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A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea

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Relation http://oar.icrisat.org/8784/
http://dx.doi.org/10.1038/srep11166
10.1038/srep11166
 
Title A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea
 
Creator Kujur, A
Bajaj, D
Upadhyaya, H D
Das, S
Ranjan, R
Shree, T
Saxena, M S
Badoni, S
Kumar, V
Tripathi, S
Gowda, C L L
Sharma, S
Singh, S
Tyagi, A K
Parida, S K
 
Subject Chickpea
 
Description 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.
 
Publisher Nature
 
Date 2015
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/8784/1/A%20genome-wide%20SNP%20scan%20accelerates%20trait-regulatory%20genomic%20loci%20identification%20in%20chickpea.pdf
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