suitability in Breeding Contexts Reference

Table 3 Important Databases and Repositories of Genomic Information

Genbank General public sequence repository http://www.ncbi.nlm.nih.gov/genbank/

Genome‑wide association study (GWAS) Genome‑based molecular breeding

Fig. 2 Trait discovery and genome based molecular breeding

improved varieties include: Plenish®, Vistive Gold®, and

Monola® [57]. MAS has been used in barley for yield-

ment. In Maize two hybrids viz. Pioneer® P1197AM and

Table 4 Genomic prediction of traits in different crops

ioneer® P1329AM have been developed using genomic

Table 5 Alternative genome editing systems

Genome editing Concept Application Reference

You might also like

s40659-024-00562-6

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s40659-024-00562-6

Uploaded by

Document Information

Copyright

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Share this document

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Did you find this document useful?

Is this content inappropriate?

Copyright:

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s40659-024-00562-6

Uploaded by

Copyright:

Available Formats

Kumar et al.

Biological Research (2024) 57:80 Biological Research

REVIEW Open Access

Advances in genomic tools for plant

Table 1 Salient features of major molecular marker

Marker type Principle Pros Cons Suitability in Breeding Contexts Reference

Table 3 Important Databases and Repositories of Genomic Information

Genbank General public sequence repository http://​www.​ncbi.​nlm.​nih.​gov/​genba​nk/

Genome‑wide association study (GWAS) Genome‑based molecular breeding

Fig. 2 Trait discovery and genome based molecular breeding

improved varieties include: ­Plenish®, Vistive ­Gold®, and

­Monola® [57]. MAS has been used in barley for yield-

ment. In Maize two hybrids viz. ­Pioneer® P1197AM and

Table 4 Genomic prediction of traits in different crops

­ ioneer® P1329AM have been developed using genomic

Table 5 Alternative genome editing systems

Genome editing Concept Application Reference

You might also like

Genbank General public sequence repository http://www.ncbi.nlm.nih.gov/genbank/

improved varieties include: Plenish®, Vistive Gold®, and

Monola® [57]. MAS has been used in barley for yield-

ment. In Maize two hybrids viz. Pioneer® P1197AM and

ioneer® P1329AM have been developed using genomic