Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms

NUR SITI KURNIASIH (Departement of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada. Jl. Teknika Selatan, Sekip Utara, Sleman 55281, Yogyakarta, Indonesia)
RATNA SUSANDARINI (Departement of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada. Jl. Teknika Selatan, Sekip Utara, Sleman 55281, Yogyakarta, Indonesia)
FEBRI ADI SUSANTO (Research Center for Biotechnology, Universitas Gadjah Mada. Jl. Teknika Utara, Depok, Sleman 55281, Yogyakarta, Indonesia)
TRI RINI NURINGTYAS (Departement of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada. Jl. Teknika Selatan, Sekip Utara, Sleman 55281, Yogyakarta, Indonesia)
GLYN JENKINS (Institute of Biological, Environmental and Rural Sciences, Aberystwyth University. Aberystwyth, United Kingdom)
YEKTI ASIH PURWESTRI (Research Center for Biotechnology, Universitas Gadjah Mada. Jl. Teknika Utara, Depok, Sleman 55281, Yogyakarta, Indonesia)

Biodiversitas Journal of Biological Diversity
Vol. 20 No. 4 (2019)

Abstract. Kurniasih NS, Susandarini R, Susanto FA, Nuringtyas TR, Jenkins G, Purwestri YA. 2019. Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms. Biodiversitas 20: 1208-1214. Indonesia has many cultivars of pigmented rice, but many variants have not been characterized using morphological characters and molecular markers. SNPs (Single Nucleotide polymorphisms) have been used in previous studies to identify the Indica and Japonica subspecies. Characterization of whether a line belongs to the Indica or Japonica subspecies is useful information for rice breeders, especially to generate line exhibiting the strong hybrid vigor. Morphological characters are used to determine the relationship between cultivars using cluster analysis. The SNP markers were amplified by PCR, sequenced and compared with sequences in the GenBank. Based on morphological characters, ten cultivars divide into two clusters. SNPs distinguish Indica and Japonica subspecies, and show that Hitam Lampung, Aek Sibundong, Melik, Hitam Toraja, Merah Kalimantan, and Merah Sumbawa belong to the Indica subspecies while Cempo Ireng and Pare Eja belong to Japonica. Abang Segreng and Hitam Toraja could not be clearly assigned to either the Indica or Japonica subspecies.