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Rice is a salt-sensitive plant. High concentration of salt will hinder the absorption of water and nutrients and ultimately affect the yield. In this study, eight seedling-stage salt-related traits within a core collection of rice landraces were evaluated under salinity stress (100 mM NaCl) and normal conditions in a growth chamber. Genome-wide association study (GWAS) was performed with the genotypic data including 2,487,353 single-nucleotide polymorphisms (SNPs) detected in the core collection. A total of 65 QTLs significantly associated with salt tolerance (ST) were identified by GWAS. Among them, a co-localization QTL  qTL4  associated with the SKC, RN/K, and SNC on chromosome 6, which explained 14.38–17.94% of phenotypic variation, was selected for further analysis. According to haplotype analysis, qRT-PCR analysis, and sequence alignment, it was finally determined that 4 candidate genes ( LOC_Os06g47720 ,  LOC_Os06g47820 ,  LOC_Os06g47850 ,  LOC_Os06g47970 ) were related to ST. The results provide useful candidate genes for marker assisted selection for ST in the rice molecular breeding programs.

Mining Beneficial Genes for Salt Tolerance From a Core Collection of Rice Landraces at the Seedling Stage Through Genome-Wide Association Mapping