QTL mapping and validation of a segment responsible for early-seedling cold tolerance in rice

Cold stress at the early-seedling stage is one of the major determinants of uniform seedling establishment. In this work, a recombinant inbred line (RIL) population consisting of 172 lines derived from a cross between Xiang743 (highly cold-tolerant) and Katy (moderately cold-sensitive) was used to map quantitative trait locus (QTL) for early-seedling cold tolerance (ESCT). A total of six QTLs were detected that were distributed on six chromosomes, and explained a total phenotypic variance of 36.8%. All alleles from Xiang743 increased ESCT. Among them, the QTL qESCT-3 was detected in the interval RM520–RM85 on chromosome 3, which was also identified in the same interval in an F2 population derived from the same parents in a previous study. To determine the effect of qESCT-3, two residual heterozygous lines (RHLs) segregating in the target segment were selected from the RILs to develop two secondary populations. The presence of QTL qESCT-3 was confirmed in the interval RM520–RM85 in the two populations, and the qESCT-3 from Xiang743 increased ESCT. The study shows that the qESCT-3 segment is responsible for cold tolerance at the early-seedling stage and provides RHL materials for fine mapping of qESCT-3. The markers flanking qESCT-3 will be useful in the improvement of ESCT in rice breeding programs.