Open Access Open Badges Research article

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

Philippe Cubry16*, Fabien de Bellis1, Komlan Avia2, Sophie Bouchet3, David Pot1, Magali Dufour4, Hyacinthe Legnate5 and Thierry Leroy1

Author Affiliations

1 CIRAD, UMR AGAP, Montpellier, F-34398, France

2 Department of Biology, University of Oulu, PO Box 3000, Oulu, FI-90014, Finland

3 INRA, UMR de Génétique Végétale, INRA/CNRS/Univ Paris-Sud/AgroParistech, Ferme du Moulon, Gif sur Yvette, F-91190, France

4 CIRAD, UMR CMAEE, Montpellier, F-34398, France

5 CNRA, Divo, BP 808, Côte d’Ivoire

6 Current address: DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Dublin, Glasnevin, Dublin 9, Ireland

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BMC Genomics 2013, 14:10  doi:10.1186/1471-2164-14-10

Published: 16 January 2013



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.


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.


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.

Africa; Association studies; Coffea canephora; Genetic diversity; Linkage disequilibrium; Microsatellite