Diversity and Population Structure of Local Rice Varieties from Indonesia Revealed by SSR Markers

  • Rerenstradika Tizar Terryana National Research and Innovation Agency, Jakarta, Indonesia
  • Puji Lestari National Research and Innovation Agency, Jakarta, Indonesia
  • I Gusti Komang Dana Arsana National Research and Innovation Agency, Jakarta, Indonesia
  • Kristianto Nugroho National Research and Innovation Agency, Jakarta, Indonesia
  • I Made Jana Mejaya National Research and Innovation Agency, Jakarta, Indonesia
  • Priatna Sasmita Indonesian Center for Food Crops Research and Development-IAARD, Bogor, Indonesia
  • Yudi Sastro Indonesian Rice Research Center-IAARD, Subang, Indonesia
  • Karden Mulya National Research and Innovation Agency, Jakarta, Indonesia
  • Dwinita Wikan Utami National Research and Innovation Agency, Jakarta, Indonesia
  • Mastur Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development-IAARD, Bogor, Indonesia

Abstract

Indonesia's local rice varieties (Oryza sativa L.) have a wide range of diversity that can be valuable sources for crop improvement with molecular markers. This study investigated local rice varieties' genetic diversity and population structure using simple sequence repeat (SSR) markers. The SSR markers demonstrated their informativeness for genotypic characterization as represented by the gene diversity indices and polymorphic information content. The UPGMA dendrogram divided 63 varieties into two distinct clusters with different levels of sub-grouping and the tendency according to their origins, as supported by PCoA. In contrast, PCA of these varieties according to agro-morphological traits was scattered in all quadrants. Thus, DNA level variation analyzed by SSR seems to complement the phenotypic traits, which were not well structured and revealed significant genetic diversity among varieties, within, and among populations (P<0.01). The pattern of grouping structure analysis of total varieties into two subpopulations is similar to the dendrogram according to SSR markers but better resembles the pedigree information of the set local varieties. These findings have implied their importance in rice breeding for genetic improvement, maintenance, and management of local genetic resources in Indonesia.

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Author Biography

Rerenstradika Tizar Terryana, National Research and Innovation Agency, Jakarta, Indonesia

Middle researcher at ICABIOGRAD

Molecular Biology division

Published
2022-06-28
How to Cite
TerryanaR. T., LestariP., ArsanaI. G. K. D., NugrohoK., MejayaI. M. J., SasmitaP., SastroY., MulyaK., UtamiD. W., & Mastur. (2022). Diversity and Population Structure of Local Rice Varieties from Indonesia Revealed by SSR Markers. HAYATI Journal of Biosciences, 29(6), 749-761. https://doi.org/10.4308/hjb.29.6.749-761