Genetic Diversity of Potato Based on Random Amplified Polymorphic DNA and Simple Sequence Repeat Marker

Sapto Nugroho Hadi, Siti Nurchasanah

Abstract


Various potato clones are cultivated by farmers in Banjarnegara and Wonosobo, Central Java, Indonesia such as MZ, NH1, NH2, Vega, Gareta, Granola, Bliss, Merah (Red Potato), Ungu (Purple Potato), Klon_17 (K17), Local Dieng, Margahayu, and X. This encourages the importance of genetic diversity and genetic similarities. This study aimed to analyze genetic diversity and genetic similarities between 13 accessions of potatoes based on seven Random Amplified Polymorphic DNA (RAPD) primers and nine pairs of Simple Sequence Repeat Marker (SSR) primers. The results showed that RAPD and SSR primers could be used to analyze genetic diversity and genetic similarities of 13 potatoes accessions from Banjarnegara and Wonosobo. The PLP value was 80.9% in the RAPD primer and 65.41% in the SSR primer. Four RAPD primers were informative based on PIC value: OPG 08, OPM 19, OPP 13, and OPX 04. Three SSR primer were informative: STM 2005, RGH- SSR 8, and StI 035. Genetic similarities presented by Phylogenetic tree analysis resulted in two main clusters. The first cluster consisted of Granola, MZ, Ungu (Purple potato), Merah (Red Potato), Local Dieng, Margahayu, Gareta, Vega, NH2, NH1, Klon_17 (K17), and Bliss. The second cluster consisted of X. Granola and MZ having a high genetic similarity with a genetic distance of 0.07 and 0.132. Meanwhile, K17 and X had a low genetic similarity with a genetic distance of 0.31 and 0.987.


Keywords


Banjarnegara; RAPD; Solanum tuberosum L.; SSR; Wonosobo

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Bakker, E., Borm, T., Prins, P., Van der Vossen, G., Uenk, G., Arens, A., de Boer, J., Van Eck, H., Muskens, M., Vossen, J., Van der Linden, G., Van Ham, R., KleinLankhorst, R., Visser, R., Smant, G., Bakker, J., & Goverse, A. (2011). A genome-wide genetic map of NB-LRR disease resistance loci in potato. Theor. Appl. Genet, 123:493–508.

Central Bureau of Statistics. (2017). Vegetable Crop Production.https://www.bps.go.id/site/resultTab. Accessed on August 3, 2018.

Collares, E. A. S., Choer, E., & da Silva Pereira, A. (2004). Characterization of potato genotypes using molecular markers. Pesq. agropec. Bras, 39 (9) : 871-878.

Doyle, J.J. & Doyle, J.L. (1987) A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue. Phytochemical Bulletin, 19: 11-15.

Fauziyah, S. (2018). Faktor-faktor yang mempengaruhi keputusan petani dalam menggunakan benih kentang bersertifikat. Studi kasus Kecamatan Cikajang, Kabupaten Garut, Jawa Barat. Skripsi. Institut Pertanian Bogor, Bogor.

Favoretto, P., Veasey, E. A., & de Melo, P. C. T. (2011). Molecular characterization of potato cultivars using SSR markers. Horticultura Brasileira, 29: 542-547.

S. Feingold, Lloyd, J., Norero, N., & Bonierbale, J.M. (2005). Lorenzen Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theor Appl Genet, 111: 456–466.

Ghislain M., Spooner, D.M., Rodriguez, F., Villamon, F., Nunez, J., Vasquez, C., Waugh, R., & Bonierbale, M. (2004). Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Gennet, 108: 881-890.

Hoque, M.E., Huq, H., & Moon, N.J. (2013). Molecular diversity analysis in potato (Solanum tuberosum L.) through RAPD markers. SAARC J. Agri, 11(2): 95-102.

Hubert,G. Y. J., Gupta, P.H., Patel, N.J., Shah, A.K., Acharya, R.R., Talati, J.G. (2015). Molecular Characterization of Indian Potato (Solanum tuberosum L.) Varieties for Cold-Induced Sweetening Using SSR Markers. Journal of Plant Sciences, 3(4): 191-196.

Jones, C.J., Edwards, K.J., Castaglione, S., Winfield, M.O., Sala, F., van deWiel, C., Bredemeijer, G., Vosman, B., Matthes, M., Daly, A., Brettschneider, R., Bettini, P., Buiatti, M., Maestri, E., Malcevschi, A., Marmiroli, N., Aert, R., Volckaert, G., Rueda, J., Linacero, R., Vazquez, A., & Karp, A. (1997). Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Molecular Breeding, 3: 381–390.

Kawengian, Y. B., Lengkong, E. & Mandang, J. (2016). Keragaman Genetik Beberapa Varietas Kentang (Solanum tuberosumL.) Berdasarkan Penanda Random Amplified Polimorphic DNA (RAPD). Jurusan Budidaya Fakultas Pertanian Universitas Sam Ratulangi Manado.

Kumar, U., Joshi, A. K., Kumar, S., Chand, R., & Roder, M.S. (2009). Mapping of resistance to spot blotch disease caused by Bipolaris sorokiniana in spring wheat. Theor Appl Genet, 118:783–792

Leksono, A. S. (2011). Keanekaragaman Hayati. UB Press, Malang.

Miah, G., Rafii, M.Y., Ismail, M.R., Puteh, A.B., Rahim, H.A., Islam, Kh.N. & Latif, M.A. (2013). A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. International Journal of Molecular Science, 14: 22499-22528.

Milbourne, B.D., Meyer, R., Bradshaw, J.E., Baird, E., Bonar, N., & Provan, J. (1997). Comparison of PCR-based marker systems for the analysis of genetic relationship in cultivated potato. Mol Breed, 3: 127-136.

Ministry of Agriculture. (2014). Berita Resmi PVT Tedjo MZ. No. Publikasi :004/BR/PVL/02/2014. Available at : pvtpp.setjen.pertanian.go.id/cms/wp.../ 04/4.-Banjarnegara-Kentang-Tedjo-MZ.pdf

Ministry of Agriculture. (2017). Potato productivity by province, 2013-2017. http://www.pertanian.go.id/Data5tahun/HortiATAP2017(.pdf)/Produktivitas%20Kentang.pdf. Accessed on February 6th, 2019.

Ministry of Agriculture. (2017). Potato Harvest Area by Province, 2013-2017. http://www.pertanian.go.id/Data5tahun/HortiATAP2017(.pdf)/L.%20Panen%20Kentang.pdf. Accessed on February 6th, 2019.

Ministry of Agriculture. (2017). Potato Production by Province, 2013-2017. http://www.pertanian.go.id/Data5tahun/HortiATAP2017(.pdf)/Produksi%20Kentang.pdf. Accessed on February 6th, 2019.

Nugroho, K., Reflinur, Lestari, P., Rosdianti, I., Terryana, R.T., Kusmana, & Tasma, I.M. (2015). Keragaman genetika empat belas aksesi kentang (Solanum tuberosum L. berdasarkan marka SSR dan STS. Jurnal AgroBiogen, 11(2):41–48.

Onamu, R., Legari, J., Rodríguez, J.L., Sahagùn, J. & Pèrez, J. (2016). Molecular characterization of potato (Solanum tuberosum L.) genotypes using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers. African Journal of Biotechnology, 15 (22) : 1015 -1025.

Rocha, E. M., Paiva, L.V., de Carvalho, H.H. & Guimaraes, C.T. (2010). Molecular characterization and genetic diversity of potato cultivars using SSR and RAPD markers. Crop Breeding and Applied Biotechnology, 10: 204-210.

Salimi, H., Bahar, M., Mirlohi, A. & Talebi, M. (2016). Assessment of the genetic diversity among potato cultivars from different geographical areas using the genomic and EST microsatellites. Iran Journal Biotech, 14(4): 270-277.

Sayaka, B. & Hestina, J. (2011). Constraints in Adopting Certified Seed in Potato Farming. Forum Penelitian Agroekonomi, 29(1): 27-41.

Sinaga, A., Putri, L. A. P. & Bangun, M.K. (2017). Analisis pola pita andaliman (Zanthoxylum Acanthopodium D.C) berdasarkan primer OPD 03, OPD 20, OPC 07, OPM 20, OPN 09. Jurnal Agroekoteknologi FP USU, 5(1) : 55-64.

Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol., 30(12): 2725–2729

Vieira, M.L.C., Santini, L., Diniz, A.L. & Munhoz Carla de Freitas. (2016). Microsatellite markers: what they mean and why they are so useful. Genetics and Molecular Biology, 39 (3): 312-328

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

Yasmin, S., Islam, S., Khondoker, Nasirrudin & Alam, S. (2006). Molecular characterization of potato germplasm by Random Amplified Polymorphic DNA markers. Biotechnology, 5 (1) : 27 -31.

Yaycili, O., & Alikamanoğlu, S. (2012). Induction of salt-tolerant potato (Solanum tuberosum L.) mutants with gamma irradiation and characterization of genetic variations via RAPD-PCR analysis. Turk Journal Biol., 36: 405-412.

Zulfahmi. (2013). Penanda DNA untuk analisis genetik tanaman. Jurnal Agroteknologi, 3 (2): 41-52.




DOI: https://doi.org/10.18196/pt.2020.114.54-62

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