Unveiling the Genetic Diversity and Demographic History of <i>Coffea stenophylla</i> in Sierra Leone Using Genotyping-By-Sequencing
<i>Coffea stenophylla</i> is a rare Coffea species boasting a flavor profile comparable to Arabica coffee (<i>Coffea arabica</i>) and has a good adaptability to lowland tropical climates. This species faces increasing threats from climate change, deforestation, and habitat fr...
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2024-12-01
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| author | Paul M. Lahai Peter O. Aikpokpodion Alieu Mohamed Bah Mohamed T. Lahai Lyndel W. Meinhardt Seunghyun Lim Ezekiel Ahn Dapeng Zhang Sunchung Park |
| author_facet | Paul M. Lahai Peter O. Aikpokpodion Alieu Mohamed Bah Mohamed T. Lahai Lyndel W. Meinhardt Seunghyun Lim Ezekiel Ahn Dapeng Zhang Sunchung Park |
| author_sort | Paul M. Lahai |
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| description | <i>Coffea stenophylla</i> is a rare Coffea species boasting a flavor profile comparable to Arabica coffee (<i>Coffea arabica</i>) and has a good adaptability to lowland tropical climates. This species faces increasing threats from climate change, deforestation, and habitat fragmentation in its West African homeland. Using 1037 novel SNP markers derived from Genotyping-by-Sequencing (GBS), we revealed the presence of three distinct natural populations (mean Fst = 0.176) in Sierra Leone. Evidence of recent bottlenecks and small effective population size (118–140) was found across all three populations, reflecting the impact of recent anthropogenic disturbances on this species. Using a model-flexible inference approach, we unveiled a strong ancient bottleneck approximately 23,000 years ago, coinciding with the last glacial maximum (LGM), followed by post-glacial expansion and divergence into distinct genetic clusters. A comparative analysis between ex situ genebanks and natural populations detected a significant gap in genetic diversity, with two out of three natural populations missing from the ex situ genebank collection. These findings highlight the urgent need to improve conservation practices for <i>C. stenophylla</i> in Sierra Leone. The novel SNP markers developed in this study provided valuable tools to support future efforts in conservation and utilization of <i>C. stenophylla</i> genetic resources in West Africa. |
| format | Article |
| id | doaj-art-b3a8eea826a447289eac29f838a01c89 |
| institution | Kabale University |
| issn | 2223-7747 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj-art-b3a8eea826a447289eac29f838a01c892025-01-10T13:19:36ZengMDPI AGPlants2223-77472024-12-011415010.3390/plants14010050Unveiling the Genetic Diversity and Demographic History of <i>Coffea stenophylla</i> in Sierra Leone Using Genotyping-By-SequencingPaul M. Lahai0Peter O. Aikpokpodion1Alieu Mohamed Bah2Mohamed T. Lahai3Lyndel W. Meinhardt4Seunghyun Lim5Ezekiel Ahn6Dapeng Zhang7Sunchung Park8Sierra Leone Agricultural Research Institute (SLARI), IDA, Kenema 42215, Sierra LeoneDepartment of Genetics and Biotechnology Faculty of Biological Sciences, University of Calabar, PMB 1115, Calabar 540271, Cross River State, NigeriaDepartment of Crops Science, Faculty of Agriculture, Njala University, Mokonde 42215, Sierra LeoneDepartment of Crop Science, Faculty of Agriculture, Eastern Technical University, Kenema 42215, Sierra LeoneSustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 2005, USASustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 2005, USASustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 2005, USASustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 2005, USASustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 2005, USA<i>Coffea stenophylla</i> is a rare Coffea species boasting a flavor profile comparable to Arabica coffee (<i>Coffea arabica</i>) and has a good adaptability to lowland tropical climates. This species faces increasing threats from climate change, deforestation, and habitat fragmentation in its West African homeland. Using 1037 novel SNP markers derived from Genotyping-by-Sequencing (GBS), we revealed the presence of three distinct natural populations (mean Fst = 0.176) in Sierra Leone. Evidence of recent bottlenecks and small effective population size (118–140) was found across all three populations, reflecting the impact of recent anthropogenic disturbances on this species. Using a model-flexible inference approach, we unveiled a strong ancient bottleneck approximately 23,000 years ago, coinciding with the last glacial maximum (LGM), followed by post-glacial expansion and divergence into distinct genetic clusters. A comparative analysis between ex situ genebanks and natural populations detected a significant gap in genetic diversity, with two out of three natural populations missing from the ex situ genebank collection. These findings highlight the urgent need to improve conservation practices for <i>C. stenophylla</i> in Sierra Leone. The novel SNP markers developed in this study provided valuable tools to support future efforts in conservation and utilization of <i>C. stenophylla</i> genetic resources in West Africa.https://www.mdpi.com/2223-7747/14/1/50climate changeconservationcrop wild relatives (CWRs)isolate-breaking effectgenetic diversityspecialty coffee |
| spellingShingle | Paul M. Lahai Peter O. Aikpokpodion Alieu Mohamed Bah Mohamed T. Lahai Lyndel W. Meinhardt Seunghyun Lim Ezekiel Ahn Dapeng Zhang Sunchung Park Unveiling the Genetic Diversity and Demographic History of <i>Coffea stenophylla</i> in Sierra Leone Using Genotyping-By-Sequencing Plants climate change conservation crop wild relatives (CWRs) isolate-breaking effect genetic diversity specialty coffee |
| title | Unveiling the Genetic Diversity and Demographic History of <i>Coffea stenophylla</i> in Sierra Leone Using Genotyping-By-Sequencing |
| title_full | Unveiling the Genetic Diversity and Demographic History of <i>Coffea stenophylla</i> in Sierra Leone Using Genotyping-By-Sequencing |
| title_fullStr | Unveiling the Genetic Diversity and Demographic History of <i>Coffea stenophylla</i> in Sierra Leone Using Genotyping-By-Sequencing |
| title_full_unstemmed | Unveiling the Genetic Diversity and Demographic History of <i>Coffea stenophylla</i> in Sierra Leone Using Genotyping-By-Sequencing |
| title_short | Unveiling the Genetic Diversity and Demographic History of <i>Coffea stenophylla</i> in Sierra Leone Using Genotyping-By-Sequencing |
| title_sort | unveiling the genetic diversity and demographic history of i coffea stenophylla i in sierra leone using genotyping by sequencing |
| topic | climate change conservation crop wild relatives (CWRs) isolate-breaking effect genetic diversity specialty coffee |
| url | https://www.mdpi.com/2223-7747/14/1/50 |
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