Morphological and Molecular Identification of Some Aromatic Rice (Oryza sativa L.) Using RAPD (Random Amplified Polymorphic DNA) Irza Guari Syah Fitri1,2, Netty Ermawati4, and Tri Handoyo1,2,3*
1Faculty of Agriculture, University of Jember, INDONESIA. 2Graduate School of Biotechnology, University of Jember, INDONESIA 3Center for Development of Advanced Science and Technology, University of Jember, INDONESIA. 4State Polytechnic of Jember, INDONESIA (*E-mail: trihandoyo.faperta[at]unej.ac.id)
Abstract
Background: Aromatic rice is one type of variance rice that had fragrant and delicious taste. The content of compound 2-acetyl-1-pyrrolin (2AP) caused the fragrant, which the compound has a higher concentration than non-aromatic rice. to development new variety of rice requires information of genetic distance that describe its character of each variety [1]. Phylogenetic analysis described genetic distance between individuals in a species. Phylogenetic analysis expressed morphological, physiological and molecular characteristics. Morphological characteristic is observation based on the planting approach in taxonomy which determinate its character. Molecular identification use RAPD (Random Amplified Polymorphic DNA) based on DNA sequences that are homologous with a single short (10-12 base) oligonucleotide sequence. Molecular marker based on PCR amplification such as RAPD is an efficient tools for plant breeding programs [2]. RAPD used to determine the kinship level between aromatic rice. The comparison of both identifications is needed to varieties development or plant breeding of aromatic rice. Aims: To determine the level of kinship and diversity in 10 varieties of aromatic rice (Oryza sativa L.) based on morphological and molecular identification. Materials and Methods: In this study, we determinated the level of kindship of 10 varieties of aromatic rice included Pendok, Pandan Wangi, Rojolele Delanggu, Genjah Arum, Kurik Kusut, Gilirang, Mentik Wangi, Inpari 7, Inpari 23, and Mentik Susu based on morphological and molecular identification. Morphological identification uses 8 variables i.e plant height, number of productive tillers, weight of 100 seeds, age of flowering, age of harvest, shape of grain, colour of grain and colour of rice. The analysis results realized in the form of a dendogram. Molecular identification using RAPD marker with 5 primers included OPB-01, OPB-04, OPB-06, OPB-7 and OPB-17. The DNA band profile translated into binary data with the provision of a value of 0 for no band and 1 for the presence of DNA bands in certain fragments. Both of data analysed into cluster using NTSYSpc software with DIST coefficient for morphological data and Jaccard-s Index for molecular data. The analysis results are realized in the form of dendogram and genetic similarity values. Results: Dendrogram of morphological data showed in 2 clusters, 2 sub-clusters and 2 groups. Cluster I was accopied by Rojolele Delanggu and Pandan Wangi. Cluster II devided into 2 groups. First group include Mentik Susu, Kurik Kusut, Inpari 23, Gilirang, Mentik Wangi, Pendok, Genjah Arum and second group include Inpari 7. Molecular kinship analysis used to determine the level of genetic similarity of 10 aromatic rice varieties based on RAPD-PCR. RAPD uses oligonucleotide primers that will bind to the complement site in the template DNA. The number of DNA bands has been amplified by each primer ranging from 4 to 8 DNA bands or an average 6 bands per pri
Keywords: Aromatic Rice, Genetic Diversity, Morphological Characteristics, and RAPD
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