The quantitative trait loci （QTLs） for the seedling vigor traits under 12℃ cold water irrigation, such as the seedling height, the seedling fresh weight, the seedling dry weight, and their cold response index, were identified using an F2：3 population including 200 individuals and lines derived from a cross of indica and japonica ＂Milyang 23/Jileng 1＂ with microsatellite markers. All seedling vigor traits exhibited a continuous distribution near normal in F3 lines; these traits were quantitative traits controlled by multiple genes. Twelve QTLs conferring the seedling vigor traits under cold water irrigation were detected on chromosomes 1, 2, 7, 8, and 12, which explained the observed phenotypic variance from 5.2% to 17.9%. Among them, qCSH2 and qCSH12 were located in RM262-RM263 on chromosome 2 and RM270-RM17 on chromosome 12, respectively, which were associated with the seedling height, qSDW12 and qCSDW1 were located in RM19-RM270 on chromosome 12 and RM 129-RM9 on chromosome 1, respectively, which were correlated with the seedling dry weight and its cold response index, and the explained 16.6%, 17.9%, 15.9%, and 16.2% of the observed phenotypic variation, respectively. These QTLs alleles were derived from cold-tolerant parent Jileng 1; the gene actions of the two front genes showed their additive effect, and the two genes belind showed dominant and over dominant effects, respectively.
