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

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 (100mM NaCI) 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 ciTL4 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_Os06g4 7820, LOC_Os06g47850, LOC_Os06g4 7970) were related to ST. The results provide useful candidate genes for marker assisted selection for ST in the rice molecular breeding programs.

Automated summary

In this study, the salt-related traits of rice under salinity stress were evaluated, and a total of 65 QTLs significantly associated with salt tolerance were identified. Four candidate genes related to salt tolerance were determined through haplotype analysis, qRT-PCR analysis, and sequence alignment.