Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition
Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from puddled to dry direct seeded rice (DDSR) cultivation system looks must in future. Genome-wi...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2019
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| Online Access: | https://hdl.handle.net/10568/164671 |
| _version_ | 1855536694657286144 |
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| author | Subedi, Sushil Raj Sandhu, Nitika Singh, Vikas Kumar Sinha, Pallavi Kumar, Santosh Singh, S.P. Ghimire, Surya Kant Pandey, Madhav Yadaw, Ram Baran Varshney, Rajeev K. Kumar, Arvind |
| author_browse | Ghimire, Surya Kant Kumar, Arvind Kumar, Santosh Pandey, Madhav Sandhu, Nitika Singh, S.P. Singh, Vikas Kumar Sinha, Pallavi Subedi, Sushil Raj Varshney, Rajeev K. Yadaw, Ram Baran |
| author_facet | Subedi, Sushil Raj Sandhu, Nitika Singh, Vikas Kumar Sinha, Pallavi Kumar, Santosh Singh, S.P. Ghimire, Surya Kant Pandey, Madhav Yadaw, Ram Baran Varshney, Rajeev K. Kumar, Arvind |
| author_sort | Subedi, Sushil Raj |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from puddled to dry direct seeded rice (DDSR) cultivation system looks must in future. Genome-wide association study was performed for traits including, roots and nutrient uptake (14 traits), plant-morphological (5 traits), lodging-resistance (4 traits) and yield and yield attributing traits (7 traits) with the aim to identify significant marker-trait associations (MTAs) for traits enhancing rice adaptability to dry direct-seeded rice (DDSR) system Study identified a total of 37 highly significant MTAs for 20 traits. The false discovery rate (FDR) ranged from 0.264 to 3.69 × 10− 4, 0.0330 to 1.25 × 10− 4, and 0.0534 to 4.60 × 10− 6 in 2015WS, 2016DS and combined analysis, respectively. The percent phenotypic variance (PV) explained by SNPs ranged from 9 to 92%. Among the identified significant MTAs, 15 MTAs associated with the traits including nodal root, root hair length, root length density, stem and culm diameter, plant height and grain yield were reported to be located in the proximity of earlier identified candidate gene. The significant positive correlation of grain-yield with seedling establishment traits, root morphological and nutrient-uptake related traits and grain yield attributing traits pointing towards combining target traits to increase rice yield and adaptability under DDSR. Seven promising progenies with better root morphology, nutrient-uptake and higher grain yield were identified that can further be used in genomics assisted breeding for DDSR varietal development Once validated, the identified MTAs and the SNPs linked with trait of interest could be of direct use in genomic assisted breeding (GAB) to improve grain yield and adaptability of rice under DDSR. |
| format | Journal Article |
| id | CGSpace164671 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1646712025-05-14T10:39:55Z Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition Subedi, Sushil Raj Sandhu, Nitika Singh, Vikas Kumar Sinha, Pallavi Kumar, Santosh Singh, S.P. Ghimire, Surya Kant Pandey, Madhav Yadaw, Ram Baran Varshney, Rajeev K. Kumar, Arvind Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from puddled to dry direct seeded rice (DDSR) cultivation system looks must in future. Genome-wide association study was performed for traits including, roots and nutrient uptake (14 traits), plant-morphological (5 traits), lodging-resistance (4 traits) and yield and yield attributing traits (7 traits) with the aim to identify significant marker-trait associations (MTAs) for traits enhancing rice adaptability to dry direct-seeded rice (DDSR) system Study identified a total of 37 highly significant MTAs for 20 traits. The false discovery rate (FDR) ranged from 0.264 to 3.69 × 10− 4, 0.0330 to 1.25 × 10− 4, and 0.0534 to 4.60 × 10− 6 in 2015WS, 2016DS and combined analysis, respectively. The percent phenotypic variance (PV) explained by SNPs ranged from 9 to 92%. Among the identified significant MTAs, 15 MTAs associated with the traits including nodal root, root hair length, root length density, stem and culm diameter, plant height and grain yield were reported to be located in the proximity of earlier identified candidate gene. The significant positive correlation of grain-yield with seedling establishment traits, root morphological and nutrient-uptake related traits and grain yield attributing traits pointing towards combining target traits to increase rice yield and adaptability under DDSR. Seven promising progenies with better root morphology, nutrient-uptake and higher grain yield were identified that can further be used in genomics assisted breeding for DDSR varietal development Once validated, the identified MTAs and the SNPs linked with trait of interest could be of direct use in genomic assisted breeding (GAB) to improve grain yield and adaptability of rice under DDSR. 2019-12 2024-12-19T12:54:10Z 2024-12-19T12:54:10Z Journal Article https://hdl.handle.net/10568/164671 en Open Access Springer Subedi, Sushil Raj; Sandhu, Nitika; Singh, Vikas Kumar; Sinha, Pallavi; Kumar, Santosh; Singh, S. P.; Ghimire, Surya Kant; Pandey, Madhav; Yadaw, Ram Baran; Varshney, Rajeev K. and Kumar, Arvind. 2019. Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition. BMC Genomics, Volume 20, no. 1 |
| spellingShingle | Subedi, Sushil Raj Sandhu, Nitika Singh, Vikas Kumar Sinha, Pallavi Kumar, Santosh Singh, S.P. Ghimire, Surya Kant Pandey, Madhav Yadaw, Ram Baran Varshney, Rajeev K. Kumar, Arvind Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition |
| title | Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition |
| title_full | Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition |
| title_fullStr | Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition |
| title_full_unstemmed | Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition |
| title_short | Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition |
| title_sort | genome wide association study reveals significant genomic regions for improving yield adaptability of rice under dry direct seeded cultivation condition |
| url | https://hdl.handle.net/10568/164671 |
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