QTL detection and fine mapping of qCTB1 for cold tolerance at the early seedling and booting stages in rice

Abstract

Key message QTLs for cold tolerance at the early seedling and booting stages were identified and qCTB1 was delimited to a 342-kb interval, and the breeding potential of QTL pyramiding was assessed. Abstract Cold stress is one of the main abiotic stresses that affects rice growth and production worldwide. Dissection of the genetic basis is important for genetic improvement of cold tolerance in rice. In this study, a new source of cold-tolerant accession from the Yunnan plateau, Lijiangxiaoheigu, was used as the donor parent and crossed with a cold-sensitive cultivar Deyou17, to develop 130 recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. In total, three QTLs for cold tolerance at the early seedling stage on chromosomes 2 and 7, and four QTLs at the booting stage on chromosomes 1, 3, 5, and 7 were identified. Under the cold stress conditions in deep water and in a high-altitude area, qCTB1 , a locus for cold tolerance at the booting stage, was fine mapped to a 342-kb interval between markers M3 and M4. Effect assessment in the RIL and BC 3 F 3 populations demonstrated that qCTB1 showed a stable effect in the genetic segregation populations. Haplotype and linear regression analyses showed that QTL pyramiding based on the additive effect of favorable loci possesses good potential for cold tolerance breeding. This study will provide genetic resources for molecular breeding and gene cloning of cold tolerance in rice.