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A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat color in chickpea

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Title A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat color in chickpea
 
Creator Bajaj, Deepak
Das, Shouvik
Upadhyaya, Hari D.
Ranjan, Rajeev
Badoni, Saurabh
Kumar, Vinod
Tripathi, Shailesh
Gowda, C. L. Laxmipathi
Sharma, Shivali
Singh, Sube
Tyagi, Akhilesh K.
Parida, Swarup K.
 
Subject Chickpea
GBS
GWAS
haplotype
QTL
seed coat color
SNP
wild accession
 
Description Accepted date: 26 October 2015
The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.
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). SD and RR acknowledge the DBT
and CSIR (Council of Scientific and Industrial Research) for
Junior/Senior Research Fellowship awards.
 
Date 2016-01-01T05:41:29Z
2016-01-01T05:41:29Z
2015
 
Type Article
 
Identifier Front. Plant Sc., 6: 979
1664-462X
http://172.16.0.77:8080/jspui/handle/123456789/486
http://journal.frontiersin.org/article/10.3389/fpls.2015.00979/full
10.3389/fpls.2015.00979
 
Language en_US
 
Publisher Frontiers Media S.A.