A major QTL conferring cold tolerance at the early seedling stage using recombinant inbred lines of rice (Oryza sativa L.)

Cold tolerance at early seedling stage of rice ( Oryza sativa L.) is one of the major determinants for the stable stand establishment in temperate and high-elevation areas. In the current study, with 269 recombinant inbred lines derived from a cross between a japonica tolerant to cold and a sensitive indica of rice, the cold tolerance at early seedling stage was evaluated by the paper-roll tests in a two-replication trial with 10- and 13-day treatments at 10 °C, respectively. The phenotype data, in combination with a complete linkage map consisting of 198 marker loci, were used to conduct composite interval mapping to locate both main-effect and digenic epistatic QTL for the trait. Three main-effect QTL were identified. The comparison of the QTL identified in these two cold treatments resulted in an intriguing finding that seedling cold tolerance in the 10-day cold treatment was regulated by many loci each with minor effect while that in the 13-day cold treatment was controlled by a major QTL as well as minor ones. Of the three main-effect QTL, QTL qSCT-11 , closely linked to microsatellite marker RM202 on chromosome 11, was found to increase its additive effect from 4.07 to 10.11% (seedling survival percentage) as the duration of cold stress was prolonged from 10 days to 13 days. In the 13-day cold treatment, QTL qSCT-11 was detected at a very high LOD score of 19, explaining up to 30% of the phenotypic variation. In addition, a total of nine digenic interactions were detected, each showing small effects on cold tolerance with R 2 ranging from 3.5 to 9.7%, with an average R 2 of 5.3%. In the 13-day cold treatment, the sum of absolute epistatic effects of all the interactions amounted up to 36% in seedling survival percentage, suggesting the importance of epistasis in the genetic control of cold tolerance. These results would favor our better understanding of the genetic control of cold tolerance in rice. The identification of QTL for the trait is important for the development of rice cultivars with a broader climatic adaptation.