Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice.

Salt stress is a major constraint in rice production worldwide. Salt stress is estimated to cause annual losses of 30-50% in rice production. Discovering and deploying salt-resistance genes are the most effective ways to control salt stress. We performed a genome-wide association study (GWAS) to detect QTLs related to salt tolerance at the seedling stage using the -multiparent advanced generation intercross (MAGIC) population. Four QTLs (, , , and ) associated with salt tolerance were identified on chromosomes 1, 2, and 9. Among these QTLs, a novel QTL, , was located between flanking SNPs (1354576 and id1028360) on chromosome 1, with the largest -log10(P) value of 5.81 and a total phenotypic variance of 15.2%. RNA-seq analysis revealed that among the seven differentially expressed genes (DEGs) commonly identified in both P6 and JM298 showing salt tolerance, two upregulated genes, (ASR transcription factor) and (), related to salt and drought tolerance, were also involved in the target region of . The results of this study can provide insights into further understanding of salt tolerance mechanisms and developing DNA markers for marker-assisted selection (MAS) breeding to improve the salt tolerance of cultivars in rice breeding programs.