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

Cubry Philippe, De Bellis Fabien, Avia Komlan, Bouchet Sophie, Pot David, Dufour Magali, Legnaté Hyacinthe, Leroy Thierry. 2013. An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis. BMC Genomics, 14 (10), 15 p.

Journal article ; Article de revue à facteur d'impact Revue en libre accès total
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Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q1, Sujet : GENETICS & HEREDITY

Abstract : 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. (Résumé d'auteur)

Mots-clés Agrovoc : Coffea canephora, Amélioration des plantes, Sélection récurrente, Microsatellite, Génome, Génétique des populations, Variation génétique

Mots-clés géographiques Agrovoc : Togo, Brésil, République centrafricaine, Ouganda, République démocratique du Congo, Bénin, Gabon, Congo, Guinée, Côte d'Ivoire

Classification Agris : F30 - Plant genetics and breeding
F70 - Plant taxonomy and geography

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

  • Cubry Philippe, National Botanic Gardens of Ireland (IRL)
  • De Bellis Fabien, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7070-7691
  • Avia Komlan, University of Oulu (FIN)
  • Bouchet Sophie, INRA (FRA)
  • Pot David, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-6144-8448
  • Dufour Magali, CIRAD-BIOS-UMR CMAEE (FRA)
  • Legnaté Hyacinthe, CNRA (CIV)
  • Leroy Thierry, CIRAD-BIOS-UMR AGAP (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/567500/)

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