Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains
Though several genes governing various major traits have been reported in rice, their superior haplotype combinations for developing ideal variety remains elusive. In this study, haplotype analysis of 120 previously functionally characterized genes, influencing grain yield (87 genes) and grain quali...
| Main Authors: | , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Wiley
2019
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| Online Access: | https://hdl.handle.net/10568/164733 |
| _version_ | 1855519147481366528 |
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| author | Abbai, Ragavendran Singh, Vikas Kumar Nachimuthu, Vishnu Varthini Sinha, Pallavi Selvaraj, Ramchander Vipparla, Abhilash Kumar Singh, Arun Kumar Singh, Uma Maheshwar Varshney, Rajeev K. Kumar, Arvind |
| author_browse | Abbai, Ragavendran Kumar, Arvind Nachimuthu, Vishnu Varthini Selvaraj, Ramchander Singh, Arun Kumar Singh, Uma Maheshwar Singh, Vikas Kumar Sinha, Pallavi Varshney, Rajeev K. Vipparla, Abhilash Kumar |
| author_facet | Abbai, Ragavendran Singh, Vikas Kumar Nachimuthu, Vishnu Varthini Sinha, Pallavi Selvaraj, Ramchander Vipparla, Abhilash Kumar Singh, Arun Kumar Singh, Uma Maheshwar Varshney, Rajeev K. Kumar, Arvind |
| author_sort | Abbai, Ragavendran |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Though several genes governing various major traits have been reported in rice, their superior haplotype combinations for developing ideal variety remains elusive. In this study, haplotype analysis of 120 previously functionally characterized genes, influencing grain yield (87 genes) and grain quality (33 genes) revealed significant variations in the 3K rice genome (RG) panel. For selected genes, meta‐expression analysis using already available datasets along with co‐expression network provided insights at systems level. Also, we conducted candidate gene based association study for the 120 genes and identified 21 strongly associated genes governing 10‐grain yield and quality traits. We report superior haplotypes upon phenotyping the subset of 3K RG panel, SD1‐H8 with haplotype frequency (HF) of 30.13% in 3K RG panel, MOC1‐H9 (HF: 23.08%), IPA1‐H14 (HF: 6.64%), DEP3‐H2 (HF: 5.59%), DEP1‐H2 (HF: 37.53%), SP1‐H3 (HF: 5.05%), LAX1‐H5 (HF: 1.56%), LP‐H13 (3.64%), OSH1‐H4 (5.52%), PHD1‐H14 (HF: 15.21%), AGO7‐H15 (HF: 3.33%), ROC5‐H2 (31.42%), RSR1‐H8 (HF: 4.20%) and OsNAS3‐H2 (HF: 1.00%). For heading date, Ghd7‐H8 (HF: 3.08%), TOB1‐H10 (HF: 4.60%) flowered early, Ghd7‐H14 (HF: 42.60%), TRX1‐H9 (HF: 27.97%), OsVIL3‐H14 (HF: 1.72%) for medium duration flowering, while Ghd7‐H6 (HF: 1.65%), SNB‐H9 (HF: 9.35%) were late flowering. GS5‐H4 (HF: 65.84%) attributed slender, GS5‐H5 (HF: 29.00%), GW2‐H2 (HF: 4.13%) were medium slender and GS5‐H9 (HF: 2.15%) for bold grains. Furthermore, haplotype analysis explained possible genetic basis for superiority of selected mega‐varieties. Overall, this study suggests the possibility for developing next‐generation tailor‐made rice with superior haplotype combinations of target genes suiting future food and nutritional demands via haplotype‐based breeding. |
| format | Journal Article |
| id | CGSpace164733 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1647332025-01-27T15:00:52Z Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains Abbai, Ragavendran Singh, Vikas Kumar Nachimuthu, Vishnu Varthini Sinha, Pallavi Selvaraj, Ramchander Vipparla, Abhilash Kumar Singh, Arun Kumar Singh, Uma Maheshwar Varshney, Rajeev K. Kumar, Arvind Though several genes governing various major traits have been reported in rice, their superior haplotype combinations for developing ideal variety remains elusive. In this study, haplotype analysis of 120 previously functionally characterized genes, influencing grain yield (87 genes) and grain quality (33 genes) revealed significant variations in the 3K rice genome (RG) panel. For selected genes, meta‐expression analysis using already available datasets along with co‐expression network provided insights at systems level. Also, we conducted candidate gene based association study for the 120 genes and identified 21 strongly associated genes governing 10‐grain yield and quality traits. We report superior haplotypes upon phenotyping the subset of 3K RG panel, SD1‐H8 with haplotype frequency (HF) of 30.13% in 3K RG panel, MOC1‐H9 (HF: 23.08%), IPA1‐H14 (HF: 6.64%), DEP3‐H2 (HF: 5.59%), DEP1‐H2 (HF: 37.53%), SP1‐H3 (HF: 5.05%), LAX1‐H5 (HF: 1.56%), LP‐H13 (3.64%), OSH1‐H4 (5.52%), PHD1‐H14 (HF: 15.21%), AGO7‐H15 (HF: 3.33%), ROC5‐H2 (31.42%), RSR1‐H8 (HF: 4.20%) and OsNAS3‐H2 (HF: 1.00%). For heading date, Ghd7‐H8 (HF: 3.08%), TOB1‐H10 (HF: 4.60%) flowered early, Ghd7‐H14 (HF: 42.60%), TRX1‐H9 (HF: 27.97%), OsVIL3‐H14 (HF: 1.72%) for medium duration flowering, while Ghd7‐H6 (HF: 1.65%), SNB‐H9 (HF: 9.35%) were late flowering. GS5‐H4 (HF: 65.84%) attributed slender, GS5‐H5 (HF: 29.00%), GW2‐H2 (HF: 4.13%) were medium slender and GS5‐H9 (HF: 2.15%) for bold grains. Furthermore, haplotype analysis explained possible genetic basis for superiority of selected mega‐varieties. Overall, this study suggests the possibility for developing next‐generation tailor‐made rice with superior haplotype combinations of target genes suiting future food and nutritional demands via haplotype‐based breeding. 2019-08 2024-12-19T12:54:14Z 2024-12-19T12:54:14Z Journal Article https://hdl.handle.net/10568/164733 en Open Access Wiley Abbai, Ragavendran; Singh, Vikas Kumar; Nachimuthu, Vishnu Varthini; Sinha, Pallavi; Selvaraj, Ramchander; Vipparla, Abhilash Kumar; Singh, Arun Kumar; Singh, Uma Maheshwar; Varshney, Rajeev K. and Kumar, Arvind. 2019. Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains. Plant Biotechnology Journal, Volume 17 no. 8 p. 1612-1622 |
| spellingShingle | Abbai, Ragavendran Singh, Vikas Kumar Nachimuthu, Vishnu Varthini Sinha, Pallavi Selvaraj, Ramchander Vipparla, Abhilash Kumar Singh, Arun Kumar Singh, Uma Maheshwar Varshney, Rajeev K. Kumar, Arvind Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains |
| title | Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains |
| title_full | Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains |
| title_fullStr | Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains |
| title_full_unstemmed | Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains |
| title_short | Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains |
| title_sort | haplotype analysis of key genes governing grain yield and quality traits across 3k rg panel reveals scope for the development of tailor made rice with enhanced genetic gains |
| url | https://hdl.handle.net/10568/164733 |
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