ORIGINAL RESEARCH article
Front. Genet.
Sec. Genomics of Plants and the Phytoecosystem
Volume 16 - 2025 | doi: 10.3389/fgene.2025.1554029
This article is part of the Research TopicTowards Crop Stress Tolerance: Germplasm Innovations and Molecular GeneticsView all articles
Genetic basis of phenotypic diversity in C. stenophylla: a stepping stone for climate-adapted coffee cultivar development
Provisionally accepted
Paul Lahai1,2
Peter Osobase Aikpokpodion1
Alieu Mohamed Bah2Mohamed T Lahai3
Lyndel Meinhardt4Seunghyun Lim4
Ezekiel Ahn4
Dapeng Zhang4*
Sunchung Park4*- 1University of Calabar, Calabar, Cross River, Nigeria
- 2Njala University, Mokonde, Sierra Leone
- 3Eastern Technical University, Kenema, Sierra Leone
- 4Sustainable Perennial Crops Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service (USDA), Beltsville, United States
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Climate change poses significant challenges to global coffee production, particularly for Arabica coffee, which is constrained by a narrow temperature tolerance and a limited genetic pool. This study explores Coffea stenophylla, a species native to West Africa, as a potential alternative to Arabica due to its adaptability to higher temperatures and high-quality flavor profile. Using genome-wide association studies (GWAS), we investigated the genetic basis of phenotypic diversity within C. stenophylla accessions from Sierra Leone, focusing on traits related to growth habit, fruit and seed morphology, and plant structural characteristics. Our findings revealed significant SNP-trait associations that underscore the genetic diversity and potential of C. stenophylla for breeding programs. Additionally, we identified potential selective sweeps and conducted functional enrichment analysis, which highlighted genes involved in inflorescence development and flowering regulation, indicating adaptive evolution to local climates. These results suggest that C. stenophylla retains valuable genetic diversity that can be harnessed for developing improved cultivars better suited to the climatic challenges.
Keywords: Coffea stenophylla, genetic diversity, Genome-wide association studies (GWAS), selective sweeps, Climate Change
Received: 31 Dec 2024; Accepted: 04 Aug 2025.
Copyright: © 2025 Lahai, Aikpokpodion, Bah, Lahai, Meinhardt, Lim, Ahn, Zhang and Park. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Dapeng Zhang, Sustainable Perennial Crops Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service (USDA), Beltsville, United States
Sunchung Park, Sustainable Perennial Crops Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service (USDA), Beltsville, United States
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