Detection of QTLs for Cold Tolerance at the Booting Stage in Near-isogenic Lines Derived from Rice Landrace Lijiangxintuanheigu

Chilling damage significantly reduces grain yield in rice, while the utilisation of major quantitative trait loci (QTLs) can potentially improve rice yielding. Mapping of QTLs for 5 cold tolerance-related traits at the booting stage was conducted with SSR markers, including composite interval mapping (ICIM). 105 near-isogenic lines, derived from a backcross between Lijiangxintuanheigu (LTH, cold-tolerant landrace) and Towada (cold-sensitive cultivar) were analysed. Phenotype values were investigated under five cold-stress environments and analysed by the best linear unbiased prediction (BLUP). Twenty-one QTLs were identified on chromosomes 1, 2, 3, 4, 6, 7, 10 and 11, and the amount of variation (R-2) explained by each QTL ranged from 7.71 to 29.66%, with five co-located QTL regions. Eight novel major loci (qSF-2, qSF-6a, qSF-7, qGW-6, qDGWP-4, qDSWPP-4, qDWPP-1 and qDWPP-4b) were detected in several environments and by using BLUP. Their alleles were derived from the cultivar LTH with R-2 variance from 12.24 to 29.66%. These favourable QTLs would help to elucidate the genetic mechanism of cold tolerance and provide strategies for breeding of high-yielding rice.