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 BC5F, 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. (c) 2007 Elsevier Ireland Ltd. All rights reserved.