An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis
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.
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dig-cirad-fr-5675002024-01-28T21:09:22Z http://agritrop.cirad.fr/567500/ http://agritrop.cirad.fr/567500/ 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. BMC Genomics, 14 (10), 15 p.https://doi.org/10.1186/1471-2164-14-10 <https://doi.org/10.1186/1471-2164-14-10> 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 eng 2013 BMC Genomics F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie Coffea canephora amélioration des plantes sélection récurrente microsatellite génome génétique des populations variation génétique http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 Togo Brésil République centrafricaine Ouganda République démocratique du Congo Bénin Gabon Congo Guinée Côte d'Ivoire http://aims.fao.org/aos/agrovoc/c_7801 http://aims.fao.org/aos/agrovoc/c_1070 http://aims.fao.org/aos/agrovoc/c_1433 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_8500 http://aims.fao.org/aos/agrovoc/c_875 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_1811 http://aims.fao.org/aos/agrovoc/c_3423 http://aims.fao.org/aos/agrovoc/c_4027 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/567500/1/document_567500.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1186/1471-2164-14-10 10.1186/1471-2164-14-10 info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-14-10 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/1471-2164-14-10 |
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F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie Coffea canephora amélioration des plantes sélection récurrente microsatellite génome génétique des populations variation génétique http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_7801 http://aims.fao.org/aos/agrovoc/c_1070 http://aims.fao.org/aos/agrovoc/c_1433 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_8500 http://aims.fao.org/aos/agrovoc/c_875 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_1811 http://aims.fao.org/aos/agrovoc/c_3423 http://aims.fao.org/aos/agrovoc/c_4027 F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie Coffea canephora amélioration des plantes sélection récurrente microsatellite génome génétique des populations variation génétique http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_7801 http://aims.fao.org/aos/agrovoc/c_1070 http://aims.fao.org/aos/agrovoc/c_1433 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_8500 http://aims.fao.org/aos/agrovoc/c_875 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_1811 http://aims.fao.org/aos/agrovoc/c_3423 http://aims.fao.org/aos/agrovoc/c_4027 |
spellingShingle |
F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie Coffea canephora amélioration des plantes sélection récurrente microsatellite génome génétique des populations variation génétique http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_7801 http://aims.fao.org/aos/agrovoc/c_1070 http://aims.fao.org/aos/agrovoc/c_1433 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_8500 http://aims.fao.org/aos/agrovoc/c_875 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_1811 http://aims.fao.org/aos/agrovoc/c_3423 http://aims.fao.org/aos/agrovoc/c_4027 F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie Coffea canephora amélioration des plantes sélection récurrente microsatellite génome génétique des populations variation génétique http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_7801 http://aims.fao.org/aos/agrovoc/c_1070 http://aims.fao.org/aos/agrovoc/c_1433 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_8500 http://aims.fao.org/aos/agrovoc/c_875 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_1811 http://aims.fao.org/aos/agrovoc/c_3423 http://aims.fao.org/aos/agrovoc/c_4027 Cubry, Philippe De Bellis, Fabien Avia, Komlan Bouchet, Sophie Pot, David Dufour, Magali Legnaté, Hyacinthe Leroy, Thierry An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis |
description |
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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie Coffea canephora amélioration des plantes sélection récurrente microsatellite génome génétique des populations variation génétique http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_27595 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_7801 http://aims.fao.org/aos/agrovoc/c_1070 http://aims.fao.org/aos/agrovoc/c_1433 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_8500 http://aims.fao.org/aos/agrovoc/c_875 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_1811 http://aims.fao.org/aos/agrovoc/c_3423 http://aims.fao.org/aos/agrovoc/c_4027 |
author |
Cubry, Philippe De Bellis, Fabien Avia, Komlan Bouchet, Sophie Pot, David Dufour, Magali Legnaté, Hyacinthe Leroy, Thierry |
author_facet |
Cubry, Philippe De Bellis, Fabien Avia, Komlan Bouchet, Sophie Pot, David Dufour, Magali Legnaté, Hyacinthe Leroy, Thierry |
author_sort |
Cubry, Philippe |
title |
An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis |
title_short |
An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis |
title_full |
An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis |
title_fullStr |
An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis |
title_full_unstemmed |
An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis |
title_sort |
initial assessment of linkage disequilibrium (ld) in coffee trees: ld patterns in groups of coffea canephora pierre using microsatellite analysis |
url |
http://agritrop.cirad.fr/567500/ http://agritrop.cirad.fr/567500/1/document_567500.pdf |
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