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

Kujur, A and Bajaj, D and Upadhyaya, H D and Das, S and Ranjan, R and Shree, T and Saxena, M S and Badoni, S and Kumar, V and Tripathi, S and Gowda, C L L and Sharma, S and Singh, S and Tyagi, A K and Parida, S K (2015) Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea. Frontiers in Plant Science, 06 (162). 01-19. ISSN 1664-462X

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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.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Cicer, chickpea, Desi, GBS, Kabuli, Linkage disequilibrium, SNP, Genome-wide SNPs
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 06 Apr 2016 09:20
Last Modified: 21 Oct 2016 06:18
URI: http://oar.icrisat.org/id/eprint/9414
Official URL: http://dx.doi.org/10.3389/fpls.2015.00162
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: The authors gratefully acknowledge the financial support for this research study provided by a research grant from the Department of Biotechnology (DBT), Government of India (102/IFD/SAN/2161/2013-14). AK and SD acknowledge the CSIR (Council of Scientific and Industrial Research) and DBT for Junior/Senior Research Fellowship awards. We thank Praveen Raj S of CromDx Solutions Pvt. Ltd. for assistance and advice concerning SNP data analysis. We are grateful to the Editor and reviewers for critically evaluating the manuscript and providing constructive comments for its improvement. This article was submitted to Plant Genetics and Genomics, a section of the journal Frontiers in Plant Science.
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