Genome-Wide Association Study Identifies Candidate Genes for Salt Tolerance in Traditional Rice Landraces

Salt stress is one of the major abiotic factors limiting rice yield, with the tillering stage-an essential growth phase that strongly influences rice productivity-being particularly sensitive to salinity. Thus, identifying salt-tolerant rice varieties is of great importance for ensuring stable rice production. In this study, we systematically evaluated the salt tolerance of 372 rice landraces at the tillering stage through dynamic phenotypic monitoring, using the average salt injury score (ASIS) as an indicator at two (T2W) and four weeks (T4W) after salt treatment. A genome-wide association study (GWAS) identified 39 loci significantly associated with salt tolerance. Among these, two high-confidence candidate genes, OsST8.1 and OsST8.2, both members of the BTB-MATH protein family, were implicated in salt tolerance during the tillering stage. Haplotype analysis revealed significant differences (p < 0.05) in salt tolerance among germplasm carrying different haplotypes, with accessions harboring the superior haplotype exhibiting enhanced tolerance. Consistently, qRT-PCR analysis showed significantly lower or higher expression levels (p < 0.05) of OsST8.1 or OsST8.2 in accessions with the superior haplotype following salt treatment, suggesting that they may regulate rice responses to salinity stress. Through the validation of a knockout transgenic experiment, OsST8.2 was identified as the causal gene for salt tolerance in rice at the tillering stage. Collectively, this study provides valuable genetic resources and a theoretical foundation for elucidating the genetic basis of salt tolerance and for breeding new salt-tolerant rice varieties.