Genetic Diversity of Black and Aromatic Rice Cultivar (Oryza sativa L.) from Various Regions in Indonesia using Random Amplified Polymorphic DNA Markers (RAPD)

Ummi Sholikhah, - Parjanto, Tri Handoyo, Ahmad Yunus

Abstract


Indonesia is one of many countries with a high potential for genetic diversity resource of rice plants, both black rice, and aromatic rice. Therefore, the kinship relationship in each cultivar of which results are not influenced by the environment can be determined by molecular methods, one of which is by using RAPD analysis. This research employed 20 RAPD primers and DNA genome materials used in isolation from ten black rice cultivars, and 15 aromatic rice cultivars. The research stage began with a collection of black rice and aromatic rice germ plasma in several regions in Indonesia, seed nursery, DNA isolation, DNA quantity, and quality testing, primary selection, RAPD, running RAPD, and phylogenetic analysis. The objectives of this research were to obtain phylogenetic diversity of black and aromatic rice in this analysis. Twenty RAPD primers used to amplify 10 black rice cultivars and 15 aromatic rice cultivars obtained 180 polymorphic DNA Ribbons, with an average percentage of 89.2%. The genetic diversity of all cultivars analyzed was considerably high. At 84% coefficient, two major groups were obtained: black rice and aromatic rice, divided into eight small groups. The results of the phylogenetic analysis demonstrate high diversity between black rice and aromatic rice. Such a thing can be a first step for selecting rice plants which will be taken as plant parent in the crossbreeding.


Keywords


RAPD; cultivar; black rice; aromatic rice.

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References


Chaudary, R.C. and D.V. Tran. 2001. Speciality Rices of the World: A Prologue. In Speciality Rices of the World; Breeding, Production and Marketing. Enfield, N.H. (USA) :Science Publishers. Inc. and FAO. p. 3-12.

Murdifin M, Pakki E, Rahim A, Syaiful SA, Ismail, EvaryYM and Baha, 2015, Physicochemical properties of Indonesian pigmented Rice (Oryza sativa Linn.)varieties from South Sulawesi.Asian JPlant Sci,14(2): 59-65.18.

Hu, C.; Kitts, D. D., 2001, Evaluation of antioxidant activity of epigallocatechin gallate in biphasic model systems in Vitro. Mol. Cell. Biochem, 218, 147-155.

Hu, C.; Zhang, Y.; Kitts, D. D.,2000, Evaluation of antioxidant and prooxidant activities of bamboo Phyllostachys nigra var. Henonisleaf extract in Vitro. J. Agric. Food Chem, 48, 3170 - 3176.

Tsuda, T.; Horio, F.; Osawa, T, 1999 . Absorption and metabolism ofcyanidin-3-O-â-glucoside in rats. FEBS Lett., 449, 179-182.

Oikawa T, Maeda H, Oguchi T, Yamaguchi T, Tanabe N, Ebana K, Yano M, Ebitani T, and Izawa T, 2015 :The birth of a black rice gene and its local spreadby introgression. Plant Cell ,27(9): 2401-14

Hu, C.; Kitts, D. D, 2001. Evaluation of antioxidant activity of epigallocatechin gallate in biphasic model systems in Vitro. Mol. Cell. Biochem, 218, 147-155.

Lee, J. C., Kim, J. D., Hsieh, F. H., & Eun, J. B. 2008. Production of black rice cake using ground black rice and medium‐grain brown rice. International journal of food science & technology, 43(6), 1078-1082

Pratiwi, R., Tunjung, W. A. S., Rumiyati, R., & Amalia, A. R. 2016. Black Rice Bran Extracts and Fractions Containing Cyanidin 3-glucoside and Peonidin 3-glucoside Induce Apoptosis in Human Cervical Cancer Cells. Indonesian Journal of Biotechnology, 20(1), 69-76.

Sui, X., Zhang, Y., & Zhou, W. 2016. Bread fortified with anthocyanin-rich extract from black rice as nutraceutical sources: Its quality attributes and in vitro digestibility. Food chemistry, 196, 910-916.

Buttery, R.G., Juliano, B.O., Ling, L.C. 1983. Identification of rice aroma compound 2-acetyl-1-pyrroline in pandan leaves.Chemical Industries (London) 20: 478.

Buttery, R.G., Ling, L.C., Juliano, 1982. B.O. 2- Acetyl-1-pyrroline: an important aroma component of cooked rice. Chemical Industries (London) 19: 958.

Chen, S., Yang, Y., Shi, W., Ji, Q., He, F., Zhang, Z., Cheng, Z., Liu, X., Xua, M. Badh2, 2008. encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell.

Rokas, Antonis, 2011 phylogenetic Analysis of Proten Sequence Data Using the Randomized Axelerated Maximum Likelihood (RAXML) Program. Wiley Online Library. UNIT 19.11

Arif S. A., Ma, N.L., Mahmoud, A, Rahmat, Z., 2016. Molekuler Phylogeny and Structure Prediction Of Rice RFTI Protein. Jurnal Tekhnologi. Vol. 78 (2)

Jonah, P. M. Bello, L. Lucky, O., Midau A., Moruppa, S.M. 2011, Review The Importance of Moleculer Markers in Plant Breeding Programmes International Research Journal Vol. 11 (5)

Sing, R., K.. 2000. Aromatic Rices., Calcuta: Oxfford & IBH Publishing Co. Pvt.

Horrike Tokumasa, 2016. An Introduction To Molecular Phylogenetic Analysis Reviews In Agriculture Science, Vol. 4, 34 -45.

Abbas, Y. A dan Radhi, G. F, 2017, Genetic Variation of Enterobacter coaceae Using Random Amplified Polymorphic DNA RAPD-PCR Technique, Donnish Journal of Microbiology and Biotechnology Research Vol 4 (3) pp. 010-123.

Doyle, JJ and Doyle, J, L, 1987, A Rapid DNA Isolation Prosedure For Small Quatities of Fresh leaf Tissue ,Phytochemical Bulletin, Vol 19, no. 1, p. 11-15

Mordechai, E, 1999. Application of PCR The Methodologies in Molecular Diagnostic, Burlington Country, USA

Saiki R.K, 1989, The Desain and Optimization of the PCR, Pages: 7- 16 in Erlich, H.A (ed) PCR Technology. Principle and Appplication for DNA Amplification.

Rohlf, F J. 2000, NT SYS-pc: Numerical Taxonomy and Multivariate Analysis System Version 2.1 User Guide. Departemen Of Ecology and Evalution State Universyty of New York

Widden B and Svwenson L, 1992 Concervation of Genetic Variation in Plant- The Importan of Population Size and Gene Flow. In: Ecological Principle Of Nature Conservation. Hansson L (ed) Elsevier Applied Science, London, pp 113 – 161

Tingey, S.V., J.A Rafalski, and M. K. Hanafey, 1994. Genetic Analysis with RAPD marker In: Corruzi, C and P Puidormenech (eds) Plant Molecular Biology Beli: Springer- Verlag.

Vi, K. 2017 Using RAPD PCR Method for Studying DNA Polymorphism of Agriculture Importance Arthropods. Agriculture Research And Technology. Vol 9 (4).




DOI: http://dx.doi.org/10.18517/ijaseit.9.3.8382

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