Clustering Analysis and Genome Inference of Pisang Raja Local Cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker

Rasyadan Taufiq Probojati(1*), Didik Wahyudi(2), Lia Hapsari(3)

(1) Department of Biology, Faculty of Mathematics and Science, State University of Malang
(2) Department of Biology, Faculty of Science and Technology, State Islamic University of Maulana Malik Ibrahim
(3) Purwodadi Botanic Garden – Research Center for Plant Conservation and Botanic Gardens, Indonesian Institute of Sciences
(*) Corresponding Author


Pisang Raja is an important local banana cultivar in the economy and cultural life in Indonesia, especially at Java. There are many Pisang Raja cultivars found on Java Island with various local names in each region, resulted in problems on taxonomic identification and grouping. Conventional research for grouping banana cultivars is still using morphological characters but considered inaccurate because of its subjectivity. This study aims to analyze the genetic diversity, grouping, and genome estimation of 13 local cultivars of Pisang Raja based on molecular approach using RAPD markers (OPA primers 1-20). Clustering and Principal Coordinates Analysis were performed to the amplified products using Paleontological Statistics (PAST) application version 3.15. Results showed that there were 12 primers which successfully amplified and produced DNA polymorphic bands in Pisang Raja, specifically OPA 1, OPA 2, OPA 3, OPA 4, OPA 5, OPA 8, OPA 16, OPA 17, OPA 18, OPA 19, and OPA 20. Pisang Raja cultivars considered have high genetic diversity, indicated by high polymorphic bands (95.17%) and low similarity coefficient values (0.2-0.6). Clustering and PCo analysis resulted in 3 clusters following its genomic group consist of AAA, AAB and ABB genomes, with Pisang Raja Bali as an outgroup (ABB). However, the separation of each cluster for genome inference was unclear. Cluster 1 consists of Pisang Raja Madu (AAB) and Raja Sereh (AAB). Cluster 2 consists of AAA and AAB genomes; includes Pisang Raja Jambe (AAA), Raja Kriyak (AAA), Raja Kutuk (AAB), Raja Brentel (AAB), Raja Seribu (AAB), and Raja Lini (AAB). Cluster 3 consists of AAA and AAB genomes, includes Pisang Raja Kisto (AAA), Raja Delima (AAA), Raja Bandung (AAB) and Raja Gareng (AAB). While Pisang Monyet (AAw) and Klutuk Wulung (BBw) as wild relatives were nested in Cluster 2. There were some different results of genome estimation based on RAPD markers compared to morphological characterization, and other molecular techniques. The use of RAPD markers is quite efficient and effective for studying genetic diversity and identifying genomes in bananas.


clustering analysis, genetic diversity genome inference, Java Island, Pisang Raja, RAPD

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Asif, M.F., Mak, C., Othman, & R.Y., 2001, Characterization of indigenous Musa species based on flow cytometric analysis of ploidy and nuclear DNA content, Caryologia, 54(2), 161-168.

Brown, N., Venkatasamy, S., Khittoo, G., Bahorun, T. & Jawaheer, S., 2009, Evaluation of genetic diversity between 27 banana cultivars (Musa spp.) in Mauritius using RAPD markers, African Journal of Biotechnology, 8(9), 1834-1840.

Bustaman, M. & Moeljopawiro, S., 1998, Utilization of DNA fingerprint technology in agriculture, Zuriat, 9, 77-90. [Indonesian].

Dayarani, M. & Dhanarajan, M.S., 2014, Diversity and phylogenetic analysis of the genus Musa, International Journal of ChemTech Research, 6(4), 2357-2762.

De Jesus, O.N., de Oliveira e Silva, S., Amorim, E.P., Ferreira, C.F., de Campos, J.M.S., de Gaspari Silva, G. & Figueira, A., 2013, Genetic diversity and population structure of Musa accessions in ex-situ conservation, BMC Plant Biology, 13, 41.

De Langhe, E., Vrydaghs, L., de Maret, P., Perrier, X., & Denham, T., 2009, Why bananas matter: An introduction to the history of banana domestication, Ethnobotany Resources and Application, 7: 165-177.

Demeke, T. & Adams, R.P., 1994, PCR Technology Current Innovation: The Use PCR RAPD Analysis in Plant Taxonomy and Evolution, CRC Press. Inc, USA.

Dolezel, J., Lysak, M.A., Van den Houwe I., Dolezelova, M. & Roux, N., 1997, Use of flow cytometry for rapid ploidy determination in Musa species, Infomusa, 6, 6-9.

Ekasari, T.W.D., Retnoningsih, A. & Widianti, T., 2012, Analysis of the diversity of banana cultivars using PCR-PFLP markers on the Internal Transcribed Spacer (ITS) ribosome DNA, J. MIPA, 35(1), 21-30. [Indonesian].

Espino, R.R.C., Jamaludin, S.H., Silayoi, Bechamas. & Nasution, R.E., 1992, Musa L. (Edible Cultivars) in E.W.M. Verheis and R.E. Coronel (Eds): ‘Plant Resources of South-East Asia No. 2 Edible Fruits and Nuts’, Prosea, Bogor, 225-229.

Firdausi, N., Hayati, A., Rahayu, T., 2015, Ethnobotany study and diversity of dessert bananas (Musaceae) in traditional communities in the Lumajang Krai Village, Biosaintropis, 1(1), 26- 34. [Indonesian].

Guzow-Krzeminska, B., Gorniak, M. & Wegrzyn, G., 2001, Molecular determination keys: construction of keys for species identification based on restriction fragment length polymorphism, Internationatal Archive of Bioscience, 1, 1057–1067.

Hammer, Ø., Harper, David, A.T., Ryan, Paul, D., 2001, Past: Paleontological Statistics Software package for education and data analysis, Palaentologia Electronica, 4(1), 4-9.

Hapsari, L., Fauziah & Trimanto, 2018, Morphology and molecular identification of local cultivars of Pisang Raja (Musa spp.) from Yogyakarta, Central Java and East Java, Indonesia, Proceeding of The International Conference on Tropical Plant Conservation and Utilization, 18-20 May 2017. “Plant and People in Harmony” Celebrating Bicentenary of Bogor Botanic Gardens and the Golden Year of LIPI. Pp 205-214.

Hapsari, L., Kennedy, J., Lestari, D.A., Masrum, A. & Lestarini, W., 2017, Ethnobotanical survey of bananas (Musaceae) in six districts of East Java Indonesia, Biodiversitas, 18(1), 160-174.

Hapsari, L., Wahyudi, D., Rodiyati, A. & Arumingtyas, E.L., 2015a, 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(03), 42-52.

Hapsari, L., Lestari, D.A., Masrum, A., 2015b. The Album of Banana Collection of Purwodadi Botanic Garden Seri 1, Purwodadi Botanic Garden – LIPI, Pasuruan. [Indonesian].

Hapsari, L, 2014, Wild Musa species collection of Purwodadi Botanic Garden: Inventory and its morpho-taxonomic review, The Journal of Tropical Life Science, 4(1), 70-80.

Indraswari, D., 2014, Ethnobotany of Musa paradisiaca in Nganjuk, J Biologi & Pembelajaran, 1(1), 1-6. [Indonesian].

[INIBAP] International Network for the Improvement of Banana and Plantain, 2002, A Strategy for the global Musa genomics consortium, Report of a meeting held in Arlington, USA, 17-20 Jul 2001, Montpellier, Italy 1-43.

Jumari & Pudjoarinto, A., 2000, Phenetic relationship of bananas in Java, Biologi, 2(9), 531-542. [Indonesian].

Ministry of Agriculture, 2016, The outlook of agricultural commodities in the horticulture (banana) sub-sector, Agricultural Information System and Data Center of the Ministry of Agriculture, Jakarta. [Indonesian].

Kiran, U., Moahnty, S. K., Roy, P. S., Behera, L., & Chand, P. K., 2015, Genetic diversity among banana cultivars from Odisha using RAPD markers, Science Research Reporter, 5(2), 118-124.

Laurentin, H. & Karlovsky, P., 2007, AFLP fingerprinting of sesame (Sesamum indicum L.) cultivars: identification, genetic relationship and comparison of AFLP informativeness parameters, Genetic Resources and Crop Evolution, 54(7), 1437–1446.

Maftuchah. 2001. Strategy for utilizing molecular markers in the development of the horticulture field. Papers presented on Seminar for the Use of Molecular Markers in the Field of Horticulture, Indonesian Biotechnology Information Centre (IndoBIC), Bogor. [Indonesian].

Makunthakumar, S., Padmesh, P., Vineesh, P. S., Skaria, R., Kumar, K. H. & Krishnan, P. N., 2013, Genetic diversity and differentiation ananlysis among wild antecedents of banana (Musa acuminata Colla) using RAPD markers, Indian Journal of Biotechnology, 12(4), 493-498.

Nair, A.S. & Resmi, L., 2016, Population genetic structure and diversity analysis of South Indian banana cultivars, Journal of Plant Breeding and Crop Science, 8(1), 1-12.

Nasution, R.E. & Yamada, I, 2001, Wild Bananas in Indonesia, Research Center of Biology-LIPI, Botany Department, Herbarium Bogorienses, Bogor. [Indonesian].

Nedha, Purmaningsih, S.L. & Damanhuri, 2017, Observation and morphological characterization of Banana plants (Musa spp.) In Ngancar District, Kediri Regency, Jurnal Produksi Tanaman, 5(5), 821-827. [Indonesian].

Ochse, J.J., 1931, Fruits and fruitculture in the Dutch East Indies, G. Kolff, Batavia, 180 pp.

Olivia, S.R., Pranay, B., Kumar, G. S., Bhushan, T. S., Deb, G. P. & Kumar, M. T, 2010, Assesment of genetic diversity in banana (Musa spp.) of North-Eastern India by RAPD. Bioremediation, Biodiversity and Bioaviabilitas, 4(1), 93-98.

Pillay, M., Nwakanma, D.C. & Tenkouano, A., 2000, Identification of RAPD markers linked to A and B genome sequences in Musa, Genome, 43, 763-767.

Poerba, Y.S. & Ahmad, F., 2013, Genetic diversity analysis of Musa balbisiana Colla based on RAPD and ISSR markers, Berita Biologi, 12(2), 259-267.

Rao, V.R. & Hodgkin, T., 2002, Genetic diversity and conservation and utilization of plant genetic Resources, Plant Cell, Tissue and Organ Culture, 68(1), 1–19.

Retnoningsih, A., Megia, R., Hartana, A., 2010, Characterization and evaluation of Musa acuminata cultivars in Indonesia based on microsatellite markers, Floribunda, 4(1), 21–32.

Roldan, I-R., Dendauw, J., Bockstaele, E.V., Depicker, A. & Loose, M.D., 2000, AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.), Molecular Breeding, 6(2), 125–134.

Sambrook, J & Russell, D.W., 1989, Molecular Cloning: A Laboratory Manual 3rd edition, Cold Spring Harbor Laboratory Press, New York.

Simmonds, N.W. & Shepherd, K., 1955, The taxonomy and origins of cultivated bananas, Journal of Linnean Society of Botany London, 55(359), 302-312.

Simmonds, N.W., 1959, Bananas, Longman Inc, New York.

Simpson, M.G., 2006, Plant Systematics, Elsevier Academic Press, USA.

Singh, H.P., Uma, S. & Sathiamoorthy, S., 2001, A Tentative Key for Identification and Classification of Indian Bananas, National Research Centre for Banana (NRCB), India, 7-16.

Slatkin, M., 1987, Gene flow and the geographic structure of population, Science Journals, 236(4803), 787-792.

Sukartini, 2007, The grouping of banana accessions using the morphological character of IPGRI, Jurnal Hortikultura, 17(1), 26-33. [Indonesian]

Sukartini, 2008, Genetic distance analysis and kinship of banana accessions based on Random Amplified Polymorphic DNA primers, Jurnal Hortikultura,18(3), 261-266. [Indonesian]

Tingey, S.V., Rafalski, J.A., & Hanafey, M.K., 1994, Genetic analysis with RAPD markers. In: Coruzzi, C. & Puidormenech, P. (Eds.), Plant Molecular Biology. Springer, Berlin.

Uma, S., Sudha, J., Saraswathi, M.S. Manickavasagam, M., Selvarajan, R., Durai, P., Sathiamoorthy, S. & Siva, S.A., 2006, Studies on the origin and diversification of Indian wild banana (Musa balbisiana) using arbitrarily Amplified DNA Marker, The Journal of Horticultural Science and Biotechnology, 79(4), 523–527.

Valmayor, R. V., Jamaluddin, S. H., Silayoi, B., Kusumo, S., Danh, L. D., Pascua, O. C. & Espino, R R.C., 2000, Banana Cultivar Names and Synonyms in Southeast Asia, International Network for the Improvement of Banana and Plantain-Asia and the Pacific Office, Los Banos, Laguna, Philippines.

Varshney, R.K., Chabane, K., Hendre, P.S., Aggarwal, R.K. & Graner, A., 2007, Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys, Plant Sciences, 173(6), 638–649.

Wahyuningtyas, W., Retnoningsih, A. & Rahayu, E.S., 2009, Genetic diversity of B genome bananas based on microsatellite marker, Biosaintifika 1(1), 1-10. [Indonesian]

Williams, J. G., Kubelik, A. R., Livak, K.J., K.J., Rafalski, K.J. & Tingey, S. V., 1990, DNA polymorphisms amplified by arbitrary promers are useful as genetic markers, Nucleic Acid Research, 18 (22), 6531-6535.

Yu, K & Pauls, K.P., 1994, PCR Technology Current Innovation: Optimation of DNA-Extraction and Procedures for RAPD Analysis in Plants, CRC Press Inc, USA.


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