Localization of QTL for cold tolerance at the germination stage of rice (Oryza sativa L.) using recombinant inbred lines

The cold tolerance of germinating direct-sown rice (Oryza sativa L.) has an increased rate of emergence, which ensures vigorous seedling growth. Research on QTL localization for cold tolerance at the germination stage can assist in molecular marker-assisted selection and enhance breeding efficiency. In this study, 94 populations of recombinant self-incompatible lines from Heigu and Ha 9366 were selected to investigate germination rates at low temperatures. It was found that two QTL loci (qLTG-3 and qLTG-12) were located at different germination times on chromosomes 3 and 12, respectively. The two QTLs at three different germination times, located using QTL, accounted for 21.3–25.9% of the phenotypic variation. Moreover, a reciprocal effect was detected between the two QTLs. The double QTLs increased the germination rate by 22–27% in this population. Additionally, qLTG-12 improved cold tolerance at the seedling stage. The results of this study might provide the materials and molecular markers for future molecular marker-assisted breeding for cold tolerance at the germination stage.