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Verleysen L, Depecker J, Bollen R, Asimonyio J, Hatangi Y, Kambale JL, Mwanga Mwanga I, Ebele T, Dhed'a B, Stoffelen P, Ruttink T, Vandelook F, Honnay O. Crop-to-wild gene flow in wild coffee species: the case of Coffea canephora in the Democratic Republic of the Congo. ANNALS OF BOTANY 2024; 133:917-930. [PMID: 38441303 PMCID: PMC11089259 DOI: 10.1093/aob/mcae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/01/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND AND AIMS Plant breeders are increasingly turning to crop wild relatives (CWRs) to ensure food security in a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridization with their nearby cultivated crops. This might be a particular problem for wild coffee species, which often occur near coffee cultivation areas. Here, we briefly review the evidence for wild Coffea arabica (cultivated as Arabica coffee) and Coffea canephora (cultivated as Robusta coffee) and then focused on C. canephora in the Yangambi region in the Democratic Republic of the Congo. There, we examined the geographical distribution of cultivated C. canephora and the incidence of hybridization between cultivated and wild individuals within the rainforest. METHODS We collected 71 C. canephora individuals from home gardens and 12 C. canephora individuals from the tropical rainforest in the Yangambi region and genotyped them using genotyping-by-sequencing (GBS). We compared the fingerprints with existing GBS data from 388 C. canephora individuals from natural tropical rainforests and the INERA Coffee Collection, a Robusta coffee field gene bank and the most probable source of cultivated genotypes in the area. We then established robust diagnostic fingerprints that genetically differentiate cultivated from wild coffee, identified cultivated-wild hybrids and mapped their geographical position in the rainforest. KEY RESULTS We identified cultivated genotypes and cultivated-wild hybrids in zones with clear anthropogenic activity, and where cultivated C. canephora in home gardens may serve as a source for crop-to-wild gene flow. We found relatively few hybrids and backcrosses in the rainforests. CONCLUSIONS The cultivation of C. canephora in close proximity to its wild gene pool has led to cultivated genotypes and cultivated-wild hybrids appearing within the natural habitats of C. canephora. Yet, given the high genetic similarity between the cultivated and wild gene pool, together with the relatively low incidence of hybridization, our results indicate that the overall impact in terms of risk of introgression remains limited so far.
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Affiliation(s)
- Lauren Verleysen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Jonas Depecker
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
| | - Robrecht Bollen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Justin Asimonyio
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, DR Congo
| | - Yves Hatangi
- Meise Botanic Garden, Meise, Belgium
- Université de Kisangani, Kisangani, DR Congo
- Liège University, Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Jean-Léon Kambale
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, DR Congo
| | | | - Thsimi Ebele
- Institut National des Etudes et Recherches Agronomique, Yangambi, DR Congo
| | | | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Filip Vandelook
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Olivier Honnay
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
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Depecker J, Verleysen L, Asimonyio JA, Hatangi Y, Kambale JL, Mwanga Mwanga I, Ebele T, Dhed'a B, Bawin Y, Staelens A, Stoffelen P, Ruttink T, Vandelook F, Honnay O. Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation to forest disturbance. Heredity (Edinb) 2023; 130:145-153. [PMID: 36596880 PMCID: PMC9981769 DOI: 10.1038/s41437-022-00588-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and West Africa, and the genetic diversity harboured in its wild populations is vital for sustainable coffee production worldwide. Here, we aimed to quantify genetic diversity, genetic structure, and pedigree relations in wild C. canephora populations, and we investigated associations between these descriptors and forest disturbance and regeneration. Therefore, we sampled 256 C. canephora individuals within 24 plots across three forest categories in Yangambi (DR Congo), and used genotyping-by-sequencing to identify 18,894 SNPs. Overall, we found high genetic diversity, and no evidence of genetic erosion in C. canephora in disturbed old-growth forest, as compared to undisturbed old-growth forest. In addition, an overall heterozygosity excess was found in all populations, which was expected for a self-incompatible species. Genetic structure was mainly a result of isolation-by-distance, reflecting geographical location, with low to moderate relatedness at finer scales. Populations in regrowth forest had lower allelic richness than populations in old-growth forest and were characterised by a lower inter-individual relatedness and a lack of isolation-by-distance, suggesting that they originated from different neighbouring populations and were subject to founder effects. Wild Robusta coffee populations in the study area still harbour high levels of genetic diversity, yet careful monitoring of their response to ongoing forest degradation remains required.
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Affiliation(s)
- Jonas Depecker
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.
- Meise Botanic Garden, Meise, Belgium.
- KU Leuven Plant Institute, Leuven, Belgium.
| | - Lauren Verleysen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium.
| | - Justin A Asimonyio
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yves Hatangi
- Meise Botanic Garden, Meise, Belgium
- Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Jean-Léon Kambale
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Ithe Mwanga Mwanga
- Centre de Recherche en Science Naturelles, Lwiro, Democratic Republic of the Congo
| | - Tshimi Ebele
- Institut National des Etudes et Recherches, Agronomique, Democratic Republic of the Congo
| | - Benoit Dhed'a
- Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yves Bawin
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Ariane Staelens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Filip Vandelook
- Meise Botanic Garden, Meise, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
| | - Olivier Honnay
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
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