Analysis of quantitative trait loci and candidate gene exploration associated with cold tolerance in rice ( L.) during the seedling stage.

Cold stress during the seedling stage significantly threatens rice ( L.) production, specifically in temperate climates. This study aimed to identify quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage. QTL analysis was conducted on a doubled haploid (DH) population derived from a cross between the cold-sensitive cultivar 93-11 and the cold-tolerant cultivar Milyang352. Phenotypic analysis was conducted over 2 years (2022-2023) under cold water treatment (13°C) at the Chuncheon Substation, South Korea. Cold tolerance scores were used to classify the DH populations and parental lines. In 2022, three QTLs were identified on chromosomes 3, 10, and 11; in 2023, a single QTL was identified on chromosome 10. The QTL on chromosome 10 was consistently observed across both years, explaining up to 16.06% and 40.55% of the phenotypic variance, respectively. Fine-mapping of narrowed the candidate region to a 300-kb interval containing 44 polymorphic single-nucleotide polymorphisms. Among the candidate genes, was significantly expressed in the cold-tolerant parent Milyang352 under cold stress, indicating its role in conferring cold tolerance. These findings offer valuable insights into the genetic mechanisms of cold tolerance and highlight as a potential target for marker-assisted selection in rice breeding programs to enhance cold tolerance.