Genetic Relationships of Yellow Berry and Red Berry Cultivars of Arabica Coffee Based on SSR Markers

Nur Kholilatul Izzah, Enny Randriani, Dani Dani


Yellow berry of Arabica coffee (AGK-1) cultivated in Garut is a local cultivar that potentially could be released as a superior variety. However, its genetic background has not been studied. Information of genetic background is one of the requirement in releasing of a new variety. The objective of this research was to analyze the genetic relationships of AGK-1 cultivar with 11 red berries Arabica coffee cultivars based on simple sequence repeats (SSR) markers to find polymorphisms and clustering. The research was carried out at the Molecular Laboratory of Indonesian Industrial and Beverage Crops Research Institute and Biology Molecular Laboratory of Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, from January to March 2015. These twelve Arabica coffee cultivars were obtained from Garut Regency. A total of 12 SSR primers were used to investigate the genetic relationships of the plant. The result showed that 12 SSR markers were adequate to identify the relationships among 12 Arabica coffee cultivars. The genetic clustering obtained in this study is related to plant morphology, particularly plant growth characters, such as tall, semi dwarf and dwarf. AGK-1 cultivar genetically related to ABP-2, one of red berries cultivars that originated from Brazil. Both of these cultivars have the same growing type characters (i.e. semi dwarf). AGK-1 cultivar that has yellow berry color presumably derived from an open pollinated red berries parents, mainly ABP-2 cultivar. Therefore, AGK-1 is a unique cultivar that could be released as a local superior variety.


Coffea arabica; genetic relationships; SSR markers

Full Text:

PDF (Indonesian)


Allen, G.C., Flores-Vergara, M.A., Krasynanski, S., Kumar, S., & Thompson, W.F. (2006). A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat Prot, 1, 2320–2325.

Combes, M.C., Andrzejewski, S., Anthony, F., Bertrand, B., Rovelli, P., Grazios, G., & Lashermes, P. (2000). Characterization of microsatellite loci in Coffea arabica and related coffee species. Molecular Ecology, 9, 1171–1193.

Geleta, M., Herrera, I., Monzon, A., & Bryngelsson, T. (2012). Genetic diversity of Arabica coffee (Coffea arabica L.) in Nicaragua as estimated by simple sequence repeat markers. The Scientific World Journal (p. 11).

Izzah, N.K., Lee, J., Perumal, S., Park, J.Y., Ahn, K., Fu, D., Kim, G-B., Nam, Y-W., & Yang, T-J. (2013). Microsatellite-based analysis of genetic diversity in 91 commercial Brassica oleracea L. cultivars belonging to six varietal groups. Genet Resour Crop Evol, 60, 1967–1986.

Jain, S., Jain, R.K., & McCouch, S.R. (2004). Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor Appl Genet, 109, 965–977.

Kalia, R.K., Rai, M.K., Kalia, S., Singh, R., & Dhawan, A.K. (2011). Microsatellite Markers: an overview of the recent progress in plants. Euphytica, 177, 309–334.

Kementerian Pertanian. (2005). Surat Keputusan Menteri Pertanian Nomor: 205/Kpts/SR.120/4/2005 tentang pelepasan varietas kopi Sigarar Utang sebagai varietas unggul. Jakarta.

Kementerian Pertanian. (2010). Surat Keputusan Menteri Pertanian Nomor: 1885/Kpts/SR.120/5/2005 tentang pelepasan varietas kopi Andungsari 2K sebagai varietas unggul. Jakarta.

Kurniasih, S., Rubiyo, Setiawan, A., Purwantara, A., & Sudarsono. (2011). Analisis keragaman genetik plasma nutfah kakao (Theobroma cacao L.) berdasarkan markaSSR. Jurnal Littri, 17(4), 156–162.

Lashermes, P., Combes, M.C., Trouslot, P., Anthony, F., Hamon, S., & Charrier, A. (1999). Molecular characterization and origin of the Coffea arabica L. genome. Molecular Genomics and Genetics, 261, 259–266.

Liu, K., & Muse, S.V. (2005). PowerMarker: Integrated analysis environment for genetic marker data. Bioinformatics, 21, 2128–2129.

Louarn, S., Torp, A.M., Holme, I.B., Andersen, S.B., & Jensen, B.D. (2007). Database derived microsatellite markers (SSRs) for cultivar differentiation in Brassica oleracea. Genet Resour Crop Evol, 54, 1717–1725.

Maluf, M.P., Silvestrini, M., Ruggiero, L., M., de C., Filho, O.G., & Colombo, C., A. (2005). Genetic diversity of cultivated Coffea arabica inbred lines assessed by RAPD, AFLP and SSR markers system. Sci. Agric. (Piracicaba, Braz), 62(4), 366–373.

Missio, R.F., Caixeta, E.T., Zambolim, E.M., Zambolim, L., & Sakiyama, N.S. (2009). Development and validation of SSR markers for Coffea arabica L.Crop Breeding and Applied Biotechnology, 9, 361–371.

Prakash, N.S., Marques, D.V., Varzea, V.M.P., Silva, M.C., Combes, M.C., & Lashermes, P. (2004). Introgression molecular analysis of a leaf rust resistance gene from Coffea liberica into Coffea arabica L. Theor. Appl. Genet., 109(6), 1311–1317.

Randriani, E., Dani, & Wardiana, E. (2014). Evaluasi ukuran biji beras, kadar kafein, dan mutu cita rasa lima kultivar kopi Arabika. Jurnal Tanaman Industri dan Penyegar, 1(1), 49–56.

Rohlf, F.J. (2000). NTSYS-PC, numerical taxonomy system for the PC, ExeterSoftware, Ver. 2.1. Setauket: Applied Biostatistics Inc.

Rubiyo, Izzah, N.K., Sulistiyorini, I., & Tresniawati, C. (2015). Genetic diversity in cacao collected from Kolaka, Southeast Sulawesi, using SSR markers. Indonesian Journal of Agricultural Science (in press).

Teressa, A., Crouzillat, D., Petiard, V., & Brouhan, P. (2010). Genetic diversity of Arabica coffee (Coffea arabica L.) collections. Ethiopian Journal of Applied Sciences and Technology, 1(1), 63–79.

Sera, T., Ruas, P.M., Ruas, C. de F., Diniz, L.E.C., Carvalho, V. de P., Rampim, L., ... da Silveira, S.R. (2003). Genetic polymorphism among 14 elite Coffea arabica L. cultivars using RAPD markers associated with restriction digestion. Genetics and Molecular Biology, 26(1), 59–64.

Zakaria, M.M. (2012). Coffee Priangan in the nineteenth century. Retrieved from historia_coffee_priangan.pdf.



  • There are currently no refbacks.

Copyright (c) 2015 Jurnal Tanaman Industri dan Penyegar

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

 Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.


P-ISSN: 2356-1297
E-ISSN: 2528-7222
Accredited No.30/E/KPT/2018 on Oktober 24, 2018 by Ministry of Research, Technology and Higher Education of the Republic of Indonesia


Jurnal Tanaman Industri dan Penyegar (JTIDP) Editorial Office :

Indonesian Industrial and Beverage Crops Research Institute
Jl. Raya Pakuwon Km. 2, Parungkuda, Sukabumi 43357 Jawa Barat Indonesia
Telp : (0266) 6542181
Fax : (0266) 6542087
Email :
Website :

View My Stats