AUTHOR=Liu Lifeng , Ma Yanling , Zhao Heng , Guo Lin , Guo Yan , Liu Chun-Ming 

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

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1384246

DOI=10.3389/fpls.2024.1384246

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p>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.</p></sec><sec><title>Methods</title><p>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.</p></sec><sec><title>Results and discussion</title><p>Three quantitative trait loci (QTLs) were identified including <italic>qGRG3-1</italic> on chromosome 3, <italic>qGRG3-2</italic> on chromosome 5, and <italic>qGRG4</italic> on chromosome 4. Assessment of candidate genes in these loci for their responses to salt stress identified a TATA modulatory factor (<italic>OsTMF</italic>) in <italic>qGRG3-2</italic>. The expression of <italic>OsTMF</italic> was up-regulated in both roots and shoots after exposure to salt stress, and <italic>OsTMF</italic> knockout mutants exhibited delayed seed germination under salt stress. Haplotype analysis showed that rice varieties carrying <italic>OsTMF-Hap2</italic> 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.</p></sec>