Mapping QTLs for cold tolerance at seedling stage using an Oryza sativa × O. rufipogon backcross inbred line population

Tolerance to low temperature is an important factor affecting the growth and development of rice (Oryza sativa L.) at an early growing season in the temperate region, and at high altitudes of tropical regions. In this study, a backcross inbred line (BIL) population derived from an interspecific cross between Xieqingzao B (O. sativa L.) and an accession of Dongxiang wild rice (O. rufipogon Griff.) was used to identify quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage. Seedlings were treated with a temperature of 6°C for 2 days and seedling mortality was measured for QTL mapping. QTL analysis was performed on the whole BIL population and on one subpopulation that showed Xieqingzao B homozygous at QTL detected in the whole population. One major QTL, qSCT8, and one QTL, qSCT4.3, with smaller effect was found in the whole population. The QTLs qSCT8 and qSCT4.3 were mapped on chromosome 8 and 4, explaining 60.96% and 8.83% of the phenotypic variance, respectively. In the subpopulation, three QTLs, qSCT4.1, qSCT4.2 and qSCT12, accounting for 56.22%, 57.62% and 53.09% of the phenotypic variance, respectively, were detected on chromosome 4 and 12. At all five loci, the alleles introduced from the Dongxiang wild rice were effective in decreasing seedling mortality. Our results provide a basis for fine mapping and cloning of QTLs associated with cold tolerance, and the markers linked with QTLs could be used to improve the cold tolerance of rice varieties by marker-assisted selection.