Unveiling the genetic diversity and demographic history of coffea stenophylla in Sierra Leone using genotyping-by-sequencing

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

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/24/2024
Publication Date: 12/27/2024
Citation: Lahai, P., Aikpokpodion, P., Lahai, M., Meinhardt, L.W., Lim, S., Ahn, E.J., Zhang, D., Park, S. 2024. Unveiling the genetic diversity and demographic history of coffea stenophylla in Sierra Leone using genotyping-by-sequencing. Plants. 14(1):50. https://doi.org/10.3390/plants14010050.
DOI: https://doi.org/10.3390/plants14010050

Interpretive Summary: Coffea stenophylla is a Coffea species native to Sierra Leone, Guinea, and Ivory Coast. This species has a flavor profile comparable to C. arabica and has a good adaptability in low elevations and hot-tropical climates, which makes it suitable for further diversification of genetic portfolio of cultivated coffee around the world. C. stenophylla genetic resources are vulnerable due to heavy deforestation and habitat fragmentation in its center of origin, West Africa. In the present study, we analyze genetic diversity and population structure of C. stenophylla germplasm in three regions and one ex situ collection in Sierra Leone. The study also includes 47 trees of Robusta and Liberica coffee. Our result unveiled the presence of three moderately distinctive genetic clusters representing Kasewa, Ngegeru, and Kpumbu forests, in Sierra Leone. Our result of comparative analysis also showed that the Kasewa cluster was not represented in the current ex situ collection. These findings bring an important message to conservation practice of C. stenophylla in Sierra Leone, affirming that there are different genetic clusters of C. stenophylla in Sierra Leone, and revealing the gap of genetic diversity in the ex-situ collection. Furthermore, we developed a panel of new molecular makers for this important species, which provides a powerful research tool for supporting conservation and genetic enhancement of C. stenophylla genetic resources. The resultant information will be used by coffee researchers to improve the efficiency in sustainable conservation and utilization of C. stenophylla genetic resources.

Technical Abstract: Coffea stenophylla is a Coffea species native to Sierra Leone, Guinea, and Ivory Coast. This species has a flavor profile comparable to C. arabica and has a good adaptability in low elevations and hot-tropical climates, which makes it suitable for further diversification of genetic portfolio of cultivated coffee around the world. C. stenophylla genetic resources are vulnerable due to heavy deforestation and habitat fragmentation in its center of origin, West Africa. In the present study, we used novel SNP markers, derived from Genotyping-by-Sequencing, to analyze genetic diversity and population structure of C. stenophylla germplasm in three regions and one ex situ collection in Sierra Leone. The study also includes 47 trees of C. canephrora and C. liberica. The GBS led to the identification of 6238 SNP markers, after rigorous filtering. Result of multivariate analysis, Bayesian clustering algorithm, and Analysis of Molecular Variance unveiled the presence of three moderately distinctive genetic clusters representing Kasewa, Ngegeru, and Kpumbu forests, with an average Fst of 0.042, and an average gene flow (Nm) of 4.80 among the three sites. Our result of comparative analysis also showed that the Kasewa cluster was not represented in the current ex situ collection. These findings bring an important message to conservation practice of C. stenophyllla in Sierra Leone, affirming the heterogenous spatial distribution, and revealing the gap of genetic diversity in the ex-situ collection. The novel SNP markers developed in this study, provided a powerful research tool for supporting conservation and genetic enhancement of C. stenophylla genetic resources.