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.

Rice is a staple food for more than half of the world’s population. However, the pervasive problem of salinity is severely undermining rice production, especially in coastal and low-lying areas where soil salinization is widespread. This stress, exacerbated by climate change, necessitates the development of salt-tolerant rice varieties to ensure food security. In this study, an F_2:3 population (n = 454) from a cross of KDML105 and its chromosome segment substitution line (CSSL) was used to identify genomic regions associated with salt tolerance at the seedling stage. Using the QTL-seq approach, a QTL significantly associated with salt tolerance was identified on chromosome 1. Annotation of candidate genes in this region revealed the potential regulators of salt tolerance, including MIKC-type MADS domain proteins, calmodulin-binding transcription factors, and NB-ARC domain-containing proteins. These and other identified genes provide insights into the genetic basis of salt tolerance. This study underscores the importance of using advanced genomics tools and CSSL populations in the study of complex traits such as salt tolerance in rice. Several candidate genes identified in this study could be used in further studies on molecular or physiological mechanisms related to the salt response and tolerance mechanism in rice. Additionally, these genes could also be utilized in plant breeding programs for salt tolerance.