title: Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea.
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.
authors: National Institute of Plant Genome Research (NIPGR) New Delhi, India.
authors: Alice
authors: A
authors: Kujur
authors: National Institute of Plant Genome Research (NIPGR) New Delhi, India.
authors: Deepak
authors: D
authors: Bajaj
authors: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Telangana, India.
authors: Hari D
authors: HD
authors: Upadhyaya
authors: National Institute of Plant Genome Research (NIPGR) New Delhi, India.
authors: Shouvik
authors: S
authors: Das
authors: National Institute of Plant Genome Research (NIPGR) New Delhi, India.
authors: Rajeev
authors: R
authors: Ranjan
authors: National Institute of Plant Genome Research (NIPGR) New Delhi, India.
authors: Tanima
authors: T
authors: Shree
authors: National Institute of Plant Genome Research (NIPGR) New Delhi, India.
authors: Maneesha S
authors: MS
authors: Saxena
authors: National Institute of Plant Genome Research (NIPGR) New Delhi, India.
authors: Saurabh
authors: S
authors: Badoni
authors: National Research Centre on Plant Biotechnology (NRCPB) New Delhi, India.
authors: Vinod
authors: V
authors: Kumar
authors: Division of Genetics, Indian Agricultural Research Institute (IARI) New Delhi, India.
authors: Shailesh
authors: S
authors: Tripathi
authors: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Telangana, India.
authors: C L L
authors: CL
authors: Gowda
authors: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Telangana, India.
authors: Shivali
authors: S
authors: Sharma
authors: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Telangana, India.
authors: Sube
authors: S
authors: Singh
authors: National Institute of Plant Genome Research (NIPGR) New Delhi, India.
authors: Akhilesh K
authors: AK
authors: Tyagi
authors: National Institute of Plant Genome Research (NIPGR) New Delhi, India.
authors: Swarup K
authors: SK
authors: Parida
keywords: Cicer; GBS; SNP; chickpea; desi; kabuli; linkage disequilibrium