Genetic Diversity and Phylogenetic Position of Traditional Rice (Oryza sativa L.) Landraces: A Case Study of South Kalimantan in Indonesia

Traditional rice (Oryza sativa L.) landraces provide many essential genes for improving yield, disease resistance, abiotic stress tolerance, and other parameters for future rice breeding. This study aimed to analyze the genetic diversity and determine the phylogenetic position of the traditional rice landraces from the tidal swamp areas of South Kalimantan, Indonesia, compared to other rice germplasm, including wild relatives, obtained from the GenBank database, using a cpDNA-rbcL marker. In this case, six traditional rice landraces from this region were collected and analyzed molecularly using the rbcL marker and compared with 16 similar others and 25 wild relatives from the GenBank database. The genetic diversity of this germplasm was determined using the nucleotide diversity index (π), whereas the phylogenetic analysis by maximum likelihood with bootstrap for 1 000 replicates. The principal component analysis (PCA) was employed to confirm this grouping. Based on this marker, the traditional rice landraces have a genetic diversity of 0.38, lower than intra-species and inter-species levels, i.e., 0.44 and 0.83, respectively. The phylogenetic analysis shows that this germplasm has separated from most O. sativa rice cultivars and their wild relatives, except for the ‘GBVN’ and ‘NARC’ (comparison cultivars obtained from GenBank). This information has substantial implications for future rice breeding and conservation efforts, locally and globally.