Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.)
Rice pericarp colour is one of the nutritional traits that is now gaining attention worldwide. In the present investigation, genome-wide association GWAS) was performed to identify loci governing pericarp colour in rice. A set of 1,349,269 SNPs and precise phenotyping across 325 diverse accessions o...
| Autores principales: | , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Indian Society of Genetics and Plant Breeding
2022
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/126477 |
| _version_ | 1855520299394531328 |
|---|---|
| author | Sonah, Humira Rana, Nitika Kumawat, Surbhi Singh, Uma Maheshwar Singh, Vikas Kumar Deshmukh, Rupesh Sharma, Tilak Raj |
| author_browse | Deshmukh, Rupesh Kumawat, Surbhi Rana, Nitika Sharma, Tilak Raj Singh, Uma Maheshwar Singh, Vikas Kumar Sonah, Humira |
| author_facet | Sonah, Humira Rana, Nitika Kumawat, Surbhi Singh, Uma Maheshwar Singh, Vikas Kumar Deshmukh, Rupesh Sharma, Tilak Raj |
| author_sort | Sonah, Humira |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Rice pericarp colour is one of the nutritional traits that is now gaining attention worldwide. In the present investigation, genome-wide association GWAS) was performed to identify loci governing pericarp colour in rice. A set of 1,349,269 SNPs and precise phenotyping across 325 diverse accessions of rice were used for the GWAS. The accessions belong to five rice isozyme classification groups viz., indica, japonica, aromatic, aus, and admix. The GWAS identified two significant loci gPC5-1and gPC7-1 on chromosomes, 5 and 7, respectively, associated with the pericarp colour in rice. The SNPs on chromosome 7 co-localized with the functionally characterized Os07g0211500 (Rc gene) known to control pericarp colour and Os07g0214900 which is similar to the Chalcone synthase 2(OsCHS2) gene involved in flavonoid synthesis pathway. Linkage disequilibrium analysis across 0.25 Mbp upstream and downstream of these markers suggested three strong linkage blocks on chromosome 7. More interestingly, the novel locus identified on chromosome 5 gPC5-1 does not harbor any homolog of previously reported genes. Therefore, the locus can serve as a basis for identifying a new gene for rice pericarp colour. The results presented here will be helpful to understand the genetic regulation of pericarp colour and for genomic-assisted breeding in rice. |
| format | Journal Article |
| id | CGSpace126477 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Indian Society of Genetics and Plant Breeding |
| publisherStr | Indian Society of Genetics and Plant Breeding |
| record_format | dspace |
| spelling | CGSpace1264772025-11-12T04:56:23Z Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.) Sonah, Humira Rana, Nitika Kumawat, Surbhi Singh, Uma Maheshwar Singh, Vikas Kumar Deshmukh, Rupesh Sharma, Tilak Raj rice genomes diversification pericarp Rice pericarp colour is one of the nutritional traits that is now gaining attention worldwide. In the present investigation, genome-wide association GWAS) was performed to identify loci governing pericarp colour in rice. A set of 1,349,269 SNPs and precise phenotyping across 325 diverse accessions of rice were used for the GWAS. The accessions belong to five rice isozyme classification groups viz., indica, japonica, aromatic, aus, and admix. The GWAS identified two significant loci gPC5-1and gPC7-1 on chromosomes, 5 and 7, respectively, associated with the pericarp colour in rice. The SNPs on chromosome 7 co-localized with the functionally characterized Os07g0211500 (Rc gene) known to control pericarp colour and Os07g0214900 which is similar to the Chalcone synthase 2(OsCHS2) gene involved in flavonoid synthesis pathway. Linkage disequilibrium analysis across 0.25 Mbp upstream and downstream of these markers suggested three strong linkage blocks on chromosome 7. More interestingly, the novel locus identified on chromosome 5 gPC5-1 does not harbor any homolog of previously reported genes. Therefore, the locus can serve as a basis for identifying a new gene for rice pericarp colour. The results presented here will be helpful to understand the genetic regulation of pericarp colour and for genomic-assisted breeding in rice. 2022-02 2023-01-03T11:59:10Z 2023-01-03T11:59:10Z Journal Article https://hdl.handle.net/10568/126477 en Open Access application/pdf Indian Society of Genetics and Plant Breeding Sonah, Humira, Nitika Rana, Surbhi Kumawat, Uma Singh, Vikas Singh, Rupesh Deshmukh, and Tilak Sharma. "Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.)." INDIAN JOURNAL OF GENETICS AND PLANT BREEDING 82, no. 01 (2022): 01-06. |
| spellingShingle | rice genomes diversification pericarp Sonah, Humira Rana, Nitika Kumawat, Surbhi Singh, Uma Maheshwar Singh, Vikas Kumar Deshmukh, Rupesh Sharma, Tilak Raj Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.) |
| title | Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.) |
| title_full | Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.) |
| title_fullStr | Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.) |
| title_full_unstemmed | Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.) |
| title_short | Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.) |
| title_sort | identification of genomic loci governing pericarp colour through gwas in rice oryza sativa l |
| topic | rice genomes diversification pericarp |
| url | https://hdl.handle.net/10568/126477 |
| work_keys_str_mv | AT sonahhumira identificationofgenomiclocigoverningpericarpcolourthroughgwasinriceoryzasatival AT rananitika identificationofgenomiclocigoverningpericarpcolourthroughgwasinriceoryzasatival AT kumawatsurbhi identificationofgenomiclocigoverningpericarpcolourthroughgwasinriceoryzasatival AT singhumamaheshwar identificationofgenomiclocigoverningpericarpcolourthroughgwasinriceoryzasatival AT singhvikaskumar identificationofgenomiclocigoverningpericarpcolourthroughgwasinriceoryzasatival AT deshmukhrupesh identificationofgenomiclocigoverningpericarpcolourthroughgwasinriceoryzasatival AT sharmatilakraj identificationofgenomiclocigoverningpericarpcolourthroughgwasinriceoryzasatival |