eprintid: 8784
rev_number: 12
eprint_status: archive
userid: 1305
dir: disk0/00/00/87/84
datestamp: 2015-06-17 09:44:27
lastmod: 2016-10-21 06:38:40
status_changed: 2015-06-17 09:44:27
type: article
metadata_visibility: show
contact_email: Library-ICRISAT@CGIAR.ORG
creators_name: Kujur, A
creators_name: Bajaj, D
creators_name: Upadhyaya, H D
creators_name: Das, S
creators_name: Ranjan, R
creators_name: Shree, T
creators_name: Saxena, M S
creators_name: Badoni, S
creators_name: Kumar, V
creators_name: Tripathi, S
creators_name: Gowda, C L L
creators_name: Sharma, S
creators_name: Singh, S
creators_name: Tyagi, A K
creators_name: Parida, S K
icrisatcreators_name: Upadhyaya, H D
icrisatcreators_name: Upadhyaya, C L L
icrisatcreators_name: Sharma, S
icrisatcreators_name: Singh, S
affiliation: National Institute of Plant Genome Research (NIPGR) (New Delhi)
affiliation: ICRISAT (Patancheru)
affiliation: National Research Centre on Plant Biotechnology (NRCPB) (New Delhi)
affiliation: Division of Genetics, Indian Agricultural Research Institute (IARI) (New Delhi)
country: India
title: A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea
ispublished: pub
subjects: s1.1
divisions: D3
crps: crp1.5
full_text_status: public
keywords: Chickpea; Natural variation in plants; Genetics
note: 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.
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.
date: 2015
date_type: published
publication: Nature Scientific Reports
volume: 5
number: 11166
publisher: Nature
pagerange: 1-20
id_number: 10.1038/srep11166
refereed: TRUE
issn: 2045-2322
official_url: http://dx.doi.org/10.1038/srep11166
related_url_url: https://scholar.google.co.in/scholar?q=allintitle%3AA+genome-wide+SNP+scan+accelerates+trait-regulatory+genomic+loci+identification+in+chickpea&btnG=&hl=en&as_sdt=0%2C5
related_url_type: pub
citation:   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     
document_url: http://oar.icrisat.org/8784/1/A%20genome-wide%20SNP%20scan%20accelerates%20trait-regulatory%20genomic%20loci%20identification%20in%20chickpea.pdf