Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice
Cold tolerance at the seedling stage of rice is an important phenotypic trait that causes normal plant growth and stable rice production in temperate regions as well as tropical high-lands in Asia and Africa. In order to find quantitative trait loci (QTLs)/genes associated with cold tolerance, we constructed a linkage map using 153 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant temperate japonica cultivar, Geumobyeo, and a cold-sensitive tropical japonica breeding line, IR66160-121-4-4-2. The RILs were phenotyped for cold tolerance or sensitivity based on the degrees of cold tolerance as cold tolerance indices at the seedling stage. The seedlings for cold-tolerance/-sensitive traits were scored on the 7th day of the recovery period at 25°C after cold treatment at 10°C. Two QTLs (qCTS4a and qCTS4b) associated with cold tolerance at the seedling stage were identified on the long and short arms of chromosome 4 with an LOD score of 2.89 and 2.75, respectively, using composite interval mapping. The QTLs were flanked by simple sequence repeat (SSR) markers RM3648-RM2799 and RM3375a-RM558 that explained 8.3 and 7.8% of the total phenotypic variation, respectively. Seven of the selected RILs expressed cold tolerance at both the seedling and reproductive stages. The SSR markers associated with the QTLs will be useful for tracking favorable QTLs/genes into cold-sensitive elite cultivars and may have potential for pyramiding different QTLs for the improvement of cold tolerance in rice.