Genetic diversity of Rhizophora mucronata in eastern region of Timor Island, Indonesia as revealed by RAPD
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Abstract. Ihwan, Uslan, Widodo, Hakim L. 2019. Genetic diversity of Rhizophora mucronata in eastern region of Timor Island, Indonesia as revealed by RAPD. Biodiversitas 20: 3364-3371. Mangrove ecosystems have essential functions in producing organic materials, protecting against erosion, and supporting the area between land and sea. Rhizophora mucronata is a dominant mangrove species in all coastal areas of Timor Island, East Nusa Tenggara, Indonesia. Recent reports suggest that mangroves have been affected by anthropogenic pressure and natural disasters. The aim of this study was to determine the genetic diversity of R. mucronata in the east region of Timor Island. This study is important in supporting mangrove protected management planning in the region. The sampling was carried out in six mangrove vegetation sites, DNA was isolated from the leaves and used for PCR-RAPD using six primers. Dendrogram analysis of the species was determined based on UPGMA (unweighted pair group method) and the similarity coefficient from Nei and Li using the MVSP program. The results showed that the six primers used generated a DNA length of 270-1345 bp, with the number of bands being 22-27. The percentage of polymorphism ranged from 73.91% to 86.96% in all primers used, with a polymorphic information content (PIC) value of 0.94. Thus, it can be concluded that the value of genetic diversity (He) from the R. mucronata mangrove population in Timor Island has a value of 0.666. The R. mucronata population in Abudenok and Tanjung Bastian has the highest genetic diversity with a value of 0.667, while the population in Tanjung Tuamese has the lowest genetic diversity with a value of 0.664. Based on the results of the dendrogram analysis, the R. mucronata population in Timor Island correlated with its geographical location. The adjacent populations have a tendency to form one subgroup.
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References
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Sambrook, J. and D. W. Russel. 2001. Molecular Cloning (A Laboratory Manual). Volume 1, Third Edition. New York: Cold Spring Harbor Laboratory Press.
Sharma, A., A. G. Namdeo and K.R.Mahadik. 2008. Molecular Markers: NewProspects in Plant Genome Analysis. Pharmacognosy Reviews 2 (3): 23-31.
Tao, J., Zhi-yong Luo, C. I. Msangi, Xiao-shun Shu, L. Wen, Shui-ping Liu,Chang-quan Zhou, Rui-xin Liu and Wei-xin Hu. 2009. Relatiomship Among Genetic Makeup, Active Ingredient Content and Place of Origin of the Medicinal Plant Gastrodia Tuber. Biochem Genet. 47:8-18.
Uslan dan Pharmawati. M. 2015. Optimasi Konsentrasi DNA dan MgCl2 pada Reaksi Polymerase Chain Reaction-Random Amplified Polymorphic DNA untuk Analisis Keragaman Genetik Tumbuhan Faloak (Sterculia quadrifida R.Br). Jurnal Bioslogos. 5(1) : 26-34.
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Mulyaningsih, E. S. dan Indrayani S. 2014. Keragaman Morfologi dan Genetik Padi Gogo Lokal Asal Banten (Phenotip and genetik variation for Banten Upland Rice Lokal Cultivars). Jurnal Biologi Indonesia, 10 (1):119-128
Dar, Aejaz Ahmad, Sushma Mudigunda, Pramod Kumar Mittal, and Neelakantan Arumugam. 2017. Comparative assessment of genetic diversity in Sesamum indicum L. using RAPD and SSR markers. 3 Biotech. 7(1): 10. doi: 10.1007/s13205-016-0578-4
Suryatini, K.Y. 2011. Analisis Keragaman Genetik Jarak Pagar (Jatropha Curcas L.) Dengan Metode Inter Simple Sequence Repeats (ISSR). Tesis. Program Magister, Program Studi Bioteknologi Pertanian, Program Pascasarjana Universitas Udayana. Denpasar.
Kayis, S. A., Hakki, E. E., and Pinarkara, E. Comparison of effectiveness of ISSR and RAPD markers in genetic characterization of seized marijuana (Cannabis sativa L.) in Turkey. African Journal of Agricultural Research, 5(21): 2925-2933
Devy, N. F. Dan Hardiyanto. 2017. Keragaman Jeruk Gunung Omeh (Citrus nobilis Lour.) di Sumatera Barat Berdasarkan Marka RAPD. J. Hort., 27(2): 155-164
Poerba, Y. S., Wawo, A. H., dan Yulita, K. S. 2007. Keragaman Fenotipe RAPD Santalum album L. di Pulau Timor Bagian Timur. Berita Biologi, 8 (6): 537-546
Giang, L. H., Geada, G. L., Hong, P. N., Tuan, M.S., Lien, N. T. H., Ikeda, S., & Harada, K.2006. Genetic variation of two mangrove species in Kandelia (Rhizophoraceae) in Vietnam and surrounding area revealed by microsatellite markers. Int. J. Plant Sci., 167(2): 291-298.
2015. Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives. Genetics Research International.
Nurtjahjaningsih, I. L.G., Haryanti, T., Widyatmoko, A.Y.P.B.C., Indrioko, S. dan Rimbawanto, A. 2015. Keragaman Genetik Populasi Calophyllum inophyllum Menggunakan Penanda RAPD (Random Amplification Polymorphism DNA). Jurnal Pemuliaan Tumbuhan Hutan, 9(2): 91-102
Sreekanth, P. M., Balasundaran, M., Nazeem, P. A., & Suma, T. B. (2012). Genetic diversity of nine natural Tectona grandis L.f. populations of the Western Ghats in Southern India. Conserv. Genet., 13, 1409-1419.
Sudheer, D.V.N., S.G. Mastan, H. Rahman and M.P. Reddy. 2010. Molecular
characterization and genetic diversity analysis of Jatropha
curcas L. in India using RAPD and AFLP analysis. Mol. Biol.
Rep., 37, 2249–2257
Tsuda, Y. and Ide, Y. (2005). Wide-range analysis of genetic structure of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in the cool temperate zone of Japan. Molecular Ecology, 14: 929-3941.
Ardiyani, M., Sulistyaningsih, L. D. dan Esthi, Y. N. 2014. Keragaman Genetik Tacca leontopetaloides (L.) Kuntze (Taccaceae) dari Beberapa Provenansi di Indonesia Berdasarkan Marka Inter Simple Sequence Repeats (ISSR). Berita Biologi, 13(1): 85-96
Manurung, Jeprianto, Iskandar Z. Siregar, Cecep Kusmana, Fifi Gus Dwiyanti. 2017. Genetic variation of the mangrove species Avicennia marina in heavy metal polluted estuaries of Cilegon Industrial Area, Indonesia. Biodiversitas. Volume 18, Number 3, July 2017. Pages: 1109-1115
Munthali, C. R. Y., Chirwa, P. W., Changadeya, W. J., & Akinnifesi, F. K. (2013). Genetic differentiation and diversity of Adansonia digitata L. (baobab) in Malawi using microsatellite markers. Agroforest Syst., 87, 117-130.
Wijayanto, T., Boer, D., dan Ente, L. 2013. Hubungan Kekerabatan Aksesi Pisang Kepok (Musa paradisiaca Formatypica) di Kabupaten Muna berdasarkan Karakter Morfologi dan Penanda RAPD. Jurnal Agroteknos, 3 (3): 163-170.
Bagindo, M. 2011. Keragaman Aksesi Pinang (Areca catechu L.) Asal Papua, Sulawesi Utara, dan Sumatera Utara berdasarkan Karakter Morfologi dan Penanda RAPD (Random Amplified Polymorphic DNA). Skripsi. Departemen Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam Institut Pertanian Bogor. Bogor.
Arisetianingsih, R. E. D., Totok, A. D. H., dan Prakoso, B. 2010. Keragaman Genetik Kedelai Berdasarkan Pola Pita DNA Hasil RAPD (Random Amplified Polymorphic DNA). Agrin, 14 (1): 37-43.
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Hamrick JL and MJW Godt. 1996. Effects of Life History Traits on Genetic Diversity in Plant Species. Phil. Trans. R. Soc. Lond. B 351, 1291-1298.
Hogbin PM and R Peakall. 1999. Evaluation of the Contribution of Genetic Research to the Management of the Endangered Plant Zieria prostata. Conservation Biology 13: 514-522.
Rahayu, S. E. dan Handayani, S. 2010. Keragaman Genetik Pandan Asal Jawa Barat Berdasarkan Penanda Inter Simple Sequence Repeat (ISSR). Makara Sains, 14 (02): 158-162
Romañach, Stephanie S., Donald L. DeAngelis, Hock Lye Koh, Yuhong Li, Su YeanTeh, Raja Sulaiman Raja Barizan, Lu Zhai. 2018. Conservation and restoration of mangroves: Global status, perspectives, and prognosis. Ocean and coastal management. 154: 72-82
Arif, Ibrahim A., Mohammad A. Bakir, Haseeb A. Khan, Ahmad H. Al Farhan, Ali A. Al Homaidan, Ali H. Bahkali, Mohammad Al Sadoon, and Mohammad Shobrak. 2010. A Brief Review of Molecular Techniques to Assess Plant Diversity. Int J Mol Sci. 11(5): 2079–2096. doi: 10.3390/ijms11052079
Bardakci, F. 2001. Random Amplified Polymorphic DNA (RAPD) Markers. Turk. J. Biol. 25:185-196.
Bekessy, S. A., Allnutt, T.R., Premoli, A. C., Lara, A., Ennos, R. A., Burgman, M.A., Cortes, M. and Newton, A. C. 2002. Genetic Variation In The Vulnerable And Endemic Monkey Puzzle Tree, Detected Using RAPDs. Heredity, 88 : 243-249.
Bengen, D. G. 2003. Pedoman teknis: Pengenalan dan pengelolaan ekosistem mangrove. PKSPL-IPB. Bogor.
Chapman, V.J. 1976. Mangrove Vegetation. J. Cramer, Valduz, 447 hal.
Chapman, V.J. editor. 1977. West Coastal Ecosystems. Ecosystems of the World: 1. Elsevier Scientific Publishing Company, 428 hal.
Demeke, T. and R. P. adams. 1994. The Use of PCR-RAPD Analysis in Plant Taxonomy and Evolution. In: Griffin, H. G. and A. M. Griffin. Eds. PCR Technology: Current Innovations. Boca Raton. CRC Press: 179-191.
Ernawati dan A. Majid. 2013. Studi Vegetasi Mangrove di Zona Intertidal Desa Oebelo Kecamatan Kupang Tengah Kabupaten Kupang. Jurnal Biologi dan Kesehatan. 1 (2); 34 – 40.
Elrod, S. dan W. Stansfield. 2007. Genetika. (Damaring Tyas W. Pentj). Jakarta: Erlangga.
Finkeldey, R. 2005. Pengantar Genetika Hutan Tropis. Jamhuri E., Siregar IZ., Siregar UJ., Kertadikarta AW., Penerjemah. Gottingen: Institute of Forest Genetics And Forest Tree Breeding Georg-August-Univerity-Gottingen. Terjemahan dari : An Introduction To Tropical Forest Genetics.
Frankham, R., Ballou, J. D. and Briscoe, D.A. 2002. Introduction to Conservation Genetics. UK: Cambridge University Press.
Yahyah, 1997. Studi Hutan Mangrove di Pulau Pasir Menifo Kecamatan Amarasi Kabupaten Kupang – NTT. Majalah Ilmiah KOPERTIS Wilayah VIII Edisi 19 tahun ke-9.
Hazarika, Dimendra, M. Thangaraj, Sunil Kumar Sahu and K. Kathiresan. 2013. Genetic diversity in three populations of Avicennia marina along the eastcoast of India by RAPD markers. Journal of Environmental Biology. 34: 663-666.
Jamsari. 2007. Bioteknologi Pemula: Prinsip Dasar dan Aplikasi Analisis Molekuler. Riau: UNRI Press.
Koda, S.H. 2013. Partisipasi Masyarakat Pesisir dalam Pelestarian Ekosistem Mangrove di Desa Nunkurus Teluk Kupang. Jurnal Biologi dan Kesehatan. 1 (2); 8 – 17.
__________. 2014. Partisipasi Masyarakat Pesisir dalam Pelestarian Ekosistem Mangrove di Desa Bipolo Teluk Kupang. Jurnal Biologi dan Kesehatan. 1 (3); 41 – 50.
Kusmana, C. 1995. Manajemen Hutan Mangrove Indonesia. Lab Ekologi Hutan. Jurusan Manajemen Hutan, Fakultas Kehutanan, IPB. Bogor
Lira-Medeiros, Catarina Fonseca, Mônica Aires Cardoso, Ricardo Avancini Fernandes and Paulo Cavalcanti Gomes Ferreira. 2015. Analysis of Genetic Diversity of Two Mangrove Species with Morphological Alterations in a Natural Environment. Diversity. 7:105-117
Noor, Y.R., Khazali R dan Suryadiputra I.N.N. 1999. Panduan Pengenalan Mangrove di Indonesia. PHKA/WI-IP, Bogor.Wetlands International-Indonesian Programme.
Pandin, D. S. 2010. Penanda DNA Untuk Pemuliaan Tumbuhan Kelapa (Cocos nucifera L.). Balai Penelitian Tumbuhan Kelapa dan Palma Lain. Perspektif, 9(1) : 21-35.
Rusydi, Ihwan, Suaedin, L.N.L. Toruan, I. Angwarmase, Y. Fajarianto. 2014. Base Line Data Kualitas Air dan Biota Perairan di Teluk Kupang Sebelum Pengoperasian PLTU di Bolok Kec. Kupang Barat. Laporan Hasil Penelitian Kerjasama dengan PT. Timor Otzuki Mutiara.
Rusydi. 2010. Studi Keanekaragaman dan Kelimpahan Jenis Mangrove di Pantai Paradiso Kota Kupang. Jurnal Madani Universitas Muhammadiyah Kupang. Edisi Februari.
Sahao, P., Jena, S., Mohanty and Bandhu, D. A. 2007. Molecular phylogenetic relationship among four species of the mangrove tree genus Bruguiera (Rhizophoeraciae), as revealed by chromosome and RAPD markersREV. Biol. Trop. 55(2): 437-448.
Sambrook, J. and D. W. Russel. 2001. Molecular Cloning (A Laboratory Manual). Volume 1, Third Edition. New York: Cold Spring Harbor Laboratory Press.
Sharma, A., A. G. Namdeo and K.R.Mahadik. 2008. Molecular Markers: NewProspects in Plant Genome Analysis. Pharmacognosy Reviews 2 (3): 23-31.
Tao, J., Zhi-yong Luo, C. I. Msangi, Xiao-shun Shu, L. Wen, Shui-ping Liu,Chang-quan Zhou, Rui-xin Liu and Wei-xin Hu. 2009. Relatiomship Among Genetic Makeup, Active Ingredient Content and Place of Origin of the Medicinal Plant Gastrodia Tuber. Biochem Genet. 47:8-18.
Uslan dan Pharmawati. M. 2015. Optimasi Konsentrasi DNA dan MgCl2 pada Reaksi Polymerase Chain Reaction-Random Amplified Polymorphic DNA untuk Analisis Keragaman Genetik Tumbuhan Faloak (Sterculia quadrifida R.Br). Jurnal Bioslogos. 5(1) : 26-34.
Weir, B. S. 1990. Genetic Data Analysis: Methods for Discrete Genetic Data. Sunderland: Sinauer Associates.
Mulyaningsih, E. S. dan Indrayani S. 2014. Keragaman Morfologi dan Genetik Padi Gogo Lokal Asal Banten (Phenotip and genetik variation for Banten Upland Rice Lokal Cultivars). Jurnal Biologi Indonesia, 10 (1):119-128
Dar, Aejaz Ahmad, Sushma Mudigunda, Pramod Kumar Mittal, and Neelakantan Arumugam. 2017. Comparative assessment of genetic diversity in Sesamum indicum L. using RAPD and SSR markers. 3 Biotech. 7(1): 10. doi: 10.1007/s13205-016-0578-4
Suryatini, K.Y. 2011. Analisis Keragaman Genetik Jarak Pagar (Jatropha Curcas L.) Dengan Metode Inter Simple Sequence Repeats (ISSR). Tesis. Program Magister, Program Studi Bioteknologi Pertanian, Program Pascasarjana Universitas Udayana. Denpasar.
Kayis, S. A., Hakki, E. E., and Pinarkara, E. Comparison of effectiveness of ISSR and RAPD markers in genetic characterization of seized marijuana (Cannabis sativa L.) in Turkey. African Journal of Agricultural Research, 5(21): 2925-2933
Devy, N. F. Dan Hardiyanto. 2017. Keragaman Jeruk Gunung Omeh (Citrus nobilis Lour.) di Sumatera Barat Berdasarkan Marka RAPD. J. Hort., 27(2): 155-164
Poerba, Y. S., Wawo, A. H., dan Yulita, K. S. 2007. Keragaman Fenotipe RAPD Santalum album L. di Pulau Timor Bagian Timur. Berita Biologi, 8 (6): 537-546
Giang, L. H., Geada, G. L., Hong, P. N., Tuan, M.S., Lien, N. T. H., Ikeda, S., & Harada, K.2006. Genetic variation of two mangrove species in Kandelia (Rhizophoraceae) in Vietnam and surrounding area revealed by microsatellite markers. Int. J. Plant Sci., 167(2): 291-298.
2015. Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives. Genetics Research International.
Nurtjahjaningsih, I. L.G., Haryanti, T., Widyatmoko, A.Y.P.B.C., Indrioko, S. dan Rimbawanto, A. 2015. Keragaman Genetik Populasi Calophyllum inophyllum Menggunakan Penanda RAPD (Random Amplification Polymorphism DNA). Jurnal Pemuliaan Tumbuhan Hutan, 9(2): 91-102
Sreekanth, P. M., Balasundaran, M., Nazeem, P. A., & Suma, T. B. (2012). Genetic diversity of nine natural Tectona grandis L.f. populations of the Western Ghats in Southern India. Conserv. Genet., 13, 1409-1419.
Sudheer, D.V.N., S.G. Mastan, H. Rahman and M.P. Reddy. 2010. Molecular
characterization and genetic diversity analysis of Jatropha
curcas L. in India using RAPD and AFLP analysis. Mol. Biol.
Rep., 37, 2249–2257
Tsuda, Y. and Ide, Y. (2005). Wide-range analysis of genetic structure of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in the cool temperate zone of Japan. Molecular Ecology, 14: 929-3941.
Ardiyani, M., Sulistyaningsih, L. D. dan Esthi, Y. N. 2014. Keragaman Genetik Tacca leontopetaloides (L.) Kuntze (Taccaceae) dari Beberapa Provenansi di Indonesia Berdasarkan Marka Inter Simple Sequence Repeats (ISSR). Berita Biologi, 13(1): 85-96
Manurung, Jeprianto, Iskandar Z. Siregar, Cecep Kusmana, Fifi Gus Dwiyanti. 2017. Genetic variation of the mangrove species Avicennia marina in heavy metal polluted estuaries of Cilegon Industrial Area, Indonesia. Biodiversitas. Volume 18, Number 3, July 2017. Pages: 1109-1115
Munthali, C. R. Y., Chirwa, P. W., Changadeya, W. J., & Akinnifesi, F. K. (2013). Genetic differentiation and diversity of Adansonia digitata L. (baobab) in Malawi using microsatellite markers. Agroforest Syst., 87, 117-130.
Wijayanto, T., Boer, D., dan Ente, L. 2013. Hubungan Kekerabatan Aksesi Pisang Kepok (Musa paradisiaca Formatypica) di Kabupaten Muna berdasarkan Karakter Morfologi dan Penanda RAPD. Jurnal Agroteknos, 3 (3): 163-170.
Bagindo, M. 2011. Keragaman Aksesi Pinang (Areca catechu L.) Asal Papua, Sulawesi Utara, dan Sumatera Utara berdasarkan Karakter Morfologi dan Penanda RAPD (Random Amplified Polymorphic DNA). Skripsi. Departemen Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam Institut Pertanian Bogor. Bogor.
Arisetianingsih, R. E. D., Totok, A. D. H., dan Prakoso, B. 2010. Keragaman Genetik Kedelai Berdasarkan Pola Pita DNA Hasil RAPD (Random Amplified Polymorphic DNA). Agrin, 14 (1): 37-43.
Nei, M. 1987. Moleculer Evolutionary Genetics. Columbia University Press. New York.
Langga, I. F., Restu, M., dan Kuswinanti, T. 2012. Optimalisasi Suhu dan Lama Inkubasi dalam Ekstraksi DNA Tumbuhan Bitti (Vitex covassus Reinw) Serta Analisis Keragaman Genetik dengan Teknik RAPD-PCR. Jurnal Sains & Teknologi, 12 (3): 265-276.
Hamrick JL and MJW Godt. 1996. Effects of Life History Traits on Genetic Diversity in Plant Species. Phil. Trans. R. Soc. Lond. B 351, 1291-1298.
Hogbin PM and R Peakall. 1999. Evaluation of the Contribution of Genetic Research to the Management of the Endangered Plant Zieria prostata. Conservation Biology 13: 514-522.
Rahayu, S. E. dan Handayani, S. 2010. Keragaman Genetik Pandan Asal Jawa Barat Berdasarkan Penanda Inter Simple Sequence Repeat (ISSR). Makara Sains, 14 (02): 158-162
Romañach, Stephanie S., Donald L. DeAngelis, Hock Lye Koh, Yuhong Li, Su YeanTeh, Raja Sulaiman Raja Barizan, Lu Zhai. 2018. Conservation and restoration of mangroves: Global status, perspectives, and prognosis. Ocean and coastal management. 154: 72-82
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