A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat colour in chickpea
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...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-11-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00979/full |
| _version_ | 1828420281550503936 |
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| author | Deepak eBajaj Shouvik eDas Hari Deo eUpadhyaya Rajeev eRanjan Rajeev eRanjan SAURABH eBADONI Vinod eKumar Shailesh eTripathi CL Laxmipathi Gowda Shivali eSharma Sube eSingh Akhilesh eTyagi SWARUP KUMAR PARIDA |
| author_facet | Deepak eBajaj Shouvik eDas Hari Deo eUpadhyaya Rajeev eRanjan Rajeev eRanjan SAURABH eBADONI Vinod eKumar Shailesh eTripathi CL Laxmipathi Gowda Shivali eSharma Sube eSingh Akhilesh eTyagi SWARUP KUMAR PARIDA |
| author_sort | Deepak eBajaj |
| collection | DOAJ |
| description | 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 colour. Five seed colour-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 colour differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat colour-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed coloured desi and kabuli accessions for their coloration/pigmentation. This seed colour-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed coloured desi and wild Cicer reticulatum accessions compared with the BE seed coloured 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 colour 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 colour types in chickpea. |
| first_indexed | 2024-12-10T15:09:30Z |
| format | Article |
| id | doaj.art-d44496d5573549e2ba756e8dbe06da64 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-10T15:09:30Z |
| publishDate | 2015-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-d44496d5573549e2ba756e8dbe06da642022-12-22T01:43:58ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2015-11-01610.3389/fpls.2015.00979139458A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat colour in chickpeaDeepak eBajaj0Shouvik eDas1Hari Deo eUpadhyaya2Rajeev eRanjan3Rajeev eRanjan4SAURABH eBADONI5Vinod eKumar6Shailesh eTripathi7CL Laxmipathi Gowda8Shivali eSharma9Sube eSingh10Akhilesh eTyagi11SWARUP KUMAR PARIDA12National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, P.O. Box: 10531, New Delhi - 110067National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, P.O. Box: 10531, New Delhi - 110067ICRISATNational Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, P.O. Box: 10531, New Delhi - 110067ICRISATNational Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, P.O. Box: 10531, New Delhi - 110067NRCPBIARIICRISATICRISATICRISATNational Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, P.O. Box: 10531, New Delhi - 110067National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, P.O. Box: 10531, New Delhi - 110067The 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 colour. Five seed colour-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 colour differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat colour-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed coloured desi and kabuli accessions for their coloration/pigmentation. This seed colour-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed coloured desi and wild Cicer reticulatum accessions compared with the BE seed coloured 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 colour 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 colour types in chickpea.http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00979/fullGWASSNPQTLGBShaplotypechickpea |
| spellingShingle | Deepak eBajaj Shouvik eDas Hari Deo eUpadhyaya Rajeev eRanjan Rajeev eRanjan SAURABH eBADONI Vinod eKumar Shailesh eTripathi CL Laxmipathi Gowda Shivali eSharma Sube eSingh Akhilesh eTyagi SWARUP KUMAR PARIDA A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat colour in chickpea Frontiers in Plant Science GWAS SNP QTL GBS haplotype chickpea |
| title | A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat colour in chickpea |
| title_full | A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat colour in chickpea |
| title_fullStr | A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat colour in chickpea |
| title_full_unstemmed | A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat colour in chickpea |
| title_short | A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat colour in chickpea |
| title_sort | genome wide combinatorial strategy dissects complex genetic architecture of seed coat colour in chickpea |
| topic | GWAS SNP QTL GBS haplotype chickpea |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00979/full |
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