Genetic Relationship of 22 Pigmented Rice from Central Java and East Java Based on Simple Sequence Repeat (SSR)

Pigmented rice contains distinct bioactive compounds compared to regular white rice. The study aimed to determine the genetic diversity of 22 pigmented local rice varieties originating from East Java and Central Java Province, Indonesia. This research used a PCR-based molecular marker approach utilizing plant pigment marker genes, namely Simple Sequence Repeat (SSR). The research commenced with planting and maintaining the rice plants, DNA isolation according to the cetyltrimethylammonium bromide (CTAB) method, DNA amplification, and PCR visualization, followed by phylogenetic tree construction using PAST 4.0 software. Based on the allele structure analysis, four main clusters of pigmented rice were identified. The identified polymorphisms and clustering patterns provide valuable insights for future plant evolution, breeding, and conservation research. In addition, genetic differentiation suggests a high level within the population. Based on allele structure analysis, black rice shares genetic characteristics with other rice colours, including red, brown, and white. In conclusion, black rice shows the most complex allele structure for colour-related genes among all rice colours.