Identification of QTLs for Rice Cold Tolerance at Plumule and 3-Leaf-Seedling Stages by Using QTLNetwork Software

A doubled haploid （DH） population consisted of 120 lines, derived from a cross between an indica vadety, TN1, and a japonica variety, Chunjiang 06, was used to identify QTLs controlling rice cold tolerance at the plumule and 3-leaf-seedling stages by using the QTLNetwork software. The percentages of normal plumules after 4~C treatments for 7 d, 9 d, 11 d, and 14 d, as well as the cold stress tolerance index （CSTI） and the withering index （WI） of rice seedling were investigated. A total of five single-effect QTLs, each for percentages of normal plumules after 4℃treatments for 9 d, 11 d and 14 d, and CSTI and WI, respectively were identified. The QTLs for the percentages of normal plumules after low temperature treatments for g d, 11 d and 14 d were on chromosomes 4, 2 and 11, accounting for 14.1%, 17.3% and 21.5% of the phenotypic variation, respectively. QTLs for CSTI and WI were on chromosomes 10 and 1, respectively. Two pairs of epistatic loci were identified, but none of the epistatic loci involved the single-effect QTLs. The RM528-RM340 interval on chromosome 6 interacted with the RM278-RM3919B interval on chromosome 9 for CSTI, and the epistatic interaction accounted for 17.7% of the phenotypic variation. A pair of epistatic loci was identified for WI, the RM246-RM5461 interval on chromosome 1 interacted with the ISA-RM447 interval on chromosome 8, which accounted for 22.6% of the phenotypic variation.