Genetic Diversity of Black and Aromatic Rice Cultivar (Oryza sativa L.) from Various Regions in Indonesia using Random Amplified Polymorphic DNA Markers (RAPD)

Abstract

Indonesia is one of many countries with a high potential for genetic diversity resource of rice plants, both black rice, and aromatic rice. Therefore, the kinship relationship in each cultivar of which results are not influenced by the environment can be determined by molecular methods, one of which is by using RAPD analysis. This research employed 20 RAPD primers and DNA genome materials used in isolation from ten black rice cultivars, and 15 aromatic rice cultivars. The research stage began with a collection of black rice and aromatic rice germ plasma in several regions in Indonesia, seed nursery, DNA isolation, DNA quantity, and quality testing, primary selection, RAPD, running RAPD, and phylogenetic analysis. The objectives of this research were to obtain phylogenetic diversity of black and aromatic rice in this analysis. Twenty RAPD primers used to amplify 10 black rice cultivars and 15 aromatic rice cultivars obtained 180 polymorphic DNA Ribbons, with an average percentage of 89.2%. The genetic diversity of all cultivars analyzed was considerably high. At 84% coefficient, two major groups were obtained: black rice and aromatic rice, divided into eight small groups. The results of the phylogenetic analysis demonstrate high diversity between black rice and aromatic rice. Such a thing can be a first step for selecting rice plants which will be taken as plant parent in the crossbreeding.