Plant Systematics and Evolution

, Volume 300, Issue 5, pp 881–897 | Cite as

ISSR fingerprinting of Coffea arabica throughout Ethiopia reveals high variability in wild populations and distinguishes them from landraces

  • Kassahun TesfayeEmail author
  • Kim Govers
  • Endashaw Bekele
  • Thomas Borsch
Original Article


Forests of SW Ethiopia constitute the native habitat of Coffea arabica and also the place where domestication of Arabica coffee started. Selection from wild populations has led to numerous landraces (farmer’s varieties) and cultivars. Inter-simple sequence repeats (ISSRs) were generated from a representative set of forest coffee populations and landraces across Ethiopia. For the broad diversity assessment, nine di- and tri-nucleotide ISSR primers were applied, as chosen from a total of 102 primers tested initially. Tetranucleotide ISSR primers differed in amplifying fingerprints that could hardly be analysed due to excessive variation. Tree building analysis (NJ, UPGMA) of 84 polymorphic loci amplified for 125 C. arabica individuals provided evidence for several groups of related genotypes occurring in certain geographical areas of Ethiopia and underscored the existence of wild coffee distinct from landraces. Landraces seem to have originated in different geographical areas of Ethiopia in a stepwise domestication process. While the overall geographical signal in the dataset was weak, analysis in a Bayesian framework using the admixture model with geographical priors in STRUCTURE recovered some genetic clustering. Based on Shannon’s diversity index, populations from Yayu (0.47) and Bonga (0.46) showed highest diversity, followed by individuals from Berhane Kontir (0.41). A likely scenario for the differentiation of C. arabica after an allopolyploidization event is that the hierarchical-geographical patterning of wild Coffea genotypes expected from stepwise range extension was obscured by recent or ancient gene flow. The diversity and geographical distribution of autochthonous C. arabica genotypes indicates the need for a multi-site in situ conservation approach.


Coffea arabica Wild populations ISSR Genetic structure Conservation Ethiopia 



This paper serves in part for the completion of a PhD dissertation of K. T. which is carried out in the framework of CoCE project (Conservation and use of wild populations of Coffea arabica in the montane rainforests of Ethiopia) in the BIOTEAM (Biosphärenforschung—InTEgrative und Anwendungsorientierte Modellprojekte) program of the German Federal Ministry of Education and Research (BMBF). We thank W. Barthlott (Nees-Institute, University of Bonn), M. Denich and F. Gatzweiler (Center for Development Research, University of Bonn), and T. W. Gole (Environment and Coffee Forest Forum, Ethiopia) for their support. We are thankful to Ludo A. H. Muller (Institut für Biologie/Botanik, Freie Universität Berlin) for his support and advise during data analyses. We appreciate the help of the Jimma Agricultural Research Center (EIAR, Ethiopia) and Institute of Biodiversity Conservation (IBC, Ethiopia) for C. arabica landraces. T.B. acknowledges support by a Heisenberg-Scholarship by the Deutsche Forschungsgemeinschaft (DFG).

Supplementary material

606_2013_927_MOESM1_ESM.eps (4.6 mb)
Supplementary material 1. Appendix S1: STRUCTURE analysis of 125 individuals of C. arabica (10 populations) sampled from wider geographical locations. Each individual coffee sample is represented by a single vertical line divided into K colours, where K (K = 2; K = 3, K = 4, K = 6) is the number of clusters assumed and the length of the coloured segment represents the individual’s estimated proportion of membership to a particular cluster. Black lines separate different populations. (a) the admixture model with the LOCPRIOR option and (b) the admixture model without any priors. Harenna = 1, Bonga = 2, Berhan Kontir = 3; Yayu = 4; Boginda = 5; Maji = 6; Anfilo = 7; Daphe = 8; Mankira = 9; Landraces and cultivars = 10. (EPS 4678 kb)


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Copyright information

© Springer-Verlag Wien 2013

Authors and Affiliations

  • Kassahun Tesfaye
    • 1
    Email author
  • Kim Govers
    • 2
  • Endashaw Bekele
    • 3
  • Thomas Borsch
    • 2
  1. 1.Institute of BiotechnologyAddis Ababa UniversityAddis AbabaEthiopia
  2. 2.Botanischer Garten und Botanisches Museum Berlin-Dahlem and Institut für Biologie/BotanikFreie Universität BerlinBerlinGermany
  3. 3.Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia

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