Table 1_QTL mapping and haplotype analysis reveal candidate genes for seedling-stage salinity tolerance in rice.xlsx

Therefore, elucidating the genetic architecture of salinity tolerance and identifying candidate genes underlying this trait are crucial for molecular design breeding. </p>Methods<p>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. </p>Results<p>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. </p>Discussion<p>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.</p>