Identification of Candidate Genes for Cold Tolerance at Seedling Stage by GWAS in Rice (Oryza sativa L.)

Due to global climate change, cold temperatures have significantly impacted rice production, resulting in reduced yield and quality. In this study, we investigated two traits related to the cold tolerance (CT) of 1992 diverse rice accessions at the seedling stage. <i>Geng</i> accessions exhibited higher levels of CT compared to <i>xian</i> accessions, with the GJ-tmp subgroup displaying the strongest CT. However, extreme CT accessions were also identified within the <i>xian</i> subspecies. Through GWAS analysis based on the survival rate (SR) and leaf score of cold tolerance (SCT), a total of 29 QTLs associated with CT at the seedling stage were identified, among which four QTLs (<i>qSR3.1a</i>, <i>qSR4.1a</i>, <i>qSR11.1x</i>, and <i>qSR12.1a</i>) were found to be important. Furthermore, five candidate genes (<i>LOC_Os03g44760</i>, <i>LOC_Os04g06900</i>, <i>LOC_Os04g07260</i>, <i>LOC_Os11g40610</i>, and <i>LOC_Os12g10710</i>) along with their favorable haplotypes were identified through gene function annotation and haplotype analysis. Pyramiding multiple favorable haplotypes resulted in a significant improvement in CT performance. Subsequently, three selected accessions (CX534, B236, and IRIS_313-8565), carrying different superior alleles for CT, were selected and recommended for molecular breeding for CT using marker-assisted selection (MAS). The findings from this study provide valuable resources for enhancing rice's ability for CT while laying a foundation for the future cloning of novel genes involved in conferring CT.