Genetic characterization and analysis of the population of selected Sarawak rice cultivars using simple sequence repeat markers

Genetic characterization refers to variation detection using genetic markers. In this study, 28 simple sequence repeat (SSR) markers were used to characterize five selected Sarawak rice cultivars, namely Bali1, Bali2, Bali3, Bubok, and Mamut. An analysis based on these 28 polymorphic SSR markers revealed that the number of alleles ranged from 2 (RM312, RM510, and RM536) to 9 (RM307) with an average of 3.86. The polymorphism information content (PIC) values ranged from 0.0175 (RM489) to 0.8174 (RM19) with an average of 0.5179. A dendogram constructed on the basis of the genetic similarity to Nei’s 1983 genetic distance showed a high similarity between Bali2 and Bali3, which was further supported by a principal coordinate analysis (PCoA). The population structure analysis illustrated the log likelihood peaking at K = 2, indicating that the entire population could be divided into two distinct groups. To develop an SSR fingerprinting panel, 10 SSR markers were selected on the basis of a high PIC value. As this panel provides a better discrimination power in cultivar identification, it could be an efficient and effective tool in cultivar identification, particularly for these selected Sarawak varieties, thus helping breeders to protect their intellectual property rights (IPR). Moreover, the markers could be used to evaluate the seed purity of the selected rice cultivars.