A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea
cg.contact | swarup@nipgr.ac.in | en_US |
cg.contributor.center | International Crops Research Institute for the Semi-Arid Tropics - ICRISAT | en_US |
cg.contributor.center | Indian Council of Agricultural Research, Indian Agricultural Research Institute - ICAR-IARI | en_US |
cg.contributor.center | National Institute of Plant Genome Research - NIPGR | en_US |
cg.contributor.center | Indian Council of Agricultural Research, National Research Centre on Plant Biotechnology - ICAR- NRCPB | en_US |
cg.contributor.crp | CGIAR Research Program on Grain Legumes - GL | en_US |
cg.contributor.funder | CGIAR System Organization - CGIAR | en_US |
cg.contributor.project-lead-institute | International Center for Agricultural Research in the Dry Areas - ICARDA | en_US |
cg.identifier.doi | https://dx.doi.org/10.3389/fpls.2015.00979 | en_US |
cg.isijournal | ISI Journal | en_US |
cg.issn | 1664-462X | en_US |
cg.issue | 979 | en_US |
cg.journal | Frontiers in Plant Science | en_US |
cg.subject.agrovoc | plant genetic resources | en_US |
cg.subject.agrovoc | seed | en_US |
cg.subject.agrovoc | gbs | en_US |
cg.subject.agrovoc | snp | en_US |
cg.subject.agrovoc | gwas | en_US |
cg.subject.agrovoc | Chickpea | en_US |
cg.volume | 6 | en_US |
dc.contributor | Das, Shouvik | en_US |
dc.contributor | Upadhyaya, Hari D. | en_US |
dc.contributor | Ranjan, Rajeev | en_US |
dc.contributor | Badoni, Saurabh | en_US |
dc.contributor | kumar, vinod | en_US |
dc.contributor | Tripathi, Shailesh | en_US |
dc.contributor | Gowda, C. L. L. | en_US |
dc.contributor | Sharma, Shivali | en_US |
dc.contributor | Singh, Sube | en_US |
dc.contributor | Tyagi, Akhilesh K. | en_US |
dc.contributor | Parida, Swarup K. | en_US |
dc.creator | Bajaj, Prasad | en_US |
dc.date.accessioned | 2017-05-14T23:33:45Z | |
dc.date.available | 2017-05-14T23:33:45Z | |
dc.description.abstract | 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 | en_US |
dc.format | en_US | |
dc.identifier | http://oar.icrisat.org/id/eprint/9696 | en_US |
dc.identifier | https://www.frontiersin.org/articles/10.3389/fpls.2015.00979/full | en_US |
dc.identifier | https://mel.cgiar.org/reporting/downloadmelspace/hash/Ze0fZLrD/v/940973c364d1fa9b73148ba1220a0c61 | en_US |
dc.identifier.citation | Prasad 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.status | Open access | en_US |
dc.identifier.uri | https://hdl.handle.net/20.500.11766/6983 | |
dc.language | en | en_US |
dc.publisher | Frontiers Media | en_US |
dc.rights | CC-BY-4.0 | en_US |
dc.source | Frontiers in Plant Science;6,(2015) Pagination 01-18 | en_US |
dc.subject | haplotype | en_US |
dc.subject | seed coat color | en_US |
dc.subject | wild accession | en_US |
dc.subject | qtl | en_US |
dc.title | A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea | en_US |
dc.type | Journal Article | en_US |
dcterms.available | 2015-12-28 | en_US |
dcterms.extent | 01-18 | en_US |
mel.impact-factor | 3.678 | en_US |