A genome-wide SNP scan accelerates trait-regulatory genomic loci identification 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) A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea. Nature Scientific Reports, 5 (11166). pp. 1-20. ISSN 2045-2322

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Abstract

We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23–47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea; Natural variation in plants; Genetics
Subjects: Mandate crops > Chickpea
Depositing User: Mr Ramesh K
Date Deposited: 17 Jun 2015 09:44
Last Modified: 21 Oct 2016 06:38
URI: http://oar.icrisat.org/id/eprint/8784
Official URL: http://dx.doi.org/10.1038/srep11166
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: Acknowledgements 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). Alice Kujur and Shouvik Das acknowledge the CSIR (Council of Scientific and Industrial Research) and the DBT for Junior/Senior Research Fellowship awards. Contributions A.K., D.B., S.D., R.R., M.S.S. and S.B. conducted all experiments and drafted the manuscript. AK, DB, TS and VK involved in data analysis. H.D.U., S.T., C.G., ShS and S.S. helped in constitution of association panel and performed phenotyping. SKP and AKT conceived and designed the study, guided data analysis and interpretation, participated in drafting and correcting the manuscript critically and gave the final approval of the version to be published. All authors have read and approved the final manuscript.
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