Abstract
The genome-wide discovery and high-throughput genotyping of SNPs in chickpea natural germplasm lines is indispensable to extrapolate their natural allelic diversity, domestication, and linkage disequilibrium (LD) patterns leading to the genetic enhancement of this vital legume crop. We discovered 44,844 high-quality SNPs by sequencing of 93 diverse cultivated desi, kabuli, and wild chickpea accessions using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays that were physically mapped across eight chromosomes of desi and kabuli. Of these, 22,542 SNPs were structurally annotated in different coding and non-coding sequence components of genes. Genes with 3296 non-synonymous and 269 regulatory SNPs could functionally differentiate accessions based on their contrasting agronomic traits. A high experimental validation success rate (92%) and reproducibility (100%) along with strong sensitivity (93–96%) and specificity (99%) of GBS-based SNPs was observed. This infers the robustness of GBS as a high-throughput assay for rapid large-scale mining and genotyping of genome-wide SNPs in chickpea with sub-optimal use of resources. With 23,798 genome-wide SNPs, a relatively high intra-specific polymorphic potential (49.5%) and broader molecular diversity (13–89%)/functional allelic diversity (18–77%) was apparent among 93 chickpea accessions, suggesting their tremendous applicability in rapid selection of desirable diverse accessions/inter-specific hybrids in chickpea crossbred varietal improvement program. The genome-wide SNPs revealed complex admixed domestication pattern, extensive LD estimates (0.54–0.68) and extended LD decay (400–500 kb) in a structured population inclusive of 93 accessions. These findings reflect the utility of our identified SNPs for subsequent genome-wide association study (GWAS) and selective sweep-based domestication trait dissection analysis to identify potential genomic loci (gene-associated targets) specifically regulating important complex quantitative agronomic traits in chickpea. The numerous informative genome-wide SNPs, natural allelic diversity-led domestication pattern, and LD-based information generated in our study have got multidimensional applicability with respect to chickpea genomics-assisted breeding.
Highlights
The second most abundantly grown food legume chickpea (Cicer arietinum L.) is a self-pollinated and diploid (2n = 2x = 16) crop species belonging to Fabaceae (Kumar et al, 2011)
We identified 303 SNPs (78 non-synonymous SNPs) in the 140 genes localized within a 0.03 Mb (10.39– 10.42 Mb) major “QTL-hotspot” region controlling drought tolerance-component root traits in chickpea (Supplementary Tables S4, S6)
GBS Assay Expedites Genome-Wide Discovery and High-Throughput Genotyping of SNPs in Chickpea GBS assay is currently considered as the most convenient approach for high-throughput SNP discovery and genotyping in crop plants, including chickpea (Mayer et al, 2012; Poland et al, 2012a,b; Byrne et al, 2013; Crossa et al, 2013; Mascher et al, 2013; Morris et al, 2013; Sonah et al, 2013; Spindel et al, 2013; Thurber et al, 2013; Uitdewilligen et al, 2013; Bastien et al, 2014; Deokar et al, 2014; He et al, 2014; Huang et al, 2014; Jaganathan et al, 2014; Jarquín et al, 2014; Liu et al, 2014; Sonah et al, 2014; Tardivel et al, 2014). It suffers from certain technical drawbacks, including non-uniform distribution of short sequence reads in different genotyped accessions and a high percentage of missing and erroneous SNP genotyping data. This assay is accompanied with difficulties in storing and handling much low quality SNP genotyping data generated from diverse crop accessions during bioinformatics analyses (Davey et al, 2011; Mir and Varshney, 2012; Poland and Rife, 2012)
Summary
The second most abundantly grown food legume chickpea (Cicer arietinum L.) is a self-pollinated and diploid (2n = 2x = 16) crop species belonging to Fabaceae (Kumar et al, 2011). It is a vital source of human dietary protein enriched with essential amino acids. The draft genomes of two major chickpea cultivars-kabuli (large seeded) and desi (small seeded) representing diverse gene pools have been successfully sequenced (Jain et al, 2013; Varshney et al, 2013a) These genome sequencing efforts signified that ∼70% of their total sequenced draft genomes are represented by low-complexity regions, which could serve as reference for subsequent resequencing of diverse desi and kabuli accessions in order to discover and validate informative sequence-based markers at a genome-wide scale by deploying suitable high-throughput genotyping assay
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