Genetic basis of phenotypic diversity in Coffea stenophylla: a stepping stone for climate-adapted coffee cultivar development

Authors: LAHAI, PAUL - Sierra Leone Agricultural Research Institute; AIKPOKPODION, PETER - University Of Calabar Nigeria; BAH, MOHAMED - Njala University; LAHAI, MOHAMED - Eastern Technical University, Sierra Leone; Meinhardt, Lyndel; LIM, SEUNGHYUN - Orise Fellow; Ahn, Ezekiel; Zhang, Dapeng; Park, Sunchung

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/4/2025
Publication Date: 8/14/2025
Citation: Lahai, P., Aikpokpodion, P., Bah, M., Lahai, M., Meinhardt, L.W., Lim, S., Ahn, E.J., Zhang, D., Park, S. 2025. Genetic basis of phenotypic diversity in Coffea stenophylla: a stepping stone for climate-adapted coffee cultivar development. Frontiers in Genetics. https://doi.org/10.3389/fgene.2025.1554029.
DOI: https://doi.org/10.3389/fgene.2025.1554029

Interpretive Summary: Climate change poses significant challenges to global coffee production, particularly for Arabica coffee, which is constrained by limited genetic diversity and poor heat tolerance. Coffea stenophylla is a wild Coffea species native to Sierra Leone, Guinea, and Ivory Coast. This species has a flavor profile comparable to Arabica coffee and is heat-tolerant, which makes it suitable for further diversification of genetic portfolio of cultivated coffee around the world. In the present study, we conducted morphological characterization on 143 C. stenophylla accessions from Sierra Leone. Using next-generation genotyping technology, we explored the association analysis to understand the genetic basis of 11 morphological traits in C. stenophylla. Our findings revealed significant molecular marker-trait associations on growth habit, fruit and seed morphology that underscore the genetic diversity and potential of using C. stenophylla in breeding programs. This study enhances our understanding of C. stenophylla genetic resources in Sierra Leone, demonstrating the viability of this species for future breeding of climate-smart coffee cultivars. The resultant information will be used by coffee researchers to improve the efficiency in utilization of C. stenophylla genetic resources in coffee breeding programs.

Technical Abstract: Climate change poses significant challenges to global coffee production, particularly for Arabica coffee, which is constrained by limited genetic diversity and poor heat tolerance. Coffea stenophylla is a wild Coffea species native to Sierra Leone, Guinea, and Ivory Coast. This species has a flavor profile comparable to C. arabica and is heat-tolerant, which makes it suitable for further diversification of genetic portfolio of cultivated coffee around the world. In the present study, we conducted morphological characterization on 143 C. stenophylla accessions from Sierra Leone. Using genome-wide association studies (GWAS), we investigated the genetic basis 11 morphological 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 using C. stenophylla in 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 of C. stenophylla to local climates. This study enhances our understanding of C. stenophylla genetic resources in Sierra Leone, demonstrating the viability of this species for future breeding of climate-smart coffee cultivars.