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

English. Received: April 5th, 2022 ; Accepted: July 20th, 2022 ; Published: August 18th, 2022 ; Correspondence: [email protected]

English. The characterization of germplasm provides information on the regional rice geneticdiversity and variety kinship classification. This study aimed to provide information on the agromorphological traits and genetic diversity of fifty local rice varieties from Java and Borneo Islandin Indonesia. The variability of thirteen agronomic traits showed the differentiation among the accessions, while the phenotypic traits were grouped into six clusters. The genotypingcharacterization was conducted using SSR (Simple Sequence Repeats) markers (22 microsatellites),and continued with genetic diversity and Polymorphism Information Content (PIC) analysis. Theagro-morphological clustering based on Ward’s Hierarchical constructed six sub-clusters. ThePC1 and PC2 had 86.3% of the total percentage. The UPGMA method was used to constructsix different groupings, as the correlation between each group and its collecting source wassignificant. Furthermore, the UPGMA dendrogram clustered the 50 accessions into six mainclusters, while the PIC showed a polymorphism value range of 0.41–0.74. RM162 located onchromosome 5, which was considered as the best marker for fifty-one genotypes. At the sametime, the lowest PIC value of 0.41 was observed in RM431 located in chromosome 1. Thisclassification can be helpful as a detailed information for plant breeders to characterize and selectthe germplasm, while conducting backcrosses between rice accessions.