Further dissection of physiological molecular mechanisms is indispensable to alleviate rice yield losses resulting from cold injury. By using 105 near-isogenic lines (NILs) derived from a backcross between cv. Lijiangxintuanheigu (LTH) and cv. Towada, we detected quantitative trait loci (QTLs) for physiological traits of the rice flag leaf, based on polymorphic simple sequence repeat (SSR) markers, inclusive composite interval mapping (ICIM), mixed composite interval mapping (MCIM) approaches and phenotypic value subjected to combine with cold-water stress and three nitrogen application rates. By using ICIM, a total of 34 QTLs with additive effects (A-QTLs) were identified on chromosomes 1, 3, 4, 5, 6, 7 and 10, and the phenotypic variation (R²) explained by each QTL ranged from 8.46 to 29.14%. By using MCIM, 20 A-QTLs and 14 pairs of QTLs with epistatic × environment interaction effects (Epistatic QTLs) were detected, the contribution of environment interaction (H²AE) was 0.87 to 7.36%, while the contribution rates of E-QTL were from 0.97 to 3.58%. Fourteen A-QTLs were detected by ICIM and MCIM, which may serve as a basis for fine-mapping and candidate gene studies, and providing strategies for the development of cold-tolerant rice cultivars and nitrogen application to alleviate chilling stress.

Chilling damage significantly reduces grain yield in rice, while exploring major quantitative trait loci (QTLs) has the potential to improve rice production. Mapping of QTLs for 5 cold tolerance-related traits at the booting stage was conducted with SSR markers and inclusive composite interval mapping (ICIM) approach, based on 105 near-isogenic lines derived from a backcross between Lijiangxintuanheigu (LTH, cold-tolerant landrace) and Towada (cold-sensitive cultivar). 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 (R²) 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 BLUP, and their alleles were contributed by LTH with R²variance from 12.24 to 29.66%. These favourable QTLs would facilitate elucidation of the genetic mechanism of cold tolerance and provide strategies for breeding high-productive rice.