Genetic Assessment of Rice Genetic Resources Using Site-Specific Amplification Based on Active Mites

Rice (Oryza sativa L.) has been domesticated and cultivated over the world as one of the staple foods for carbohydrate source, and diverse accessions (about 35 thousand) conserved in Korean National Agrobiodiversity Center (RDA, NAAS). For the genetic assessment of rice germplasm, we focused on active miniature inverted-repeat transposable elements (MITEs) such as mPing in that the movement of transposons might reflect the history of genetic diversification and domestication. We used site-specific primers designed in TE-flanking sequences of MITEs, and applied to diverse 91 rice accestions for genetic assessment. Finally, we acquired amplicons of several site-specific primers; mPing – 46, Akan – 92, Kiddo – 41, Toya – 26, nDaiZ – 6. The ratio of monomorphic loci of mPing, Akan, Kiddo, Toya and nDaiZ was 6.5%, 85.9%, 24.4%, 88.5% and 50.0%, respectively. Based on DNA profiles of polymorphic loci, the phylogenetic tree was constructed, and japonica and indica ecotype were divergent and accessions belonging to japonica showed greater genetic diversity. These selected polymorphic site-specific markers could be used for revealing genetic relationship of rice genetic resources.