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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 <i>japonica</i>-multiparent advanced generation intercross (MAGIC) population. Four QTLs (<i>qDTS1-1</i>, <i>qDTS1-2</i>, <i>qDTS2</i>, and <i>qDTS9</i>) associated with salt tolerance were identified on chromosomes 1, 2, and 9. Among these QTLs, a novel QTL, <i>qDTS1-2</i>, 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, <i>Os01g0963600</i> (ASR transcription factor) and <i>Os01g0975300</i> (<i>OsMYB48</i>), related to salt and drought tolerance, were also involved in the target region of <i>qDTS1-2</i>. 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.