Journal of Plant Sciences

Submit a Manuscript

Publishing with us to make your research visible to the widest possible audience.

Propose a Special Issue

Building a community of authors and readers to discuss the latest research and develop new ideas.

Review on Coffee (Coffea arabica L.) Genetic Diversity Studies Using Molecular Markers

Coffee (Coffea arabica L.) is one of the most consumed beverages in the world and is the second largest traded commodity after petroleum. It greatly contributes to the economy of many developing countries in South and Central America, Asia, and Africa. Currently, many countries are producing and supplying coffee to the world market and there is a high competition among producers to meet the demand both in quantity and quality. Hence, it is vital to improve the current productivity as well as the quality of coffee for each producing country. In this regard, variability study is a pre-requisite for improvement of any crop and knowledge of the genetic variability among genotypes is important for the transfer of useful genes and to maximize the use of available germplasm resources. Hence, genetic diversity analysis in coffee (Coffea arabica L.) has paramount importance in continuously developing coffee varieties through hybridization and selection. Morphological markers allow the assessment of genetic variability based on individual phenotypic differences yet there are limitations associated with these markers. These limitations led to the development of molecular markers. Molecular marker techniques are based on naturally occurring polymorphisms in DNA sequences. Studies, which have been conducted to assess the level of genetic diversity of Coffee arabica L. using different DNA markers (RAPD, AFLP, ISSR, and SSR), demonstrated that all DNA marker techniques could be applied for measuring the degree of variability within, and between wild and cultivated coffee populations. Despite all the four DNA markers are efficient in coffee genetic diversity analysis, all have their own disadvantages. However, the previous studies showed that the polymorphism observed in coffee Arabica is generally low as compared to other diploid coffee species and this is probably the result of a narrow genetic basis of the cultivated coffee (Coffea arabica L.) as well as the mating system of the crop. Hence, it is recommended to use the observed variability for the coffee breeding program to improve the yield and quality of coffee.

Coffea Arabica, Molecular Markers, Polymorphisim, Simple Sequence Repeat Markers, Variability

APA Style

Getachew Weldemichael. (2023). Review on Coffee (Coffea arabica L.) Genetic Diversity Studies Using Molecular Markers. Journal of Plant Sciences, 11(5), 164-170.

ACS Style

Getachew Weldemichael. Review on Coffee (Coffea arabica L.) Genetic Diversity Studies Using Molecular Markers. J. Plant Sci. 2023, 11(5), 164-170. doi: 10.11648/j.jps.20231105.14

AMA Style

Getachew Weldemichael. Review on Coffee (Coffea arabica L.) Genetic Diversity Studies Using Molecular Markers. J Plant Sci. 2023;11(5):164-170. doi: 10.11648/j.jps.20231105.14

Copyright © 2023 Authors retain the copyright of this article.
This article is an open access article distributed under the Creative Commons Attribution License ( which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

1. Lashermes, P., M. C. Comes, J. Robert, P. Trouslot, A. D’Hont, F. Anthony & A. Charrier (1999) Molecular characterization and origin of the Coffea arabica L. genome. Mol. Gen. Genet, 261: 259–266.
2. Carvalho A, Medina Filho HP, Fazuoli LC, GuerreiroFilho O, Lima MMA (1991) Aspectosgenéticos do cafeeiro. Rev Bras Genet l4: 135–183.
3. Sakiyama, NS (2000) DNA markers for coffee tree breeding. pp. 179-185. In: T. Sera, C. R. Soccol, A. pandy and S. Roussos (Eds.), Coffee biotechnology and quality. Kluwer Academic Publishers, Dordrecht.
4. Barbosa, A. M. M., I. O. Geraldi, L. L. Benchimol, A. A. F. Gracia, C. L. Souza Jr. and A. P. Souza (2003) Relationship of intra- and inter-population tropical maize single cross hybrid performance and genetic distances computed from AFLP and SSR markers. Euphytica 130: 87-99.
5. Esayas Aga (2005) Molecular genetic diversity study of forest coffee tree (Coffea arabica L.) populations in Ethiopia: implications for conservation and breeding (Vol. 2005, No. 79).
6. Alemayehu Teressa. Crouzillat, D., Petiard, V. and Brouhan, P (2010) Genetic diversity of Arabica coffee (Coffea arabica L.) collections. Ejast, 1 (1): 63-79.
7. Weising, K., Nybom, H., Pfenninger, M., Wolff, K. and Kahl, G (2005) DNA fingerprinting in plants: principles, methods, and applications. CRC press.
8. Kasahun Tesfaye (2006) Genetic diversity of wild Coffea arabica populations in Ethiopia as a contribution to conservation and use planning, Ecology and Development Series No. 44, 2006.
9. Joshi, S. P., Prabhakar K., Ranjekar, P. K and Gupta, VS (2011) Molecular markers in plant genome analysis. http/ 15.htm. Pp 1-19.
10. Acquaah and George (2012) Principles of plant genetics and breeding. John Wiley & Sons.
11. Williams, J. G., Kubelik, A. R., Livak, K. J., Rafalski, J. A. and Tingey, S. V (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic acids research, 18 (22): 6531-6535.
12. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van De Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M. and Zabeau, M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res, 23: 4407-4414.
13. Zietkiewicz E, Rafalski A, Labuda D (1994) Genomic fingerprinting by simple sequence repeat (SSR)- anchored polymerase chain reaction amplification. Genomics 20: 176–183.
14. Morgante, M. & Olivieri, A. M (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J. 3: 175–182.
15. Mohler, V. and Schwarz, G (2004) Genotyping tools in plant breeding: from restriction fragment length polymorphisms to single nucleotide polymorphisms. In Molecular marker systems in plant breeding and crop improvement Springer Berlin Heidelberg. pp. 23-38.
16. Williams MNV, Pande N, Nair M (1991) Restriction fragment length polymorphism analysis of polymerase chain reaction products amplified from mapped loci of rice (Oryza sativa L.) genomic DNA. TheorAppl Genet 82: 489–498.
17. Kumar, P., Gupta, V. K., Misra, A. K., Modi, D. R. and Pandey, B. K (2009) Potential of molecular markers in plant biotechnology. Plant Omics, 2 (4): 141-162.
18. Anthony, F, Bertrand, B, Quiros, O, Wilches, A. Lashermes, J. Berthaud, J &Charrier, A (2001) Genetic diversity of wild coffee (Coffea arabica L.) using molecular markers, Euphytica 118: 53–65.
19. Esayas Aga, Bryngelsson, Endeshaw Bekele, and Salomon Bealami (2003) Genetic diversity of forest arabica coffee (Coffea arabica L.) in Ethiopia as revealed by random amplified polymorphic DNA (RAPD) Analysis, Hereditas 138: 36–46.
20. Chaparro, A. P., Cristancho, M. A., Cortina, H. A. and Gaitan, A. L (2004) Genetic variability of Coffea arabica L. accessions from Ethiopia evaluated with RAPDs. Genetic resources and crop evolution, 51 (3): 291-297.
21. Lashermes, P., Trouslot, P., Anthony, F., Combes, M. C. and Charrier, A (1996) Genetic diversity for RAPD markers between cultivated and wild accessions of Coffea arabica. Euphytica, 87: 59-64.
22. Masumbuko, L. I., Bryngelsson, T., Mneney, E. E. and SALOMON, B (2003) Genetic diversity in Tanzanian Arabica coffee using random amplified polymorphic DNA (RAPD) markers. Hereditas, 139 (1): 56-63.
23. Crochemore, M. L., Nunes, L. M., Andrade, G. A., Molinari, H. B. C. and Vasconcellos, M. E (2004) Varietal identification of coffee seeds by RAPD technique. Brazilian Archives of Biology and Technology, 47 (1): 7-11.
24. Maluf, M. P., Silvestrini, M., Ruggiero, L. M. D. C., GuerreiroFilho, O. and Colombo, C. A (2005) Genetic diversity of cultivated Coffea arabica inbred lines assessed by RAPD, AFLP and SSR marker systems. Scientia Agricola, 62(4): 366-373.
25. Kathurima C. W., Kenji G. M., Muhoho S. M., Boulanger R., Gichimu B. M. and Gichuru (2012) Genetic diversity among commercial coffee varieties, advanced selections and museum collections in Kenya using molecular markers E. K. International Journal of Biodiversity and Conservation 4(2): 39-46.
26. Sera, T., Ruas, P. M., Ruas, C. D. F., Diniz, L. E. C., Carvalho, V. D. P., Rampim, L., Ruas, E. A. and Silveira, S. R. D (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.
27. Silveira, S. R., Ruas, P. M., Ruas, C. D. F., Sera, T., Carvalho, V. D. P. and Coelho, A. S. G (2003) Assessment of genetic variability within and among coffee progenies and cultivars using RAPD markers. Genetics and Molecular Biology, 26 (3): 329-336.
28. Diniz, L. E. C., Ruas, C. D. F., Carvalho, V. D. P., Torres, F. M., Ruas, E. A., Santos, M. D. O., Sera, T. and Ruas, P. M (2005) Genetic diversity among forty coffee varieties assessed by RAPD markers associated with restriction digestion. Brazilian Archives of Biologyand Technology, 48 (4): 511-521.
29. Atnafua Bekele and Endashaw Bekele (2014) Overview: Morphological and Molecular Markers role in Crop Improvement Programs, International Journal of Current Research in Life Sciences, 3 (3): 035-042.
30. Anthony, F., M. C. Combes, C. Astorga, B. Bertrand, G. Graziosi and P. Lashermes (2002) The rigin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers. Theoretical and Applied Genetics, 104: 894-900.
31. Steiger, D. L., Nagai, C., Moore, P. H. Morde C. W, Osgood, R. V and Ming, R (2002) "AFLP analysis of genetic diversity within and among Coffea arabica cultivars." Theoretical and applied genetics 105 (2-3): 209-215.
32. Tran, T. M. H (2005) Genetic variation in cultivated coffee (Coffea arabica L.) accessions in northern New South Wales, Australia (Doctoral dissertation, Southern Cross University).
33. Yigzaw Desalegn., Herselman, L. and Labuschagne, M. T (2008) AFLP analysis among Ethiopian arabica coffee genotypes. African Journal of Biotechnology, 7 (18). 3193-3198.
34. Reddy, M. P., Sarla, N. and Siddiq, E. A (2002) Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. euphytica, 128 (1): 9-17.
35. Bornet, B. and Branchard, M (2001) Non anchored inter -simple sequence repeat (ISSR) markers: reproducible and specific tools for genome fingerprinting. Plant molecular biology reporter, 19 (3): 209-215.
36. KojimaT, Nagaoka T, Noda N, Ogihara Y (1998) Genetic linkage map of ISSR and RAPD markers in Einkorn wheat in relation to that of RFLP markers. Theor. Appl. Genet. 96: 37–45.
37. Solomon Belami (2007) Genetic diversity analysis of the wild Coffea arabica L. populations from Harennaforest, Bale Mountains of Ethiopia, using inter simple sequence repeats (ISSR) marker, AAU.
38. Shemkit Tadele (2012) Genetic diversity of coffee (Coffea arabica L.) Land races from major coffee growing areas of souther Ethiopia as revealed by inter simple sequence repeat marker, An MSc Thesis submitted to Haramaya university.
39. Meyer FG (1965) Notes on wild Coffea arabica from southwestern Ethiopia with some historical considerations. Economic Botany 19: 136-151.
40. Gezaghen Berecha Yadessa (2014). Genetic diversity, pollination ecology and organoleptic characteristics of Coffea arabica L. Ethiopian moist forests of different management Intensity. (Doctoral dissertation in the degree of Doctor Biology), pp. 1-200.
41. Farooq, S; and Azam, F (2002). Molecular markers in plant breeding: concepts and characterization. Pakistan journal of biological sciences 5 (10): 11351140.
42. Combes, M. C., S. Andrzejewski, F. Anthony, B. Bertrand, P. Rovelli, G. Graziosi, and P. Lashermes ( 2000) “Characterization of microsatellite loci in Coffea arabica and related coffee species.” Mol. Ecol. 9: 1178–1180.
43. Baruah, A., Naik, V., Hendre, P. S., Rajkumar, R., Rajendrakumar, P., and Aggarwal, R K (2003) Isolation and characterization of nine microsatellite markers from Coffea arabica L., showing wide cross-species amplifications. Molecular Ecology Notes 3: 647–650.
44. Cubry, P., Musoli, P., Legnate, H., Pot, D., De Bellis, F., Poncet, V., Anthony, F., Dufour, M. and Leroy, T (2008) Diversity in coffee assessed with SSR markers: structure of the genus Coffea and perspectives for breeding. Genome, 51 (1): 50-63.
45. Missio, R. F., Caixeta, E. T., Zambolim, E. M., Pena, G. F., Zambolim, L. Dias, A. S. and Sakiyama, N. S (2011) "Genetic characterization of an elite coffee germplasm assessed by gSSR and EST-SSR markers." Genet Mol Res 10 (4): 2366-2381.
46. Omingo, D. O., Omondi, C. O., Cheserek, J., Runo, S. and Okun, D (2017) Diversity analysis of selected coffee genotypes using microsatellites and random amplified polymorphic DNA in Kenya.
47. Moncada, P. and S. McCouch (2004). "Simple sequences repeat diversity in diploid and tetraploid Coffea species." Genome 47(3): 501-509.
48. Silvestrini, M., Junqueira, M. G., Favarin, A. C., Guerreiro-Filho, O., Maluf, M. P., Silvarolla, M. B. and Colombo, C. A (2007) Genetic diversity and structure of Ethiopian, Yemen and Brazilian C offea arabica L. accessions using microsatellites markers. Genetic Resources and Crop Evolution, 54: 1367-1379.
49. Yigzaw Desalegn (2005) Assessment of genetic diversity of Ethiopian arabica coffee genotypes using morphological, biochemical and molecular markers. APhD Dissertation, University of the Free State, South Africa. 197p.
50. Mulatu Geleta, Isabel Herrera, Arnulfo Monzon and Tomas Bryngelsson (2012) "Genetic diversity of arabica coffee (Coffea arabica L.) in Nicaragua as estimated by simple sequence repeat markers." The Scientific World Journal.
51. Tadesse Benti, Endale Gebre, Kassahun Tesfaye, Gezahegn Berecha, Philippe Lashermes, Martina Kyallo&Nasser Kouadio Yao (2020): Genetic diversity among commercial arabica coffee (Coffeaarabica L.) varieties in Ethiopia using simple sequence repeat markers, Journal of Crop Improvement,. Journal of Crop Improvement, 35 (2): 147-168.
52. Tadesse Benti, Endale Gebre, Kassahun Tesfaye, Gezahegn Berecha, Philippe Lashermes, Martina Kyalo and Nasser Kouadio Yao (2022). Assessment of Genetic Diversity among Elite Breeding Lines of Arabica Coffee (Coffea arabica L.) in Ethiopia using Simple Sequence Repeats Markers, American Journal of Biochemistry and Biotechnology, 18 (4): 394-404.