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

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Title Employing genome- wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea
 
Creator Kujur, Alice
Bajaj, Deepak
Upadhyaya, Hari D.
Das, Shouvik
Ranjan, Rajeev
Shree, Tanima
Saxena, Maneesha S.
Badoni, Saurabh
Kumar, Vinod
Tripathi, Shailesh
Gowda, C. L. L.
Sharma, Shivali
Singh, Sube
Tyagi, Akhilesh K.
Parida, Swarup K.
 
Subject Cicer
chickpea
desi
GBS
kabuli
linkage disequilibrium
SNP
 
Description Accepted date: 01 March 2015
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.
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.
 
Date 2016-01-07T04:56:36Z
2016-01-07T04:56:36Z
2015
 
Type Article
 
Identifier Front. Plant Sc., 6: 162
1664-462X
http://172.16.0.77:8080/jspui/handle/123456789/529
http://journal.frontiersin.org/article/10.3389/fpls.2015.00162/abstract
10.3389/fpls.2015.00162
 
Language en_US
 
Publisher Frontiers Media S.A.