Morpho-molecular diversity of improved Indonesia’s rice varieties based on grain morphology and three types of DNA-based markers

Genetic improvement of rice (Oryza sativa L.) requires a clear understanding of both phenotypic and molecular diversity. This study examined 82 improved Indonesian rice varieties using grain morphological traits and three DNA-based marker systems: Simple Sequence Repeat (SSR), Subspecies-Specific Sequence-Tagged Site (SS-STS), and Start Codon Targeted (SCoT). Phenotypic evaluation revealed significant variation in grain length, width, and thickness. Principal component analysis condensed four traits into two axes explaining 94.4% of variance, separating genotypes into three clusters largely corresponding to indica and japonica types. Across 32 markers, 157 alleles were detected, with average gene diversity (He) values of 0.30 (SSR), 0.29 (SS-STS), and 0.22 (SCoT). Polymorphic information content (PIC) was generally low. SS-STS markers revealed fixation of indica-type alleles, consistent with major varieties IR64 and Ciherang, while rare alleles were scarce (1.1-1.5 per locus). Although SCoT markers generated 8.5 bands per locus, heterozygosity remained low (0.005-0.010). Analysis of molecular variance (AMOVA) showed that 90-91% of the genetic variation was distributed within subpopulations, while only 5-8% was explained by differences among subpopulations, indicating weak population structure (FST = 0.055 for SSR; 0.084 for SS-STS). STRUCTURE analysis inferred different subpopulation numbers for each marker type (K = 7 for SS-STS, K = 2 for SSR, K = 4 for SCoT). Phylogenetic clustering separated the genotypes into two to three subpopulations, which partly corresponded to grain type and inferred subspecies background. These results reveal limited molecular diversity despite observable phenotypic variation, suggesting genetic narrowing associated with the repeated use of closely related parental lines during breeding. Broader germplasm, including landraces and wild relatives, is essential for future rice breeding.