Coffea Species Research Articles

Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico.

BackgroundThe coffee species Coffea canephora is commercially identified as “Conilon” when produced in Brazil, or “Robusta” when produced elsewhere in the world. It represents approximately 40 % of coffee production worldwide. While the genetic diversity of wild C. canephora has been well studied in the past, only few studies have addressed the genetic diversity of currently cultivated varieties around the globe. Vietnam is the largest Robusta producer in the world, while Mexico is the only Latin American country, besides Brazil, that has a significant Robusta production. Knowledge of the genetic origin of Robusta cultivated varieties in countries as important as Vietnam and Mexico is therefore of high interest.ResultsThrough the use of Sequencing-based diversity array technology-DArTseq method-on a collection of C. canephora composed of known accessions and accessions cultivated in Vietnam and Mexico, 4,021 polymorphic SNPs were identified. We used a multivariate analysis using SNP data from reference accessions in order to confirm and further fine-tune the genetic diversity of C. canephora. Also, by interpolating the data obtained for the varieties from Vietnam and Mexico, we determined that they are closely related to each other, and identified that their genetic origin is the Robusta Congo – Uganda group.ConclusionsThe genetic characterization based on SNP markers of the varieties grown throughout the world, increased our knowledge on the genetic diversity of C. canephora, and contributed to the understanding of the genetic background of varieties from very important coffee producers. Given the common genetic origin of the Robusta varieties cultivated in Vietnam, Mexico and Uganda, and the similar characteristics of climatic areas and relatively high altitude where they are grown, we can state that the Vietnamese and the Mexican Robusta have the same genetic potential to produce good cup quality.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0933-y) contains supplementary material, which is available to authorized users.

Estimation of stem and leaf dry biomass using a non-destructive method applied to African Coffea species

The coffee tree is an important economic plant for several developing countries. Stem and leaf dry biomass, which are key traits of plant production, are used in functional-structural plant models to simulate plant growth and predict yield. These values are difficult to obtain since they classically rely on time-consuming protocols and require destructive measurements. Measuring stem and leaf dimensions (length and width) to estimate them provides a non-destructive and rapid approach for use in the field. In this study we sought the best allometric relationships existing between stem and leaf dimensions and their corresponding dry mass in order to avoid destructive measurements which are also time-consuming. This was investigated in three coffee species: Coffea canephora, Coffea liberica var. liberica and Coffea liberica var. dewevrei in Ivory Coast. For each species, the internodes and leaves of three axis categories (stem, branch and branchlet) comprising the main compartments were sampled. Two different equations were found to estimate the stem and leaf dry mass whatever the species and the axis categories: (1) a linear equation for the relation between the stem volume (V) and its corresponding dry mass (IWe), IWe = 0.70 × V and (2) a power law for the relation between the leaf area [as the product of length (LL) and width (Wi)] and its dry mass (LWe), LWe = 0.007 (LL × LWi)1.02. Finally, stem and leaf dry mass could be easily obtained without destructive measurements. This method could be applied to estimate the plant total leaf area and the total stem and leaf biomass of a plant in an agroforestry system.

Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories.

The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7%. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53% of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes.

Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species.

The frequency of plant species introductions has increased in a highly connected world, modifying species distribution patterns to include areas outside their natural ranges. These introductions provide the opportunity to gain new insight into the importance of flowering phenology as a component of adaptation to a new environment. Three Coffea species, C. arabica, C. canephora (Robusta), and C. liberica, native to intertropical Africa have been introduced to New Caledonia. On this archipelago, a secondary contact zone has been characterized where these species coexist, persist, and hybridize spontaneously. We investigated the impact of environmental changes undergone by each species following its introduction in New Caledonia on flowering phenology and overcoming reproductive barriers between sister species. We developed species distribution models and compared both environmental envelopes and climatic niches between native and introduced hybrid zones. Flowering phenology was monitored in a population in the hybrid zone along with temperature and precipitation sequences recorded at a nearby weather station. The extent and nature of hybridization events were characterized using chloroplast and nuclear microsatellite markers. The three Coffea species encountered weak environmental suitability compared to their native ranges when introduced to New Caledonia, especially C. arabica and C. canephora. The niche of the New Caledonia hybrid zone was significantly different from all three species' native niches based on identity tests (I Similarity and D Schoener's Similarity Indexes). This area appeared to exhibit intermediate conditions between the native conditions of the three species for temperature‐related variables and divergent conditions for precipitation‐related ones. Flowering pattern in these Coffea species was shown to have a strong genetic component that determined the time between the triggering rain and anthesis (flower opening), specific to each species. However, a precipitation regime different from those in Africa was directly involved in generating partial flowering overlap between species and thus in allowing hybridization and interspecific gene flow. Interspecific hybrids accounted for 4% of the mature individuals in the sympatric population and occurred between each pair of species with various level of introgression. Adaptation to new environmental conditions following introduction of Coffea species to New Caledonia has resulted in a secondary contact between three related species, which would not have happened in their native ranges, leading to hybridization and gene flow.

Analysis of Phosphorus Use Efficiency Traits in Coffea Genotypes Reveals Coffea arabica and Coffea canephora Have Contrasting Phosphorus Uptake and Utilization Efficiencies.

Background and Aims: Phosphate (Pi) is one of the most limiting nutrients for agricultural production in Brazilian soils due to low soil Pi concentrations and rapid fixation of fertilizer Pi by adsorption to oxidic minerals and/or precipitation by iron and aluminum ions. The objectives of this study were to quantify phosphorus (P) uptake and use efficiency in cultivars of the species Coffea arabica L. and Coffea canephora L., and group them in terms of efficiency and response to Pi availability.Methods: Plants of 21 cultivars of C. arabica and four cultivars of C. canephora were grown under contrasting soil Pi availabilities. Biomass accumulation, tissue P concentration and accumulation and efficiency indices for P use were measured.Key Results: Coffee plant growth was significantly reduced under low Pi availability, and P concentration was higher in cultivars of C. canephora. The young leaves accumulated more P than any other tissue. The cultivars of C. canephora had a higher root/shoot ratio and were significantly more efficient in P uptake, while the cultivars of C. arabica were more efficient in P utilization. Agronomic P use efficiency varied among coffee cultivars and E16 Shoa, E22 Sidamo, Iêmen and Acaiá cultivars were classified as the most efficient and responsive to Pi supply. A positive correlation between P uptake efficiency and root to shoot ratio was observed across all cultivars at low Pi supply. These data identify Coffea genotypes better adapted to low soil Pi availabilities, and the traits that contribute to improved P uptake and use efficiency. These data could be used to select current genotypes with improved P uptake or utilization efficiencies for use on soils with low Pi availability and also provide potential breeding material and targets for breeding new cultivars better adapted to the low Pi status of Brazilian soils. This could ultimately reduce the use of Pi fertilizers in tropical soils, and contribute to more sustainable coffee production.

Antioxidant potential, tannin and polyphenol contents of seed and pericarp of three Coffea species.

To investigate the antioxidant activity, total phenolic and total tannin content of the pericarp and the seed of Coffea benghalensis (C.benghalensis) and Coffea liberica compared to Coffea arabica (C.arabica). The antioxidant potential, total tannin and polyphenol contents of the immature and mature seed and pericarp of C.benghalensis and Coffea liberica were quantified and compared to C.arabica. Enhanced chemiluminescence (ECL), 2,2-diphenyl-1-picrylhydrazyl (DPPH), oxygen radical absorbance capacity, Folin-Ciocalteau method and total tannin content assays were used. Trolox equivalent (TE/g plant material) values obtained by ECL and DPPH methods showed loose correlation (r(2)=0.587) while those measured by oxygen radical absorbance capacity assay were higher without correlation in each plant. A closer correlation was detected between the ECL method and the percentage antioxidant activity of the DPPH technique (r(2)=0.610 7) in each species, however the immature pericarp of C.benghalensis showed much higher DPPH scavenging potential than was seen in the ECL assay. The immature pericarp of C.benghalensis expressed the highest tannin and polyphenol content, and a high polyphenol level was also detected in the immature seed of C.arabica. The immature pericarp of Bengal and Liberian coffees showed the largest amount of phenolic contents. The obtained data highlight the potential role of C.benghalensis as a new source of natural antioxidants and polyphenols compared to C.arabica.

Current status of coffee genetic resources: implications for conservation – case study in Madagascar

Coffee genetic resources are being lost at a rapid pace, leading to loss of genetic diversity. Various threats contribute to the erosion of coffee genetic diversity such as human population pressures leading to conversion of land to agriculture, deforestation and land degradation; low coffee prices leading to abandoning of coffee trees in forests and gardens and shifting cultivation to other more remunerative crops; and climate change. Additionally, the cultivated species of coffee (Coffea arabica L.) has a very narrow genetic base. Increased incidence of pests and diseases associated with climate change is leading to significant crop losses, threatening livelihoods in many coffee growing countries. A comprehensive conservation strategy for coffee should take into account complementary methods of in situ and ex situ conservation. The development of molecular techniques has expanded the possibilities and tools for genetic analysis for efficient conservation and use of coffee genetic resources. Before it is too late, a thorough evaluation of existing germplasm should be performed based upon which a comprehensive conservation strategy could be developed. A case study using four different Coffea species in Madagascar is discussed.

Manipulators live better, but are they always parasites?

A recent study reports partner manipulation for an interaction that was considered a reward-for-defence mutualism. Secretions of lycaenid caterpillars altered ant locomotion and aggressiveness, likely by manipulating dopaminergic signalling. This study opens the question whether such manipulation is common and whether manipulation necessarily characterises an interaction as parasitism.

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.

Estudo tecnológico da madeira de Coffea arabica L. Visando à combustão completa e pirólise

The objective of this study was to evaluate the quality of the wood from Coffea arabica L. in different cultivars and cultivation systems, aiming for the production of charcoal and its complete combustion. Wood from three cultivation systems (natural, conventional and organic) and two cultivars (Mundo Novo and Catuai) was used, totaling six treatments. Chemical compositions (molecular and immediate), basic density, carbon stock, heating values (higher and lower) and energy densities of the woods analyzed were evaluated. Furthermore, an energy dispersive X-ray spectroscopy was performed, as well as the thermogravimetric analysis of the wood. Wood residues from the species Coffea arabica L. presented technological properties that demonstrate its viability as an energy source, especially for cultivar Catuai, which showed higher basic density, carbon stock and energy densities. The woods from the conventional system (cultivars Mundo Novo and Catuai) are more suitable for complete combustion in boilers or furnaces, due to the K2O/CaO ratio. By thermogravimetric analysis, it can be stated that woods from the organic system (cultivars Mundo Novo and Catuai) and the natural system (cultivar Mundo Novo) tend to present a higher yield in charcoal, if carbonized at low temperatures.

Spatial estimation of foliar phosphorus in different species of the genus Coffea based on soil properties

Information underlying analyses of coffee fertilization systems should consider both the soil and the nutritional status of plants. This study investigated the spatial relationship between phosphorus (P) levels in coffee plant tissues and soil chemical and physical properties. The study was performed using two arabica and one canephora coffee variety. Sampling grids were established in the areas, and the points georeferenced. The assessed properties of the soil were levels of available phosphorus (P-Mehlich), remaining phosphorus (P-rem) and particle size, and of the plant tissue, phosphorus levels (foliar P). The data were subjected to descriptive statistical analysis, correlation analysis, cluster analysis, and probability tests. Geostatistical and trend analyses were only performed for pairs of variables with significant linear correlation. The spatial variability for foliar P content was high for the variety Catuai and medium for the other evaluated plants. Unlike P-Mehlich, the variability in P-rem of the soil indicated the nutritional status of this nutrient in the plant.

Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta).

Caffeine is a metabolite of great economic importance, especially in coffee, where it influences the sensorial and physiological impacts of the beverage. Caffeine metabolism in the Coffea species begins with the degradation of purine nucleotides through three specific N-methyltransferases: XMT, MXMT and DXMT. A comparative analysis was performed to clarify the molecular reasons behind differences in caffeine accumulation in two Coffea species, namely Coffea arabica and Coffea canephora var. robusta. Three different genes encoding N-methyltransferase were amplified in the doubled haploid Coffea canephora: CcXMT1, CcMXMT1 and CcDXMT. Six genes were amplified in the haploid Coffea arabica: CaXMT1, CaXMT2, CaMXMT1, CaMXMT2, CaDXMT1, and CaDXMT2. A complete phylogenic analysis was performed to identify specific key amino acids defining enzymatic function for each protein identified. Furthermore, a quantitative gene-expression analysis was conducted on leaves and on maturing coffee beans, simultaneously analyzing caffeine content. In the different varieties analyzed, caffeine accumulation is higher in leaves than in the coffee bean maturation period, higher in Robusta than in Arabica. In Robusta, CcXMT1 and CcDXMT gene expressions are predominant and transcriptional activity is higher in leaves than in maturing beans, and is highly correlated to caffeine accumulation. In Arabica, the CaXMT1 expression level is high in leaves and CaDXMT2 as well to a lesser extent, while global transcriptional activity is weak during bean maturation, suggesting that the transcriptional control of caffeine-related genes differs within different organs and between Arabica and Robusta. These findings indicate that caffeine accumulation in Coffea species has been modulated by a combination of differential transcriptional regulation and genome evolution.Electronic supplementary materialThe online version of this article (doi:10.1007/s00425-014-2170-7) contains supplementary material, which is available to authorized users.

The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event.

The stochastic process of long-distance dispersal is the exclusive means by which plants colonize oceanic islands. Baker's rule posits that self-incompatible plant lineages are unlikely to successfully colonize oceanic islands because they must achieve a coordinated long-distance dispersal of sufficiently numerous individuals to establish an outcrossing founder population. Here, we show for the first time that Mauritian Coffea species are self-incompatible and thus represent an exception to Baker's rule. The genus Coffea (Rubiaceae) is composed of approximately 124 species with a paleotropical distribution. Phylogenetic evidence strongly supports a single colonization of the oceanic island of Mauritius from either Madagascar or Africa. We employ Bayesian divergence time analyses to show that the colonization of Mauritius was not a recent event. We genotype S-RNase alleles from Mauritian endemic Coffea, and using S-allele gene genealogies, we show that the Mauritian allelic diversity is confined to just seven deeply divergent Coffea S-RNase allelic lineages. Based on these data, we developed an individual-based model and performed a simulation study to estimate the most likely number of founding individuals involved in the colonization of Mauritius. Our simulations show that to explain the observed S-RNase allelic diversity, the founding population was likely composed of fewer than 31 seeds that were likely synchronously dispersed from an ancestral mainland species.

Why is Your Cup of Coffee so Expensive? Because of a Tiny Bark Beetle!

Sometimes an insect pest attacking crops in places as far away as Indonesia or Ethiopia can be very important to us here in Florida. One such insect is the coffee berry borer, Hypothenemus hampei Ferrari (Coleoptera: Curculionidae: Scolytinae), a tiny (1.5 mm) bark beetle that originated in the highlands of central Africa. It would probably remain one of the many inconspicuous little beetles in the tropics, if not for the choice of its host: seeds of several Coffea species. This 3-page fact sheet was written by Jiri Hulcr, and published by the UF Department of School of Forest Resources and Conservation, October 2013. http://edis.ifas.ufl.edu/fr382

Ultrastructural Characterization of Oil Bodies in Different Coffea Species

In the coffee seed, the lipid component known as coffee oil is stored in the endosperm tissue as an energy reserve for germination and post-germination growth. This coffee constituent is present in the form of subcellular spherical oil bodies (“oleosomes”) in a typical size range of 0.2–2.5 μm. These particles are filled with an osmiophilic matrix of triglycerides, delimited by a single protein membrane, typical of oleaginous plant tissues. The object of this study is to characterize the morphology and distribution of oil bodies in different coffee species. In particular, we studied Indian samples of Coffea arabica, C. canephora, C. liberica, C. stenophylla and C. salvatrix. After appropriate fixation and preparation, the samples were examined and oil bodies characterized by optical microscopy and transmission electron microscopy. Oil bodies morphology, tissue distribution and size distribution were determined and several features of these subcellular structures were observed and discussed for the first time in the framework of a coffee inter-species comparative study.

Phospholipids profile in chloroplasts of Coffea spp. genotypes differing in cold acclimation ability

Environmental temperature change may induce modifications in membrane lipid properties and composition, which account for different physiological responses among plant species. Coffee plants, as many tropical species, are particularly sensitive to cold, but genotypes can present differences that can be exploited to improve crop management and breeding. This work intended to highlight the changes promoted by low non-freezing temperatures (chilling) in phospholipid (PL) composition of chloroplast membranes of genotypes from two Coffea species, Coffea arabica cv. Catuaí (moderately tolerant) and Coffea canephora cv. Conilon (Clone 153, more susceptible), and relate them with cold sensitivity differences. Such evaluation was performed considering a gradual temperature decrease, chilling (4°C) exposure and a recovery period under rewarming conditions. Catuaí presented an earlier acclimation response than Clone 153 (CL 153). It displayed a higher metabolic activity during acclimation (total fatty acids and total PL increases) and chilling (phosphatidylglycerol increases), and an overall better recovery. Catuaí also showed the highest phosphatidylglycerol unsaturation (higher double bond index) after chilling, in contrast with CL 153 (gradual unsaturation decrease). Higher unsaturation degree in Catuaí than in CL 153 was also observed for phosphatidylcholine and phosphatidylinositol, resulting, mainly, from raises in unsaturated C18:2 and C18:3. It is suggested that an enhanced PL synthesis and turnover induced by a gradual cold exposure, as well as unsaturation increases in major PL classes, is related to decreased Catuaí susceptibility to low temperatures and strongly contributes to sustain photosynthetic activity in this genotype under chilling conditions, as reported in previous work by this team.

Identificação e Caracterização de Microssatélites de Coffea arabica a partir de dados de sequenciamento de RNA e de BACs

O café é uma das principais commodities agrícolas comercializados. A estreita base genética de Coffea arabica tem-se refletido em diferentes formas. Além disso, em C. arabica, o desenvolvimento de novas cultivares é demorado. A utilização de marcadores moleculares como ferramenta para análises da diversidade e seleção de genótipos representa uma importante ferramenta para tentar diminuir tempo e custo de seleção do melhoramento de espécies perenes como C. arabica. Neste trabalho foi realizada identificação e análise in silico de SSR a partir de dados de RNA-seq de C. arabica-Iapar 59 e de sequenciamento de BACs de C. arabica HDT832/2. Para Iapar 59 foram analisados 77 contigs, encontrados 39 SSR’s e desenhados 21 primers. Para HDT832/2 foram analisados também 77 contigs, encontrados 35 SSR’s e desenhados 29 primers. Os motivos mais frequentes foram di, tri e tetra, sendo AT o mais frequente entre os genótipos. Esta busca de sequências repetitivas é de grande importância para futura validação e aumento desses marcadores para estudos de diversidade genética.

High genetic diversity of in situ and ex situ populations of Madagascan coffee species: further implications for the management of coffee genetic resources

The genetic diversity of endemic Madagascan Coffea species has not received any considerable attention, despite the high extinction threat facing most of the species on the island. In order to address this shortfall, we assessed and compared the genetic diversity and allelic richness of ex situ and in situ populations for four selected species, and 18 ex situ populations maintained at the Kianjavato Coffee Research Station. We also investigated the possibility of in situ and ex situ hybridization events for Madagascan coffee, both within and between species. For these purposes, we used 18 nuclear microsatellite markers, on a total of 37 Coffea populations (4 in situ and 33 ex situ) representing a total of 398 genotypes (96 in situ and 302 ex situ) for 23 species. Our study showed (1) strong differentiation between Madagascan Coffea species; (2) good differentiation between all the populations studied, including those from the same locality (even when the area of the locality was restricted); (3) good evidence for both in situ and ex situ hybridization, although in situ hybridization appeared to be limited; (4) much higher genetic diversity within in situ collections compared to ex situ collections; and (5) that, despite limitations, the Kianjavato Coffee Research Station collection is an extremely valuable resource of Madagascan coffee germplasm. Recommendations for in situ and ex situ germplasm conservation are discussed.

Genetic investigations on the caffeine and chlorogenic acid relationship in an interspecific cross between Coffea liberica dewevrei and C. pseudozanguebariae

The objective of the paper was to identify the number of major loci explaining caffeine content in coffee seeds. Investigations were based on previously published results: (1) Caffeine binds to chlorogenic acids in a 1:1 molecular ratio; (2) Between species, the caffeine content is correlated to the chlorogenic acid content; (3) Only a part of chlorogenic acids is bound to caffeine. Especially, the content ratio between caffeine and chlorogenic acids varied between species. For identifying the number of major loci, a quantitative trait locus (QTL) approach was carried out using an interspecific cross between two highly differentiated species—Coffea liberica dewevrei and Coffea pseudozanguebariae, the latter being a caffeine-free species. As main finding, two QTLs, i.e., RCQ1 and CQA1, were identified allowing us to explain up to 97 % of the caffeine content variance. RCQ1 explained variation of the caffeine/chlorogenic acid ratio and was genetically independent of the second QTL. The latter explained the part of the caffeine content which was dependent on the chlorogenic acid content. The findings also confirmed that only a part of chlorogenic acids were trapped by caffeine, as in wild species.

Impact of Roasting Time on the Sensory Profile of Arabica and Robusta Coffee

Roasted coffee samples of the two major trade species (Coffea arabica and C. canephora) were studied to identify sensory descriptors that might be used to determine blends production and evaluation, following the expectations of consumers. Coffee beans were roasted at 220 + 10 °C, for 7, 9, and 11 min, and the sensory profiles of the beverages were assessed. From descriptive analysis the eigenvalues allowed the identification of two principal components (PCs), being the variance between samples 68.9% and 21.1%. In the first PC the characteristic odor, astringency, body, bitter flavor, burned aroma, and residual, typical, and burned tastes prevailed. The correlation coefficient between the second PC and citric acid flavor and aroma reached 0.96 and 0.78, respectively. It was concluded that in beverages of these species, the descriptors of both components can be separated according to bean roasting time. Considering roasting time, the overall quality was also rated.