Genetic diversity analysis of Indonesian rice germplasm (Oryza sativa L.) with simple sequence repeat markers
¹University of Jember, Graduate School of Biotechnology, Jember, ID6812 East Java, Indonesia
²University of Jember, Faculty of Agriculture, Study Program of Agronomy, Jember, ID6812 East Java, Indonesia
³Kyungpook National University, College of Agriculture and Life Science, School of Applied BioSciences, Division of Plant Biosciences, Daegu, South Korea
⁴University of Jember, Faculty of Agriculture, Study Program of Agrotechnology, Jember, ID6812 East Java, Indonesia
*Correspondence: moh.ubaidillah.pasca@unej.ac.id
Abstract:
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 t
he 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.
Key words:
agro-morphological, diversity, germplasm, rice, SSR