Molecular Diversity of Tidal Swamp Rice (Oryza sativa L.) in South Kalimantan, Indonesia

Abstract

Tidal swamp rice has long been cultivated by the local people of the South Kalimantan, Indonesia. This germplasm possess some important traits for adapted to a wide range of abiotic and biotic stresses. In this study, a total of 16 cultivars of the tidal swamp rice, consisting of 15 from the South Kalimantan Provinces and 1 from South Sumatera, Indonesia (an outgroup) were analyzed phylogenetically based on the chloroplast trnL-F and nuclear intergenic spacer region (IGS). The results showed that this germplasm has a relatively more extraordinary genetic diversity than other local rice. On a nucleotide level, the tidal swamp rice showed a genetic diversity of 0.61 for nuclear IGS and 0.58 for trnL-F. The phylogenetic reconstruction also exhibited that the tidal swamp rice has the unique phylogenetic trees, particularly for the combined sequence datasets. This information would be useful for the rice conservation and breeding programs in the future.

DNA barcoding of the tidal swamp rice (Oryza sativa) landraces from South Kalimantan, Indonesia

“…However, the genetic insight of the local rice germplasm of these areas is not generally understood. Partially in the tidal swamp areas of South Kalimantan, Indonesia, the local rice germplasm has been limited to characterized morphologically, both in macro and microstructure (Mursyidin et al 2018a, Mursyidin and Khairullah 2020. While these markers are essential in evaluating rice germplasm, they were strongly influenced by the environmental factors (Nadeem et al 2018).…”

Profiling SNP and Nucleotide Diversity to Characterize Mekong Delta Rice Landraces in Southeast Asian Populations

“…Because of their affordability, these newly improved methods can be exploited for use in small research projects with limited budgets. In particular, many currently untouched bio-resource collections preserved in local institutions are now ready for characterization (Mursyidin et al, 2018;Tu et al, 2007;Yamanaka et al, 2011). Before characterization of these local resource collections, however, the most appropriate methods and genomic indicators must be determined for application in these evaluations.…”