Identification and mapping of quantitative trait loci for cold tolerance at the booting stage in a japonica rice near-isogenic line

Near-isogenic lines (NILs) are preferred materials for mapping quantitative trait loci (QTLs) and for evaluating gene action or interaction. We developed a set of NILs with cold tolerance at the booting stage by backcrossing the strongly cold-tolerant japonica landrace, Kunmingxiaobaigu (KMXBG) to cold-sensitive japonica cultivar, Towada, as the recipient parent. A BC4F5 line was selected as a parent to construct a BC5F2 segregating population from which BC5F3 lines were developed. Cold tolerance at the booting stage was evaluated on the basis of spikelet fertility of main panicles over 2 years and two locations. Using a LOD significance threshold of 3.0, compositive interval mapping based on a mixed linear model revealed eight QTLs on chromosomes 1, 4, 5, 10 and 11. They were tentatively designated qCTB-1-1, qCTB-4-1, qCTB-4-2, qCTB-5-1, qCTB-5-2, qCTB-10-1, qCTB-10-2 and qCTB-11-1. All alleles for cold tolerance were contributed by KMXBG, and the marker intervals containing them were narrowed to 0.6–5.6 cM. Genetic distances between the peaks of the QTL and nearest markers varied from 0 to 1.3 cM. The variance explained by a single QTL ranged from 0.90 to 14.86%. Four QTLs, qCTB-1-1, qCTB-4-1, qCTB-5-1, qCTB-5-2 and qCTB-10-1, were detected in two or more trials. Comparisons with previous studies indicated that these QTLs were reliable. Our study sets a foundation for cloning cold-tolerance genes and provides opportunities to understand the mechanism of cold tolerance at the booting stage.