Sachdeva, S and Singh, R and Maurya, A and Singh, V K and Singh, U M and Kumar, A and Singh, G P (2024) Multi-model genome-wide association studies for appearance quality in rice. Frontiers in Plant Science (TSI), 14. 01-16. ISSN 1664-462X
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Abstract
Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.
| Item Type: | Article |
|---|---|
| Divisions: | Others |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | rice, grain quality, QTNs, candidate genes, GWAS |
| Subjects: | Others > Rice |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 23 Feb 2024 10:20 |
| Last Modified: | 23 Feb 2024 10:20 |
| URI: | http://oar.icrisat.org/id/eprint/12512 |
| Official URL: | https://www.frontiersin.org/journals/plant-science... |
| Projects: | UNSPECIFIED |
| Funders: | Government of India - Department of Biotechnology |
| Acknowledgement: | We would like to thank the International Rice Research Institute South Asia Regional Centre (IRRI-SARC), Varanasi, India for providing the rice accessions for this study, and Dr. A. K. Singh, Director, ICAR-Indian Agricultural Research Institute for providing the agricultural land for conducting the experiments. |
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