Coffea stenophylla is a rare Coffea species boasting a flavor profile comparable to Arabica coffee (Coffea arabica) 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 C. stenophylla in Sierra Leone. The novel SNP markers developed in this study provided valuable tools to support future efforts in conservation and utilization of C. stenophylla genetic resources in West Africa.

Coffee is a major cash and export crops in Sierra Leone and is mainly cultivated in southern and eastern provinces. Kenema, Kailahun, Moyamba, Bo, Pujehun and Kono are major coffee growing districts in the country. This study looks at the extent of phenotypic diversity of the rare and wild Coffea stenophylla in Kenema and Moyamba districts. The Shannon-Weaver diversity were computed for the 13 qualitative parameters of the International Plant Genetic Resources Institute. The Shannon-Weaver diversity revealed variations among the samples for the observed 13 morphological traits which ranges from (H'=0) for both fruit colour and calyx limb persistence to (H'=0.87) for angle of insertion of primary branches on the main stem. Among the 13 qualitative traits assessed, angle of insertion of primary branches on main stem (H' = 0.87), growth habit (H' = 0.78), bean size (H' = 0.75), young leaf colour (H' = 0.66), stem habit (H' = 0.66) and fruit shape (H' = 0.65) exhibited high level of diversity while seed shape (H' = 0.58), stipule shape (H' = 0.46), leaf shape (H' = 0.43), seed uniformity (H' = 0.31) and leaf apex shape (H' = 0.06) showed low level of diversity. This is the first report of phenotypic diversity of Coffea stenophylla in Sierra Leone and the study thus unraveled existence of diversity among samples. It is recommended that these observed variabilities be exploited in order to develop better accessions that are high yielding yet maintaining the same taste. Additionally, genetic fingerprinting need to be applied to provide a complementary assessment of the observed phenotypic diversity.

Global coffee production is dominated by Coffea arabica (Arabica coffee) and C. canephora (Robusta coffee) due to their relatively high-yielding and quality attributes as opposed to other coffee species. Despite these advantages, production of Arabica and Robusta coffee is facing mounting challenges though not limited to increasing prevalence and severity of biotic and abiotic stresses. These challenges bring forth an indication that the global coffee crop portfolio requires diversification to ensure resilience to the key challenges for sustainable production. Sierra Leone is in the center of genetic diversity of genus Coffea, and the country hosts rich coffee genetic resources. The C. stenophylla, C. affinis and possibly other wild relative species are indigenous to Sierra Leone and these species offer great potential for a new coffee market and income generation. However, more efforts of conservation and genetic improvement on these species, are needed to realize these opportunities. The objective of this paper is to review the coffee genetic resources in Sierra Leone with an emphasis on the wild coffee species including their conservation status, and the phenotypic and molecular characterization. We also present perspectives for future genetic improvement of C. stenophylla, and discuss breeding methods, combining ability, and molecular marker-assisted prediction of hybrid vigor. Moreover, with the availability of recently developed single nucleotide polymorphisms (SNP) markers on C. stenophylla, we suggest that new technologies of molecular breeding, such as genomic selection can significantly accelerate the breeding progress and deliver improved varieties with high yield, good adaptability, and disease resistance.