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

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Title A genome-wide SNP scan accelerates trait-regulatory genomic loci identification 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 Natural variation in plants
Plant sciences
 
Description Accepted date: 18 May 2015
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 2016-01-07T06:40:19Z
2016-01-07T06:40:19Z
2015
 
Type Article
 
Identifier Scientific Reports, 5: 11166
2045-2322
http://172.16.0.77:8080/jspui/handle/123456789/530
http://www.nature.com/articles/srep11166
10.1038/srep11166
 
Language en_US
 
Publisher Nature Publishing Group