Genetic diversity of Sterculia quadrifida in Kupang, Indonesia based on RAPD (Random Amplified Polymorphic DNA) markers
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Abstract. Uslan, Pharmawati M. 2020. Genetic diversity of Sterculia quadrifida in Kupang, Indonesia based on RAPD (Random Amplified Polymorphic DNA) markers. Biodiversitas 21: 3407-3414. This study aims to determine the genetic diversity of Sterculia quadrifida R.Br. in Kupang based on RAPD markers. Samples of S. quadrifida were collected from the yard and community forest in Kupang City (Sub-districts of Oebobo, Kelapa Lima, Maulafa, and Alak) and mixed forest in the Kupang District (Sub-districts of Kupang Barat, Nekamese, Taebenu, and Fatuleu). DNA was isolated by the CTAB method and amplified by six RAPD primers (OPD-11, OPF-11, UBC-106, UBC-127, UBC-250, and OPB-04). The data were analyzed in the MVSP software using UPGMA method and Nei & Li similarity coefficient. Total of 131 DNA bands ranging from 250-1400 bp was obtained. Populations of S. quadrifida in Kupang were divided into two main clusters and 12 sub-clusters with. The highest genetic diversity was found in Kelapa Lima of 0.1050, while the lowest genetic diversity was found in S. quadrifida population in Fatuleu of 0.0305. The population of S. quadrifida in Kupang has high genetic diversity and also clustered based on their geographical distribution
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References
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Hahn CZ, Michalski SG, Fischer M, Durka W. 2017. Genetic Diversity and Differentiation Follow Secondary Succession in a Multi-Species Study on Woody Plants from Subtropical China. Journal of Plant Ecology 10 (1): 213-221.
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Nikmah IA, Azrianingsih R, Wahyudi D. 2016. Genetic diversity of porang populations (Amorphophallus muelleri Blume) in Central Java and West Java based on LEAFY second intron marker. Journal of Tropical Life Science 6 (1), 23-27
Ozbek O, Kara A. 2013. Genetic variation in natural populations of Capparis from Turkey, as revealed by RAPD analysis. Plant Systematics and Evolution 299: 1911–1933.
Pharmawati M. 2009. Optimalisasi Ekstraksi DNA dan PCR-RAPD pada Grevillea spp. (Proteaceae). Jurnal Biologi 13(1): 12-16. [Indonesian]
Plenk K, Bardy K, Höhn M, Kropf M. 2019. Long?term survival and successful conservation? Low genetic diversity but no evidence for reduced reproductive success at the north?westernmost range edge of Poa badensis (Poaceae) in Central Europe. Biodiversity and Conservation 28:1245–1265. DOI: https://doi.org/10.1007/s10531-019-01722-x
Pratiwi P. 2012. Analisis Variasi Genetik Beberapa Populasi Globba leucantha Miq. di Sumatera Barat Dengan Random Amplified Polymorphic DNA (RAPD). [Thesis]. Program Pascasarjana Universitas Andalas, Padang. [Indonesian]
Probojati RT, Wahyudi D, HapsariL. 2019. Clustering Analysis and Genome Inference of Pisang Raja Local Cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker. Journal of Tropical Biodiversity and Biotechnology 4 (02): 42-53
Rahiman FOM, Balasubramanian T, Pawan K, Shejina M. 2015. National conference on Advances in Laboratory Medicine: P-44 Random Amplified polymorphic DNA (RAPD) – A Tool for Gene Mapping.
Ranta F. 2011. Sifat Anti Mikroba Zat Ekstraktif Pohon Faloak. [Thesis]. Program Pascasarjana Institut Pertanian Bogor, Bogor. [Indonesian]
Rimbawanto, A, Widyatmoko, Sulistyowati P. 2006. Distribusi Keragaman Genetik Santalum album Berdasarkan Penanda RAPD (Random Amplified Polymorphic DNA) . Jurnal Pemuliaan Tanaman Hutan 3: 175-181. [Indonesian]
Sambrook J, Russel DW. 2001. Molecular Cloning (A Laboratory Manual). Cold Spring Harbor Laboratory Press, New York.
Saragih GS, Siswadi S. 2019. Antioxidant Activity of Plant Parts Extracts from Sterculia quadrifida R.Br. Asian Journal of Pharmeceutical and Clinical Research 12 (7): 143-148.
Elly JB, Abdurrouf, Juswono UP. 2015. Effect of Sterculia quadrifide Extract R.Br. Against Free Radical in Liver Organs Oreochromis niloticus Due to Heavy Metal Pollution. Natural B, Journal of Health and Environmental Sciences 3(2): 175-181 doi:http://dx.doi.org/10.21776/ub.natural-b.2015.003.02.11.
Siswadi, Grace SS, Heny R. 2013. Potential Distributions And Utilization of Faloak (Sterculia quadrifida R.Br. 1844) on Timor Island, East Nusa Tenggara. Prooceding International Conference Forest and Biodiversity. Balai Penelitian Kehutanan Kupang Press, Kupang. [Indonesian]
Sukhumsirichart W. 2018. Polymorphisms. In: Yamin L (eds) Genetic diversity and Disease Susceptibility. IntechOpen, Arizona.
Sundari, Arumingtyas EL, Hakim L, Azrianingsih R, Wahyudi D. 2017. Genetic variability of local durian (Durio zibethinus Murr.) in Ternate Island based on RAPD markers. Plant Cell Biotechnology and Molecular Biology 18 (1): 68-75.
Suryatini KY. 2011. Analisis Keragaman Genetik Jarak Pagar (Jatropha curcas L.) dengan Metode Inter Simple Sequence Repeats (ISSR). [Thesis]. Program Magister, Program Studi Bioteknologi Pertanian, Program Pascasarjana Universitas Udayana, Denpasar. [Indonesian]
Wahyudi D, Hapsari L, Sundari. 2020. RAPD Analysis for Genetic Variability Detection of Mutant Soybean (Glycine max (L.) Merr). Journal of Tropical Biodiversity and Biotechnology 5 (1): 68-77.
Wahyudi D, Rifliyah K, Uslan. 2020. Genome evaluation of banana cultivars based on morphological character and Inter-Simple Sequence Repeat (ISSR) molecular marker. 21(7): 2982-2990. https://doi.org/10.13057/biodiv/d210715
Winata A, Triana H, Purwantiningsih, Siswadi. 2019. In vivo Immunomodulatory Activity of Faloak Bark Extract (Sterculia quadrifida R.Br). Pakistan Journal of Biological Sciences 22 (12): 590-596.
Wistiani, L. A. J. 2014. Induksi Mutasi Kromosom Dengan Kolkisin pada Tanaman Kesuna Bali (Allium sativum Linn.) dan Analisis DNA Dengan Mrka RAPD (Random Amplified Polymorphic DNA). [Thesis]. Program Magister, Program Studi Ilmu Biologi, Program Pascasarjana Universitas Udayana, Denpasar. [Indonesian]
Yulita KS, Rahmat HH. 2019. Population Genetic Structure and Diversity of a Critically Endangared Ramin [Gonystylus bancanus Miq.(Kurz),Thymelaeaceae] form Kalimantan and Sumatera based on Sequence Random Amplified Polymorphism. Earth and Environmental Science 308: 1-9
Bhandari HR, Bhanu AN, Srivastava K, Singh MN, Shreya, Hemantaranjan A. 2017. Assessment of Genetic Diversity in Crop Plants – An Overview. Advances in Plants & Agriculture Research 7 (3): 0025.
Bzdega K, Agnieszka J, Tomasz K, Agata L, Ma?gorzata G, Elwira S, Barbara TG. 2016. A Survey of Genetic Variation and Genome Evolution within the Invasive Fallopia Complex. PloS ONE 11(8): e0161854.
Candra IP. 2011. Keragaman Genetik Nilam (Pogostemon cablin Benth) yang di Budidayakan di Bali Berdasarkan Marka Random Amplified Polymorphic DNA (RAPD). [Thesis]. Program Magister, Program Studi Bioteknologi Pertanian, Program Pascasarjana Universitas Udayana, Denpasar. [Indonesian]
Carvalho YGS , Luciana CV, Ueric JBS, Layara AB. 2019. Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation. Diversity 11 (62): 1-21.
Damayanto IPGP. 2012. Keragaman Genetik dan Kunci Sidik Jari DNA Kultivar Salak Bali [Salacca zalacca var. amboinensis (Beccari) Mogea] Berdasarkan Penanda RAPD (Random Amplified Polymorphic DNA). [Thesis]. Program Magister, Program Studi Ilmu Biologi, Program Pascasarjana Universitas Udayana, Denpasar. [Indonesian]
Dayarani M, Dhanarajan MS. 2014. Diversity and phylogenetic analysis of the genus Musa. International Journal of ChemTech Research 6 (4): 2357-2762.
Doyle JJ, Doyle JL. 1990. Isolation of Plant DNA from Fresh Tissue. Focus 12: 13-15.
Ellegren H, Galtier N. 2016. Determinants of genetic diversity. Nature Reviews Genetics 17(7): 422-33.
Finkeldey R. 2005. Pengantar Genetika Hutan Tropis. Jamhuri E., Siregar IZ., Siregar UJ., Kertadikarta AW., Penerjemah. Institute Of Forest Genetics And Forest Tree Breeding Georg-August-Univerity-Gottingen, Gottingen. Terjemahan dari : An Introduction To Tropical Forest Genetics.
Graebner RC, Hayes PM, Hagerty CH, Cuesta-Marcos A. 2016. A comparison of polymorphism information content and mean of transformed kinships as criteria for selecting informative subsets of barley (Hordeum vulgare L. s. l.) from the USDA Barley Core Collection. Genet Resour Crop Evol (2016) 63:477–482. DOI 10.1007/s10722-015-0265-z
Govindaraj M, Vetriventhan M and Srinivasan M. 2015. Gen Res Int 431487: 1-14. DOI: https://doi.org/10.1155/2015/431487
Gusmiati LH, Hapsari L, Wahyudi D. 2018. Keragaman dan pengelompokan morfologi 10 pisang olahan (Musa cv. Grup ABB) koleksi Kebun Raya Purwodadi LIPI. Floribunda 5 (8): 299-313. [Indonesian]
Hahn CZ, Michalski SG, Fischer M, Durka W. 2017. Genetic Diversity and Differentiation Follow Secondary Succession in a Multi-Species Study on Woody Plants from Subtropical China. Journal of Plant Ecology 10 (1): 213-221.
Hapsari L, Wahyudi D, Azrianingsih R, Arumingtyas EL. 2015. Genome identification of bananas (Musa L.) from East Java Indonesia assessed with PCR-RFLP of the internal transcribed spacers nuclear ribosomal DNA. International Journal of Biosciences 7 (3): 42-52
Hertiani T, Purwantiningsih, Aji W, Widyandani S, Rima M, Erna PS, Retno M, Siswadi. 2019. In Vitro Immunomodulatory and Cytotoxic Potentials of Faloak (Sterculia quadrifida R.Br.) Bark. OnLine Journal of Biological Sciences 19 (4): 222-231.
Kusumadewi Y, Poerba YS, Partomihardjo T. 2010. Keragaman Genetika Ramin (Gonystylus bancanus (Miq.) Kurz) dari Provinsi Riau Berdasarkan Profil Random Amplified Polymorphic DNA (RAPD). Jurnal Biologi Indonesia 6 (2): 173-183. [Indonesian]
Lorenz TC. 2012. Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies. Journal of Visualized Experiments 63: 1-15.
Nikmah IA, Azrianingsih R, Wahyudi D. 2016. Genetic diversity of porang populations (Amorphophallus muelleri Blume) in Central Java and West Java based on LEAFY second intron marker. Journal of Tropical Life Science 6 (1), 23-27
Ozbek O, Kara A. 2013. Genetic variation in natural populations of Capparis from Turkey, as revealed by RAPD analysis. Plant Systematics and Evolution 299: 1911–1933.
Pharmawati M. 2009. Optimalisasi Ekstraksi DNA dan PCR-RAPD pada Grevillea spp. (Proteaceae). Jurnal Biologi 13(1): 12-16. [Indonesian]
Plenk K, Bardy K, Höhn M, Kropf M. 2019. Long?term survival and successful conservation? Low genetic diversity but no evidence for reduced reproductive success at the north?westernmost range edge of Poa badensis (Poaceae) in Central Europe. Biodiversity and Conservation 28:1245–1265. DOI: https://doi.org/10.1007/s10531-019-01722-x
Pratiwi P. 2012. Analisis Variasi Genetik Beberapa Populasi Globba leucantha Miq. di Sumatera Barat Dengan Random Amplified Polymorphic DNA (RAPD). [Thesis]. Program Pascasarjana Universitas Andalas, Padang. [Indonesian]
Probojati RT, Wahyudi D, HapsariL. 2019. Clustering Analysis and Genome Inference of Pisang Raja Local Cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker. Journal of Tropical Biodiversity and Biotechnology 4 (02): 42-53
Rahiman FOM, Balasubramanian T, Pawan K, Shejina M. 2015. National conference on Advances in Laboratory Medicine: P-44 Random Amplified polymorphic DNA (RAPD) – A Tool for Gene Mapping.
Ranta F. 2011. Sifat Anti Mikroba Zat Ekstraktif Pohon Faloak. [Thesis]. Program Pascasarjana Institut Pertanian Bogor, Bogor. [Indonesian]
Rimbawanto, A, Widyatmoko, Sulistyowati P. 2006. Distribusi Keragaman Genetik Santalum album Berdasarkan Penanda RAPD (Random Amplified Polymorphic DNA) . Jurnal Pemuliaan Tanaman Hutan 3: 175-181. [Indonesian]
Sambrook J, Russel DW. 2001. Molecular Cloning (A Laboratory Manual). Cold Spring Harbor Laboratory Press, New York.
Saragih GS, Siswadi S. 2019. Antioxidant Activity of Plant Parts Extracts from Sterculia quadrifida R.Br. Asian Journal of Pharmeceutical and Clinical Research 12 (7): 143-148.
Elly JB, Abdurrouf, Juswono UP. 2015. Effect of Sterculia quadrifide Extract R.Br. Against Free Radical in Liver Organs Oreochromis niloticus Due to Heavy Metal Pollution. Natural B, Journal of Health and Environmental Sciences 3(2): 175-181 doi:http://dx.doi.org/10.21776/ub.natural-b.2015.003.02.11.
Siswadi, Grace SS, Heny R. 2013. Potential Distributions And Utilization of Faloak (Sterculia quadrifida R.Br. 1844) on Timor Island, East Nusa Tenggara. Prooceding International Conference Forest and Biodiversity. Balai Penelitian Kehutanan Kupang Press, Kupang. [Indonesian]
Sukhumsirichart W. 2018. Polymorphisms. In: Yamin L (eds) Genetic diversity and Disease Susceptibility. IntechOpen, Arizona.
Sundari, Arumingtyas EL, Hakim L, Azrianingsih R, Wahyudi D. 2017. Genetic variability of local durian (Durio zibethinus Murr.) in Ternate Island based on RAPD markers. Plant Cell Biotechnology and Molecular Biology 18 (1): 68-75.
Suryatini KY. 2011. Analisis Keragaman Genetik Jarak Pagar (Jatropha curcas L.) dengan Metode Inter Simple Sequence Repeats (ISSR). [Thesis]. Program Magister, Program Studi Bioteknologi Pertanian, Program Pascasarjana Universitas Udayana, Denpasar. [Indonesian]
Wahyudi D, Hapsari L, Sundari. 2020. RAPD Analysis for Genetic Variability Detection of Mutant Soybean (Glycine max (L.) Merr). Journal of Tropical Biodiversity and Biotechnology 5 (1): 68-77.
Wahyudi D, Rifliyah K, Uslan. 2020. Genome evaluation of banana cultivars based on morphological character and Inter-Simple Sequence Repeat (ISSR) molecular marker. 21(7): 2982-2990. https://doi.org/10.13057/biodiv/d210715
Winata A, Triana H, Purwantiningsih, Siswadi. 2019. In vivo Immunomodulatory Activity of Faloak Bark Extract (Sterculia quadrifida R.Br). Pakistan Journal of Biological Sciences 22 (12): 590-596.
Wistiani, L. A. J. 2014. Induksi Mutasi Kromosom Dengan Kolkisin pada Tanaman Kesuna Bali (Allium sativum Linn.) dan Analisis DNA Dengan Mrka RAPD (Random Amplified Polymorphic DNA). [Thesis]. Program Magister, Program Studi Ilmu Biologi, Program Pascasarjana Universitas Udayana, Denpasar. [Indonesian]
Yulita KS, Rahmat HH. 2019. Population Genetic Structure and Diversity of a Critically Endangared Ramin [Gonystylus bancanus Miq.(Kurz),Thymelaeaceae] form Kalimantan and Sumatera based on Sequence Random Amplified Polymorphism. Earth and Environmental Science 308: 1-9
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