Zhang, W.-B., Jiang, H.-W., Qiu, P.-C., Liu, C.-Y., Chen, F.-L., Xin, D.-W., Li, C.-D., Hu, G.-H. and Chen, Q.-S. 2012. Genetic overlap of QTL associated with low-temperature tolerance at germination and seedling stage using BILs in soybean. Can. J. Plant Sci. 92: 1381-1388. Low temperature is one of the critical environmental factors that limit agricultural production worldwide. In northeast China soybean frequently suffers low temperature stress, especially at germination stage and seedling stage. The most effective way to solve this problem is to breed cultivars with low-temperature tolerance. A set of advanced backcross introgression lines was constructed with Hongfeng 11 as recurrent parent, which was a local variety in Heilongjiang province, and Harosoy as donor parent, which was introduced from Canada. Their BC₂F₄ lines were screened in low-temperature condition at the two stages, and 41 transgressive lines were selected out at germination stage and 45 lines at seedling stage. Sixty-four and fifty-one pairs of simple sequence repeat primers with fine polymorphism were used for genotyping the selected population and random population at the two stages, respectively. Related quantitative trait loci (QTL) were obtained by chi-test and ANOVA analysis with genotypic and phenotypic data. Finally, 25 QTL at germination stage and 13 QTL at seedling stage were mapped. Among them, 10 QTL overlapped between two stages, which showed a partial genetic crossover on low-temperature tolerance stages in soybean. This would play an important role in marker-assisted selection for breeding elite variety with low-temperature tolerance at both stages.