Fine mapping of the qSCT12 locus conferring seedling cold tolerance in Oryza nivara

Cold stress severely limits rice growth and yield, making it crucial to identify cold-tolerant QTLs and genes for effective molecular breeding. In this study, we detected four QTLs for seedling cold tolerance using the introgression lines derived from wild rice (Oryza nivara) and identified an introgression line Ra47 harboring the major QTL qSCT12, which exhibited a higher seedling survival rate under cold stress than its recipient parent 9311 (an elite indica cultivar). Using the F_2:3 population developed by backcrossing Ra47 with 9311, we confirmed the major QTL qSCT12 for seedling cold tolerance, which explained up to 29.92% of the phenotypic variation in cold tolerance traits, and which allele from wild rice could enhance seedling cold tolerance. Using additional 2744 F₂ individuals, we narrowed the QTL qSCT12 to a 21.8-kb region on chromosome 12 between markers CT321 and 3-F. This interval contains 2 candidate genes LOC_Os12g10700 and LOC_Os12g10710. Further RNA-seq analysis of Ra47 and 9311 before and after cold treatment revealed that DEGs were enriched in primary metabolic process, cellular metabolic process, hydrolase activity and pyrophosphatase activity. These findings will provide important insights into the genetic basis of cold tolerance in rice seedlings and offer new genetic resources for developing cold-tolerant rice varieties.