Genomic resources in chickpea (original) (raw)
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A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea
Scientific Reports, 2015
We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome-and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23-47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/ plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea. Chickpea (Cicer arietinum L.), a member of family Fabaceae is an annual, diploid, self-pollinated crop species with a very small genome size of ~740 Mbp. It is the most cultivated food legume/pulse crop worldwide that serves as an important dietary source of protein with essential amino acids for human. The seed and pod characters are major yield contributing traits of chickpea and vary widely across global germplasm collections, landraces and cultivated desi and kabuli accessions. Considering the agronomic importance of seed and pod traits, multiple efforts have been made for molecular mapping of quantitative trait loci (QTLs) governing major seed and pod yield contributing traits, including seed and pod number, double podding and seed weight in chickpea 1-31. Unfortunately, due to lack of requisite intra-specific polymorphism in chickpea, no such robust genes/QTLs associated with seed and pod traits have been identified/fine mapped hitherto, which can be utilized for marker-assisted genetic
Impact of Genomics on Chickpea Breeding
Compendium of Plant Genomes
Chickpea is an economical source of vegetable protein for the poor living in the semi-arid regions globally. As a consequence of climate change and increasing climate variability, the incidences of drought and heat stresses and severity of some diseases, such as dry root rot and collar rot, have increased in chickpea crop, resulting in poor and unstable yields. By improoving the efficiency of crop breeding programs, climate resilient varieties with traits desired by the farmers, industries and consumers can be developed more rapidly. Excellent progress has been made in the development of genomic resources for chickpea in the recent past. Several national and international chickpea breeding programs have started utilizing these genomic resources and tools for genetic improvement of complex traits. One of such examples includes the introgression of "QTL-hotspot" containing quantitative trait loci (QTLs) for several drought tolerance-related traits, including root traits, through marker-assisted backcrossing (MABC) for enhancing drought tolerance in popular cultivars. Several drought-tolerant introgression lines with higher yield as compared to the popular cultivars have been identified. Multi-parent advanced generation intercross (MAGIC) populations developed from using 8 parents created large genetic diversity consequently several promising lines. Marker-assisted recurrent selection (MARS) has also been explored for yield improvement in chickpea. Development of diagnostic markers or the identification of candidate genes for several traits is essential for greater use of genomic resources in chickpea improvement.
Springer eBooks, 2013
Chickpea (Cicer arietinum L.), the second largest consumed pulse crop of the world after common bean, is grown in over 50 countries and traded across 140 countries. The beneficial effects of chickpea on soil health and human health are well recognized. There has been a slow progress in improving average global productivity of chickpea, which continued to remain below 1.0 ton ha-1. The breeding efforts in chickpea have mainly focused on improving its adaptation to different growing conditions. The changing scenario of chickpea cultivation, particularly the large shift in its area to warmer growing environments, and expected effects of climate change further impose challenges on chickpea breeding programs. After several decades of slow progress, the recent years have witnessed extraordinary growth in development of genetic (mapping populations) and genomic resources (structural and functional molecular markers, integrated genetic map, mapping of genes/quantitative trait loci, whole genome sequencing) for chickpea. Now, chickpea is one of the most advanced grain legumes in terms of availability of genomic resources. Efforts have already begun on application of genomics technologies in chickpea improvement. The coming years are expected to have an exponential growth in integration of genomics technologies in chickpea breeding programs. This book chapter provides an update on the development of genetic and genomic resources for chickpea and their current and potential uses in chickpea improvement.
Advances in Chickpea Genomic Resources for Accelerating the Crop Improvement
Compendium of Plant Genomes
Chickpea plays a major role in food and nutritional security worldwide. Its productivity is severely affected by various biotic and abiotic stresses; hence development of stress resilience varieties that can yield higher under stress environment remains the call of the hour. Conventional breeding approaches clubbed with the genome information, commonly known as genomic-assisted breeding (GAB) have the potential to accelerate the crop improvement efforts. In order to deploy the GAB for crop improvement in chickpea, there was need to convert an orphan crop chickpea into the genomic resource-rich crop. Advent of sequencing technology has resulted in reduction of cost and led to development of huge genomic resources in chickpea. A variety of markers have been developed, used for various mapping studies including linkage mapping and association mapping and finally deployed for developing the superior varieties using GAB approached such as marker assisted backcrossing and genomic selection. The chapter reviews the journey of chickpea status from orphan crop with almost no marker resources to a genome resource-rich crop, which are being used for achieving the genetic gains at a momentum.
Scientific Reports, 2018
We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars. Chickpea (Cicer arietinum) is a self-pollinated, diploid (2n = 16) and economically important legume food crop rich in human dietary proteins 1. The chickpea is primarily represented by its desi and kabuli cultivars exhibiting a distinct differentiation in both agro-morphological and architecture traits, which genomes have been sequenced recently 2-5. Substantial enhancement of its yield and productivity by developing high-yielding a/biotic stress tolerant and climate-ready cultivars is essential at present to sustain the global food security. To accomplish these objectives, many significant efforts involving classical genetics as well as genomics-assisted breeding strategies like quantitative trait loci (QTL) mapping, fine-mapping/map-based cloning and association analysis have been made to decipher the inheritance pattern and quantitative dissection of complex yield and stress tolerance traits for genetic improvement of chickpea 6-30. However, these are constrained by narrow genetic base and low intra-specific marker polymorphism among desi and kabuli accessions due to combined strong impact of four major domestication bottlenecks in chickpea as compared to other food crop plants 2,3,31-35. To overcome the aforesaid limitations, development and high-throughput genotyping of large-scale sequence-based informative markers like single nucleotide polymorphism (SNPs) exhibiting a higher potential of polymorphism among cultivated desi and kabuli accessions is a prerequisite for their use in genomics-assisted breeding applications and genetic improvement of chickpea. The next-generation sequencing (NGS)-led genome and transcriptome sequencing of multiple cultivated (desi and kabuli) and wild accessions are found efficient in fast discovery of numerous SNPs at a genome-wide scale in chickpea 2,3,13,18,30,36-44. The large-scale validation and high-throughput genotyping of these SNPs mined from limited number of sequenced accessions using diverse array-based genotyping assays commonly exhibit
Nature Genetics
We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement
Nature Biotechnology, 2013
Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ~738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea-desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.
Chickpea (Cicer arietinum L.) is an important crop legume plant with high nutritional value. The transcriptomes of desi and wild chickpea have already been sequenced. In this study, we sequenced the transcriptome of kabuli chickpea, C. arietinum (genotype ICCV2), having higher commercial value, using GS-FLX Roche 454 and Illumina technologies. The assemblies of both Roche 454 and Illumina datasets were optimized using various assembly programs and parameters. The final optimized hybrid assembly generated 43,389 transcripts with an average length of 1065 bp and N50 length of 1653 bp representing 46.2 Mb of kabuli chickpea transcriptome. We identified a total of 5409 simple sequence repeats (SSRs) in these transcript sequences. Among these, at least 130 and 493 SSRs were polymorphic with desi (ICC4958) and wild (PI489777) chickpea, respectively. In addition, a total of 1986 and 37,954 single nucleotide polymorphisms (SNPs) were predicted in kabuli/desi and kabuli/wild genotypes, respectively. The SNP frequency was 0.043 SNP per kb for kabuli/desi and 0.821 SNP per kb for kabuli/wild, reflecting very low genetic diversity in chickpea. Further, SSRs and SNPs present in tissue-specific and transcription factor encoding transcripts have been identified. The experimental validation of a selected set of polymorphic SSRs and SNPs exhibited high intra-specific polymorphism potential between desi and kabuli chickpea, suggesting their utility in large-scale genotyping applications. The kabuli chickpea gene index assembled, and SSRs and SNPs identified in this study will serve as useful genomic resource for genetic improvement of chickpea.
Frontiers in Plant Science, 2016
The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10-15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.
DNA Research, 2014
The identification and fine mapping of robust quantitative trait loci (QTLs)/genes governing important agro-morphological traits in chickpea still lacks systematic efforts at a genome-wide scale involving wild Cicer accessions. In this context, an 834 simple sequence repeat and single-nucleotide polymorphism marker-based high-density genetic linkage map between cultivated and wild parental accessions (Cicer arietinum desi cv. ICC 4958 and Cicer reticulatum wild cv. ICC 17160) was constructed. This inter-specific genetic map comprising eight linkage groups spanned a map length of 949.4 cM with an average inter-marker distance of 1.14 cM. Eleven novel major genomic regions harbouring 15 robust QTLs (15.6 -39.8% R 2 at 4.2 -15.7 logarithm of odds) associated with four agro-morphological traits (100-seed weight, pod and branch number/plant and plant hairiness) were identified and mapped on chickpea chromosomes. Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number. One robust SW-influencing major QTL region (qSW4.2) has been narrowed down by combining QTL mapping with high-resolution QTL regionspecific association analysis, differential expression profiling and gene haplotype-based association/LD mapping. This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at traitspecific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development. The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea.