Chloroplast Genetic Comparison of Siam and Siputih Swamp Rice (Oryza sativa L.) from South Sumatra Based on rbcL and matK

Abstract

Traditional swamp rice landraces are important components of South Sumatra’s local rice genetic resources, yet their chloroplast sequence variation remains poorly documented. This study assessed chloroplast sequence similarity between two representative accessions of the traditional swamp rice landraces Siam and Siputih using the rbcL and matK markers. Both loci yielded reproducible amplification products of approximately 600 bp (rbcL) and 900 bp (matK), with high-quality bidirectional sequencing results. BLAST analysis revealed 99.66–100% sequence similarity to Oryza sativa and related Oryza references, including O. nivara, O. rufipogon, and O. glaberrima. Comparative analysis detected limited chloroplast variation: rbcL contained one single-nucleotide polymorphism (SNP) and two insertion–deletion (InDel) events, whereas matK showed no SNPs but three short InDel events. Nucleotide diversity was low (rbcL: π = 0.00170; matK: π = 0.00000), indicating minimal sequence divergence. Neighbour-Joining phylogenetic analysis using the Kimura 2-parameter model placed both accessions within the same major clade, with strong bootstrap support for rbcL and moderate support for matK. These results suggest closely related chloroplast sequences and a potentially shared maternal plastid lineage between the sampled accessions. This study provides baseline molecular evidence for chloroplast variation in traditional South Sumatran swamp rice and may inform future germplasm conservation and breeding research. However, because each landrace was represented by a single genotype, the findings are restricted to comparisons between the two sampled accessions. This study contributes to the limited chloroplast DNA-based molecular characterization of traditional swamp rice landraces from South Sumatra.