QTL-seq Identifies Pokkali-Derived QTLs and Candidate Genes for Salt Tolerance at Seedling Stage in Rice ( Oryza sativa L.)

Rice is a staple food crop that plays a pivotal role in global food security, feeding more than half of the world’s population. Soil salinity is one of the most important global problems affecting rice productivity. Salt stress at the seedling stage inhibits root growth, impairs nutrient and water uptake, and affects overall plant vigor, resulting in poor establishment and reduced growth. Therefore, acquiring salt tolerance, especially at the seedling stage, is critical for successful rice production in salinity-affected areas. In this study, 160 RILs derived from a cross between Pokkali and KDML105 were evaluated for their salt tolerance at the seedling stage. QTL-seq analysis with this population identified nine QTLs associated with salt tolerance. Through a comprehensive examination of the effects of coding sequence variants of the 360 annotated genes within the QTLs and gene expression under salt stress, 47 candidate genes were prioritized. In particular, Os01g0200700 (metallothionein-like protein) and Os12g0625000 (O-acetylserine (thiol)lyase) were suggested as potential candidates based on annotated functions and expression data. The results provide valuable insights for improving rice productivity and resistance under salt stress conditions during the critical seedling stage.