Genome-wide association studies identified OsTMF as a gene regulating rice seed germination under salt stress

Lifeng Liu; Yanling Ma; Heng Zhao; Lin Guo; Yan Guo; Chun-Ming Liu

doi:10.3389/fpls.2024.1384246

Genome-wide association studies identified OsTMF as a gene regulating rice seed germination under salt stress

Front Plant Sci. 2024 Mar 27:15:1384246. doi: 10.3389/fpls.2024.1384246. eCollection 2024.

Authors

Lifeng Liu^{1

2}, Yanling Ma¹, Heng Zhao¹, Lin Guo¹, Yan Guo², Chun-Ming Liu^{1

3

4

5}

Affiliations

¹ Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
² State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China.
³ Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
⁴ College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
⁵ School of Advanced Agricultural Sciences, Peking University, Beijing, China.

Abstract

Introduction: Salt tolerance during seed germination is an important trait for direct seeding and low-cost rice production. Nevertheless, it is still not clear how seed germination under salt stress is regulated genetically.

Methods: In this study, genome-wide association studies (GWAS) were performed to decipher the genetic basis of seed germination under salt stress using 541 rice varieties collected worldwide.

Results and discussion: Three quantitative trait loci (QTLs) were identified including qGRG3-1 on chromosome 3, qGRG3-2 on chromosome 5, and qGRG4 on chromosome 4. Assessment of candidate genes in these loci for their responses to salt stress identified a TATA modulatory factor (OsTMF) in qGRG3-2. The expression of OsTMF was up-regulated in both roots and shoots after exposure to salt stress, and OsTMF knockout mutants exhibited delayed seed germination under salt stress. Haplotype analysis showed that rice varieties carrying OsTMF-Hap2 displayed elevated salt tolerance during seed germination. These results provide important knowledge and resources to improve rice seed germination under salt stress in the future.

Keywords: GWAS; OsTMF; rice; salt stress; seed germination.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was supported by grants from the National Key R&D Program of China (2020YFE0202300).