Journal article
Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition
BMC Genomics, Vol.20(1), Art. 471
2019
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.
Details
- Title
- Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition
- Authors/Creators
- S.R. Subedi (Author/Creator) - International Rice Research InstituteN. Sandhu (Author/Creator) - Punjab Agricultural UniversityV.K. Singh (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsP. Sinha (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsS. Kumar (Author/Creator) - ICAR Research Complex for NEH RegionS.P. Singh (Author/Creator) - Bihar Agricultural UniversityS.K. Ghimire (Author/Creator) - Agriculture and Forestry UniversityM.K. Pandey (Author/Creator)R.B. Yadaw (Author/Creator) - National Rice Research Program, Hardinath, Nepal.R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsA. Kumar (Author/Creator) - International Rice Research Institute
- Publication Details
- BMC Genomics, Vol.20(1), Art. 471
- Publisher
- BioMed Central Ltd as part of Springer Nature
- Identifiers
- 991005541440607891
- Copyright
- © 2019 The Authors.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics