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

Abstract

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.

Phenotypic Diversity of Super Local Durian (Durio zibethinus Murr.) Varieties from South Kalimantan, Indonesia: A Case Study

“…In other words, plants with a cross-pollination mechanism (like durians) are derived from natural crosses and are very difficult to obtain with potentially superior character (Kurniadinata et al, 2019). In this context, plant breeders utilize this aspect to assemble new-improved varieties with desired traits, particularly for abiotic and biotic stress adaptation, including consumer-preferred (Swarup et al, 2021;Mursyidin, 2022). In addition, only populations with high genetic diversity can adapt rapidly to environmental changes (Lloyd et al, 2016).…”

Genetic Diversity and Its Relationship of Dendrobium (Orchidaceae) Based on Bioactive Compounds and Their Biological Activities: A Meta-Analysis

“…According to Govindaraj et al (2015), genetic diversity is necessary to develop a new line population for future evolutionary processes and adaptive environmental changes. Hence, this parameter is critical for future preservation and improvement programs for endangered plants (Lloyd et al, 2016;Mursyidin, 2022). For preservation, assessing genetic diversity has a beneficial impact on increasing the effectiveness and efficiency of that program (Salgotra and Chauhan, 2023).…”