Identification of Genetic Relationship of Local Rice in East Java Based on gene matK

Kurniawan Setia Putra, Dwi Listyorini, Suharti Suharti


Genetic diversity in living things is very important in the fulfillment of germplasm and conservation activities. East Java local rice is not so much cultivated farmers, so that the existence of local rice has begun to be replaced with new varieties and it is feared will happen genetic erosion of local rice. The purpose of this study to identify the genetic relationships of local rice and phylogenetic position of the rice contained in the Gene Bank. The method used to identify a molecular genetic using short pieces of DNA called DNA barcode. The results of this study indicate that the three local varieties of Berlian (Br), Genjah Harum (Gh) and Jawa (Jw) varieties can be identified by the matK gene barcode. The results of electrophoresis visualization showed that the DNA bands of the three samples were 900 bp. The results of DNA BLAST analysis show that the genetic relationships level with Oryza sativa and Oryza rufipogon is 100%. The results of the phylogenetic tree analysis showed that East Java's local rice was in one taxa with other rice and had a confidence level above 50


Genetic, Local rice, DNA barcode, Gene matK

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Claverie, J.-M., & Notredame, C. (2007). Bioinformatics for Dummies. 2nd edition. Wiley Publishing, Inc. Indiana, 417 pp.

Djong, H. T., Iskandar, D. T., & Gusman, D. (2010). Hubungan Filogenetik Spesies Limnonectes (Ranidae: Amphibia) Asal Sumatera Barat Dan Asal Asia Tenggara Berdasarkan Gen 16s Ribosomal RNA. Makara, Sains, 14(1), 79–87.

Dong, L., Lv, L.-B., & Lai, R. (2012). [Molecular cloning of Tupaia belangeri chinensis neuropeptide Y and homology comparison with other analogues from primates]. Zool. Res. (Vol. 33).

Ge, H., Sun, L., & Yu, J. (2017). Fast batch searching for protein homology based on compression and clustering. BMC Bioinformatics, 18(1), 1–12.

Hairmansis, A. (2017). Variability of upland rice genotypes response to low light intensity. Biodiversitas, Journal of Biological Diversity, 18(3), 1122–1129.

Hajibabaei, M., Smith, M. A., Janzen, D. H., Rodriguez, J. J., Whitfield, J. B., & Hebert, P. D. N. (2006). A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes, 6(4), 959–964.

Hebert, P. D. N., Cywinska, A., Ball, S. L., & DeWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270(1512), 313–321.

Hollingsworth, P. M., Graham, S. W., & Little, D. P. (2011). Choosing and using a plant DNA barcode. PLoS ONE, 6(5).

Kalangi, C., Kamu, V. S., & Kumaunang, M. (2014). DNA Tanaman Leilem minahassae L .) Berdasarkan Gen matK ( Clerodendrum, 3(2), 108–112.

Molecular Systematics of Plants II. (1998).

Nugraha, F., Roslim, D. I., Ardilla, Y. P., & Herman. (2014). Biosaintifika. Biosaintifika, 6(2), 94–103.

Nurhasanah, N. (2015). Keragaman genetik padi lokal Kalimantan Timur, 1, 1553–1558.

Rabbani, M. A., Pervaiz, Z. H., & Masood, M. S. (2008). Genetic diversity analysis of traditional and improved cultivars of Pakistani rice (Oryza sativa L.) using RAPD markers. Electronic Journal of Biotechnology, 11(3).

Sitaresmi, T., Wening, R. H., Rakhmi, A. T., Yunani, N., & Susanto, U. (2013). Pemanfaatan Plasma Nutfah Padi Varietas Lokal dalam Perakitan Varietas Unggul. Iptek Tanaan Pangan, 8(1), 22–30.

Subhas Chandra, R. (2015). DNA Barcoding for Wild Rice [Oryza rufipogon Griff.] of NBU Campus Based on matK gene and Assessment of Genetic Variation Using DREB and BAD2 Gene Sequences. Plant Gene and Trait, 6(5), 1–10.

Suhartini, T., Somantri, I. H., & Abdullah, B. (2003). Rejuvenasi dan Karakterisasi Plasma Nutfah Spesies Padi Liar. Buletin Plasma Nutfah, 9, 16–25.

Ward, P. S., Brady, S. G., Fisher, B. L., & Schultz, T. R. (2010). Phylogeny and biogeography of dolichoderine ants: Effects of data partitioning and relict taxa on historical inference. Systematic Biology, 59(3), 342–362.

Zodinpuii, D., Ghatak, S., Mukherjee, S., & Kumar, N. S. (2013). Genetic relatedness of genus Oryza from Eastern Himalayan region as revealed by chloroplast matK gene, 2(2), 144–151.



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