Genetic diversity analysis of Indonesian rice germplasm (Oryza sativa L.) with simple sequence repeat markers

The characterization of germplasm provides information on the regional rice genetic diversity and variety kinship classification. This study aimed to provide information on the agro-morphological traits and genetic diversity of fifty local rice varieties from Java and Borneo Island in Indonesia. The variability of thirteen agronomic traits showed the differentiation among the accessions, while the phenotypic traits were grouped into six clusters. The genotyping characterization was conducted using SSR (Simple Sequence Repeats) markers (22 microsatellites), and continued with genetic diversity and Polymorphism Information Content (PIC) analysis. The agro-morphological clustering based on Ward’s Hierarchical constructed six sub-clusters. The PC1 and PC2 had 86.3% of the total percentage. The UPGMA method was used to construct six different groupings, as the correlation between each group and its collecting source was significant. Furthermore, the UPGMA dendrogram clustered the 50 accessions into six main clusters, while the PIC showed a polymorphism value range of 0.41–0.74. RM162 located on chromosome 5, which was considered as the best marker for fifty-one genotypes. At the same time, the lowest PIC value of 0.41 was observed in RM431 located in chromosome 1. This classification can be helpful as a detailed information for plant breeders to characterize and select the germplasm, while conducting backcrosses between rice accessions.