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Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content in Chickpea

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Relation http://oar.icrisat.org/9401/
http://dx.doi.org/10.3389/fpls.2016.00302
10.3389/fpls.2016.00302
 
Title Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content in Chickpea
 
Creator Upadhyaya, H D
Bajaj, D
Narnoliya, L
Das, S
Kumar, V
Gowda, C L L
Sharma, S
Tyagi, A K
Parida, S K
 
Subject Chickpea
Genetics and Genomics
 
Description Identification of potential genes/alleles governing complex seed-protein content (SPC) is essential in marker-assisted breeding for quality trait improvement of chickpea. Henceforth, the present study utilized an integrated genomics-assisted breeding strategy encompassing trait association analysis, selective genotyping in traditional bi-parental mapping population and differential expression profiling for the first-time to understand the complex genetic architecture of quantitative SPC trait in chickpea. For GWAS (genome-wide association study), high-throughput genotyping information of 16376 genome-based SNPs (single nucleotide polymorphism) discovered from a structured population of 336 sequenced desi and kabuli accessions [with 150–200 kb LD (linkage disequilibrium) decay] was utilized. This led to identification of seven most effective genomic loci (genes) associated [10–20% with 41% combined PVE (phenotypic variation explained)] with SPC trait in chickpea. Regardless of the diverse desi and kabuli genetic backgrounds, a comparable level of association potential of the identified seven genomic loci with SPC trait was observed. Five SPC-associated genes were validated successfully in parental accessions and homozygous individuals of an intra-specific desi RIL (recombinant inbred line) mapping population (ICC 12299 × ICC 4958) by selective genotyping. The seed-specific expression, including differential up-regulation (>four fold) of six SPC-associated genes particularly in accessions, parents and homozygous individuals of the aforementioned mapping population with a high level of contrasting SPC (21–22%) was evident. Collectively, the integrated genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in six potential candidate genes regulating SPC trait in chickpea. Of these, a non-synonymous SNP allele-carrying zinc finger transcription factor gene exhibiting strong association with SPC trait was found to be the most promising in chickpea. The informative functionally relevant molecular tags scaled-down essentially have potential to accelerate marker-assisted genetic improvement by developing nutritionally rich chickpea cultivars with enhanced SPC.
 
Publisher Frontiers Media
 
Date 2016-03-23
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/9401/1/fpls-07-00302.pdf
Upadhyaya, H D and Bajaj, D and Narnoliya, L and Das, S and Kumar, V and Gowda, C L L and Sharma, S and Tyagi, A K and Parida, S K (2016) Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content in Chickpea. Frontiers in Plant Science, 07 (302). 01-13. ISSN 1664-462X