Genetic diversity of selected Malaysian rice accessions using microsatellite markers

Genetic diversity of plant genetic resources provides the foundation for breeding programmes aimed at developing high-yielding rice varieties with tolerance to biotic and abiotic stresses. Given the abundance of available genetic resources, efficient approaches for their characterisation are essential. In this study, 182 Malaysian rice accessions representing different maturity groups were characterised using 20 polymorphic simple sequence repeat (SSR) markers. The analysis identified 183 alleles, ranging from two (RM507) to 22 (RM154), with an average of 9.15 alleles per locus. Observed and expected heterozygosity ranged from 0.000 to 0.506 and 0.319 to 0.864, respectively. Polymorphism information content (PIC) values ranged from 0.2744 (RM495) to 0.8475 (RM154), with an average of 0.6216 per locus. Unweighted pair group method with arithmetic mean (UPGMA) analysis revealed two major groups. In general, the accessions were clustered according to their adaptive ecosystem type, with most lowland varieties, including lowland breeding lines (92.4%), assigned to Group I, whereas most upland varieties (86.7%) belonged to Group II. This grouping pattern was supported by STRUCTURE analysis, which identified K = 2 as the optimal number of clusters, indicating that the studied accessions were structured into two major genetic groups. Principal coordinate analysis (PCoA) further supported this grouping pattern, with the first three axes explaining 39.63% of the total variation. Analysis of molecular variance (AMOVA) showed that 31% of the total variation occurred among populations, 63% among accessions, and 6% within accessions. The results also indicated the possible presence of duplicate accessions within the collection. This study provides valuable insights for future breeding programmes aimed at developing high-yielding rice varieties with a broad genetic base and supports the effective management and conservation of rice genetic resources.