Subedi, S R and Sandhu, N and Singh, V K and Sinha, P and Kumar, S and Singh, S P and Ghimire, S K and Pandey, M and Yadaw, R B and Varshney, R K and Kumar, A (2019) Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition. BMC Genomics (TSI), 20(1) (471). pp. 1-20. ISSN 1471-2164
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Abstract
Background 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. Results 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. Conclusions 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.
| Item Type: | Article |
|---|---|
| Divisions: | Research Program : Genetic Gains |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Dry direct seeded, Marker-trait association, Nutrient uptake, Rice, Root, Yield |
| Subjects: | Others > Rice Others > Genetics and Genomics |
| Depositing User: | Mr Ramesh K |
| Date Deposited: | 21 Aug 2019 05:12 |
| Last Modified: | 21 Aug 2019 05:12 |
| URI: | http://oar.icrisat.org/id/eprint/11256 |
| Official URL: | https://doi.org/10.1186/s12864-019-5840-9 |
| Projects: | TA8441-Development and dissemination of climate resilient rice varieties for water short areas of South Asia and Southeast Asia |
| Funders: | Asian Development Bank, Government of Finland |
| Acknowledgement: | We thank Ma. Teresa Sta. Cruz and Paul Maturan for the management of field experiments, Jocelyn Guevarra and RuthErica Carpio for assistance with seed preparations and data management respectively. Funding We thank Asian Development Bank and Government of Finland for the financial support to conduct the experiments and publish this study through the project “TA8441-Development and dissemination of climate resilient rice varieties for water short areas of South Asia and Southeast Asia.” |
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