Coffee (Coffea spp.) is one of the most important beverages and cash crops worldwide, providing economic livelihood to millions of people in developing countries [1]. It is ranked second in international trade after crude oil [2]. Globally, green coffee production is estimated to be above 134.16 million bags (60 kg capacity per bag) with a retail sales value in excess of $22.7 billion during the 2010-11 sales in the world market [3]. Spanning over 80 countries in Africa, Asia and Latin America, coffee is grown on about 10.2 million hectares of land in the tropical and subtropical regions of the world [2]. Coffee trees belong to the genus Coffea in the family Rubiaceae. The genus Coffea has a record of more than 130 species, but only three species are commercially cultivated: C. arabica L. (2n = 4x = 44) known for its allotetraploidy and self-fertility [4], C. canephora P. (2n = 2x = 22), and C. liberica L. (2n = 2x = 22). Of recent times, C. stenophyllais beginning to gain attention globally due to its superiority taste comparable to C. arabica [5]. C. arabica is preferred in the consumer market due to its beverage quality, aromatic characteristics, and low-caffeine content, compared to robusta, which is characterized by a stronger bitterness and higher-caffeine content. Globally, C. arabica contributes 65% of the total global coffee production [6]. Considering the number of species on record with only a few being commercially viable, this presents limitation for their genetic improvement through conventional breeding programs because of their perennial nature and differences in level of ploidy and incompatibility. Most importantly, characteristics such as resistance to pathogens or pests are seen to be lacking in the available germplasm globally, although conventional and advanced breeding techniques are in progress to address these challenges [1]. Genetic engineering techniques have been utilized to solve this barrier, leading to significant advances during the last decades.

Global coffee production is dominated by C. 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 [5]. 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 [7]. However, more efforts of conservation and genetic improvement on these species are needed to realize these opportunities [5].

C. arabica is mainly native to the highlands of Southwestern Ethiopia with additional populations in South Sudan (Boma Plateau) and North Kenya (Mount Marsabit) [8]. The varieties of C. arabicagrown all over the world are derivatives from either the “Typica” or “Bourbon” genetic base, resulting in low-genetic diversity among cultivated arabicas. In contrast, however, C.canephora has a wide geographic distribution, extending from the western to central tropical and subtropical regions of the African continent, from Guinea, Sierra Leone and Liberia to Sudan and Uganda with high genetic diversity in the Democratic Republic of the Congo [9]. Additionally, C. canephora maintains heterozygosity due to its cross-pollinating nature.

More than a decade ago, considerable advances were made in the genetic transformation of coffee. A number of research groups in the world have been able to transform coffee through genetic manipulations for insect resistance, production of decaffeinated coffee, resistance to herbicide and control of fruit maturation. Although the majority of the research is seen to be still limited to laboratory and greenhouse studies, initial field tests with transformed coffee progenies are beginning to appear in the literature.

This study collected, collated and synthesized existing evidence on Advances in coffee germplasm enhancement and utilization in Sierra Leone. The review followed a structured process comprising literature identification, screening, eligibility assessment, data extraction, and synthesis to ensure transparency and reproducibility.

A search was conducted across Web of Science, Scopus, ScienceDirect, Springer Nature, PubMed/PubMed Central, MDPI, Google Scholar, and the Food and Agriculture Organization (FAO) repository. Additional studies were identified through manual screening of reference lists from relevant publications. Searches were performed using combinations of keywords and Boolean operators related to germplasm collection, characterization, conservation and maintenance; trait profiling, discovery and utilization for coffee germplasm improvement; association mapping of important traits in coffee; breeding for abiotic stress resistance in coffee; and impact of drought stress in the production and productivity of coffee.

Studies were included if they focused on coffee in the highlighted subject areas, and were excluded if they did not focus on the coffee, lacked clear variables of the subject studied, were duplicate publications, or provided insufficient methodological information.

Plant genetic transformation expands the gene pool beyond conventional breeding, enabling efficient gene transfer across species. This technique is vital for perennial crops, allowing rapid introduction of new traits while preserving the original cultivar’s genetic base, thus advancing plant science and agriculture. Transgenic crop production is beginning to reach 90 million hectares ten years after release of commercially viable genetically modified plants [10]. Plant transformation aids breeding programs and is essential in research, enabling gene knockout and over-expression. It is valuable across plant physiology, biochemistry, and phytopathology.

Conventional breeding has effectively developed rust-resistant coffee cultivars, but introducing new traits typically takes 20 to 35 years. Genetic engineering can significantly shorten this timeframe, allowing for the quicker development of cultivars with enhanced disease resistance and quality. This technique also facilitates the introduction of traits from different species, enabling characteristics like insect resistance, herbicide resistance, and improved tolerance to abiotic stresses such as drought or frost, which are challenging to achieve through traditional methods.

Genetically Modified (GM) coffee plants have been produced by different research groups in the world [11]-[15]. Despite significant advances over the last 15 years, coffee transformation is still very laborious, with bottlenecks in the methodology that make it far from a routine laboratory technique [16][17].

Plant Genetic Resources (PGR) are crucial for agro-biodiversity, encompassing primitive, modern, obsolete, breeding lines, weedy, and related wild species [18]. Genetic diversity in farmers’ fields and wild relatives enhances crop productivity through plant breeding, but PGRs are finite and vulnerable to losses due to new crop varieties, urbanization, and natural hazards [19]. The PGR significantly contributes to achieving the Millennium Development Goals through genebanks, with over six million accessions conserved in over 1400 genebanks worldwide [20]. The Sierra Leone Agricultural Research Institute (SLARI) has responded to this need by establishing a Genetic Resources Unit for assembly, characterization, evaluation, maintenance, conservation, documentation and distribution of germplasm of selected tree crops such as coffee (Coffea species), cacao (Theobromacacao L.), cashew (Anacardium occidentale) and oil palm (Elaeis guineensis).

Genetic variation, once considered unlimited, is rapidly eroding as modern cultivars replace traditional ones, causing the destruction of natural habitats of wild relatives of cultivated species. Several land races of some of the enlisted crops conserved under SLARI’s jurisdiction have disappeared, except for C. stenophylla, which has resurfaced since 2018 and is beginning to gain momentum due to its superior flavor and ability to withstand changing climatic conditions. Seed conservation is crucial for crop genetic diversity preservation, as it is cost-effective, simple, and maintains genetic stability over long periods. It involves collection, characterization, conservation, distribution, and utilization of plant germplasm for global germplasm conservation.

Germplasm collection is costly and time-consuming, so it’s crucial to review past crop collections and secure germplasm from those who have already explored the area. The collection offers protection against genetic erosion, resistance to diseases, pests, and environmental stresses, and improved crop quality and yield traits.

The primary goal of collecting PGR is to capture the maximum amount of genetic variation in the smallest number of samples [21]. Efficient strategies for germplasm collection are influenced by the available information on genetic variation in target taxa populations and their distribution in the target geographical region [22]. However, in cases where there is a lack of information about the target species and the collection area, it may be beneficial to conduct an exploration mission.

The establishment of the Institute of Agricultural Research (IAR), which was later transformed into SLARI in 2009, aimed at the assemblage of germplasm of its mandate crops through donation and exchange with various West African sub-region research institutes. This effort was also complemented by the collection, characterization and management of various land races spanning across tree crops, root and tuber crops, cereals and horticultural crops. The IAR received the first set of introduced T. cacaoin the 1960s from the West African Cocoa Research Institute (dubbed as WACRI Series I and II). During these periods, Sierra Leone was served alongside her West African Counter parts such as Ghana, Nigeria, Cote d’Ivoire and Togo. This was followed by the introduction of eight varieties of C.canephorafrom Uganda and Nigeria. These materials were initially deposited at the Njala Lower Nursery, Mokonde. They were later propagated and established at SLARI’s cocoa and coffee clonal gardens at Kpuwabu and Pendembu. In 2019, SLARI acquired its first-ever set of ten C. arabicavarieties from Embapra, Brazil through a European Union Funded Project called Boosting Agriculture and Food Security (BAFS). The 10 varieties including MGSCATIGUA’ 3, CATUCAI AMARELO (2SL), IAC 125 RN, CATUCAI AMARELO (IAC 62), PAQAISO 2, PAQAISO (H 419-1), TOPAZIO MG 1190, MUNDO NOVO (IAC 379-19), CATUAI VEQMELHO (IAC 144), and OEIRAS MG 6851 were established at Bambawo, Pendembu and Kpuwabu clonal gardens for onward characterization (Table A1). The current collections account for 65% - 70% of the available diversity, and there is a continuous need to protect endangered germplasm, especially C. stenophylla.

Recently, we obtained wild saplings of C. stenophyllafrom the Kambui and Kasewe Hills for establishment at Bambawo (due to its proximity to the Kambui Forest). Similarly, the Welthungerhilfe (WHH) organization through Greenwich University has been collecting and nursing both seeds and saplings of stenophylla from ex-situ and distributing them to smallholder coffee farmers as a form of conservation of wild coffee relatives. Additionally, coffee culture has established 10 ha of wild C. stenophylla at Ngegeru (entry point into the Kambui Forest for collection of stenophylla seeds and saplings).

The national agricultural research programs in most countries, universities, regional organizations, and international centers are working on developing crop cultivars/elite breeding lines. Most of these collected lines are conserved in constituent centers of SLARI’s genebank for future utilization.

Germplasm utilization by breeders requires accurate characterization of agronomic and morphological traits, continuous screening against stresses, and joint estimation of yield traits with contributions from scientists across different disciplines. For instance, at SLARI, germplasm sets for coffee have been evaluated for agronomic performance by scientists from the Kenema Forestry and Tree Crops Research Centre (KFTCRC) of SLARI. The results of joint evaluation by a team of KFTCRC scientists have resulted in better understanding of the germplasm materials conserved at SLARI’s tree crops genebank so that they could be characterized for important morpho-agronomic traits.

Germplasm characterization is the systematic recording of heritable, identifiable traits with precision in fields, contrasting with preliminary evaluation, which records limited agronomic traits for crop improvement. The major objectives of germplasm characterization are as follows:

1) Describe accessions, establish their diagnostic characteristics and identify duplicates;

2) Classify groups of accessions using sound criteria;

3) Identify accessions with desired agronomic traits and select entries for more precise evaluation;

4) Develop interrelationships between, or among traits and between geographic groups of cultivars; and

5) Estimate the extent of variation in the collection.

Achieving the above objectives would lead to the identification of a wide range of sources for desirable traits in the assembled germplasm.

Breeding programs require efficient selection strategies for low heritability traits in univariate or multivariate models for high genetic gains. Multiple trait selection in perennial crops allows for more assertive identification of genetic divergence [58][59]. High-throughput metabolic phenotyping offers rapid plant characterization, but technical issues and data processing and statistical evaluation strategies must be developed for accurate results [60].

Trait profiling and its subsequent discovery and utilization are crucial for the genetic enhancement of coffee germplasm, particularly in response to challenges like climate change and market dynamics. This process allows for the systematic identification and integration of desirable traits from various coffee accessions into breeding programs to create resilient cultivars. Comprehensive characterization of coffee germplasm evaluates numerous traits such as yield, drought tolerance, and pest resistance, utilizing advanced phenotyping and statistical tools to assess trait variation and stability [61]. Breeding efforts increasingly focus on traits critical for climate adaptation, such as leaf rust resistance and drought tolerance, to bolster agricultural resilience and farmer livelihoods.

Trait discovery in coffee leverages advances in molecular biology, using tools like SNP markers, GBS, and Genome-Wide Association Studies (GWAS) to identify novel genetic markers linked to traits such as heat tolerance and pest resistance. Researchers have therefore taken advantage of these tools to critically examine the genetic architecture of complex traits and uncover rare alleles in wild species such as C. stenophylla, C. liberica, and C. racemosa, offering unique attributes like heat tolerance, pest resistance, and low caffeine content [62]. Techniques such as transcriptomic and metabolomic analyses explain the relationship between gene expression and traits like flavor. To utilize these traits, breeding programs employ marker-assisted and Genomic Selection (GS), alongside hybridization strategies, ensuring alignment with market demands through participatory breeding approaches [62]. Core collections and pre-breeding programs further enhance the use and preservation of genetic diversity.

In Sierra Leone, trait-based coffee improvement has significant potential due to the country’s biodiversity and underutilized germplasm, including indigenous Coffea species. This approach can lead to the development of climate-resilient and market-oriented cultivars, supporting national breeding programs and aligning with agricultural innovation, biodiversity conservation, and export competitiveness. Integrating these strategies into policy frameworks and extension systems will enhance their effectiveness, benefiting farmers and stakeholders. Transgenic approaches for coffee focus on utilizing the genetic resources of the native species. C. stenophylla, which is rich in genetic diversity [5][7]. Technologies such as GS and SNP markers have been exploited to enhance breeding progress and produce improved coffee genotypes with better adaptability and disease resistance. These technologies aimed at leveraging the genetic potential of C. stenophylla to develop sustainable coffee production in Sierra Leone [5][7]. To make the recommended approach actionable, the following minimum enabling requirements are essential: establish a robust phenotyping network that includes standardized protocols for capturing and analyzing phenotypic data, ensuring consistency across experiments; 1) ensure assess to high-quality genotyping resources, including tools and databases that support accurate genetic data collection and analysis; 2) implement effective data management practices that facilitate the storage, retrieval, and analysis of phenotypic and genotypic data, ensuring data integrity and accessibility; 3) foster collaborations with researchers, breeders, and industry stakeholders to share knowledge and resources, enhancing the overall effectiveness of the phenotyping and genotyping efforts.

Developing coffee varieties that are resilient to abiotic stress has become a critical necessity due to increased variability in climate and environmental challenges. Coffee species, especially C. arabicaand C. canephora, have been observed to be vulnerable to drought, high temperatures, salinity, and excessive sunlight factors that threaten consistency in yield and yield-related parameters, quality of beans, and the livelihoods of farmers in tropical regions. The Sierra Leone scenario seems to be worsened by limited availability of resilient genetic material and insufficient adaptive breeding infrastructure.

Recent developments in coffee breeding have concentrated on the integration of physiological, molecular, and genomic techniques to fast-track the development of cultivars that can withstand prevailing stress. Research by dos Santos et al. [72] indicates that genomic-assisted breeding allows for the discovery of Quantitative Trait Loci (QTLs) and genes that respond to stress, which are linked to drought tolerance, heat resilience, and the ability to manage oxidative stress. These findings are being utilized in marker-assisted selection and transcriptomic profiling, enabling breeders to identify and select genotypes with enhanced traits for adaptation. In addition to molecular methods, physiological assessments are crucial. Traits such as stomatal conductance, management of leaf temperature, chlorophyll fluorescence, and the activity of antioxidant enzymes are increasingly employed to assess the performance of clones under stressful conditions. Borgo et al. [73] emphasized on the necessity of integrating plant nutrition with stress physiology in breeding strategies, highlighting that efficiency in nutrient usage and the ability to adjust osmotically are essential indicators of resilience. Additionally, Borgo etal. [73] gave a general description of the main effects of drought, heat, excess light, and salinity on plant growth, presenting the mechanisms employed by coffee plants to deal with environmental stresses.

Furthermore, breeding initiatives are embracing a holistic approach that merges traditional selection methods with contemporary stress biology. For instance, Partelli and Vieira [74] presented a scenario that illustrates efforts to create cultivars that are appropriate for various agro-climatic regions through participatory breeding, field experiments, and studies on genotype-by-environment interactions. The goal of these programs is to produce coffee varieties that can withstand abiotic stresses while also fulfilling market and quality expectations.

For the national research institutions and clonal seed garden projects in Sierra Leone, these insights provide a guide for improving local breeding capabilities. By utilizing genomic resources, physiological indicators, and building strategic collaborations, these organizations can enhance the development of climate-resilient coffee clones that align with national goals for restoration and productivity.

Drought stress presents a major challenge to coffee cultivation, especially as climate change exacerbates the intensity and frequency of dry periods in key coffee-producing areas. Researchers globally have taken initiative by investigating the intricate physiological, biochemical, and molecular processes that facilitate drought tolerance in coffee plants.

A recent investigation conducted by Ramalho et al. [75] delivers a comprehensive examination of stress resilience in C. arabica and C. canephora amid severe drought and heat circumstances. The investigators underscored crucial genes, proteins, and lipid reactions that aid in drought adaptation. Their results emphasize the significance of antioxidant enzymes, osmoprotectants, and membrane-stabilizing lipids in reducing oxidative damage and preserving cellular integrity during periods of water scarcity. Notably, C. canephora showed a stronger response, indicating its higher potential for developing drought-resistant cultivars. In addition to this molecular viewpoint, Borgo et al. [73] assessed the combined impacts of drought, heat, excessive light, and salinity on coffee physiology and productivity. They highlighted the necessity of integrated mitigation approaches, including plant breeding, soil management, and nutritional strategies. Their research stresses the combined advantages of merging genetic enhancements with agronomic practices to bolster drought resilience. For example, selecting genotypes with deeper root structures and improved water-use efficiency has demonstrated potential in field experiments across Brazil and East Africa.

Ramirez-Builes et al. [76] illustrated that boron supplementation significantly enhances resistance to drought stress in coffee. When paired with calcium, boron not only improves physiological resilience but also boosts long-term yield and seed quality. These findings indicate that managing micronutrients could serve as a cost-effective solution for smallholder farmers dealing with unpredictable rainfall.

Beyond physiological and nutritional methods, researchers are also investigating remote sensing and modeling technologies to forecast drought effects and inform adaptive management practices. Satellite-based indicators and crop simulation models are being customized for coffee growing systems in Latin America and Africa, allowing for early warnings and tailored recommendations.

Sustaining growth and increasing crop yield in highly stressful environmental situations like water scarcity is one of the primary challenges faced by contemporary agriculture [77].

High-Throughput Plant Phenotyping (HTPP) is considered as a very relevant technique used to speed up discoveries in many areas of plant science, including plant physiology [78][79], genetics [80], breeding [81], and phytopathology [82]. The technique was found to be efficient in detecting plant stress response under open field and greenhouse conditions. A wide gap exists between the discovery and practical use of QTL for crop improvement, especially for several important agronomic traits of interest. This limitation is attributable to the low accuracy in QTL detection resulting from low marker density and the manual collection of phenotypes of complex agronomic traits. Combined utilization of High-Throughput Genotyping (HTG) and high-throughput digital phenotyping has revealed the possibility of increasing marker density and improving the precision and resolution of QTL detection [83]. The quantitative measurement of Drought Resistance (DR) phenotyping markers, including transpiration or leaf moisture content in addition to automated HTPP platforms, provides an opportunity to correlate traditional and novel DR traits as well as perform DR-related genes mining. Using LemnaTec’s Scanalyzer3D, Honsdorf et al. [84] and Parent et al. [85] identified 44 and 21 DR QTLs in a set of wild barley introgression lines and a wheat Recombinant Inbred Line (RIL) population under water stress, respectively. Similarly, 51 DR traits were detected in an association panel and a RIL population. Consequently, 93% of the loci found by GWAS co-localized with previously reported DR-related QTLs and different loci containing known DR-related genes were identified. Through GWAS and linkage analysis, 69 trait-locus associations were identified, and the role of a DR gene, OsPP15, was confirmed by genetic transformation experiments, demonstrating that the combination of HTPP and genetic mapping is a promising technique for the discovery of novel DR genes [86] and other important traits.

Arbuscular Mycorrhizal Fungi (AMF) are among the beneficial soil microbes with a role in improving coffee tolerance to abiotic stresses. Exploitation of AMF has been suggested for consideration in the context of agriculture, since the AM symbiosis is the dominant mycorrhizal symbiosis formed by most crops (except for the Brassicaceae species) and its potentially positive, multifunctional role in plant nutrition, pathogen protection, stress tolerance, and soil structure provision [87]. Applied research focused on these symbioses should consider improving the production and application of the mycorrhizal fungal inoculum, which directly addresses the decline in mycorrhizal abundance in agricultural fields. Mycorrhizal technology involving the set of measures utilized for optimization of local mycorrhizal abundance and diversity in terms of functioning for attaining sustainability of agroecosystems [88], should be supported by research including: 1) a better understanding of the relative contribution of AM symbiosis to any aspect of sustainability; 2) defining which parameters influence symbiosis effectiveness, helping to prevent other agricultural management approaches from interfering with the mycorrhizal-mediated benefit; and 3) expanding the response variables for documenting mycorrhizal effects. Translation of the information derived from fundamental research to innovation in crop, soil, and water management, with the development of beneficial microbial-based strategies and practices designed for environmentally sustainable coffee production and tailored to a specific environment, should be exploited. Such a holistic approach necessitates a tight linkage of highly controlled phenotyping trials, a network of field experiments in contrasting environments, field phenotyping approaches, long-term experiments under field conditions and the development of accessible data repositories. Development and application of bioinformatics tools useful to study the complex interactions among different functional groups of microorganisms should be exploited in future studies. Various bioinformatic approaches have been developed to study the microbial diversity as well as the interaction networks discovered by high-throughput DNA sequencing, although they are often applied separately for bacteria and fungi [89]. Microbiome-based innovations may contribute to the policies for the development of sustainable practices, in line with the Sustainable Development Goals (SDGs, https://sdgs.un.org/goals), and international cooperation in microbiome research projects has been suggested to be an essential point for a sustainable future [90]. Notably, diversity and efficiency of microorganisms, as well as the microbial networks, are correlated to crop plant species/varieties and soil/environmental conditions [89].

Domestication of coffee has focused more on yield-related traits compared to stress tolerance or disease resistance traits, which consequently need to be recovered from wild relatives by introgression that takes long periods, and fails when concurring stress conditions appear. Priming strategies, such as rhizosphere and root-associated microbiota, exhibit a huge potential in the development of a next-generation coffee. These approaches will contribute to boosting the existing endogenous plant potential to endure abiotic and biotic constrictors. Priming strategies also exhibit potential long-lasting effects and non-negative modification of other interesting traits, including quality of edible organs and yield. Moreover, advancement in technology, such as the use of high-throughput platforms to quantify crop performance and tolerance traits of different coffee genotypes upon different treatments (e.g., inoculation with beneficial microbes, plant response to diverse environmental stresses, etc.), provides an opportunity to characterize the plant responses of selected breeding lines under controlled growth conditions or in the field, where real-life agricultural conditions are found.

Advances in breeding technologies and methodologies, as well as the availability of high-quality historical trial data, continue to drive improvements in coffee genotypes for desired end-user traits.

Information from this monograph could be useful in designing future marker-based breeding as well as genetic conservation of coffee. The exploitation of AMF for improvement of coffee tolerance to biotic and abiotic stresses, priming strategies, combined utilization of high-throughput genotyping and high-throughput digital phenotyping, and assessment of long-term effects of plant domestication, pleiotropy and selective breeding for desired agronomic traits of coffee forms part of future work on the crop.

This research received financial aid from the Agricultural Value Chain Development Project (AVDP) under the grant number ID AVDP2000001544 through the International Fund for Agricultural Development (IFAD), Fund for International Development (OPEC Fund) and Adaptation fund for increasing production and improving the marketing of rice, palm oil, cocoa and vegetables. The technical support from the Kenema Forestry and Tree Crops Research Centre, is dully acknowledged.

Table A1.Arabica coffee introductions in Sierra Leone.