Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

• Main Authors: Alice eKujur, Deepak eBajaj, Hari Deo eUpadhyaya, Shouvik eDas, Rajeev eRanjan, Tanima eShree, Maneesha S Saxena, Saurabh eBadoni, Vinod eKumar, Shailesh eTripathi, CL Laxmipathi Gowda, Shivali eSharma, Sube eSingh, Akhilesh eTyagi, SWARUP KUMAR PARIDA
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2015-03-01
• Series: Frontiers in Plant Science
• Subjects: Cicer; Linkage Disequilibrium; SNP; GBS; chickpea; Desi
• Online Access: http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00162/full

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 44844 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, 22546 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 23798 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 importan