Identification of QTLs for cold tolerance at seedling stage in rice (Oryza sativa L.) using two distinct methods of cold treatment

Cold water irrigation and growth in low temperature phytotron are two commonly used methods to evaluate cold tolerance of rice at the seedling stage and the cold sensitive seedlings exhibit different injury symptoms, respectively. However, so far no one has systematically dissected the differences of cold tolerance at seedling stage in rice under the two cold environments. We used a recombinant inbred line (RIL) population derived from a cross of a cold-tolerant japonica cultivar, Lijiangxintuanheigu and a cold sensitive indica cultivar, Sanhuangzhan-2 for this study. The cold sensitive seedlings exhibited leaf yellowing after cold water irrigation and leaf rolling during growth in the low temperature phytotron. Leaf yellowing and leaf rolling in RILs was significantly correlated, but the correlation coefficient was low. A total of four quantitative trait locus (QTLs) on chromosomes 1, 6, 9 and 12 were detected using leaf yellowing and percent seedling survival as indicators of cold tolerance after cold water irrigation, while five QTLs on chromosomes 7, 8, 9, 11 and 12 were detected using leaf rolling and percent seedling survival as indicators of cold tolerance during growth in the low temperature phytotron. The two QTLs, qCTS-9 and qCTS-12 were detected using different evaluation indicators under the two cold environments. Our results suggest that rice cold tolerance mechanisms at the seedling stage differ between the two environments, but the detection of common QTL implies the existence of overlap in the metabolic pathways for cold tolerance. The two common QTLs have potential value in rice breeding.