SSR diversity on rice landraces collected from Yogyakarta Province

Abstract

Abstract In Indonesia, rice is the most common food, and many areas have a lot of rice landraces. Therefore, characterization is very important to be done to identify potential gene sources to be used for the breeding program. The current study aims to learn more about the genetic diversity of rice landrace accessions collected from Yogyakarta province using simple sequence repeat (SSR) markers. A total of 56 accessions of rice landraces originated from Yogyakarta province, and 7 accessions of standard varieties, were used in the study. The DNA sample was extracted from young leaves and isolated for further molecular analysis by using eleven SSR markers. Data analysis was conducted using Power Marker v3.25 for genetic analysis, and DARwin v6.0.021 for cluster analysis and dendrogram visualization. The results of the genetic analysis showed that the average values of major allele frequency, number of alleles, gene diversity, heterozygosity, and polymorphic information content (PIC) were 0.27, 10.1, 0.83, 0.15, and 0.80, respectively. All eleven SSR markers were highly informative (PIC>0.50), as their PIC values ranged from 0.69 to 0.85. These markers have great potential to be used for marker-assisted selection of the germplasm collections. The result of cluster analysis showed that all the rice landrace accessions were separated into three different groups, each consisting of 29, 28, and 6 accessions.