A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea

cg.contactswarup@nipgr.ac.inen_US
cg.contributor.centerInternational Crops Research Institute for the Semi-Arid Tropics - ICRISATen_US
cg.contributor.centerIndian Council of Agricultural Research, Indian Agricultural Research Institute - ICAR-IARIen_US
cg.contributor.centerNational Institute of Plant Genome Research - NIPGRen_US
cg.contributor.centerIndian Council of Agricultural Research, National Research Centre on Plant Biotechnology - ICAR- NRCPBen_US
cg.contributor.crpCGIAR Research Program on Grain Legumes - GLen_US
cg.contributor.funderCGIAR System Organization - CGIARen_US
cg.contributor.project-lead-instituteInternational Center for Agricultural Research in the Dry Areas - ICARDAen_US
cg.identifier.doihttps://dx.doi.org/10.3389/fpls.2015.00979en_US
cg.isijournalISI Journalen_US
cg.issn1664-462Xen_US
cg.issue979en_US
cg.journalFrontiers in Plant Scienceen_US
cg.subject.agrovocplant genetic resourcesen_US
cg.subject.agrovocseeden_US
cg.subject.agrovocgbsen_US
cg.subject.agrovocsnpen_US
cg.subject.agrovocgwasen_US
cg.subject.agrovocChickpeaen_US
cg.volume6en_US
dc.contributorDas, Shouviken_US
dc.contributorUpadhyaya, Hari D.en_US
dc.contributorRanjan, Rajeeven_US
dc.contributorBadoni, Saurabhen_US
dc.contributorkumar, vinoden_US
dc.contributorTripathi, Shaileshen_US
dc.contributorGowda, C. L. L.en_US
dc.contributorSharma, Shivalien_US
dc.contributorSingh, Subeen_US
dc.contributorTyagi, Akhilesh K.en_US
dc.contributorParida, Swarup K.en_US
dc.creatorBajaj, Prasaden_US
dc.date.accessioned2017-05-14T23:33:45Z
dc.date.available2017-05-14T23:33:45Z
dc.description.abstractThe 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 chickpeaen_US
dc.formatPDFen_US
dc.identifierhttp://oar.icrisat.org/id/eprint/9696en_US
dc.identifierhttps://www.frontiersin.org/articles/10.3389/fpls.2015.00979/fullen_US
dc.identifierhttps://mel.cgiar.org/reporting/downloadmelspace/hash/Ze0fZLrD/v/940973c364d1fa9b73148ba1220a0c61en_US
dc.identifier.citationPrasad Bajaj, Shouvik Das, Hari D. Upadhyaya, Rajeev Ranjan, Saurabh Badoni, vinod kumar, Shailesh Tripathi, C. L. L. Gowda, Shivali Sharma, Sube Singh, Akhilesh K. Tyagi, Swarup K. Parida. (28/12/2015). A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea. Frontiers in Plant Science, 6 (979), pp. 01-18.en_US
dc.identifier.statusOpen accessen_US
dc.identifier.urihttps://hdl.handle.net/20.500.11766/6983
dc.languageenen_US
dc.publisherFrontiers Mediaen_US
dc.rightsCC-BY-4.0en_US
dc.sourceFrontiers in Plant Science;6,(2015) Pagination 01-18en_US
dc.subjecthaplotypeen_US
dc.subjectseed coat coloren_US
dc.subjectwild accessionen_US
dc.subjectqtlen_US
dc.titleA Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpeaen_US
dc.typeJournal Articleen_US
dcterms.available2015-12-28en_US
dcterms.extent01-18en_US
mel.impact-factor3.678en_US

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