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Recombinant inbred lines (RILs) derived from a Japonica parent Hygokithanishiki (HGKN) and Indica parent Hokuriku (HOK) were used to identify quantitative trait loci (QTLs) controlling cold tolerance at the seedling stage in rice (Oryza sativa L). Genetic map with 95 SSR markers were used for QTL analysis and 163 RILs were subjected to two consecutive cold stresses at 4 o C for cold tolerance evaluation. Five major QTLs were identified in two different cold stresses and among these QTLs, QTL on chromosome 11 scored 9.39 and 5.43 LOD values at the first and the second cold stresses respectively. In rice expression sequence tags (EST) data base, cold responsive ESTs were found in the QTL region of chromosome 11 and they were analyzed by reverse transcriptase polymerase chain reaction (RT-PCR). RT-PCR was done under cold stress and control conditions in parental rice cultivars and in selected cold tolerant RILs with relevant chromosome fragment from HGKN parent and in selected cold susceptible RILs with relevant chromosome fragment from HOK parent. Results showed that ESTs numbered CI047516.1, CI049555 and CI049229 expressed highly in cold tolerant parent and in selected cold tolerant RILs at cold stress giving evidence on possible candidate ESTs in cold tolerant QTL.

Expression analysis of some cold responsive ESTs in seedling- stage cold-tolerant QTL in rice (Oryza sativa l.)