Abstract
The QTLSD7-1/Rc is a pleiotropic locus that controls seed dormancy and pericarp color in rice. DNA sequence variation in promoter region, exon1, and intron 1 in wild rice from Thailand and Laos, weedy rice accessions from Thailand, as well as cultivated rice were investigated using re-sequencing DNA technique. For promoter region, three types of DNA variation were observed including variation in number of nucleotide (T)n (n=9,10,11), five SNPs and 19-bp indel. For coding region exon 1, no DNA sequence variation was observed. For non-coding region intron1, weedy rice had the 10-bp insertion in the region, but there was the deletion in wild rice. In addition, deletion of 34-bp in intron1 was observed in all wild rice accessions examined, while weedy rice had the 34-bp insertion. Haplotype analysis of weedy rice indicated that the pairwise nucleotide diversity parameter, Pi (ℼ) and the level of the Watterson estimator (Өw) in the DNA sequences were 0.00401 and 0.0048, respectively. This finding enhances knowledge of the DNA sequence
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