Mapping quantitative trait loci for cold tolerance in rice at seedling stage

Rice plants are sensitive to cold stress at various growth stages starting from germination to maturity. Exploitation of cold tolerance for the development of cold tolerant varieties may help in saving crop loss or cost of production in the cold prone environment. Introgression of quantitative trait loci (QTLs) conferring cold tolerance in the elite variety may be the most effective and sustainable approach to address this issue. A F2:3 mapping population of a cross between a cold susceptible variety (BR1) and a cold tolerant variety (BR18) was used to map QTLs for cold tolerance at seedling stage. Three significant QTLs on chromosomes 1, 3 and 12 associated with cold tolerance were mapped between the markers intervals of RM220-RM10829, RM546-RM7 and RM27877-RM463, respectively at a threshold LOD of 4.3 through composite interval mapping. Phenotypic contributions of these QTLs were 50.7, 39 and 52.7%, respectively. Marker information of such a large effect QTL could be used in the breeding program after necessary validation to develop cold tolerant high yielding rice varieties. Introduction Cold stress is one of the major abiotic stresses affecting rice crop at seedling stage in the northern parts of Bangladesh. Germination and seedling establishment are very sensitive growth stages of rice to cold stress. Seedling mortality ranging from 10 90% is observed in some years at early establishement stage of Boro rice crop in the northern districts of Bangladesh when severe cold spell occurs in late December to mid January. This entails increased cost of production for replanting, which is a great problem for the marginal farmers. Farmers sometimes delay planting to avoid seedling mortality caused by low temperature, which eventually lowers the grain yield of Boro rice due to exposure of reproductive phase in high temperature in April. To overcome this problem, use of rice varieties tolerant to cold stress at seedling stage could be a sustainable crop management approach. In the cold prone area in Bangladesh, farmers commonly grow major high yielding varieties like, BRRI dhan28 and BRRI dhan29 but they lack cold tolerance. Although, there are other few cold tolerant rice varieties (BRRI dhan36 and BRRI dhan55) that were developed through conventional breeding method by BRRI, but their performance is not good enough to address the cold injury problem in Boro rice. Furthermore, the rice varieties which are popularly grown in South and South-east Asian countries and are preferred by the consumers usually lack cold tolerance. However, there are rice germplasm that can tolerate cold stress and can maintain better growth than the intolerant one under low temperature stress conditions. Exploitation and use of cold tolerance from such germplasm in development of high yielding rice varieties could save crop loss or cost of cultivation. Therefore, exploring genetic resources to develop cold tolerant rice variety is essential. Molecular analysis of QTLs underlying cold tolerance is the best approach to develop cold tolerant varieties. Author for correspondence: . Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur-1701, Bangladesh.