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Background  A reciprocal recurrent selection program has been under way for the  Coffea canephora  coffee tree for approximately thirty years in the Ivory Coast. Association genetics would help to speed up this program by more rapidly selecting zones of interest in the genome. However, prior to any such studies, the linkage disequilibrium (LD) needs to be assessed between the markers on the genome. These data are essential for guiding association studies.    Results  This article describes the first results of an LD assessment in a coffee tree species. Guinean and Congolese breeding populations of  C. canephora  have been used for this work, with the goal of identifying ways of using these populations in association genetics. We identified changes in the LD along the genome within the different  C. canephora  diversity groups. In the different diversity groups studied, the LD was variable. Some diversity groups displayed disequilibria over long distances (up to 25 cM), whereas others had disequilibria not exceeding 1 cM. We also discovered a fine structure within the Guinean group.    Conclusions  Given these results, association studies can be used within the species  C. canephora . The coffee recurrent selection scheme being implemented in the Ivory Coast can thus be optimized. Lastly, our results could be used to improve  C. arabica  because one of its parents is closely related to  C. canephora .

An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis