| Summary: | <p>Abstract</p> <p>Background</p> <p>Among <it>Coffea </it>species, <it>C. canephora </it>has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". In this study, we used both microsatellite (simple sequence repeat, SSR) and restriction fragment length polymorphism (RFLP) markers to investigate the genetic variation pattern of <it>C. canephora </it>in the Guineo-Congolean distribution zone.</p> <p>Results</p> <p>Both markers were first compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among wild <it>C. canephora </it>genotypes. As expected, SSR markers were found to have a higher genetic distance detection capacity than RFLP. Nevertheless, similarity matrices showed significant correlations when Mantel's test was carried out (r = 0.66, p < 0.0001). Finally, both markers were equally effective for group discrimination and phylogenetic studies, but SSR markers tended to outperform RFLP markers in discriminating the source of an individual among diversity groups and in putative hybrid detection. Five well defined genetic groups, one in the Upper Guinean forests, the four others in the Lower Guinean forests, were identified, corresponding to geographical patterning in the individuals.</p> <p>Conclusion</p> <p>Our data suggested that the Dahomey Gap, a biogeographical barrier, played a role in wild <it>C. canephora </it>differentiation. Climatic variations during the Pleistocene and/or Holocene probably caused the subgroup differentiation in the Congolese zone through the presence of a mosaic of putative refugia. Recent hybridization between <it>C. canephora </it>diversity groups, both for spontaneous individuals and cultivars, was further characterised according to their geographic dissemination or breeding history as a consequence of human activities.</p>
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