Multi-model genome-wide association studies for appearance quality in rice

Supriya Sachdeva; Rakesh Singh; Avantika Maurya; Vikas Kumar Singh; Uma Maheshwar Singh; Arvind Kumar; Gyanendra Pratap Singh

doi:10.3389/fpls.2023.1304388

Multi-model genome-wide association studies for appearance quality in rice

Front Plant Sci. 2024 Jan 11:14:1304388. doi: 10.3389/fpls.2023.1304388. eCollection 2023.

Authors

Supriya Sachdeva¹, Rakesh Singh¹, Avantika Maurya¹, Vikas Kumar Singh², Uma Maheshwar Singh³, Arvind Kumar⁴, Gyanendra Pratap Singh⁵

Affiliations

¹ Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India.
² International Rice Research Institute, South Asia Hub, International Crop Reseach Institute for Semi Arid Tropics (ICRISAT), Hyderabad, India.
³ International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India.
⁴ International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India.
⁵ Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India.

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.

Keywords: GWAS; QTNs; candidate genes; grain quality; rice.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by Department of Biotechnology Government of India, grant number “BT/PR32853/AGIII/103/1059/2019”. The funder has no role in the design of the study and data collection, analysis, interpretation and in writing the manuscript.