A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea
OAR@ICRISAT
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Relation |
http://oar.icrisat.org/8784/
http://dx.doi.org/10.1038/srep11166 10.1038/srep11166 |
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Title |
A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea
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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 |
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Subject |
Chickpea
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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.
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Publisher |
Nature
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Date |
2015
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Type |
Article
PeerReviewed |
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Format |
application/pdf
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Language |
en
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Rights |
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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 |
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