QTL mapping and haplotype analysis reveal candidate genes for seedling-stage salinity tolerance in rice

Abstract

Soil salinization is a major constraint on rice production, and severe salinity levels lead to pronounced yield losses. Therefore, elucidating the genetic architecture of salinity tolerance and identifying candidate genes underlying this trait are crucial for molecular design breeding. In this study, a population of 253 recombinant inbred lines (RILs) derived from the salt-sensitive japonica cultivar Jileng 1 (JL1) and the salt-tolerant indica cultivar Milyang 23 (MY23) was evaluated for seedling-stage salinity tolerance under 0.9% NaCl stress. Using multiple phenotypic indices and a high-density genetic map constructed from whole-genome resequencing data, we identified 43 QTLs associated with seedling-stage salinity tolerance, including 11 major-effect loci, each explaining more than 10% of the phenotypic variance. By integrating functional annotation, haplotype analysis, RNA-seq-based co-expression network analysis, and qRT-PCR validation, OsFBX29 ( LOC_Os01g59910 ) was prioritized as a strong candidate gene associated with seedling-stage salinity tolerance. Lines carrying the Hap2 haplotype exhibited enhanced salinity tolerance, and qRT-PCR analysis revealed significantly lower OsFBX29 expression levels ( p  < 0.05) in Hap2-carrying lines after salt treatment, suggesting a potential association between reduced OsFBX29 expression and enhanced salinity tolerance. These findings provide new insights into the genetic architecture of seedling-stage salinity tolerance and offer potential genetic resources for breeding salinity-tolerant rice varieties.