Genetic diversity of Some Indonesian Local Rice Varieties based on Simple Sequence Repeat (SSR) marker related to Aromatic Genes

Abstract

Rice plant (Oryza sativa L.) has various varieties. People generally prefers to rice with good taste and aroma. The aroma is part of the physicochemical properties of the rice plant. The aroma of rice arises because of the gene that controls the nature of the aroma. PCR (polymerase chain reaction) is an in vitro method for generating a large amount of specific DNA fragments with defined lengths and sequences in a small number of complex templates. The objective of this study was to analyze the genetic diversity of some Indonesian local rice varieties based on SSR marker related to aromatic genes. The selected Simple Sequence Repeat (SSR) primers associated with aromatic genes were: RM 484, RM 410, RM 251, RM 247, RM 223, and RM 9. Based on the DNA band pattern, 6 primers were derived, in which there were 14 loci related to the aromatic gene. The resulting dendrogram showed that two main groups of rice achieved a 57% similarity. Group A consisted of aromatic rice accessions, i.e. Rojolele, Rabeg, Rumbah, Cere Lintang, Manikam, Cao, Jawara Hawara, Jalawara, Pare Racik, Godok, Mayang, Caragol, Segubal, Konjal, Beuruem Batu, Tambleg, Parajaketra, Pondok Leger, Seungkeuhan, Waren, Pare Emas, Kapundung, and Cireh Hudang. Group B consisted of non-aromatic rice accessions, i.e. Ciherang, Care Wari, Care Beuruem, Cokrom, Kewal Bulu Hideung, Maninjau, Seren, Sidenuk, Tampai Beureum, Mira, and Pare Caok.