Genetic Variability Among Indigenous Robusta Coffee Clones from Pagar Alam Based on SSR Marker Analysis

Syafaruddin Syafaruddin, Dani Dani, Marcia Bunga Pabendon


Robusta coffee (Coffea canephora var. robusta) is the most extensive developed in Indonesia, including Pagar Alam, South Sumatra. In the last few decades, many farmers in Pagar Alam conducted clonal selection and rehabilitation of Robusta coffee trees that generated indigenous clonal populations. This pattern in the long period can damage important alleles and reduce the genetic diversity of indigenous Robusta coffee in farmland. The research aimed to know the genetic diversity among indigenous Robusta coffee clones developed in Pagar Alam based on SSR markers. The study was conducted at Molecular Biology Laboratory, Cereals Research Institute, Maros, from February to April 2017. Molecular characterization of 19 indigenous Robusta coffee clones was conducted using 33 polymorphic SSR markers. The resulting binary data was then analyzed using PowerMarker program to determine polymorphism value (PIC), number and diversity of alleles, and heterozygosity values. The results showed that 33 polymorphic SSR loci produced 134 alleles with an average of 4.06 alleles/locus, whereas PIC values ranged from 0.090.77 with an average of 0.48. Of the 33 SSR loci, 19 loci (57.58%) exhibited very informative PIC value (> 0.55). Dendrogram generated using NTSYS program divided 19 indigenous Robusta coffee clones into 4 clusters at 0.53 similarity coefficient. KPA41clone was separated in its own cluster, potentially crossed with other clones. Based on genetic distance values >0.55, could arrange 14 combinations of interclonal crosses that potentially increase the genetic variability of indigenous Robusta coffee from Pagar Alam.


Coffea canephora var robusta; genetic diversity; genetic distance value; microsatellite markers

Full Text:

PDF (Indonesian)


Anim-Kwapong, G. J., Anim-Kwapong, E., & Oppong, F. K. (2010). Evaluation of some Robusta coffee (Coffea canephora Pierre ex a. Froehner) clones for optimal density planting in Ghana. African Journal of Agricultural Research, 5(1), 84–89. Retrieved from

Anthony, F., Astorga-Domian, C. G., Quiros, O., Bertrand, B., Etienne, H., Topart, P., & Lashermes, P. (2002). Genetic diversity of wild and cultivated coffees (Coffea Arabica), revealed by molecular markers. Boletin PROMECAFE, 96, 7–12.

Baruah, A., Naik, V., Hendre, P. S., Rajkumar, R., Rajendrakumar, P., & Aggarwal, R. K. (2003). Isolation and characterization of nine microsatellite markers from Coffea arabica L., showing wide cross-species amplifications. Molecular Ecology Notes, 3(4), 647–650. doi:10.1046/j.1471-8286.2003.00544.x

Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32(3), 314–331. Retrieved from

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

Cubry, P., De Bellis, F., Pot, D., Musoli, P., Legnate´, H., Leroy, T., & Dufour, M. (2005). Genetic diversity analyses and linkage disequilibrium evaluation in some natural and cultivated popula- tions of Coffea canephora. In Proceedings of the 4th Plant Genomics European Meeting, Amsterdam, 20–23 September 2005.

Cubry, P., de Bellis, F., Pot, D., Musoli, P., & Leroy, T. (2013). Global analysis of Coffea canephora Pierre ex Froehner (Rubiaceae) from the Guineo-Congolese region reveals impacts from climatic refuges and migration effects. Genetic Resources and Crop Evolution, 60(2), 483–501. doi:10.1007/s10722-012-9851-5

Cubry, P., Musoli, P., Legnaté, H., Pot, D., de Bellis, F., Poncet, V., … Leroy, T. (2008). Diversity in coffee assessed with SSR markers: structure of the genus Coffea and perspectives for breeding. Genome, 51(1), 50–63. doi:10.1139/G07-096

Dalcomo, J. M., Vieira, H. D., Ferreira, A., Lima, W. L., Ferrão, R. G., Fonseca, A. F. A., … Partelli, F. L. (2015). Evaluation of genetic divergence among clones of conilon coffee after scheduled cycle pruning. Genetics and Molecular Research, 14(4), 15417–15426. doi:10.4238/2015.November.30.19

DaMatta, F. M., Ronchi, C. P., Maestri, M., & Barros, R. S. (2007). Ecophysiology of coffee growth and production. Brazilian Journal of Plant Physiology, 19(4), 485–510. doi:10.1590/S1677-04202007000400014

Direktorat Jenderal Perkebunan. (2015). Statistik perkebunan Indonesia 2014-2016: Kopi. (E. Subiyantoro & Y. Arianto, Eds.). Jakarta: Direktorat Jenderal Perkebunan.

George, M. L., Regalado, E., Li, W., Cao, M., Dahlan, M., Pabendon, M., … Hoisington, D. (2004). Molecular characterization of Asian maize inbred lines by multiple laboratories. Theor Appl Genet., 109(1), 80–91.

Gichuru, E. K., Agwanda, C. O., Combes, M. C., Mutitu, E. W., Ngugi, E. C. K., Bertrand, B., & Lashermes, P. (2008). Identification of molecular markers linked to a gene conferring resistance to coffee berry disease (Colletotrichum kahawae) in Coffea arabica. Plant Pathology, 57(6), 1117–1124.

Gomez, C., Dussert, S., Hamon, P., Hamon, S., Kochko, A. de, & Poncet, V. (2009). Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: Cumulative impact of ancient climatic changes and recent human activities. BMC Evolutionary Biology, 9(1), 167. doi:10.1186/1471-2148-9-167

Hendre, P. S., & Aggarwal, R. K. (2014). Development of genic and genomic SSR markers of Robusta coffee (Coffea canephora Pierre ex A. Froehner). PLoS ONE, 9(12), 1–34. doi:10.1371/journal.pone.0113661

Indonesia-Investment. (2015). Coffee. Retrieved from

Khan, I. A., Awan, F. S., Ahmad, A., & Khan, A. A. (2004). A modified mini-prep method for economical and rapid extraction of genomic DNA in plants. Plant Molecular Biology Reporter, 22(1), 89–89. doi:10.1007/bf02773355

Lashermes, P., Andrzejewski, S., Bertrand, B., Combes, M. C., Dussert, S., Graziosi, G., … Anthony, F. (2000). Molecular analysis of introgressive breeding in coffee (Coffea arabica L.). Theoretical and Applied Genetics, 100, 139–146. Retrieved from

Lashermes, P., Combes, M.-C., Ansaldi, C., Gichuru, E., & Noir, S. (2011). Analysis of alien introgression in coffee tree (Coffea arabica L.). Molecular Breeding, 27(2), 223–232. doi:10.1007/s11032-010-9424-2

Liu, K., & Muse, S. V. (2005). PowerMaker: An integrated analysis environment for genetic maker analysis. Bioinformatics, 21(9), 2128–2129. doi:10.1093/bioinformatics/bti282

Mishra, M. K., & Slater, A. (2012). Recent advances in the genetic transformation of coffee. Biotechnology Research International, 2012, 1–17. doi:10.1155/2012/580857

Missio, R., Caixeta, E., Zambolin, E., Zambolin, L., Cruz, C., & Sakiyama, N. (2010). Polymorphic information content of SSR markers for Coffea spp. Crop Breeding and Applied Biotechnology, 10, 89–94.

Moncada, P., & McCouch, S. (2004). Simple sequence repeat diversity in diploid and tetraploid Coffea species. Genome, 47(3), 501–509. doi:10.1139/g03-129

Montagnon, C., Guyot, B., Cilas, C., & Leroy, T. (1998). Genetic parameters of several biochemical compounds from green coffee, Coffea canephora. Plant Breeding, 117, 576–578.

Moysés Alves, R., Rogério De Sousa Silva, C., Sérgio, P., Albuquerque, B. De, Silva, V., & Santos, D. (2017). Phenotypic and genotypic characterization and compatibility among genotypes to select elite clones of cupuassu. Acta Amazonica, 47(3), 175–184. doi:10.1590/1809-4392201602104

Musoli, P., Cubry, P., Aluka, P., Billot, C., Dufour, M., De Bellis, F., … Leroy, T. (2009). Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda. Genome, 52(7), 634–646. doi:10.1139/G09-037

Nowak, M. D., Davis, A. P., Anthony, F., & Yoder, A. D. (2011). Expression and trans-specific polymorphism of self-incompatibility rnases in Coffea (Rubiaceae). PLoS ONE, 6(6). doi:10.1371/journal.pone.0021019

Pejic, I., Ajmone-Marsan, P., Morgante, M., Kozumplick, V., Castiglioni, P., Taramino, G., & Motto, M. (1998). Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theoretical and Applied Genetics, 97(8), 1248–1255. doi:10.1007/s001220051017

Prakash, N. S., Combes, M. C., Somanna, N., & Lashermes, P. (2002). AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybrid. Euphytica, 124(3), 265–271. doi:10.1023/A:1015736220358

Prastowo, B., Karmawati, E., Rubijo, Siswanto, Indrawanto, C., & Munarso, S. J. (2010). Budidaya dan Pasca Panen Kopi. Pusat Penelitian dan Pengembangan Perkebunan. Retrieved from

Rohlf, F. J. (2000). NTSYSpc Numerical Taxonomy and Multivariate Analysis System Version 2.1. Applied Biostatistics Inc.

Rovelli, P., Mettulio, R., Anthony, F., Anzueto, F., Lashermes, P., & Graziosi, G. (2000). Microsatellites in Coffea Arabica L. In T. Sera, C. R. Soccol, A. Pandey, & S. Roussos (Eds.), Coffee biotechnology and quality: Proceedings of the 3rd international seminar on biotechnology in the Coffee Agro-Industry, Londrina, Brazil (pp. 123–133). Dordrecht: Springer Netherlands. doi:10.1007/978-94-017-1068-8_9

Syafaruddin, Randriani, E., Dani, Sulistyorini, I., & Pabendon, M. B. (2014). Genetic variability of 15 Robusta coffee genotypes selected by farmer based on SSRs markers. J. TIDP, 1(2), 87–94.

Usatov, A. V., Klimenko, A. I., Azarin, K. V., Gorbachenko, O. F., Markin, N. V., Tikhobaeva, V. E., … Getmantseva, L. (2014). The relationship between heterosis and genetic distances based on SSR markers in Helianthus annuus. American Journal of Agricultural and Biological Science, 9(3), 270–276. doi:10.3844/ajabssp.2014.270.276

Yu, R. H., Wang, Y. L., Sun, Y., & Liu, B. (2012). Analysis of genetic distance by SSR in waxy maize. Genetics and Molecular Research, 11(1), 254–260.



  • There are currently no refbacks.

Copyright (c) 2017 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