The QTLSD7-1/Rc Locus Variation between Weedy (O. sativa f. spontanea) and Wild Rice (O. rufipogon) Populations

This chapter reports on newly discovered DNA sequences which resulted from exploring DNA polymorphism of the QTL/Rc locus in the representatives of wild rice and weedy rice accessions geographically originating in Thailand.A pleiotropic locus, QTLSD7-1/Rc, regulates rice seed dormancy and pericarp colour. Re-sequencing DNA technology was used to examine the promoter region, exon 1, and intron 1 DNA sequence variation in wild rice from Thailand and Laos, weedy rice accessions from Thailand, as well as cultivated rice. A sample of 54 wild and weedy rice accessions including 4 accessions of wild rice and 50 accessions of weedy rice were used in this study. For wild rice, young leaves were collected from mother plants from natural habitats of Savannakhet province, Laos (code Rc-OR-LSK1). For promoter region, three types of DNA variation were observed including variation in number of nucleotide T, five SNPs and 19-bp indel. For 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. The QTLSD7-1/Rc is a pleiotropic locus of seed dormancy and pericarp color in rice seed. Results from this study exhibit DNA sequence variation in weedy rice and wild rice from Thailand and Laos. Haplotype analysis of weedy rice indicated that the pairwise nucleotide diversity parameter, Pi ( ) and the level of the Watterson estimator ( w) in the DNA sequences were 0.00401 and 0.0048, respectively. Furthermore, DNA variation show not only as DNA markers in terms of molecular evolution, but also weedy rice germplasm would be domestication rice toward direct-seeded rice could be achieved by precisely editing some disadvantaged genes by using the advanced DNA technology.