Genetic diversity analysis of Korean rice (Oryza sativa L.) varieties using microsatellite markers

Rice is an important staple to majority of the world's population particularly to Asian countries such as Korea. While some of the Korean varieties have been utilized for the development of improved lines much of the accessions from this region remain uncharacterized. This study was conducted to analyze and establish the genetic relationships within and among nine representative Korean rice varieties (classified into four different variety names, namely 'koryeong 2', 'koryeong 8', 'suk na', and 'san dudo' with nine individuals comprising each variety) and to estimate the percentage of labeling errors through the use of microsatellite markers (SSR). A total of 73 alleles, with a mean of 9.125 per locus across all the accessions were detected using eight SSR markers. Allele sizes ranged from 78 base pairs, bp (RM 271) to 298 bp (RM 124). Mean Polymorphism Information Content, PIC (0.7054), average gene diversity (0.7404) and Wright's F. statistics (fixation index, whole group level) (Fst = 0.5978) values for these varieties indicated a diverse nature of the population of selected genotypes. Phylogenetic tree analysis revealed putative incidences of mislabeled samples (homonymous and duplicate errors) belonging to the 'suk na' (IRGC 2374, IRGC 19862), 'san du do' (IRGC 19848), and 'koryeong 2' (IRGC 112793) which clustered with individuals from different varieties on which they should not group with. It is suggested that further genotyping be done with an increased number of markers and samples to confirm these incidences of mislabeling. The minimal number of microsatellite markers utilized in this study, however, was already able to differentiate Korean varieties from each other on the basis of their SSR fingerprints. Results from these analyses could be used for establishing future breeding programs towards the development of improved varieties of Korean rice and can be utilized for structuring a protocol for the identification of mislabeling among rice accessions.