In our previous study, we identified a QTL for cold tolerance at the booting stage of ‘Ukei840’, the cold tolerance of which is derived from one of the most tolerant cultivars, ‘Lijiangxintuanheigu’, in Yunnan province of China, in a 1.2-Mb region between RM7000 and RM3719 markers on chromosome 3. In the present study, we delimited the previously identified QTL to a region of about 35 kb by SSR and dot-blot-SNP marker analysis and nucleotide sequencing using a newly produced near-isogenic line having the ‘Lijiangxintuanheigu’ allele in the QTL region. Comparison of nucleotide sequences of the published ‘Nipponbare’ and ‘Hitomebore’ genome sequences and our previously determined sequence of ‘Ukei840’ revealed nine SNPs in the delimited 35-kb region harboring six genes. LOC-Os03g59190 containing two SNPs in its coding region was a retrotransposon-like sequence having long terminal repeats, which has at least seven other copies in the rice genome. Expression levels of the other five genes in spikelets at the booting stage were not different between ‘Ukei840’ and ‘Hitomebore’. There was one SNP in the coding region of Os03g0806700 which causes amino acid substitution in ‘Ukei840’. However, in Os03g0806700, the genotype of ‘Ukei840’ is the same as that of cold sensitive Indica cultivars. Among the other six SNPs in intergenic regions, one SNP was present in a locus for small RNAs. Possible candidates for the cold-tolerance gene derived from ‘Lijiangxintuanheigu’ are discussed.
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