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Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation to forest disturbance

Jonas Depecker, Lauren Verleysen, Justin A. Asimonyio, Yves Hatangi, Jean-Léon Kambale, Ithe Mwanga Mwanga, Tshimi Ebele, Benoit Dhed’a, Yves Bawin, Ariane Staelens, et al.
(2023) HEREDITY. 130(3). p.145-153
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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.
Keywords
Genetics (clinical), Genetics, TROPICAL FORESTS, ANTHROPOGENIC DISTURBANCE, ALLELIC RICHNESS, GLOBAL PATTERNS, PIERRE, TREE, DIFFERENTIATION, PARENTAGE, SOFTWARE, BIODIVERSITY

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MLA
Depecker, Jonas, et al. “Genetic Diversity and Structure in Wild Robusta Coffee (Coffea Canephora A. Froehner) Populations in Yangambi (DR Congo) and Their Relation to Forest Disturbance.” HEREDITY, vol. 130, no. 3, 2023, pp. 145–53, doi:10.1038/s41437-022-00588-0.
APA
Depecker, J., Verleysen, L., Asimonyio, J. A., Hatangi, Y., Kambale, J.-L., Mwanga Mwanga, I., … Honnay, O. (2023). Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation to forest disturbance. HEREDITY, 130(3), 145–153. https://doi.org/10.1038/s41437-022-00588-0
Chicago author-date
Depecker, Jonas, Lauren Verleysen, Justin A. Asimonyio, Yves Hatangi, Jean-Léon Kambale, Ithe Mwanga Mwanga, Tshimi Ebele, et al. 2023. “Genetic Diversity and Structure in Wild Robusta Coffee (Coffea Canephora A. Froehner) Populations in Yangambi (DR Congo) and Their Relation to Forest Disturbance.” HEREDITY 130 (3): 145–53. https://doi.org/10.1038/s41437-022-00588-0.
Chicago author-date (all authors)
Depecker, Jonas, Lauren Verleysen, Justin A. Asimonyio, Yves Hatangi, Jean-Léon Kambale, Ithe Mwanga Mwanga, Tshimi Ebele, Benoit Dhed’a, Yves Bawin, Ariane Staelens, Piet Stoffelen, Tom Ruttink, Filip Vandelook, and Olivier Honnay. 2023. “Genetic Diversity and Structure in Wild Robusta Coffee (Coffea Canephora A. Froehner) Populations in Yangambi (DR Congo) and Their Relation to Forest Disturbance.” HEREDITY 130 (3): 145–153. doi:10.1038/s41437-022-00588-0.
Vancouver
1.
Depecker J, Verleysen L, Asimonyio JA, Hatangi Y, Kambale J-L, Mwanga Mwanga I, et al. Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation to forest disturbance. HEREDITY. 2023;130(3):145–53.
IEEE
[1]
J. Depecker et al., “Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation to forest disturbance,” HEREDITY, vol. 130, no. 3, pp. 145–153, 2023.
@article{01HN04HK7JHJ7QK2QD9Z5XRV0D,
  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.}},
  author       = {{Depecker, Jonas and Verleysen, Lauren and Asimonyio, Justin A. and Hatangi, Yves and Kambale, Jean-Léon and Mwanga Mwanga, Ithe and Ebele, Tshimi and Dhed’a, Benoit and Bawin, Yves and Staelens, Ariane and Stoffelen, Piet and Ruttink, Tom and Vandelook, Filip and Honnay, Olivier}},
  issn         = {{0018-067X}},
  journal      = {{HEREDITY}},
  keywords     = {{Genetics (clinical),Genetics,TROPICAL FORESTS,ANTHROPOGENIC DISTURBANCE,ALLELIC RICHNESS,GLOBAL PATTERNS,PIERRE,TREE,DIFFERENTIATION,PARENTAGE,SOFTWARE,BIODIVERSITY}},
  language     = {{eng}},
  number       = {{3}},
  pages        = {{145--153}},
  title        = {{Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation to forest disturbance}},
  url          = {{http://doi.org/10.1038/s41437-022-00588-0}},
  volume       = {{130}},
  year         = {{2023}},
}
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