Potential beverage quality of three wild coffee species (Coffea brevipes, C. congensis and C. stenophylla) and consideration of their agronomic use.

BACKGROUND: Of the 130 known coffee (Coffea) species, very few have been properly evaluated for their beverage quality. The diversity of wild coffee species is considered critical to the long-term sustainability of the coffee sector, particularly under climate change. The challenge is finding coffee crops that satisfy agronomic criteria, now and under the altered climatic conditions of the future, as well as consumer requirements for flavour. We evaluated the sensory characteristics of three wild coffee species with four independent sensory panels, and the key environmental/agronomic requirements of these wild species based on a literature review. RESULTS: Coffea congensis and C. stenophylla have a lower unroasted seed weight compared to C. arabica and C. canephora, while C. brevipes has the largest. Sensory analysis showed that the main differences between species was for the fruitiness attribute. Coffea stenophylla was the fruitiest wild species, and was considered an Arabica-like coffee. The flavour profile range of C. stenophylla covers herb-like, vegetal, floral and fruit; C. brevipes resembles C. stenophylla in some respects. Opinions concerning C. congensis were contradictory and several judges considered the industry-standard coffee flavour wheel not suitable for the beverage produced from this species. CONCLUSION: The three wild species have the required sensory qualities for commercialization. According to published data, C. stenophylla has agronomic potential, especially in warmer climates than Arabica areas. Coffea brevipes and C. congensis have the potential to be easily crossed with C. canephora to form interspecific hybrids capable of adapting to different climatic and agronomic conditions. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Vapour pressure deficit determines critical thresholds for global coffee production under climate change.

Our understanding of the impact of climate change on global coffee production is largely based on studies focusing on temperature and precipitation, but other climate indicators could trigger critical threshold changes in productivity. Here, using generalized additive models and threshold regression, we investigate temperature, precipitation, soil moisture and vapour pressure deficit (VPD) effects on global Arabica coffee productivity. We show that VPD during fruit development is a key indicator of global coffee productivity, with yield declining rapidly above 0.82 kPa. The risk of exceeding this threshold rises sharply for most countries we assess, if global warming exceeds 2 °C. At 2.9 °C, countries making up 90% of global supply are more likely than not to exceed the VPD threshold. The inclusion of VPD and the identification of thresholds appear critical for understanding climate change impacts on coffee and for the design of adaptation strategies.

A review of the indigenous coffee resources of Uganda and their potential for coffee sector sustainability and development.

Uganda is a major global coffee exporter and home to key indigenous (wild) coffee resources. A comprehensive survey of Uganda's wild coffee species was undertaken more than 80 years ago (in 1938) and thus a contemporary evaluation is required, which is provided here. We enumerate four indigenous coffee species for Uganda: Coffea canephora, C. eugenioides, C. liberica (var. dewevrei) and C. neoleroyi. Based on ground point data from various sources, survey of natural forests, and literature reviews we summarise taxonomy, geographical distribution, ecology, conservation, and basic climate characteristics, for each species. Using literature review and farm survey we also provide information on the prior and exiting uses of Uganda's wild coffee resources for coffee production. Three of the indigenous species (excluding C. neoleroyi) represent useful genetic resources for coffee crop development (e.g. via breeding, or selection), including: adaptation to a changing climate, pest and disease resistance, improved agronomic performance, and market differentiation. Indigenous C. canephora has already been pivotal in the establishment and sustainability of the robusta coffee sector in Uganda and worldwide, and has further potential for the development of this crop species. Coffea liberica var. dewevrei (excelsa coffee) is emerging as a commercially viable coffee crop plant in its own right, and may offer substantial potential for lowland coffee farmers, i.e. in robusta coffee growing areas. It may also provide useful stock material for the grafting of robusta and Arabica coffee, and possibly other species. Preliminary conservation assessments indicate that C. liberica var. dewevrei and C. neoleroyi are at risk of extinction at the country-level (Uganda). Adequate protection of Uganda's humid forests, and thus its coffee natural capital, is identified as a conservation priority for Uganda and the coffee sector in general.

Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes.

PREMISE: Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS: Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS: We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS: The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.

Arabica-like flavour in a heat-tolerant wild coffee species.

There are numerous factors to consider when developing climate-resilient coffee crops, including the ability to tolerate altered climatic conditions, meet agronomic and value chain criteria, and satisfy consumer preferences for flavour (aroma and taste). We evaluated the sensory characteristics and key environmental requirements for the enigmatic narrow-leaved coffee (Coffea stenophylla), a wild species from Upper West Africa1. We confirm historical reports of a superior flavour1-3 and uniquely, and remarkably, reveal a sensory profile analogous to high-quality Arabica coffee. We demonstrate that this species grows and crops under the same range of key climatic conditions as (sensorially inferior) robusta and Liberica coffee4-9 and at a mean annual temperature 6.2-6.8 °C higher than Arabica coffee, even under equivalent rainfall conditions. This species substantially broadens the climate envelope for high-quality coffee and could provide an important resource for the development of climate-resilient coffee crop plants.

The potential for income improvement and biodiversity conservation via specialty coffee in Ethiopia.

The specialty coffee sector represents opportunities for coffee farmers and other actors due to increased value within the supply chain, driven by elevated consumer purchase prices. We investigated these relationships up to the export stage, as well as the potential for specialty coffee to improve stakeholder participation in biodiversity conservation. Household data was collected from a sample of 272 coffee farmers belonging to five primary cooperatives, in the heavily forested area of Yayu, in the Illubabor administrative zone of Oromia regional state in south-western Ethiopia, for the 2017/2018 harvest season. Qualitative and quantitative data, gathered between 2015 and 2019, from focus group discussions, was used to supplement the survey and to explain the empirical findings. We show that the income from coffee (and thus household income) can be increased, in some cases substantially, via participation in the specialty coffee market. The unit price for coffee was much higher than standard market prices and those including certification premiums. Whilst quality is a key factor for specialty coffee, income increases via the specialty market are caveat bound. In particular, there is a critical requirement for efficient and effective cooperative management, and we provide suggestions for improvements. In the long-term, more focus is needed to increase the financial and human capacities of Ethiopian coffee cooperatives, to make them more effective partners in the specialty coffee value chain. The high conversion rates from harvested to clean exportable specialty coffee (8:1, or higher) is identified as a major constraint on profitability. We show that specialty coffee can bring about positive environmental benefits. Elevating coffee prices and farm profitability to bring household income levels to around or above the global poverty line may ensure the continuation of forest coffee production, and thus the retention of forest. The increases in income via specialty coffee production, reported in the study, were achieved without increasing land use or the application of environmentally costly inputs. Moreover, analysis of satellite data shows that a large proportion of the coffee farms surveyed retain a level of forest cover and quality approaching primary (undisturbed) forest, and that the coffee production area at Yayu has not experienced any significant deforestation (since 2000). We recommend that coffee premiums linked to environmental benefit should demonstrate clearly defined and appropriate metrics, as we have demonstrated here for forest (canopy) quality and coverage (area).

Lost and Found: Coffea stenophylla and C. affinis, the Forgotten Coffee Crop Species of West Africa.

Coffea arabica (Arabica) and C. canephora (robusta) almost entirely dominate global coffee production. Various challenges at the production (farm) level, including the increasing prevalence and severity of disease and pests and climate change, indicate that the coffee crop portfolio needs to be substantially diversified in order to ensure resilience and sustainability. In this study, we use a multidisciplinary approach (herbarium and literature review, fieldwork and DNA sequencing) to elucidate the identity, whereabouts, and potential attributes, of two poorly known coffee crop species: C. affinis and C. stenophylla. We show that despite widespread (albeit small-scale) use as a coffee crop species across Upper West Africa and further afield more than 100 years ago, these species are now extremely rare in the wild and are not being farmed. Fieldwork enabled us to rediscover C. stenophylla in Sierra Leone, which previously had not been recorded in the wild there since 1954. We confirm that C. stenophylla is an indigenous species in Guinea, Sierra Leone, and Ivory Coast. Coffea affinis was discovered in the wild in Sierra Leone for the first time, having previously been found only in Guinea and Ivory Coast. Prior to our rediscovery, C. affinis was last seen in the wild in 1941, although sampling of an unidentified herbarium specimen reveals that it was collected in Guinea-Conakry in 2015. DNA sequencing using plastid and ITS markers was used to: (1) confirm the identity of museum and field collected samples of C. stenophylla; (2) identify new accessions of C. affinis; (3) refute hybrid status for C. affinis; (4) identify accessions confused with C. affinis; (5) show that C. affinis and C. stenophylla are closely related, and possibly a single species; (6) substantiate the hybrid C. stenophylla × C. liberica; (7) demonstrate the use of plastid and nuclear markers as a simple means of identifying F1 and early-generation interspecific hybrids in Coffea; (8) infer that C. liberica is not monophyletic; and (9) show that hybridization is possible across all the major groups of key Africa Coffea species (Coffee Crop Wild Relative Priority Groups I and II). Coffea affinis and C. stenophylla may possess useful traits for coffee crop plant development, including taste differentiation, disease resistance, and climate resilience. These attributes would be best accessed via breeding programs, although the species may have niche-market potential via minimal domestication.

Early growth phase and caffeine content response to recent and projected increases in atmospheric carbon dioxide in coffee (Coffea arabica and C. canephora).

While [CO2] effects on growth and secondary chemistry are well characterized for annual plant species, little is known about perennials. Among perennials, production of Coffea arabica and C. canephora (robusta) have enormous economic importance worldwide. Three Arabica cultivars (Bourbon, Catimor, Typica) and robusta coffee were grown from germination to ca. 12 months at four CO2 concentrations: 300, 400, 500 or 600 ppm. There were significant increases in all leaf area and biomass markers in response to [CO2] with significant [CO2] by taxa differences beginning at 122-124 days after sowing (DAS). At 366-368 DAS, CO2 by cultivar variation in growth and biomass response among Arabica cultivars was not significant; however, significant trends in leaf area, branch number and total above-ground biomass were observed between Arabica and robusta. For caffeine concentration, there were significant differences in [CO2] response between Arabica and robusta. A reduction in caffeine in coffee leaves and seeds might result in decreased ability against deterrence, and consequently, an increase in pest pressure. We suggest that the interspecific differences observed (robusta vs. Arabica) may be due to differences in ploidy level (2n = 22 vs. 2n = 4x = 44). Differential quantitative and qualitative responses during early growth and development of Arabica and robusta may have already occurred with recent [CO2] increases, and such differences may be exacerbated, with production and quality consequences, as [CO2] continues to increase.

Elucidation of Hosts, Native Distribution, and Habitat of the Coffee Berry Borer (Hypothenemus hampei) Using Herbaria and Other Museum Collections.

The coffee berry borer (Hypothenemus hampei) is the most damaging insect pest of global coffee production. Despite its importance, our knowledge on the insect's natural habitat, range, and wild host species remains poorly known. Using archival sources (mainly herbaria but also other museum collections), we surveyed 18,667 predominantly wild-collected herbarium specimens mostly from Africa, Madagascar, and Asia for coffee berry borer occurrence. A total of 72 incidences were confirmed for presence of the coffee berry borer, with identifications assisted by micro-CT for SEM. Of the 72 positive infestations, all were from tropical African coffee (Coffea) species, of which 32 were from wild (non-cultivated) plants. Of the 32 wild occurrences, 30 were found in C. canephora (robusta coffee), 1 in C. liberica (Liberica coffee), and 1 in C. arabica (Arabica coffee). Our herbarium survey confirms literature and anecdotal reports that the coffee berry borer is indigenous to tropical Africa, and that coffee species, and particularly robusta coffee, are important hosts. We identify the wetter type of Guineo-Congolian forest as either the preferred or exclusive native habitat of the coffee berry borer. Other than coffee, we find no evidence of other naturally occurring hosts. Characters of infestation (e.g., hole position on coffee fruits) infers a certain degree of specificity between the coffee berry borer and its host.

High extinction risk for wild coffee species and implications for coffee sector sustainability.

Wild coffee species are critical for coffee crop development and, thus, for sustainability of global coffee production. Despite this fact, the extinction risk and conservation priority status of the world's coffee species are poorly known. Applying IUCN Red List of Threatened Species criteria to all (124) wild coffee species, we undertook a gap analysis for germplasm collections and protected areas and devised a crop wild relative (CWR) priority system. We found that at least 60% of all coffee species are threatened with extinction, 45% are not held in any germplasm collection, and 28% are not known to occur in any protected area. Existing conservation measures, including those for key coffee CWRs, are inadequate. We propose that wild coffee species are extinction sensitive, especially in an era of accelerated climatic change.

Enset in Ethiopia: a poorly characterized but resilient starch staple.

BACKGROUND: Enset (Ensete ventricosum, Musaceae) is an African crop that currently provides the staple food for approx. 20 million Ethiopians. Whilst wild enset grows over much of East and Southern Africa and the genus extends across Asia to China, it has only ever been domesticated in the Ethiopian Highlands. Here, smallholder farmers cultivate hundreds of landraces across diverse climatic and agroecological systems. SCOPE: Enset has several important food security traits. It grows over a relatively wide range of conditions, is somewhat drought-tolerant, and can be harvested at any time of the year, over several years. It provides an important dietary starch source, as well as fibres, medicines, animal fodder, roofing and packaging. It stabilizes soils and microclimates and has significant cultural importance. In contrast to the other cultivated species in the family Musaceae (banana), enset has received relatively little research attention. Here, we review and critically evaluate existing research, outline available genomic and germplasm resources, aspects of pathology, and explore avenues for crop development. CONCLUSION: Enset is an underexploited starch crop with significant potential in Ethiopia and beyond. Research is lacking in several key areas: empirical studies on the efficacy of current agronomic practices, the genetic diversity of landraces, approaches to systematic breeding, characterization of existing and emerging diseases, adaptability to new ranges and land-use change, the projected impact of climate change, conservation of crop wild relatives, by-products or co-products or non-starch uses, and the enset microbiome. We also highlight the limited availability of enset germplasm in living collections and seedbanks, and the lack of knowledge of reproductive and germination biology needed to underpin future breeding. By reviewing the current state of the art in enset research and identifying gaps and opportunities, we hope to catalyse the development and sustainable exploitation of this neglected starch crop.

Least concern to endangered: Applying climate change projections profoundly influences the extinction risk assessment for wild Arabica coffee.

Arabica coffee (Coffea arabica) is a key crop in many tropical countries and globally provides an export value of over US$13 billion per year. Wild Arabica coffee is of fundamental importance for the global coffee sector and of direct importance within Ethiopia, as a source of harvestable income and planting stock. Published studies show that climate change is projected to have a substantial negative influence on the current suitable growing areas for indigenous Arabica in Ethiopia and South Sudan. Here we use all available future projections for the species based on multiple general circulation models (GCMs), emission scenarios, and migration scenarios, to predict changes in Extent of Occurrence (EOO), Area of Occupancy (AOO), and population numbers for wild Arabica coffee. Under climate change our results show that population numbers could reduce by 50% or more (with a few models showing over 80%) by 2088. EOO and AOO are projected to decline by around 30% in many cases. Furthermore, present-day models compared to the near future (2038), show a reduction for EOO of over 40% (with a few cases over 50%), although EOO should be treated with caution due to its sensitivity to outlying occurrences. When applying these metrics to extinction risk, we show that the determination of generation length is critical. When applying the International Union for Conservation of Nature's Red list of Threatened Species (IUCN Red List) criteria, even with a very conservative generation length of 21 years, wild Arabica coffee is assessed as Threatened with extinction (placed in the Endangered category) under a broad range of climate change projections, if no interventions are made. Importantly, if we do not include climate change in our assessment, Arabica coffee is assessed as Least Concern (not threatened) when applying the IUCN Red List criteria.

The use and misuse of herbarium specimens in evaluating plant extinction risks.

Herbarium specimens provide verifiable and citable evidence of the occurrence of particular plants at particular points in space and time, and are vital resources for assessing extinction risk in the tropics, where plant diversity and threats to plants are greatest. We reviewed approaches to assessing extinction risk in response to the Convention on Biological Diversity's Global Strategy for Plant Conservation Target 2: an assessment of the conservation status of all known plant species by 2020. We tested five alternative approaches, using herbarium-derived data for trees, shrubs and herbs in five different plant groups from temperate and tropical regions. All species were previously fully assessed for the IUCN Red List. We found significant variation in the accuracy with which different approaches classified species as threatened or not threatened. Accuracy was highest for the machine learning model (90%) but the least data-intensive approach also performed well (82%). Despite concerns about spatial, temporal and taxonomic biases and uncertainties in herbarium data, when specimens represent the best available evidence for particular species, their use as a basis for extinction risk assessment is appropriate, necessary and urgent. Resourcing herbaria to maintain, increase and disseminate their specimen data is essential to guide and focus conservation action.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

16-O-methylcafestol is present in ground roast Arabica coffees: Implications for authenticity testing.

High-field and low-field proton NMR spectroscopy were used to analyse lipophilic extracts from ground roast coffees. Using a sample preparation method that produced concentrated extracts, a small marker peak at 3.16 ppm was observed in 30 Arabica coffees of assured origin. This signal has previously been believed absent from Arabicas, and has been used as a marker for detecting adulteration with robusta. Via 2D 600 MHz NMR and LC-MS, 16-O-methylcafestol and 16-O-methylkahweol were detected for the first time in Arabica roast coffee and shown to be responsible for the marker peak. Using low-field NMR, robusta in Arabica could be detected at levels of the order of 1-2% w/w. A surveillance study of retail purchased "100% Arabica" coffees found that 6 out of 60 samples displayed the 3.16 ppm marker signal to a degree commensurate with adulteration at levels of 3-30% w/w.

Resilience potential of the Ethiopian coffee sector under climate change.

Coffee farming provides livelihoods for around 15 million farmers in Ethiopia and generates a quarter of the country's export earnings. Against a backdrop of rapidly increasing temperatures and decreasing rainfall, there is an urgent need to understand the influence of climate change on coffee production. Using a modelling approach in combination with remote sensing, supported by rigorous ground-truthing, we project changes in suitability for coffee farming under various climate change scenarios, specifically by assessing the exposure of coffee farming to future climatic shifts. We show that 39-59% of the current growing area could experience climatic changes that are large enough to render them unsuitable for coffee farming, in the absence of significant interventions or major influencing factors. Conversely, relocation of coffee areas, in combination with forest conservation or re-establishment, could see at least a fourfold (>400%) increase in suitable coffee farming area. We identify key coffee-growing areas that are susceptible to climate change, as well as those that are climatically resilient.

Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content.

A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.

Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species.

The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascar were divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.

Can Coffee Chemical Compounds and Insecticidal Plants Be Harnessed for Control of Major Coffee Pests?

Pests and pathogens threaten coffee production worldwide and are difficult to control using conventional methods, such as insecticides. We review the literature on the chemistry of coffee, concentrating on compounds most commonly reported from Coffea arabica and Coffea canephora. Differences in chemistry can distinguish coffee species and varieties, and plants grown under different biogeographic conditions exhibit different chemotypes. A number of chemical groups, such as alkaloids and caffeoylquinic acids, are known to be insecticidal, but most studies have investigated their effects on coffee quality and flavor. More research is required to bridge this gap in knowledge, so that coffee can be bred to be more resistant to pests. Furthermore, we report on some pesticidal plants that have been used for control of coffee pests. Locally sourced pesticidal plants have been underutilized and offer a sustainable alternative to conventional insecticides and could be used to augment breeding for resilience of coffee plants.