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Global analysis of Coffea canephora Pierre ex Froehner (Rubiaceae) from the Guineo-Congolese region reveals impacts from climatic refuges and migration effects
Abstract
As the second species used for commercial coffee, evaluation of Coffea canephora Pierre ex Froehner population genetics is a challenging task for coffee breeding. This study examined the pattern of genetic variability and genetic relationships of cultivated and wild populations of C. canephora sampled across the Guineo-Congolese region of Africa and some improved populations maintained in field genebanks. A total of 293 individuals, sampled from 17 populations, were genotyped with 39 nuclear microsatellite markers. Genetic diversity and structure were investigated with both a model-based and a graphical approach; isolation by distance was also tested. Relationships between the diversity clusters are discussed with regard to differentiation due to several glacial refuges during the Last Glacial Maximum (LGM). High genetic diversity within C. canephora is confirmed with a mean number of alleles of 11.85 per marker, a mean gene diversity of 0.72 and a mean observed heterozygosity of 0.36. An overall structure of two main groups (Guinean and Congolese) subdivided in six subgroups (2 for the Guinean and 4 for the Congolese) was found, including one described for the first time in the Guinean group. A fine structure within the Guinean group was also newly detected. Genetic structure of C. canephora appears to be consistent with its geographic repartition at the continent scale. Structure of diversity was found in accordance with localizations of refuge zones during LGM and migration from this period. Results from this genetic structure study raise our capabilities to better manage and use the collections of genetics resources for breeding purposes. Those results will be used in future association studies to optimize the number of genotypes to be phenotyped.
... Kiwuka et al. (2021) detected wild accessions exhibiting signals of hybridization and introgression in fragmented natural forests. Within the Congo Basin, from which many of the currently cultivated Robusta coffee genotypes originate and which harbours genetically highly diverse wild C. canephora populations (Cubry et al., 2013;Ferrão et al., 2019;Merot-L'anthoene et al., 2019;Depecker et al., 2023), Vanden Abeele et al. (2021 identified two putative cultivated-wild hybrids in the rainforests. All previous studies used a limited number of SSR markers, yet a more comprehensive assessment, with genome-wide molecular markers, of the occurrence of cultivated-wild hybrids and the potential impact on the genetic composition of wild populations of C. canephora remains to be done. ...
... We found a relatively high allelic richness and observed heterozygosity in the cultivated reference group that was similar to that observed in the wild reference group, which was in contrast to our expectations. Typically, CWRs are considered to exhibit greater genetic diversity than their cultivated counterparts (Cubry et al., 2013;Zhang et al., 2017). For instance, Vanden Abeele et al. (2021) previously reported higher levels of observed heterozygosity in cultivated materials in the Yangambi region, as compared to the wild populations of C. canephora in the region, and equivalent or higher levels of observed heterozygosity were found in cultivated C. canephora elsewhere in the Afrotropical region compared to wild C. canephora populations (Musoli et al., 2009;Kiwuka et al., 2021). ...
... Not only was within-genetic group allelic richness and observed heterozygosity similar in the cultivar and wild reference groups in our study, but also between-reference group genetic diversity comparisons showed a relatively high overlap in allele composition, albeit at different allele frequency per group (no strictly private alleles and only 24 out of 8131 SNPs with an F ST > 0.8 in our study). The relatively close genetic relatedness between cultivated and wild C. canephora was also highlighted by Cubry et al. (2013), and Kiwuka et al. (2021) found a low number of private alleles in cultivated C. canephora populations. This is probably related to the long generation time of coffee, limited breeding selection and a broad genetic base (Stoffelen, 1998;Cubry et al., 2013;Gomez et al., 2016), and because 'Lula' cultivars probably came from sources relatively close to the Yangambi region . ...
Background and aims
Plant breeders are increasingly turning to crop wild relatives (CWRs) to ensure food security in a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridisation with their nearby cultivated crops. This might be especially a problem for wild coffee species, which often occur near coffee cultivation areas. Here, we briefly review the evidence for wild Coffea arabica (cultivated as Arabica coffee) and Coffea canephora (cultivated as Robusta coffee) and then focussed on C. canephora in the Yangambi region in the Democratic Republic of the Congo. There, we examined the geographical distribution of cultivated C. canephora and the incidence of hybridisation between cultivated and wild individuals within the rainforest.
Methods
We collected 71 C. canephora individuals from home gardens and 12 C. canephora individuals from the tropical rainforest in the Yangambi region and genotyped those with Genotyping-by-Sequencing (GBS). We compared those fingerprints with existing GBS data from 388 C. canephora individuals from natural tropical rainforests and the INERA Coffee Collection, a Robusta coffee field gene bank and the most likely source of cultivated genotypes in the area. We then established robust diagnostic fingerprints that genetically differentiate cultivated from wild coffee, identified cultivated-wild hybrids, and mapped their geographical position in the rainforest.
Key results
We identified cultivated genotypes and cultivated-wild hybrids in zones with clear anthropogenic activity, and where cultivated C. canephora in the home gardens may serve as a source for crop-to-wild gene flow. We found relatively few hybrids and backcrosses in the rainforests.
Conclusions
The cultivation of C. canephora in close proximity to its wild gene pool has led to cultivated genotypes and cultivated-wild hybrids appearing within the natural habitats of C. canephora. Yet, given the high genetic similarity between the cultivated and wild gene pool, together with the relatively low incidence of hybridisation, our results indicate that the overall impact in terms of risk of introgression remains limited so far.
... The species Coffea arabica differs from the other species by undergoing fruit maturation in shorter time, ranging from 7 to 9 months; also, Arabica coffee is more susceptible to pests and abiotic variations (temperature, humidity, pH, and altitude) due to its shape [27,28]. Regarding cultivation, this species needs altitudes greater than 600 m and a mild climate (15-22 °C), since without these abiotic factors, the development of the plant is impaired [29]. ...
... The species Coffea arabica differs from the other species by undergoing fruit maturation in shorter time, ranging from 7 to 9 months; also, Arabica coffee is more susceptible to pests and abiotic variations (temperature, humidity, pH, and altitude) due to its shape [27,28]. Regarding cultivation, this species needs altitudes greater than 600 m and a mild climate (15)(16)(17)(18)(19)(20)(21)(22) • C), since without these abiotic factors, the development of the plant is impaired [29]. ...
... Since they are diploid, Coffea robusta plants have two copies of the basic chromosome number (n = 11), resulting in a total of 22 chromosomes per cell nucleus [27]. It presents characteristics of allogamous reproduction and gametophytic self-incompatibility, making cross-fertilization the only form of sexual reproduction of the species [28,35]. Coffee trees of Coffea robusta are multi-stem, with a phenological cycle (9-11 months) longer than Coffea arabica [31]. ...
Roasting is responsible for imparting the main characteristics to coffee, but the high temperatures used in the process can lead to the formation of several potentially toxic substances. Among them, polycyclic aromatic hydrocarbons, acrylamide, furan and its derivative compounds, α-dicarbonyls and advanced glycation end products, 4-methylimidazole, and chloropropanols stand out. The objective of this review is to present a current and comprehensive overview of the chemical contaminants formed during coffee roasting, including a discussion of mitigation strategies reported in the literature to decrease the concentration of these toxicants. Although the formation of the contaminants occurs during the roasting step, knowledge of the coffee production chain as a whole is important to understand the main variables that will impact their concentrations in the different coffee products. The precursors and routes of formation are generally different for each contaminant, and the formed concentrations can be quite high for some substances. In addition, the study highlights several mitigation strategies related to decreasing the concentration of precursors, modifying process conditions and eliminating/degrading the formed contaminant. Many of these strategies show promising results, but there are still challenges to be overcome, since little information is available about advantages and disadvantages in relation to aspects such as costs, potential for application on an industrial scale and impacts on sensory properties.
... comm.). Eight distinct genetic groups of Robusta coffee are known to exist [6,9,10,[13][14][15][16][17][18][19], including a Ugandan group [13,18]. ...
... The significance of difference in tolerance to watering deficit stress with stressprimed plants exhibiting better tolerance and recovery than controls suggest a potential of breeding for resilience to drought stress in C. canephora using the half-sib selection Specific examination of data sets on WS for both tolerance and recovery reveals 10 genotypes that appear in both sets and possess between 0 (no leaf is wilted) and 2 (only 26-50% of leaves are wilted), as wilting scores include 14 ...
... This study's findings indicate that C. canephora populations differ in their ability to acquire tolerance to drought and high temperatures. Individuals, namely 14 Our view is that the observed distribution of best genotypes is a result of (i) the genetic background of mother clone KR7 being more drought tolerant than that of the rest of the studied materials, but (ii) there is also a random pollen grain movement due to an exclusive cross pollination tendency in Robusta coffee thereby increasing geneflow among the study half-sib offspring. The random mating facilitated by self-incompatibility of C. canephora [24,49] and pollination agents [24,50] creates unlimited genetic diversity that suites the crop to recurring climate change effects (biotic and abiotic) [2,22,23], including the studied watering deficit tolerance and recovery from the stress. ...
Coffea canephora has high but inadequately exploited genetic diversity. This diversity, if well exploited, can sustain coffee productivity amidst climate change effects. Drought and heat stress are major global threats to coffee productivity, quality, and tradable volumes. It is not well understood if there is a selectable variation for drought stress tolerance in Robusta coffee half-sibs as a result of watering deficit pre-exposure at the germination stage. Half-sib seeds from selected commercial clones (KR5, KR6, KR7) and a pipeline clone X1 were primed with deficit watering at two growth stages followed by recovery and later evaluated for tolerance to watering deficit stress in three different temperature environments by estimation of plant growth and wilt parameters. Overall, the KR7 family performed the best in terms of the number of individuals excelling for tolerance to deficit watering. In order of decreasing tolerance, the 10 most promising individuals for drought and heat tolerance were identified as: 14.KR7.2, 25.X1.1, 35.KR5.5, 36.KR5.6, 41.KR7.5, 46.KR6.4, 47.KR6.5, 291.X1.3, 318.X1.3, and 15.KR7.3. This is the first prospect into the potential of C. canephora half-sibs’ diversity as an unbound source of genetic variation for abiotic stress tolerance breeding.
... comm.). Eight distinct genetic groups of Robusta coffee are known to exist [6,9,10,[13][14][15][16][17][18][19], including a Ugandan group [13,18]. ...
... The majority (33%) of cluster 3 members belong to the KR7 family, followed by 25% X1, 22% KR6, and 19% belong to the KR5 family. The cluster 3 members include 4.X1. 4 Specific examination of data sets on WS for both tolerance and recovery reveals 10 genotypes that appear in both sets and possess between 0 (no leaf is wilted) and 2 (only 26-50% of leaves are wilted), as wilting scores include 14 ...
... This study's findings indicate that C. canephora populations differ in their ability to acquire tolerance to drought and high temperatures. Individuals, namely 14 Our view is that the observed distribution of best genotypes is a result of (i) the genetic background of mother clone KR7 being more drought tolerant than that of the rest of the studied materials, but (ii) there is also a random pollen grain movement due to an exclusive cross pollination tendency in Robusta coffee thereby increasing geneflow among the study half-sib offspring. The random mating facilitated by self-incompatibility of C. canephora [24,49] and pollination agents [24,50] creates unlimited genetic diversity that suites the crop to recurring climate change effects (biotic and abiotic) [2,22,23], including the studied watering deficit tolerance and recovery from the stress. ...
Coffea canephora has high but inadequately exploited genetic diversity. This diversity, if well exploited, can sustain coffee productivity amidst climate change effects. Drought and heat stress are major global threats to coffee productivity, quality, and tradable volumes. It is not well understood if there is a selectable variation for drought stress tolerance in Robusta coffee half-sibs as a result of watering deficit pre-exposure at the germination stage. Half-sib seeds from selected commercial clones (KR5, KR6, KR7) and a pipeline clone X1 were primed with deficit watering at two growth stages followed by recovery and later evaluated for tolerance to watering deficit stress in three different temperature environments by estimation of plant growth and wilt parameters. Overall, the KR7 family performed the best in terms of the number of individuals excelling for tolerance to deficit watering. In order of decreasing tolerance, the 10 most promising individuals for drought and heat tolerance were identified as: 14.KR7.2, 25.X1.1, 35.KR5.5, 36.KR5.6, 41.KR7.5, 46.KR6.4, 47.KR6.5, 291.X1.3, 318.X1.3, and 15.KR7.3. This is the first prospect into the potential of C. canephora half-sibs' diversity as an unbound source of genetic variation for abiotic stress tolerance breeding.
... Yangambi (Tshopo province, northeastern DR Congo) became the principal research station of the INEAC, both in general and for Robusta coffee (Leplae, 1936). In the years following the second World War, DR Congo and Uganda took over Java's role as principal research and breeding centers for C. canephora (Jaroget and Descroix, 2002 (Cubry et al., 2013;Bramel et al., 2017). ...
... The Congo Basin is hypothesized to be the region of origin of many cultivated Robusta coffee genotypes (Dulloo et al., 1998;Cubry et al., 2013). Consequently, populations of C. canephora native to this region contain a valuable part of the wild gene pool, but the extent of this genetic reservoir remains unknown. ...
... Nonetheless, the 'Lula' varieties are assumed to have originated from the Congo Basin and probably root back to the early introduction of 'Coffea robusta' by Linden from Sankuru, but additional sampling and research is needed to trace the region of origin. Cultivated material from the former INEAC Yangambi collection is still present in the CNRA collection in Ivory Coast (Cubry et al., 2013), but this cultivated material dates back to 1935 (Bodard, 1965). The CNRA C. canephora material originating from the former INEAC was shown to be closely related to C. canephora growing in Uganda Accepted Article (Cubry et al., 2013;Leroy et al., 2014). ...
Premise:
Many cultivated coffee varieties descend from Coffea canephora, commonly known as Robusta coffee. The Congo Basin has a century long history of Robusta coffee cultivation and breeding, and is hypothesized to be the region of origin of many of the cultivated Robusta varieties. Since little is known about the genetic composition of C. canephora in this region, we assessed the genetic diversity of wild and cultivated C. canephora shrubs in the Democratic Republic of the Congo.
Methods:
Using 18 microsatellite markers, we studied the genetic composition of wild and backyard-grown C. canephora shrubs in the Tshopo and Ituri provinces, and from the INERA Yangambi Coffee Collection. We assessed genetic clustering patterns, genetic diversity, and genetic differentiation between populations.
Key results:
Genetic differentiation was relatively strong between wild and cultivated C. canephora shrubs, and both gene pools harbored multiple unique alleles. Strong genetic differentiation was also observed between wild populations. The level of genetic diversity in wild populations was similar to that of the INERA Yangambi Coffee Collection, but local wild genotypes were mostly missing from that collection. Shrubs grown in the backyards were genetically similar to the breeding material from INERA Yangambi.
Conclusions:
Most C. canephora that is grown in local backyards originated from INERA breeding programs, while a few shrubs were obtained directly from surrounding forests. The INERA Yangambi Coffee Collection could benefit from an enrichment with local wild genotypes, to increase the genetic resources available for breeding purposes, as well as to support ex situ conservation. This article is protected by copyright. All rights reserved.
... Although robusta beverage is less prized than arabica, there is a high variability in quality traits within this species and the presence of consistent quantitative trait loci provides breeders with promising tools to improve the cup quality of robusta coffee (Leroy et al. 2011). Coffea canephora is a perennial forest shrub with the largest natural distribution range for a coffee tree species, stretching from Guinea to Uganda with a discontinuity in the Togo-Benin region (Dahomey Gap) (Cubry et al. 2013b). The type specimen of the species C. canephora was collected in Gabon in 1895 by the Reverend Théophile Klaine and sent to the botanist Jean Baptiste Louis Pierre at the Muséum National d'Histoire Naturelle (MNHN) in Paris, France under the name "Café indigène des Ishira" [specimen Klaine 247 (P)]. ...
... Following the chorological system established by White (1979), Berthaud proposed to classify the wild populations growing in Upper Guinea as "Guinean", and those from Lower Guinea and Congolia as "Congolese". Further studies based on the use of DNA markers (RFLP and SSR) validated this classification in two major genetic groups and led to the recognition of five sub-groups (SG1, SG2, B, C, and UW) within the Congolese group (Dussert et al 2003;Gomez et al. 2009;Musoli et al. 2009;Cubry et al. 2013b;Leroy et al. 2014). ...
... The largest gene bank of C. canephora is located at the Centre National de Recherche Agronomique (CNRA) research station near Divo, Côte d'Ivoire, where about 1900 clonal accessions are conserved in the field. Many of these accessions have been genetically characterized over the past 30 years using isozymes, RFLP, or SSR markers, e.g. by Montagnon et al. (1992aMontagnon et al. ( , 1993, Dussert et al. (2003), Gomez et al. (2009), andCubry et al. (2013b). Only 205 accessions (about 10%) of C. canephora germplasm in the CNRA gene bank belong to the Guinean group. ...
Backgrounds and aims – Previous studies showed that robusta coffee (Coffea canephora Pierre ex A.Froehner), one of the two cultivated coffee species worldwide, can be classified in two genetic groups: the Guinean group originating in Upper Guinea and the Congolese group in Lower Guinea and Congolia. Although C. canephora of the Guinean group is an important resource for genetic improvement of robusta coffee, its germplasm is under-represented in ex situ gene banks and its genetic diversity and population structure have not yet been investigated. Methods – To overcome the limitations of living collections, we explored old herbarium specimens collected in Guinea and Côte d’Ivoire and conserved at the Muséum National d’Histoire Naturelle, Paris. First, we reviewed the history of collection missions in both countries and how the C. canephora herbaria from the Muséum were assembled. Then, using 23 nuclear microsatellite markers, factorial and model-based Bayesian analyses, we investigated the genetic diversity of 126 specimens and 36 controls, analysed their distribution among the Congolese and Guinean groups, and estimated admixture proportions for each individual.Key results – For the first time, we detected population genetic structure within the Guinean group of C. canephora. The Guinean genotypes can be assigned to five sub-groups with distinct geographic distribution, especially in Guinea where two sub-groups (Maclaudii and Gamé) are characterized by a low level of admixture due to geographical isolation.Conclusions – We showed how combining a literature review and genetic data from old herbarium specimens can shed light on previous observations made by botanists and guide further actions to better preserve native coffee plants in forest remnants of West Africa.
... Production of Robusta increased by 11% in 2018/2019 to 70.67 million bags (International Coffee Organization, 2019), so Robusta coffee has an important role in improving the economy of coffee farmers. Robusta coffee is cultivated at low to moderate altitudes in tropical Africa, America, and Asia (Cubry, de Bellis, Pot, Musoli, & Leroy, 2013). The main problem with Robusta coffee cultivation is the availability of superior seeds for plant propagation, because propagation by seed will produce new plants that have different genetic properties from the parent plant. ...
... The main problem with Robusta coffee cultivation is the availability of superior seeds for plant propagation, because propagation by seed will produce new plants that have different genetic properties from the parent plant. The nature of Robusta coffee is self-incompatible, so it tends to be cross-pollinated (Cubry et al., 2013;Hetzel, 2015;Moraes et al., 2018). The results of crosspollination tend to produce seeds with different genetic characteristics from the parent plant. ...
Robusta coffee plant propagation is recommended to be performed by vegetative methods, one of which is cuttings. Among plant organs that can be used for cuttings is the stem. The research objective was to determine which stem segment from cuttings was able to provide the best root and leaf growth. The layout study used a completely randomized block design (RBD) with an experimental treatment consisting of five stem segments, namely (1) the first stem segment from the upper shoot (A); (2) the second stem segment from the upper shoot (B); (3) the third stem segment from the upper shoot (C); (4) the fourth stem segment from the upper shoot (D); and (5) the fifth stem segment from the upper shoot (E); each treatment had five replications. Data analysis was performed statistically with analysis of variance (ANOVA) and Tukey's HSD (honestly significant difference) test with a significance level of P < 0.05. Robusta coffee cuttings stems from the second stem segment from the upper shoot were able to provide the optimal root growth (root length) and shoot growth (leaf sprout height and leaf sprout growth rate). Leaf sprout number derived from the cuttings was not affected by the stem segment.
... Other studies on C. canephora have also highlighted the genetic variability of the species (Cubry et al. 2013;Ferrão et al. 2013Ferrão et al. , 2009Montagnon et al. 2012;Musoli et al. 2009;Rodrigues et al. 2015;Souza et al. 2013). The great variability of the species is due to its reproductive system, presenting allogamy with gametophytic self-incompatibility mechanism (Conagin and Mendes 1961; Berthaud 1980), which further expands the heterogeneity and heterozygosity of the species. ...
Coffee is one of Brazil’s main commodities. Among the goals of crop improvement, the search for drought-tolerant materials has stood out, mainly due to the water scarcity of the producing regions. The knowledge of genetic diversity and the morphophysiological analysis of plants allow the identification of genotypes with potential use in genetic improvement. Thus, this study aimed to evaluate the diversity, by morphophysiological characteristics, in 173 genotypes of Coffea canephora, from populations of contrasting crosses regarding the drought tolerance of the breeding program of Incaper, and to identify the relative importance of traits, subsidizing the selection for drought tolerance, based on the factor analysis index (FAI). The experiment was conducted in three evaluation periods, under field conditions without irrigation at the Incaper Experimental Farm of Marilândia, in the state of Espírito Santo. There was great variability between and within populations, which was affected by the evaluation season. Based on the traits of greater relative importance identified in this work (LL, LW, SLA, LAR, LT, TLA, PBL, CHL, NO3⁻, TSP, PRO, A, and iWUE), the FAI identified the genotypes 76 × 48 − 1, 76 × 48 − 10, 76 × 48 − 16, 76 × 48 − 76, 76 × 48 − 77, 76 × 48 − 83, 76 × 48 − 90, 76 × 48 − 128, 76 × 04 − 1, and 76 × 04 − 32 as more promising, from the ideotype of lower LL, LW, SLA, and LAR, and higher LT, TLA, PBL, CHL, NO3⁻, TSP, PRO, A, and iWUE.
... Extant taxonomic diversity has been influenced by several environmental and geographic factors. For example, the Dahomey Gap, an arid savannah region separating West and Central African forests, is known to have influenced the genetic diversity and speciation within Coffea by acting as a barrier to gene flow (Berthaud, 1986;Maurin et al., 2007;Gomez et al., 2009;Cubry et al., 2013). Further, speciation on the West Indian Ocean Islands has been shown to be rapid and radial, suggesting a possible adaptive radiation in the WIOI subclade (Davis et al., 2006;Anthony et al., 2010). ...
Background and Aims
Leaf traits are known to be strong predictors of plant performance and can be expected to (co)vary along environmental gradients. We investigated the variation, integration, environmental relationships, and evolutionary history of leaf functional traits in the genus Coffea L., typically a rainforest understory shrub, across Africa. A better understanding of the adaptive processes involved in leaf trait evolution can inform the use and conservation of coffee genetic resources in a changing climate.
Methods
We used phylogenetic comparative methods to investigate the evolution of six leaf traits measured from herbarium specimens of 58 African Coffea species. We added environmental data and data on maximum plant height for each species to test trait-environment correlations in various (sub)clades, and we compared continuous trait evolution models to identify variables driving trait diversification.
Key Results
A substantial leaf trait variation was detected across the genus Coffea in Africa, which was mostly interspecific. Of these traits, stomatal size and stomatal density exhibited a clear trade-off. We observed low densities of large stomata in early branching lineages and higher densities of smaller stomata in more recent taxa, which we hypothesise to be related to declining CO 2 levels since the mid-Miocene. Brownian Motion evolution was rejected in favour of White Noise or Ornstein-Uhlenbeck models for all traits, implying these traits are adaptively significant rather than driven by pure drift. The evolution of leaf area was likely driven by precipitation, with smaller leaves in dryer climates across the genus.
Conclusions
Generally, Coffea leaf traits appear to be evolutionarily labile and governed by stabilising selection, though evolutionary patterns and correlations differ depending on the traits and clades considered. Our study highlights the importance of a phylogenetic perspective when studying trait relationships across related taxa, as well as the consideration of various taxonomic ranges.
... Distribution: Throughout Uganda but mainly in central and western parts of the country. Uganda is a major centre of diversity for C. canephora 11,[43][44][45] and is the only country on the eastern side of the Great Rift Valley holding substantial wild populations of this species. Figure 5a. ...
Coffee natural capital for environmental and livelihood sustainability in Uganda was a three-year project (October 2020 to September 2023) funded by the Darwin Initiative and undertaken by a team in Uganda (The National Agricultural Research Organization (NARO), Makerere University, and Kyagalanyi Coffee Ltd. (Volcafe) and the UK (Royal Botanic Gardens, Kew). The main objectives of the project were to:
undertake a detailed survey of Uganda’s wild coffee species (coffee natural capital), including conservation status and extinction risk; conduct farm and field trials, agronomic assessments, and value chain appraisals for excelsa coffee; undertake preliminary agronomic assessment of eugenioides coffee; and demonstrate the value of Uganda’s coffee natural capital for ecosystem service provision, livelihood improvement, and coffee sector sustainability.
This report should be cited as: Davis, A.P., Kiwuka, C., Faruk, A.,
Walubiri, M. J., Lumu, M., Mulumba, J.W., Heusinkveld, G.J. and
Kalema, J. (2023). The wild coffee resources of Uganda: a precious heritage. Royal Botanic Gardens, Kew (UK). Pp. 44.
... The results of exploration in Dusun Tuo Village and Nilo Dingin Village, Sub-district of Lembah Masurai, Koto Renah Village, Jangkat Sub-district, and Simpang Talang Tembago Village, Jangkat Timur Sub-district, revealed that most Robusta coffee farmers planted coffee seeds from non-recommended varieties/clones. Robusta coffee is self-incompatible in nature, so it tends to cross-pollinate [14,15]. The barrier to self-pollination is caused by cessation of pollen tube development, which makes fertilization of the female gametophyte impossible [16,17]. ...
Jambi known as one of the Robusta coffee producing areas in Indonesia. Many of promising Robusta coffee clones were found at coffee plantations in Jambi and have adapted to local agroecosystems. The study aimed to evaluate the quality of Robusta coffee in Merangin Regency, Jambi Province. The exploration and evaluation were carried out in July 2020 and December 2021 using the survey method. In this study, several Robusta coffees clones that had developed in the community were found, such as Prima, Tugusari Kuning, Bengko, Mendo, and Tugusari Hijau. These clones are preferred because they have good taste and high productivity as well as adaptive in the highlands. The result of cupping test for Prima, Bengko, Local, Tugusari Kuning, Mendo, and Tugusari Hijau clones showed a final score of >80 (Fine Robusta) with a final score ranging from 80.50-81.63, while Parabola and Curup clones were categorized as not specialty with the score of 70.50 and 78.375, respectively. On the other hand, the results of caffeine content analysis of the Curup, Mendo, Parabola, Tugusari Hijau, and Tugusari Kuning clones ranged from 1.33-1.74%. This initial evaluation is expected to provide an overview of the existence of promising Robusta coffee clones in Jambi. Hence, these coffee clones can be developed as local superior clones in the future.
... Distribution: Throughout Uganda but mainly in eastern and western parts of the country. Uganda is a centre of diversity for C. canephora (Gomez et al., 2009;Cubry et al., 2013;Merot-L'anthoene et al., 2019;Kiwuka et al., 2021), and is the only country on the eastern side of the Great Rift Valley that holds substantial wild populations of this species. Figure 1A. ...
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.
... Coffea canephora is a self-incompatible species, without a persistent soil seed bank (Oryem-Origa 1999;Nowak et al. 2011). Natural populations of C. canephora are usually disconnected, with 10-20 individuals per ha, and few offspring scattered across the forest floor (Musoli et al. 2009;Cubry et al. 2013;Depecker and Vandelook pers. obs.). ...
Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and West Africa, and the genetic diversity harboured in its wild populations is vital for sustainable coffee production worldwide. Here, we aimed to quantify genetic diversity, genetic structure, and pedigree relations in wild C. canephora populations, and we investigated associations between these descriptors and forest disturbance and regeneration. Therefore, we sampled 256 C. canephora individuals within 24 plots across three forest categories in Yangambi (DR Congo), and used genotyping-by-sequencing to identify 18,894 SNPs. Overall, we found high genetic diversity, and no evidence of genetic erosion in C. canephora in disturbed old-growth forest, as compared to undisturbed old-growth forest. In addition, an overall heterozygosity excess was found in all populations, which was expected for a self-incompatible species. Genetic structure was mainly a result of isolation-by-distance, reflecting geographical location, with low to moderate relatedness at finer scales. Populations in regrowth forest had lower allelic richness than populations in old-growth forest and were characterised by a lower inter-individual relatedness and a lack of isolation-by-distance, suggesting that they originated from different neighbouring populations and were subject to founder effects. Wild Robusta coffee populations in the study area still harbour high levels of genetic diversity, yet careful monitoring of their response to ongoing forest degradation remains required. Heredity; https://doi.
... Cubry et al., 2013;Gomez et al., 2009;Kiwuka et al., 2021) as well as SNP array(Mérot-L'Anthoene et al., 2019). Note however that our analysis merged the previously separated B and O groups (using higher sample sizes inGomez et al., 2009). ...
The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species’ native range can provide valuable insights about habitat loss and the species’ adaptive potential, allowing to identify genotypes that may act as a resource for varietal improvement. By applying species distribution models, we assessed ecological vulnerability as the decrease in climatic suitability under future climatic conditions from 492 occurrences. We then quantified genomic vulnerability (or risk of maladaptation) as the allelic composition change required to keep pace with predicted climate change. Genomic vulnerability was estimated from genomic environmental correlations throughout the native range. Suitable habitat was predicted to diminish to half its size by 2050, with populations near coastlines and around the Congo River being the most vulnerable. Whole‐genome sequencing revealed 165 candidate SNPs associated with climatic adaptation in C. canephora, which were located in genes involved in plant response to biotic and abiotic stressors. Genomic vulnerability was higher for populations in West Africa and in the region at the border between DRC and Uganda. Despite an overall low correlation between genomic and ecological vulnerability at broad scale, these two components of vulnerability overlap spatially in ways that may become damaging. Genomic vulnerability was estimated to be 23% higher in populations where habitat will be lost in 2050 compared to regions where habitat will remain suitable. These results highlight how ecological and genomic vulnerabilities are relevant when planning on how to cope with climate change regarding an economically important species. We characterized the ecological and genomic vulnerability of the wild Robusta coffee (Coffea canephora). Using species distribution modelling, we predicted a loss of ~50% in suitable habitat area in 2050. We detected 165 genetic markers that could be involved in facilitating adaptation to future climate conditions. Yet, we estimated that genomic vulnerability was higher for populations at the West and East margins of the current distribution and ~23% higher in populations where habitat will be lost in 2050. Our study highlights how ecological and genomic vulnerabilities are relevant for conservation policies and when planning for varietal improvement.
... Robusta/Conilon coffees are characterized by a wide genetic diversity and subdivided into several groups and subgroups. Within the species C. canephora, the so-called Congolese group includes the two most commonly cultivated botanical varieties, Conilon (SG1) and Robusta (SG2) [7,8]. Since allogamy and self-incompatibility can both be observed in the ...
The objective of this study was to evaluate nutrient concentrations in the flowers, leaves (pre-flowering and grain-filling period), grains, and husks of Robusta coffee genotypes cultivated in the Amazon region, as well as to identify their genetic diversity. This experiment was carried out in Alta Floresta D’Oeste, Rondônia, Brazil, in randomized blocks with three replications; for the leaves, a factorial experimental design of sampling periods was included. The nutrient concentrations of the different evaluated organs were subjected to analysis of variance by the F test (p < 0.01), and the genetic parameters were estimated. To determine the genetic diversity, the genotypes were grouped by the UPGMA hierarchical method, and to predict it the relative importance of traits was analyzed. Genetic divergence among Coffea canephora genotypes was indicated by the leaf nutrient concentrations. At a maximum dissimilarity threshold of 82% for the genotypes, the UPGMA method formed six groups. Concentrations of nitrogen (N) and phosphorus (P) in the leaf sampling periods of pre-flowering and grain filling were not influenced by genotypes. The leaf and flower iron (Fe) concentrations contributed most to genetic divergence. For a nutritional diagnosis of Robusta coffee, it is important to take into account the comparisons of genetic diversity as well as the nutritional requirements during the flowering and grain-filling periods.
... High diversity prevails within the species for many agronomic traits, such as pest and disease resistance and abiotic stress tolerance (Leroy et al., 1993;Montagnon et al., 1992). Regarding the genetic structure of wild African C. canephora, a marked separation between accessions from Upper-Lower Guinean (West Africa) and Congolese (Central Africa) regions has been described, with further subdivision into eight well-defined genetic groups, that is, four in the Guinean region and four in the Congolese region (Cubry et al., 2013;Gomez et al., 2009;Merot-L'Anthoene et al., 2019;Musoli et al., 2009) ( Figure S1A). The Ugandan group is organized in well-structured wild populations (Kiwuka et al., 2021) presenting a wide range of phenotypic variations regarding tree morphology, agronomic traits, green bean physical and biochemical characteristics (Aluka, 2013;Berthaud & Charrier, 1988;Kiwuka, 2020). ...
Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programs. To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long‐lived species such as trees. We conducted a population genomics study of 207 Coffea canephora trees from seven forests along different climate gradients in Uganda. For this, we sequenced 323 candidate genes involved in key metabolic and defense pathways in coffee. Seventy‐one SNPs were found to be significantly associated with bioclimatic variables, and were thereby considered as putatively adaptive loci. These SNPs were linked to key candidate genes, including transcription factors, like DREB‐like and MYB family genes controlling plant responses to abiotic stresses, as well as other genes of organoleptic interest, like the DXMT gene involved in caffeine biosynthesis and a putative pest repellent. These climate‐associated genetic markers were used to compute genetic offsets, predicting population responses to future climatic conditions based on local climate change forecasts. Using these measures of maladaptation to future conditions, substantial levels of genetic differentiation between present and future diversity were estimated for all populations and scenarios considered. The populations from the forests Zoka and Budongo, in the northernmost zone of Uganda, appeared to have the lowest genetic offsets under all predicted climate change patterns, while populations from Kalangala and Mabira, in the Lake Victoria region, exhibited the highest genetic offsets. The potential of these findings in terms of ex‐situ conservation strategies are discussed.
... The Robusta coffee germplasm collected came from seeds so that there was diversity in the characteristic of fruit weight per tree with a variation coefficient value of 19.72%. This is because Robusta coffee is self-incompatible, so it tends to be cross-pollinated [15,16,17] that causes genetic diversity in its offspring. Thus, in its cultivation it must be planted side by side with other coffee plants of different types. ...
To produce superior varieties, gene sources of high diversity are needed. The study was intended to reveal the diversity of qualitative and quantitative characters and the quality of Robusta coffee germplasm. The study conducted at Pakuwon Experimental Garden, Sukabumi Indonesia, used 14 accessions of Robusta coffee grown by a single stem system. The observed characteristics were qualitative and quantitative characteristics, caffeine content, and cup quality. The data were analyzed descriptively and grouped by cluster analysis using the PBSTAT program. The results revealed variations in the angle of insertion of primary branches, stipule shape, immature leaf color, leaf shape, leaf apex shape, young shoot color, mature leaf color, ripe fruit color, and fruit shape. The number of bunches/branch is the characteristic of the highest variation coefficient. Eleven accessions had cupping scores between 80 and 86 with a caffeine content of 1.39 - 2.06%. The accession B4-17-1 had the lowest yield, but its final cupping test score was the highest. At the dissimilarity coefficient of 0.25, 14 accessions of Robusta coffee are divided into two large groups, while at the dissimilarity coefficient of 0.15 they consist of four groups.
... Nevertheless, when the 12 SSR loci (Table 5) of the 10 clones were amplified, the genetic dissimilarity between them was found to be reduced. These clones belong to the Congolese Group, with CcK1 representing the botanical variety Kouilou of subgroup SG1; the other clones belonged to the botanical variety Robusta, of subgroup SG2 (Berthaud 1986;Cubry et al. 2013). The Robusta clones were derived from accessions from the Democratic Republic of Congo (DRC) (CcR3 and CcR4) or from Indonesia (CcR2, CcR6, CcR8, CcR9 and CcR10), while the exact geographical origin of CcR5 and CcR7 is unknown. ...
The cultivars of most Brazilian Arabica coffee plantations are susceptible to root knot nematodes (RKN), Meloidogyne spp. By planting resistant rootstocks of the species Coffea canephora, a successful strategy in some producing regions, coffee can be cultivated in RKN-infested areas. However, the only currently available rootstock cultivar in Brazil has a segregation rate close to 20% for susceptibility. To breed new rootstock cultivars resistant to the main RKN species, with a lower segregation rate, 10 C. canephora clones were selected in areas infested by these nematodes, with confirmed resistance to Meloidogyne exigua, M. incognita and M. paranaensis, under controlled conditions. The genetic compatibility analysis of the clones detected only one incompatible combination (CcK1xCcR5 and its reciprocal). Almost all F1 hybrids resulting from the cross between the selected clones were resistant to M. exigua and M. incognita. According to the reproduction factor, 77% of the evaluated F1 hybrids proved resistant to M. paranaensis, and those classified as susceptible had variable segregation rates within the progeny, generally lower than 25%. Based on these data, different hybrid combinations can be suggested for the development of new rootstock cultivars of C. canephora with simultaneous resistance to coffee RKN. This approach has immediate practical applications in grafting Arabica coffee scion cultivars in areas where nematodes restrict cultivation.
... Development of molecular markers such as SSR (single sequence repeat), RFLP (restriction fragment length polymorphism) and RAPD (random amplification of polymorphic DNA) markers, or more recently SNPs, derived from DNA sequencing has enabled researchers to further understand the phylogenetic relationships between different Coffea species [20,21], but also the relationships within wild C. canephora populations [22,23]. Genetic characterization of C. canephora diversity has been greatly facilitated by the availability of a large repository of simple sequence repeat (SSR) based microsatellite markers, which provides efficiency and high-resolution in genetic analyses [24][25][26][27][28]. Globally, the genetic diversity of C. canephora is linked to the geographical location [22,23,29,30]. Isoenzyme analyses initially highlighted that C. canephora diversity was pooled within two different genetic groups, namely: (i) a Guinean group including wild populations from Côte d'Ivoire, and (ii) a Congolese group consisting of accessions from the Central African Republic and Cameroon [30]. ...
Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.
... Regarding the structure of the collection, the Bayesian model-based STRUCTURE method and the PCoA gave similar results, as was also observed in coconut data [45]. The INRA collection consists of two well-differentiated clusters, as is often reported in other plant germplasm collections, for example, soybean, cherry, maize, apple and coffee [46][47][48][49][50]. The two genetic clusters of the INRA walnut collection fit well with the geographical origin of the accessions. ...
... Brazil will harvest between 13.95 million and 16.04 million bags of C. canephora in 2020, representing around 20% of the world's production. 2 Studies about C. canephora converge for the existence of two large groups of economic importance: Congolese and Guinean. 3 These two distinct genetic groups differ in relation to tolerance to drought stress, disease resistance, yield, and quality. Robusta belongs to the Congolese group and is native to Central Africa, whereas conilon belongs to Guinean group, originated in West Africa. ...
BACKGROUND
The terrain slope and field altitude where the plant is cultivated influence the composition of coffee cherries. The aim of this study was to analyze the effects of different levels of altitude and terrain slope on the Coffea canephora cherries, as well as on the quality of the final beverage. C. canephora harvested in fields with 300 and 600 m altitude and with southeast‑ and northwest‐facing slopes was evaluated.
RESULTS
Lower pH values were observed for cherries cultivated at higher altitudes. The highest percentage of soluble solids (525.00 g kg⁻¹) was found on northwest‐facing slopes at 300 m. The highest values of phenolic compounds were observed at 600 m. Significant differences were found in the moisture of coffee cherries grown in different terrain slope and in the fiber content at different altitudes. The results do not enable us to conclude how the altitude and terrain slope influence the mineral content of cherries. Acidity, proteins, lipids, and carbohydrates were not influenced by altitude or terrain slope. The scores of cup quality were significantly affected by the altitude but not by the terrain slope. Coffees from cherries harvested in fields with 600 m altitude obtained the higher scores.
CONCLUSION
Results show that altitude and terrain slope influence some compounds of coffee fruits, whereas others remain unaffected. The findings are important because, during coffee fruits processing, these compounds are used to produce others that will have an influence on the bean and coffee beverage quality. © 2020 Society of Chemical Industry
... It is cultivated low to medium altitude in the intertropical region of Africa, America and Asia. C. canephora is a self incompatible diploid species indigenous to some areas of the tropical African forest, from West Africa via Cameroon, Central African Republic, Democratic Republic of Congo and Northern Tanzania down to Northern Angola (Cubry et al. 2012). Coffee has been the most commercially used food product and a most widely consumed beverage in the world since the opening of the first coffee house in Meca at the end of Fifteenth century. ...
The evaluation of nutritional and medicinal potentials of seeds of Fluted pumpkin (Telfairia occidentalis) and Coffea robusta (Coffea
canephora) leaves was carried out using various analytical techniques. Proximate parameters: ash, moisture, crude protein, crude fibre,
crude fat and carbohydrate as well as phytochemicals: alkaloids, cardiac glycosides, saponins, anthranoids, flavonoids, polyphenols, tannins,
anthraquinones and phlobatannins were assessed. The results of proximate analysis revealed the following compositions: ash (7.20 ±0.32%),
moisture (6.40±0.41%), crude fibre (7.00±0.79%), crude lipid (6.20±0.40%), crude protein (6.10±0.43%) and carbohydrate (73.50±0.87%)
for fluted pumpkin (T. occidentalis) seeds, while the proximate composition of the leaves of Coffea robusta revealed: ash (16.00±0.11%),
moisture (26.00±0.18%), crude fibre (38.00±0.42%), crude lipid (10.00±0.05%), crude protein (1.14±0.01%) and carbohydrate
(34.86±0.51%). The phytochemical screening of T. occidentalis showed the presence of polyphenols in moderate amount in both water
extract (WE) and petroleum ether (PE) extract while flavonoids, saponins and cardiac glycosides were only present in petroleum ether but
absent in water extract, while alkaloids was only present in water extract. Tannins, reducing sugar, anthraquinones and anthranoids were
however absent in both extracts. For C. canephora, polyphenol was present in small amount in both extracts, cardiac glycosides, alkaloids,
saponins and anthranoids were present in water extracts but absent in petroleum ether extract. Tannins was only present in petroleum ether
extract while reducing sugar and phlobatanins were absent in both extracts. The result shows that T. occidentalis and C. canephora have
good nutritional and pharmaceutical potentials.
... Brazil is the largest producer and exporter of coffee in the world (Meinhart et al., 2017), with a total of 2 million ha planted (CONAB, 2019). Production areas in Brazil are distributed in the south-central region, in the states of Minas Gerais, São Paulo, and Espírito Santo (Andrade et al., 2012;Cubry et al., 2013). Minas Gerais represents about 50% of the total production of Brazil and is the largest producer of coffee in the country , Ronchi et al., 2015. ...
... Brazil is the largest producer and exporter of coffee in the world (Meinhart et al., 2017), with a total of 2 million ha planted (CONAB, 2019). Production areas in Brazil are distributed in the south-central region, in the states of Minas Gerais, São Paulo, and Espírito Santo (Andrade et al., 2012;Cubry et al., 2013). Minas Gerais represents about 50% of the total production of Brazil and is the largest producer of coffee in the country , Ronchi et al., 2015. ...
O café é a bebida mais consumida no mundo e uma das principais causas para a redução da produtividade e qualidade são os problemas fitossanitários. A estratégia mais comum de controle dessas doenças e pragas é a aplicação de fungicidas e inseticidas foliares, dependendo da intensidade dos mesmos na região. Esse método tradicional pode ser melhorado utilizando de sistemas de alertas por meio de modelos de estimativas dos índices de doenças e pragas. Este trabalho tem como OBJETIVOS: A) Calibrar as variáveis meteorológicas: temperatura do ar e precipitação pluviométrica do sistema ECMWF em relação aos dados de reais de superfície mensurados pelo sistema nacional de meteorologia (INMET) para o estado de Minas Gerais; B) Avaliar quais os elementos meteorológicos exercem maior influência nas principais pragas (broca e bicho-mineiro) e doenças (ferrugem e cercosporiose) do cafeeiro arábica nas principais localidades cafeeiras do Sul de Minas Gerais e do Cerrado Mineiro; C) Desenvolver modelos agrometeorológicos para previsão de pragas e doenças em função das variáveis meteorológicas usando algoritmos de machine learning e procurando uma antecipação temporal suficiente para tomada de decisões. MATERIAL E MÉTODOS: Para o objetivo “A” foram utilizados dados climáticos mensais de temperatura do ar (T, ºC) e precipitação pluviométrica (P, mm) provenientes do ECMWF e do INMET no período de 1979 a 2017. A evapotranspiração potencial foi estimada por Thornthwaite (1948) e balanço hídrico por Thornthwaite e Mather (1955). As comparações entre o ECMWF e INMET foram realizadas pelos índices: acurácia (mean absolute percentage error, MAPE, e root mean squared error, RMSE) e precisão (coeficiente de determinação ajustado, R2adj). Para o objetivo “B” foram utilizados dados climáticos e fitossanitários de Boa Esperança, Carmo de Minas, Muzambinho e Varginha, situadas na região Sul de Minas (SOMG) e as localidades de Araxá, Araguari e Patrocínio situadas na região do Cerrado Mineiro (CEMG). Foram simulados a tendência de progresso das doenças e pragas ao longo de tempo usando modelos não lineares em função do índice térmico acumulado. Também foi estimada dos níveis de infestação de pragas e severidade de doenças usando regressão linear múltipla. A variável dependente foi os níveis de doenças e pragas e as variáveis independentes: graus dias (DD) acumulado, enfolhamento do café estimado por DD e número de nós estimado por DD. Para o objetivo “C” foram utilizados dados climáticos e fitossanitários da SOMG e CEMG. Os algoritmos calibrados e testados para a previsão das doenças e pragas do café foram 1) Regressão linear múltipla, 2) K-Neighbors, 3) Random Forest e 4) Redes Neurais. RESULTADOS E DISCUSSÃO: Os maiores desvios entre PINMET e PECMWF foram de 75 mm mo-1 e ocorreram no verão. O cafeeiro implantado no CEMG tem maiores índices de doenças e pragas em relação ao café do SOMG. O algoritmo random forest foi mais acurado na previsão da ferrugem, cercospora, bicho-mineiro e broca-do-cafeeiro em ambas as regiões. CONCLUSÃO: As variáveis climáticas oriundas do ECMWF são acuradas e podem modelar o balanço hídrico climatológico. É possível simular a tendência e ainda prever os índices de pragas e doenças do café usando como variáveis regressoras os dados climáticos e metodologia o machine learning.
... Coffee is one of the most consumed beverages in the world, reaching a worldwide consumption of 150-160 million bags between 2014 and 2017 (ICO, 2019;FAO, 2020). This crop constitutes one of the most important agricultural activities due to high employment and income generation (Cubry et al., 2013;Rodríguez-Lopes et al., 2013;DaMatta et al., 2018). However, growers face challenges from arthropods pests and diseases that limit coffee productivity (Avelino et al., 2018). ...
The acaricidal bioactivity of an oxymatrine-based commercial formulation was assessed against Oligonychus ilicis (McGregor) (Acari: Tetranychidae), a pest in coffee cropping systems. For this purpose, a series of assays were carried out under laboratory and greenhouse conditions using different concentrations (from 0.25 to 1.0 mL c.p. L⁻¹) of the oxymatrine formulation. In the laboratory, a significant reduction in egg hatchability was observed in treatment using 1.00 mL c. p. L⁻¹ of the oxymatrine formulation. Egg hatchability rates ranging from 69.9 to 91.7% were observed in eggs treated with 0.25–0.75 mL c. p. L⁻¹ of the bioacaricide. Although the ovicidal activity was low, all tested bioacaricide concentrations caused significant larval mortality for newly hatched larvae in relation to the negative control. For adult females, the highest concentrations (0.75–1.00 mL c. p. L⁻¹) of the bioacaricide caused high acute toxicity and residual (≥86.7% mortality) at 10 days after exposure, which were similar to the synthetic acaricide spirodiclofen. In the greenhouse, the bioacaricide caused ∼74% reduction in population levels of O. ilicis, while spirodiclofen provided a population reduction of ∼96%. In this study, no phytotoxic effect was observed on the coffee nursery trees treated with the bioacaricide. The oxymatrine-based commercial formulation has potential to be used for O. ilicis management in coffee, though field trials are needed to validate findings of our study.
... In the last glacial maximum (LGM, 22 ka), due to the rapid deterioration of the climate, several species have become extinct, and the distribution of most surviving species has shrunk sharply. As such, many biological refugia have appeared in many regions around the world [5][6][7]. The surviving terrestrial plants spread from their refuge under the conditions of post-glacial climate warming, and then redistributed. ...
Semiliquidambar cathayensis is a special and endangered plant in China, used for traditional Chinese medicine and in landscape applications. Predicting the impact of climate change on the distribution of S. cathayensis is crucial for its protection and the sustainable use of resources. We used the maximum entropy (MaxEnt) model optimized by the ENMeval data packet to analyze the potential geographic distribution changes of S. cathayensis in 12 provinces of Southern China for the different periods since the last interglacial period (LIG, 120–140 ka). Considering the potential geographic distribution changes in the province, and based on the two climate scenarios of Representative Concentration Pathways (RCP) 2.6 and RCP 8.5, the distribution range of S. cathayensis was analyzed and we predicted the range for the 2050s (average for 2041–2060) and 2070s (average for 2061–2080). The area under AUC (Area under the receiver operating characteristic (ROC) curve) is 0.9388 under these parameters, which indicates that the model is very accurate. We speculate that the glacial period refugia were the Nanling and Wuyi Mountains for S. cathayensis, and central and Western Fujian and Taiwan are likely to be the future climate refugia. In the mid-Holocene (MH, 6 ka), the growth habitat was 32.41% larger than the modern habitat; in the 2050s and 2070s (except RCP2.6–2070s), the growth habitat will shrink to varying degrees, so efforts to support its in situ and ex situ conservation are urgently needed. The jackknife test showed that the main factors affecting the geographical distribution of S. cathayensis were annual precipitation, precipitation of the wettest month, and precipitation of the driest month. The annual precipitation may be the key factor restricting the northward distribution of S. cathayensis. In general, the centroid of the distribution of S. cathayensis will move northward. The centroid of the adaptive habitats will move northward with the highest degree of climate abnormality. We think that Hainan Island is the most likely origin of S. cathayensis. These findings provide a theoretical basis for the establishment of genetic resources protection measures, the construction of core germplasm resources, and the study of the formation and evolution of Hamamelidaceae.
... O Brasil ocupa o ranking de maior produtor e exportador mundial de café, além de ser o segundo maior consumidor do produto, o que faz da cafeicultura uma atividade de extrema importância para o país (CARVALHO et al., 2015). A produção de café no Brasil possui grande importância para geração de empregos e renda nas regiões produtoras (CUBRY et al., 2013;RODRÍGUEZ et al., 2013), sendo o café arábica (Coffea arabica L.) o mais produzido no Brasil e no mundo (CONAB, 2016). ...
p>Objetivou-se neste trabalho avaliar os estádios de maturação dos frutos do cafeeiro com os parâmetros sensoriais de Coffea arabica L. no município de Monte Carmelo-MG. O experimento foi implantado na Fazenda Vitória no município de Monte Carmelo, em outubro de 2011. O delineamento experimental utilizado foi o de blocos casualizados com três repetições, sendo que cada parcela foi composta por 5 plantas. As cultivares estudadas foram Acauã, Catucaí 2 SL, Catucaí Amarelo 3 SM, Catucaí Vermelho 19/8, Sarchimor MG 8840 e Paraíso MG H 419-1. Em julho de 2015 foi realizada a colheita por derriça manual para a avaliação dos estádios de maturação dos frutos e posteriormente feita análise sensorial na COOXUPÉ - Núcleo de Monte Carmelo (Cooperativa Regional dos Cafeicultores em Guaxupé Ltda.). Os dados foram submetidos à análise de variância, com aplicação do teste F. Para as comparações entre as médias, foi realizado o teste de Tukey, a 5% de probabilidade. Os resultados demonstraram que os estádios de maturação influenciaram na qualidade da bebida de algumas das cultivares. A cultivar Paraíso MG H 419-1 e Catucaí Amarelo 3 SM foram classificadas com o tipo de bebida dura verde e dura e com as maiores porcentagens de frutos verdes. Em conclusão, não se pode relacionar a qualidade da bebida somente ao grau de maturação dos frutos, sendo que diversos fatores também influenciam nesta caracterização. Estudos adicionais devem ser realizados para relacionar os diversos fatores que interferem na qualidade da bebida do café.
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... RNA-seq data from accessions of C. canephora were used to ascertain present procedure and model settings. C. canephora is a widely distributed species in the west and central African rainforest whose demographic history is rather well documented (Maley, 1987(Maley, , 1996Anhuf et al., 2006;Gomez et al., 2009;Cubry et al., 2013;Hardy et al., 2013;Tournebize, 2017). Evidence from paleoenvironmental reconstructions and patterns of endemism showed that tree species of the Guineo-Congolian region contracted to refugia during the LGM and subsequently migrated from Pleistocene refugia, causing large-scale changes in vegetation patterns (Maley, 1987(Maley, , 1996Anhuf et al., 2006;Gomez et al., 2009;Hardy et al., 2013). ...
Past climatic fluctuations have played a major role in shaping the current plant biodiversity. Although harbouring an exceptional biota, oceanic islands have received little attention in studies on species demographic history and past vegetation patterns.
We investigated the impact of past climatic changes on the effective population size of a tree (Coffea mauritiana) that is endemic to Reunion Island, located in the south‐western Indian Ocean (SWIO). Demographic changes were inferred using summary statistics calculated from genomic data. Using ecological niche modelling and the current distribution of genetic diversity, the paleodistribution of the species was also assessed.
A reduction in the effective population size of C. mauritiana during the last glaciation maximum was inferred. The distribution of the species was reduced on the western side of the island, due to low rainfall. It appeared that a major reduction in rainfall and a slight temperature decrease prevailed in the SWIO.
Our findings indicated that analyses on the current patterns of intraspecific genetic variations can efficiently contribute to past climatic changes characterisation in remote islands. Identifying area with higher resilience in oceanic islands could provide guidance in forest management and conservation faced to the global climate change.
... To ascertain whether a coffee species is held within a coffee germplasm collection (ex situ), we surveyed literature sources (32,42,43,73,(80)(81)(82)(83)(84)(85)(86) and herbarium collections [which often house herbarium vouchers for germplasm collections (for recording and verification purposes)]. Site visits were made to the living collections at the Kianjavato Coffee Research Station in Madagascar (in 2000Madagascar (in , 2006Madagascar (in , and 2011 and to the L'Institut de recherche pour le développement (IRD), Montpellier, France (in 2001). ...
... The species Coffea canephora, also known as conilon or robusta coffee, is currently cultivated at low to medium elevations in the intertropical regions of Africa, America and Asia, adapting well to warmer climates without large variations in temperature and with precipitation above 1200 mm per year (Montagnon et al., 2012;Cubry et al., 2013;Barbosa et al., 2014). C. canephora presents a higher growth rate when cultivated in climates with minimum air temperatures above 17°C (Partelli et al., 2010(Partelli et al., , 2013 and mean maximum air temperature below 33°C (Covre et al., 2016;Dubberstein et al., 2017). ...
Climate change prospections indicate large fluctuations in terrestrial temperature, what may change the zoning of coffee cultivation. This is particularly true for Coffea canephora (conilon or robusta coffee) to which some suitable areas may become inappropriate. Thus, conilon cultivation at high altitudes may be an option to establish C. canephora, mitigating the possible effects of productive areas loss. In this context, the aim of this work was to evaluate the productivity, adaptability and stability of 28 C. canephora genotypes cultivated at 850 m above sea level, under climatic conditions where the minimum temperature is the limiting factor for the species. A random block design with four replicates x five plants per replicate was used. The genotype x environment interaction was investigated using stability and adaptability analyzes based on the mixed model of restricted maximum likelihood / best linear unbiased prediction (REML/BLUP). The genotypes presented heritability of high magnitude, indicating the precision of selection. Six genotypes (NV2, NV8, P1, 3V, Verdim TA and A1) were highlighted for productivity, adaptability and stability at high-altitude and low temperature.
... To ascertain whether a coffee species is held within a coffee germplasm collection (ex situ), we surveyed literature sources (32,42,43,73,(80)(81)(82)(83)(84)(85)(86) and herbarium collections [which often house herbarium vouchers for germplasm collections (for recording and verification purposes)]. Site visits were made to the living collections at the Kianjavato Coffee Research Station in Madagascar (in 2000Madagascar (in , 2006Madagascar (in , and 2011 and to the L'Institut de recherche pour le développement (IRD), Montpellier, France (in 2001). ...
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.
... Regarding the structure of the collection, the Bayesian model-based STRUCTURE method and the PCoA gave similar results, as was also observed in coconut data [45]. The INRA collection consists of two well-differentiated clusters, as is often reported in other plant germplasm collections, for example, soybean, cherry, maize, apple and coffee [46][47][48][49][50]. The two genetic clusters of the INRA walnut collection fit well with the geographical origin of the accessions. ...
Persian or English walnut (Juglans regia L.), the walnut species cultivated for nut production, is one of the oldest food sources known and is grown worldwide in temperate areas. France is the 7th leading producer as of 2016 with 39 kt. Deciphering walnut genetic diversity and structure is important for efficient management and use of genetic resources. In this work, 253 worldwide accessions from the INRA walnut germplasm collection, containing English walnut and several related species, were genotyped using 13 SSR (Single Sequence Repeat) markers selected from the literature to assess diversity and structure. Genetic diversity parameters showed a deficiency of heterozygotes and, for several SSRs, allele-specificities among the accessions tested. Principal Coordinate Analysis (PCoA) showed the 253 accessions clustered in largely in agreement with the existing botanical classification of the genus. Among the 217 J. regia accessions, two main clusters, accessions from Eastern Europe and Asia, and accessions from Western Europe and America, were identified using STRUCTURE software. This was confirmed by Principal Coordinate Analysis and supported by Neighbor-Joining tree construction using DARwin software. Moreover, a substructure was found within the two clusters, mainly according to geographical origin. A core collection containing 50 accessions was selected using the maximum length sub-tree method and prior knowledge about their phenotype. The present study constitutes a preliminary population genetics overview of INRA walnut genetic resources collection using SSR markers. The resulting estimations of genetic diversity and structure are useful for germplasm management and for future walnut breeding programs.
... Since C. canephora is an allogamous species and also presents the widest geographic distribution among Coffea species in Africa, it was chosen for comparison. Bearing C. canephora evolutionary history in mind (Cubry et al. 2013), one would thus expect much higher levels of genetic diversity in C. canephora than in C. mauritiana. Surprisingly, compared to C. canephora, genetic diversity indices in C. mauritiana were not so restricted as its evolutionary context would lead one to suppose (Ho: 0.1381and He: 0.1763in C. mauritiana versus Ho: 0.1405and He: 0.1933in C. canephora, Garavito et al. 2016. ...
Oceanic islands are commonly considered as natural laboratories for studies on evolution and speciation. The evolutionary specificities of islands associated with species biology provide unique scenarios to study the role of geography and climate in driving population divergence. However, few studies have addressed this subject in small oceanic islands with heterogeneous climates. Being widely distributed in Reunion Island forest, Coffea mauritiana represents an interesting model case for investigating patterns of within-island differentiation at small spatial scale. In this study, we examined the genetic diversity and population divergences of C. mauritiana using SNP markers obtained from 323 individuals across 34 locations in Reunion Island. Using redundancy analysis, we further evaluated the contribution of geographic and climatic factors to shaping genetic divergence among populations. Genetic diversity analyses revealed that accessions clustered according to the source population, with further grouping in regional clusters. Genetic relationships among the regional clusters underlined a recent process of expansion in the form of step-by-step colonization on both sides of the island. Divergence among source populations was mostly driven by the joint effect of geographic distance and climatic heterogeneity. The pattern of isolation-by-geography was in accordance with the dispersal characteristics of the species, while isolation-by-environment was mostly explained by the heterogeneous rainfall patterns, probably associated with an asynchronous flowering among populations. These findings advance our knowledge on the patterns of genetic diversity and factors of population differentiation of species native to Reunion Island, and will also usefully guide forest management for conservation.
... Today, the species C. canephora, also known as 'conilon' or 'robusta' coffee, is cultivated at low to medium elevations in the intertropical regions of Africa, America, and Asia. It adapts well to warmer climates without major variations in temperature, with precipitation greater than 2,000 mm yr -1 (Montagnon et al. 2012, Cubry et al. 2013. ...
Knowledge of the genetic variability of a population is essential to guide its preservation and maintenance in addition to increasing the efficiency of genetic breeding programs. On this basis, this study was conducted to evaluate the genetic diversity of Coffea canephora genotypes using multivariate statistical procedures applied to a set of morpho-agronomic variables. The materials employed in this study constitute a crop located in Vila Valério - ES, Brazil, where the genotypes are arranged in a randomized-blocks experimental design with four replicates. Significant differences were detected by the F test at the 1% or 5% probability levels among the genotypes for all evaluated traits, demonstrating heterogeneity of genetic constitution in the studied population, which is favorable to breeding, as it indicates the possibility to identify superior and divergent individuals. Based on the generalized Mahalanobis distance, the most divergent combinations were obtained between genotypes 23 and 10 (256.43) and 23 and 17 (250.09). The clusters formed by Tocher's optimization and the UPGMA hierarchical method agreed, both similarly grouping the genotypes into three clusters. Of the analyzed traits, mature fruit weight (19.08%), yield (15.50%), plant diameter (12.42%), and orthotropic-shoot internode length (10.94%) were the most efficient to explain the dissimilarity among the genotypes.
... Hasil penelitian sebelumnya menunjukkan bahwa keragaman genetik C. canephora dapat dianalisis menggunakan beberapa tipe marka, antara lain marka isozyme (Montagnon, Guyot, Cilas, & Leroy, 1998), mikrosatelit atau SSR (Cubry et al., 2008;Musoli et al., 2009;Cubry, de Bellis, Pot, Musoli, & Leroy, 2013;Hendre & Aggarwal, 2014) dan RFLP (Gomez et al., 2009). Di antara beberapa marka tersebut, marka SSR diketahui mempunyai keunggulan dibandingkan dengan marka yang lain, yaitu dapat digunakan untuk mengidentifikasi C. arabica, C. canephora, dan spesies terkait . ...
em>Robusta coffee ( Coffea canephora var. robusta) is the most extensive developed in Indonesia, including Pagar Alam, South Sumatra. In the last few decades, many farmers in Pagar Alam conducted clonal selection and rehabilitation of Robusta coffee trees that generated indigenous clonal populations. This pattern in the long period can damage important alleles and reduce the genetic diversity of indigenous Robusta coffee in farmland. The research aimed to know the genetic diversity among indigenous Robusta coffee clones developed in Pagar Alam based on SSR markers. The study was conducted at Molecular Biology Laboratory, Cereals Research Institute, Maros, from February to April 2017. Molecular characterization of 19 indigenous Robusta coffee clones was conducted using 33 polymorphic SSR markers. The resulting binary data was then analyzed using PowerMarker program to determine polymorphism value (PIC), number and diversity of alleles, and heterozygosity values. The results showed that 33 polymorphic SSR loci produced 134 alleles with an average of 4.06 alleles/locus, whereas PIC values ranged from 0.09 – 0.77 with an average of 0.48. Of the 33 SSR loci, 19 loci (57.58%) exhibited very informative PIC value (> 0.55). Dendrogram generated using NTSYS program divided 19 indigenous Robusta coffee clones into 4 clusters at 0.53 similarity coefficient. KPA41clone was separated in its own cluster, potentially crossed with other clones. Based on genetic distance values >0.55, could arrange 14 combinations of interclonal crosses that potentially increase the genetic variability of indigenous Robusta coffee from Pagar Alam.</em
Background and Aims
Leaf traits are known to be strong predictors of plant performance and can be expected to (co)vary along environmental gradients. We investigated the variation, integration, environmental relationships, and evolutionary history of leaf functional traits in the genus Coffea L., typically a rainforest understory shrub, across Africa. A better understanding of the adaptive processes involved in leaf trait evolution can inform the use and conservation of coffee genetic resources in a changing climate.
Methods
We used phylogenetic comparative methods to investigate the evolution of six leaf traits measured from herbarium specimens of 58 African Coffea species. We added environmental data and data on maximum plant height for each species to test trait-environment correlations in various (sub)clades, and we compared continuous trait evolution models to identify variables driving trait diversification.
Key Results
A substantial leaf trait variation was detected across the genus Coffea in Africa, which was mostly interspecific. Of these traits, stomatal size and stomatal density exhibited a clear trade-off. We observed low densities of large stomata in early branching lineages and higher densities of smaller stomata in more recent taxa, which we hypothesise to be related to declining CO2 levels since the mid-Miocene. Brownian Motion evolution was rejected in favour of White Noise or Ornstein-Uhlenbeck models for all traits, implying these traits are adaptively significant rather than driven by pure drift. The evolution of leaf area was likely driven by precipitation, with smaller leaves in dryer climates across the genus.
Conclusions
Generally, Coffea leaf traits appear to be evolutionarily labile and governed by stabilising selection, though evolutionary patterns and correlations differ depending on the traits and clades considered. Our study highlights the importance of a phylogenetic perspective when studying trait relationships across related taxa, as well as the consideration of various taxonomic ranges.
Despite the differences between the two cultivated species Coffea arabica and C. canephora, in terms of breeding system and genetic diversity, there are some key elements in common for creating C. arabica and C. canephora varieties adapted to global warming (GW). The main existing farming systems are common to both species, and impose, for each farming system, specifications to the breeders that are quite similar for these species. To speed-up the selection of C. canephora, we propose a crossbreeding program using the widest possible genetic diversity including very closely related species (C. congensis and C. brevipes), followed by clonal selection and assisted by multi-trait and multi-environment genomic-phenomic selection. Since C. arabica contains an entire sub-genome of C. canephora, this makes the latter, the cornerstone of C. arabica breeding. For this species with very low polymorphism, the use of specific hybridisation for the introgression of resistance and adaptation genes is an absolute necessity. Introgressed materials can then be crossed with wild Ethiopian male-sterile genotypes to create high-yielding F1 hybrid. However, given the length of selection cycles, the use of genome-editing techniques enabling the transfer of large and precise quantities of DNA seems essential for introgressing several traits at once. Most of the main target traits seeking sustainability and resilience for the main
farming systems are currently considered, but some constitute “blind spots”. However, for both producing species, breeding based on performance, high yield and yield stability in environments representing targeted stress scenarios, remains the proven
method for selecting GW-adapted coffee varieties in the next decade.
Coffee is one of the most preferred beverages consumed by millions of people throughout the world. It is cultivated in more than 80 countries in tropical and subtropical zones of Asia, Africa, and Latin America and provides livelihood to 125 million people worldwide. Among 125 coffee species known so far, only two coffee species, Coffea arabica (arabica coffee) and Coffea canephora (robusta coffee), are commercially cultivated for beverage production. Coffee is a perennial plant and therefore subjected to constant environmental stress. However, during the last few decades, sustainable coffee cultivation has been threatened by unprecedented climate change. This calls for unified efforts, including cutting-edge research and modified management practices. Although conventional breeding efforts have been developed to address some issues, emerging biotechnology research, especially in-vitro propagation technology, could augment the coffee cultivation landscape. Despite the tangible progress made in coffee tissue culture, there were some grey areas, such as the level of somaclonal variation and the genomic changes associated with somatic embryogenesis in coffee, which needs to be addressed imminently. This chapter provides detailed progress on coffee tissue culture and addresses some of the critical issues associated with the genetic homogeneity of tissue culture plants.
Cultivation of Robusta coffee is likely to gain importance because of its high disease resistance and climate envelope. Robusta coffee genetic resources conserved in field genebanks can play an important role to further improve its cupping quality and other agronomic traits, but such Coffea canephora collections are limited and still poorly characterized. In this study, we characterized the genetic composition of the historically important but until recently neglected INERA Coffee Collection in Yangambi (the Democratic Republic of Congo). We used GBS to discover genome-wide genetic diversity, created and validated a novel multiplex amplicon sequencing (HiPlex) screening assay to genetically screen 730 coffee shrubs of the Yangambi Coffee Collection, grouped clonal material and delineated 263 accessions with unique genetic fingerprints. Comparison to reference material of three genetic origins revealed that the majority of the Yangambi accessions were assigned a ‘Lula’ cultivar origin, four accessions were assigned to Congolese subgroup A and nine accessions were most closely related to local wild accessions. About one-quarter of the accessions was likely derived from hybridization between these groups, which could result from seed-based propagation of the collection, breeding efforts, or natural cross-pollination. Parental analyses discovered eight preferentially used accessions, which may correspond to historically selected founders, or direct descendants thereof, whose seed material was once widely used to establish coffee plantations. Finally, two core collections were proposed using the maximization strategy (CC-I; 100 accessions) and genetic distance method (CC-X; 10 accessions). Our study demonstrates a method for the genetic characterization of Robusta coffee collections in general and contributes to the re-evaluation and exploration of the Robusta coffee genetic resources in the Democratic Republic of the Congo in particular.
Humans have had a major influence on the dissemination of crops beyond their native range, thereby offering new hybridization opportunities. Characterizing admixed genomes with mosaic origins generates valuable insight into the adaptive history of crops and the impact on current varietial diversity. We applied the ELAI tool-an efficient local ancestry inference method based on a two-layer hidden Markov model to track segments of wild origin in cultivated accessions in the case of multiway admixtures. Source populations-which may actually be limited and partially admixed-must be generally specified when using such inference models. We thus developed a framework to identify local ancestry with admixed source populations. Using sequencing data for wild and cultivated Coffea canephora (commonly called Robusta), our approach was found to be highly efficient and accurate on simulated hybrids. Application of the method to assess elite Robusta varieties from Vietnam led to the identification of an accession derived from a likely backcross between two genetic groups from the Congo Basin and the western coastal region of Central Africa. Admixtures resulting from crop hybridization and diffusion could thus lead to the generation of elite high-yielding varieties. Our methods should be widely applicable to gain insight into the role of hybridization during plant and animal evolutionary history.
Coffea canephora (2n = 2x = 22 chromosomes) is a species with extensive genetic diversity and desirable agronomic traits for coffee breeding programs. However, obtaining a new coffee cultivar through conventional breeding techniques may require more than 30 years of crossing cycles and selection, which hampers the effort of keeping up with market demands and rapidly proposing more resilient to climate change varieties. Although, the application of modern biotechnology tools such as precision genetic engineering technologies may enable a faster cultivar development process. Therefore, we aimed to validate the CRISPR/Cas9 system to generate mutations on a selected genotype of C. canephora, the clone 14. Embryogenic calli and a multiplex binary vector containing two sgRNAs targeting different exons of the CcPDS gene were used. The sgRNAs were under the C. canephora U6 promoter regulation. The target gene encodes phytoene desaturase, an enzyme essential for photosynthesis involved in β-carotene biosynthesis. Somatic seedlings and embryos with albino, variegated and green phenotypes regenerated after Agrobacterium tumefaciens-mediated genetic transformation were analyzed by verifying the insertion of the Cas9 gene and later by sequencing the sgRNAs target regions in the genome of Robusta modified seedlings. Among them, 77% had the expected mutations, and of which, 50% of them had at least one target with a homozygous mutation. The genotype, temperature of co-cultivation with the bacteria, and light intensity used for subsequent embryo regeneration appeared to strongly influence the successful regeneration of plants with a mutated CcPDS gene in the Coffea genus.
Cremastraappendiculata (Orchidaceae) is a perennial medicinal herb, which is included in the national second-class protected plant catalog in China. Due to the influences of climate change and anthropogenic activities, in conjunction with soaring commercial prices, the wild sources of C.appendiculata have been drastically reduced and are in danger of extinction. Consequently, it is important to predict the distribution of potentially suitable growth/propagation areas for C.appendiculata under the backdrop of climate change for its protection and sustainable use. For this study, an optimized maximum entropy model was employed to analyze the distribution patterns and changes of potentially suitable regions for C.appendiculata during different periods since the Last Glacial Maximum (LGM, 18–24 ka). Based on multiple climate change scenarios (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5), the distribution range of C. appendiculata was predicted for the 2050s (average for 2041–2060), 2070s (average for 2061–2080), and 2090s (average for 2081–2100). The results revealed that during the LGM period, the highly suitable growth area for C.appendiculata was 0.28 × 104 km2, which accounted for only 3.26% of the current highly suitable growth area. During the mid-Holocene (MH, 6 ka) period, the area of highly suitable regions increased to 8.38 × 104 km2, which accounted for 99.30% of the present highly suitable growth area. Further, the cumulative existing potentially suitable growth area for C. appendiculata is 213.9 × 104 km2, which accounts for 22.28% of China’s territory. Of these lands, the low, medium, and high suitable areas are 147.76 × 104 km2, 57.71 × 104 km2, and 8.44 × 104 km2, respectively. The highly suitable areas are primarily distributed across Sichuan, Gansu, Shaanxi, Chongqing, Guizhou, Hubei, and Anhui Provinces. Moreover, in the future the potentially suitable growth areas for C. appendiculata will decrease to varying degrees. Further, the results of this study found that the relatively low impact areas for C. appendiculata were mainly distributed across Shaanxi, Sichuan, Chongqing, and Guizhou Provinces. Centroid transfer analysis indicated that the center of potentially suitable growth areas for C.appendiculata shifted to the northwest in SSP2-4.5 and SSP3-7.0, while they initially shifted to the northwest and then to the southeast in SSP1-2.6 and SSP5-8.5.
The sensory profile from the Coffea canephora stands out for being denser, less sweet, presenting less acidity, and having characteristics of a marked aroma of roasted cereals. Coffee is essentially a terroir product, that is, directly influenced by environmental aspects, both natural and anthropic, in this sense, it has been argued that Coffea canephora is linked to the context of inferior coffees in sensory terms by the terroir conditions. This study aimed to characterize and investigate the terroir in different areas of Conilon coffee production, with the application of different fermentation methods, and to observe their possible gains and losses in the sensory quality of Coffea canephora. Cherry coffee samples were collected in six municipalities in the state of Espírito Santo, Brazil, which has an altitude variation from 376 m to 866 m. The study showed that the local characteristics of altitude and temperature directly influence the sensory quality, as well as demonstrated that natural fermentation in a specific altitude zone delivered good results, fixing the terroir factor. Finally, it was demonstrated that induced fermentation helps to improve sensory quality for higher altitude areas, indicating the possibility of reformulating the terroir of Conilon coffee production.
Coffee is a popular beverage with significant economic importance. The economies of many developing countries depend heavily on the earnings from this crop. Besides increasing demand, coffee productivity has not increased in many coffee-growing countries and remained desolately low or on a plateau for the last several years. Genetic improvement of coffee through conventional breeding approaches has several limitations primarily due to the insufficient understanding of the genetic and molecular mechanism associated with various agronomic traits. However, recent development in omics approaches and technological advancements has accelerated research on understanding the basic mechanisms related to crop improvement. In coffee, significant progress has been made in the genomics front especially whole-genome sequencing, transcriptomics, marker development, and gene identification. Besides, other omics tools such as metabolomics are now being integrated along with genomics to further expand our knowledge on the key mechanism underlying various physiological and cellular processes. This review article highlights up-to-date information on the available omics resources (genomics, transcriptomics, proteomics, and metabolomics) and their applications in coffee for genetic improvement.
Genetic base-broadening of crop plants with local germplasm which are repositories of important alleles for key traits is vital to facilitate the breeding process and lead to the development of improved varieties. This study was to estimate the genetic variability among local Robusta coffee accessions and determine the relationships among agro-morphological traits to guide selection for improved variety development. The 166 accessions collected from seven localities in Ghana and unknown sources were planted in June 2011 in a randomized complete block design with four replications and assessed based on 14 agro-morphological traits. There were significant variation among the accessions for all the traits assessed adjudged by the wide trait ranges and relatively high coefficient of variations. Cluster analysis based on the unweighted pair-group method with arithmetic mean grouped the accessions into four main clusters with membership ranging from one in cluster II to 97 in cluster IV. The clustering indicated no parallelism between genetic and geographical diversities. Principal component analysis (PCA) revealed that five PCs which cumulatively accounted for 70.35% of the total variability were enough in explaining the diversity within the coffee accessions. Furthermore, the PCA showed that appearance, angle of lateral insertion, branching habit, diameter of laterals, number of nodes per lateral and yield were the key characters that discriminated the accessions and should be the primary focus in Robusta coffee improvement. The study provides evidence of the potential for broadening the gene pool of Robusta coffee through the use of local germplasm beyond foreign introductions in Ghana.
Les présents travaux réalisés sur le noyer ont consisté en l’exploitation des riches ressources génétiques disponibles à l’INRAE de Nouvelle-Aquitaine-Bordeaux, afin d’apporter les outils qui pourront être utilisés dans un nouveau programme de création variétale mené par le CTIFL, centre opérationnel de Lanxade. En effet, au regard du développement économique important de la noix, le choix variétal en France ne semble pas suffisant pour répondre aux futures nouvelles contraintes telles que la concurrence mondiale et le changement climatique. Le travail de prospection que l’on doit principalement à l’équipe d’Éric Germain a permis de rassembler sur l’UEA de Toulenne la majeure partie des espèces du genre Juglans et de nombreuses accessions de noyer cultivé, Juglans regia L. L’exploitation de ses archives accumulées pendant 30 ans a permis de rendre publiques d’importantes données chronologiques de phénotypage concernant cette collection. Ces données ont permis de montrer l’avancée de la phénologie des deux variétés témoins ‘Lara’ and ‘Franquette’, en lien avec le changement climatique. Grâce à un ensemble de 13 marqueurs SSR, des allèles spécifiques aux espèces Juglans ont été identifiés et la structure de la collection a été étudiée. Cette structure montre deux sous-groupes principaux, l’un comprenant des accessions d’Europe de l’est et d’Asie et l’autre, d’Europe de l’ouest et des Etat-Unis. Aussi, une core collection a été définie pour réaliser des études de GWAS sur les principaux caractères d’intérêt agronomique, de la fleur au fruit, grâce à l’utilisation d’une puce de 600 000 SNP mise au point par l’Université de Davis en Californie. Des associations entre des SNP et plusieurs caractères liés à la phénologie ont été mises en évidence, grâce aux données des archives et à celles nouvellement acquises. Un SNP fortement lié à la date de débourrement des feuilles et fleurs femelles a été identifié sur le chromosome 1 et co-localise avec un QTL détecté en parallèle sur une descendance F1. Un marqueur de type KASP a été validé avec du matériel végétal de l’Université de Davis. D’autres associations ont également été identifiées pour le type de dichogamie et de fructification, caractère intervenant directement sur le rendement, et ont mené à la définition de gènes candidats. D’autres analyses GWAS ont été conduites sur les caractères liés au fruit, comme la taille de la noix, son poids, le rendement au cassage et la force nécessaire pour rompre la coque. En parallèle, des méthodes utilisant des techniques de phénotypage robustes ont été développées, comme l’utilisation de la microtomographie à rayons X pour mesurer tous les caractères morphologiques, sans casser la noix. Enfin, un travail de comparaison de l’efficacité des deux types de marqueurs utilisés dans ces travaux, SSR et SNP, a été mené. Les résultats montrent que les 13 marqueurs SSR donnent des résultats similaires à plusieurs milliers de SNP en ce qui concerne les étapes de détermination de structure et de construction de core collections, incontournables dans le management des ressources génétiques. A terme, les résultats de ces travaux permettront d’initier une sélection assistée par marqueurs pour la création de nouvelles variétés, dans le cadre d’un nouveau programme d’amélioration qui sera mené par le CTIFL. Ces nouvelles variétés seront aptes à répondre aux critères recherchés dans les années à venir, prenant en compte le changement climatique.
Coffea canephora Pierre ex Frohener is popularly known as robusta coffee contributes to about 39% of the total world coffee production. Coffea canephora a native to West Africa was introduced to India as early as 1900 AD. However adequate information regarding the diversity and genetic structure of C. canephora germplasm available in India is not yet available. In the present study, Sequence related amplified polymorphism (SRAP) and start codon targeted (SCoT) molecular markers were employed to access the genetic diversity and
relationships of 58 C. canephora germplasm accessions available in the Indian gene bank. Forty-nine SRAP and thirty-one SCoT primers amplified 632 and 331 fragments respectively, of which 507 (80.22%) and 225 (67.97%) were polymorphic. The average polymorphism
information content (SRAP, 0.48; SCoT, 0.37) and resolving power (SRAP, 15.60; SCoT,14.84) revealed high genetic diversity among the accessions The SRAP markers were found more informative with regards to the amount of diversity detected which is evident
from effective multiplex ratio (SRAP=8.59, SCoT=5.61) and marker index (SRAP=4.60, SCoT=2.58). The neighbour-joining clustering revealed that 58 accessions were grouped into four major clusters which were also supported by Principal coordinate analysis. An
admixture model-based clustering method in STRUCTURE grouped all the accessions in four subpopulations (K= 4) as similar to NJ clustering. Our study demonstrated the suitability of SRAP and SCoT markers for coffee genetic diversity and discovered thirty-one diverse genotypes in the germplasm that could be integrated into the C. canephora genetic improvement program.
The development of Coffea canephora cultivars is based on the characterization of genotype × environment interaction, which is interpreted to quantify the differential behavior of clones at different cultivation sites. The objective of this research was to study the genotype x environment interaction aiming to select clones of broad and specific adaptation to different environments of the Western Amazon. Twelve clones with hybrid characteristics of the botanical varieties Conilon and Robusta and four open pollinated clones, had their performance evaluated in comparison with four controls. The genotype × environment interaction was interpreted based on the environmental quality index, the non-parametric estimator of Lin and Binns, 1988 and on the dispersion of the centroid method. Effects of the genotypes, environment, and genotype × environment interaction were all significant (p<0.01). The environmental quality index (Ij) classified three environments as favorable for coffee production. In terms of the Lin and Binn’s estimator (Pi), hybrid genotypes 16, 10, 13, 09 and 14 presented lower Pi indices than others, and were classified as being more stable. Five clones of low adaptability, seven clones of specific adaptability to favorable or unfavorable environments and two clones of broad adaptability to all environments were identified interpreting the dispersion of the centroid method.
Coffee is an important agricultural export commodity in many Asian,
African and Latin American countries. It provides a livelihood for more than
125 million people worldwide. The genus Coffea comprises more than 125 species
of which only 2 species Coffea arabica (arabica coffee) and C. canephora (robusta
coffee) are commercially cultivated for beverage production. Climate change presents
unprecedented challenges to sustainable coffee cultivation on a global scale.
Besides, both arabica and robusta coffee are subjected to biotic and abiotic stress
conditions that limit their production and productivity. Although conventional
breeding approaches are followed to attenuate some of these problems, they were
slow and time-consuming. Furthermore, arabica coffee has a narrow genetic base
and needs to be addressed immediately by incorporating diverse germplasm with
potential agronomic values, using focused breeding programs. In both arabica and
robusta, the full potential of germplasm has not been exploited. Recent progress in
the biotechnological field particularly on molecular markers and new generation
sequencing platform hold great promise to discover new genes and accelerate coffee
breeding programs. The progress achieved in coffee transgenic technology also has
unparalleled opportunities to develop new cultivars with improved agronomic traits.
Recent progress in gene editing techniques has a significant impact on the genetic
improvement of coffee. This chapter provides current and innovative information
about coffee’s origin and distribution, genetic resource diversity and conventional
breeding strategies and application. Current advances in the field of tissue culture,
genetic transformation, gene editing and molecular breeding are also discussed.
This paper gives a historical overview of the African rain forest from its origins, towards, the end of the Cretaceous period. The areas around the Gulf of Guinea, in particular from Ivory Coast to Nigeria and especially Cameroon, Gabon and Congo, appear to have been already occupied at this time by wet tropical forest formations mainly composed of Angiosperms. In the course of the Tertiary period the combined effect of the equator being situated further north than now and the development of the Antarctic ice cap favoured the development of wet tropical conditions over a large part of North Africa. Towards the end of the Tertiary, the equator reached its present position and the northern hemisphere ice caps appeared, and these phenomena resulted in the disappearance of the forest formations spread across the north of Africa, and the concentration of these formations near the equatorial zone around the Gulf of Guinea and in the Congo-Zaire basin. From 800 000 years ago onwards the marked glacial variations at middle and high latitudes in both hemispheres, lowered temperatures in equatorial areas and brought arid climates at times of maximum glacial extension. -Author
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multilocus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
DNA polymorphism has became a widespread tool in biotechnology; in fact, they are frequently used for a number of technical approaches as, for example, in agronomic traits identification, variety characterisation, and marker-assisted breeding programmes. Coffea arabica is expected to show polymorphic DNA sequences as any other species and indeed some polymorphisms have been described. However, it has been reported that restriction fragment length polymorphism (RFLP) (Lashermes et al.,1996a) and polymorphism based on polymerase chain reactions (PCR, RAPD) (Orozco-Castillo et al., 1994; Lashermes et al., 1996b) have a relatively low degree of polymorphism (Paillard et al, 1993, 1996). To-date, a high degree of polymorphism has been found only through AFLP (Lashermes et al., 2000). As this species of coffee is autogamous and has a restricted genetic base, its heterozygosity is expected to be relatively low and the probability of finding a polymorphism is correspondingly reduced.
Morphological and molecular phylogenetic studies show that there is a close relationship between Coffea and Psilanthus. In this study we reassess species relationships based on improved species sampling for Psilanthus, including P. melanocarpus, a species that shares morpho-taxonomic characters of both genera. Analyses are performed using parsimony and Bayesian inference, on sequence data from four plastid regions [trnL–F intron, trnL–F IGS, rpl16 intron and accD–psa1 intergenic spacer (IGS)] and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (ITS 1/5.8S/ITS 2). Several major lineages with geographical coherence, as identified in previous studies based on smaller and larger data sets, are supported. Our results also confirm previous studies showing that the level of sequence divergence between Coffea and Psilanthus species is negligible, particularly given the much longer branch lengths separating other genera of tribe Coffeeae. There are strong indications that neither Psilanthus nor Coffea is monophyletic. Psilanthus melanocarpus is nested with the Coffea–Psilanthus clade, which means that there is only one critical difference between Coffea and Psilanthus; the former has a long-emergent style and the latter a short, included style. Based on these new data, in addition to other systematically informative evidence from a broad range of studies, and especially morphology, Psilanthus is subsumed into Coffea. This decision increases the number of species in Coffea from 104 to 124, extends the distribution to tropical Asia and Australasia and broadens the morphological characterization of the genus. The implications for understanding the evolutionary history of Coffea are discussed. A group of closely related species is informally named the ‘Coffea liberica alliance’. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167, 357–377.
Coffea canephora breeding requires combining sustainable productivity with improved technological and cup quality characteristics. Beverage quality is a complex and subjective trait, and breeding for this trait is time consuming and depends on knowledge of the genetics of its components. A highly variable C. canephora progeny resulting from an intraspecific cross was assessed for 63 traits over 5 years. To identify quantitative trait loci (QTLs) controlling agronomic, technological, and quality-related traits, a genetic map comprising 236 molecular markers was constructed, and composite interval mapping was performed. Beverage quality was evaluated in relation to biochemical and cup tasting traits. QTLs were identified for almost half of the traits evaluated, with effects ranging from 6% to 80% of phenotypic variation. Most of them present a consistent detection over years. The strongest QTLs explained a high percentage of the variation for yield in 2006 (34% to 57%), bean size (25% to 35%), content of chlorogenic acids (22% to 35%), sucrose and trigonelline content (29% to 81%), and acidity and bitterness of coffee beverages (30% to 55%). Regions of the C. canephora genome influencing beverage quality were identified. Five QTL zones were co-localized with candidate genes related to the biosynthesis of the analyzed traits: two genes coding for caffeine biosynthesis, one gene implicated in the biosynthesis of chlorogenic acids, and two genes implicated in sugar metabolism. This is one of the first studies on the identification of QTLs combining agronomic and quality traits in coffee. The high variability of quality traits within C. canephora and the presence of consistent QTLs offer breeders a promising tool to improve coffee cup quality.
Summary: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G′ST, G′′ST, Jost’s Dest and F′ST through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised.Availability and implementation: GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx.Contact:
rod.peakall@anu.edu.au
An annotated taxonomic conspectus of the genus Coffea (coffee) is presented, with 103 species and seven infraspecific taxa enumerated. The taxonomic history of Coffea is summarized and details of the circumscription of Coffeeae, Coffea, and the subgeneric groups of Coffea are given. For each accepted name, the author, place of publication, type species, and synonyms are given. Useful illustrations and literature are cited, where available. The distribution of each accepted taxon is summarized as a text note and using the Taxonomic Database Working Group (TDWG) system; the vegetation type and altitude are given in an ecological summary. A list of potentially new taxa is included. Two lectotypes are designated. Conservation assessments are given based on the World Conservation Union (IUCN) Red List Categories. Of the 103 Coffea species, 72 (c. 70%) are threatened with extinction as a result of a combination of decline in quantity and quality of habitat. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society, 2006, 152, 465–512.
Phylogeographic analysis of the Coffea subgenus Coffea was performed using data on plastid DNA sequences and interpreted in relation to biogeographic data on African rain forest
flora. Parsimony and Bayesian analyses of trnL-F, trnT-L and atpB-rbcL intergenic spacers from 24 African species revealed two main clades in the Coffea subgenus Coffea whose distribution overlaps in west equatorial Africa. Comparison of trnL-F sequences obtained from GenBank for 45 Coffea species from Cameroon, Madagascar, Grande Comore and the Mascarenes revealed low divergence between African and Madagascan
species, suggesting a rapid and radial mode of speciation. A chronological history of the dispersal of the Coffea subgenus Coffea from its centre of origin in Lower Guinea is proposed. No relation was found between phylogenetic topology and the age of
emergence of the volcanic islands that Coffea species have colonised in the Indian Ocean, suggesting dispersal from mainland Africa after the emergence of the youngest
island, Grande Comore, 500,000years ago. Additional sequences were obtained from GenBank for 24 species of other Rubiaceae
genera, including the Rubia genus whose origin has been dated from the Upper Miocene. Estimates of substitution rates suggested that diversification
in Coffea subgenus Coffea occurred about 460,000years ago or as recently as the last 100,000years, depending on the cpDNA region considered and calibration.
The phylogenetic relationships based on plastid sequences confirmed biogeographic differentiation of coffee species, but they
were not congruent with morphological and biochemical classifications, or with the capacity to grow in specific environments.
Examples of convergent evolution in the main clades are given using characters of leaf size, caffeine content and reproductive
mode.
KeywordsAfrica-Biogeography-
Coffea
-Evolution-Phylogeny-Plastid sequences-Rubiaceae
Synopsis
This chapter sets out to give a historical overview of the African rain forest from its origins, towards the end of the Cretaceous period. The areas around the Gulf of Guinea, in particular from Ivory Coast to Nigeria and especially Cameroon, Gabon and Congo, appear to have been already occupied at this time by wet tropical forest formations mainly composed of Angiosperms which were then becoming established. In the course of the Tertiary period the combined effect of the equator being situated further north than now and the development of the Antarctic ice cap favoured the development of wet tropical conditions over a large part of North Africa which in turn led to the extension of tropical forest to various sites on the shores of the Tethys Sea. There were probably at this time common taxa and similar vegetation patterns stretching from the Gulf of Guinea to the Tethys Sea.
Towards the end of the Tertiary, the equator reached its present position and the northern hemisphere ice caps appeared, and these phenomena resulted in the disappearance of the forest formations spread across the north of Africa, and the concentration of these formations near the equatorial zone around the Gulf of Guinea and in the Congo–Zaïre basin. From 800 000 years ago onwards the marked glacial variations at middle and high latitudes in both hemispheres, with a periodicity of about 100 000 years determined by the orbital variations of the earth around the sun, lowered temperatures in equatorial areas and brought arid climates at times of maximum glacial extension. The most arid periods resulted in the fragmentation of the forest cover, and the forest biotopes and their biodiversity were preserved in a series of refugia. The lowering of temperatures also resulted in the extension of montane flora to low altitudes, with migration of montane flora and fauna between main mountain ranges. These compounded phenomena of isolation and migration, probably involving genie exchange, must have resulted in numerous speciation phenomena. Subsequently, such montane flora or fauna became isolated on mountain areas during periods of maximum warming, in the last instance in the course of the Holocene, when a vast forest cover became re-established from Guinea westwards, and to the East as far as the Lake Victoria area. The phases of maximum fragmentation, which appear to have been connected with only the coldest periods – in the last instance during the second part of isotopic stages 6 (from c. 160 to 130 000 years) and 2 (from c. 24 to 12000 years BP) – relate to less than 10% of the last 800 000 years, and the phases of maximum forest extension would likewise appear to be less than 10% of the period. The remaining 80–90% of the time relates to ‘intermediate situations’ which varied from period to period, and these intermediate extension situations seem to have been the norm over the larger part of the Quaternary, rather than the present situation which is closer to a situation of maximum extension.
Among Coffea species, C. canephora has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". In this study, we used both microsatellite (simple sequence repeat, SSR) and restriction fragment length polymorphism (RFLP) markers to investigate the genetic variation pattern of C. canephora in the Guineo-Congolean distribution zone.
Both markers were first compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among wild C. canephora genotypes. As expected, SSR markers were found to have a higher genetic distance detection capacity than RFLP. Nevertheless, similarity matrices showed significant correlations when Mantel's test was carried out (r = 0.66, p < 0.0001). Finally, both markers were equally effective for group discrimination and phylogenetic studies, but SSR markers tended to outperform RFLP markers in discriminating the source of an individual among diversity groups and in putative hybrid detection. Five well defined genetic groups, one in the Upper Guinean forests, the four others in the Lower Guinean forests, were identified, corresponding to geographical patterning in the individuals.
Our data suggested that the Dahomey Gap, a biogeographical barrier, played a role in wild C. canephora differentiation. Climatic variations during the Pleistocene and/or Holocene probably caused the subgroup differentiation in the Congolese zone through the presence of a mosaic of putative refugia. Recent hybridization between C. canephora diversity groups, both for spontaneous individuals and cultivars, was further characterised according to their geographic dissemination or breeding history as a consequence of human activities.
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
Several estimators of population differentiation have been proposed in the recent past to deal with various types of genetic markers (i.e., allozymes, nucleotide sequences, restriction fragment length polymorphisms, or microsatellites). We discuss the relationships among these estimators and show how a single analysis of variance framework can accomodate these qualitatively different data types.
Primer sets were developed from 85 Coffea arabica sequences in addition to 25 already published primer sets. They were subsequently used for amplification in six African Coffea species: Coffea canephora (CAN), Coffea eugenioides (EUG), Coffea heterocalyx (HET), Coffea liberica (LIB), Coffea sp. Moloundou (MOL) and Coffea pseudozanguebariae (PSE). The amplification percentages for these 110 primer pairs ranged from 72.7% for LIB to 86.4% for PSE. Good transferability was thus obtained within the Coffea genus. When focusing on the two species CAN and PSE, high genetic diversity, high polymorphic locus rates (above 80%) and a mean allele number per polymorphic locus of more than 3 were noted. The estimated null allele percentage was -11% for PSE and -9% for CAN. Sixty three percent (CAN) and 79.5% (PSE) of the fixation index (Fis) values were positive. The within-species polymorphism information content (PIC) distribution showed two modes for both species. Although the two species shared 30 polymorphic loci, no correlation between CAN and PSE PIC values was obtained. All of these data are discussed in relation to the polymorphism level and the potential use of these SSRs for subsequent analysis of genetic diversity or genetic mapping.
The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.
The first bacterial artificial chromosome (BAC) library of Robusta coffee (Coffea canephora) was constructed, with the aim of developing molecular resources to study the genome structure and evolution of this perennial crop. Clone 126, which is highly productive and confers good technological and organoleptic qualities of beverage, was chosen for development of this library. The BAC library contains 55,296 clones, with an average insert size of 135 Kb per plasmid, therefore representing theoretically nine haploid genome equivalents of C. canephora. Its validation was achieved with a set of 13 genetically anchored single-copy and 4 duplicated RFLP probes and yielded on average 9 BAC clones per probe. Screening of this BAC library was also carried out with partial cDNA probes coding for enzymes of sugar metabolism like invertases and sucrose synthase, with the aim of characterizing the organization and promoter structure of this important class of genes. It was shown that genes for both cell wall and vacuolar forms of invertases were probably unique in the Robusta genome whereas sucrose synthase was encoded by at least two genes. One of them (CcSUS1) was cloned and sequenced, showing that our BAC library is a valuable tool to rapidly identify genes of agronomic interest or linked to cup quality in C. canephora.
An EST database has been generated for coffee based on sequences from approximately 47,000 cDNA clones derived from five different stages/tissues, with a special focus on developing seeds. When computationally assembled, these sequences correspond to 13,175 unigenes, which were analyzed with respect to functional annotation, expression profile and evolution. Compared with Arabidopsis, the coffee unigenes encode a higher proportion of proteins related to protein modification/turnover and metabolism-an observation that may explain the high diversity of metabolites found in coffee and related species. Several gene families were found to be either expanded or unique to coffee when compared with Arabidopsis. A high proportion of these families encode proteins assigned to functions related to disease resistance. Such families may have expanded and evolved rapidly under the intense pathogen pressure experienced by a tropical, perennial species like coffee. Finally, the coffee gene repertoire was compared with that of Arabidopsis and Solanaceous species (e.g. tomato). Unlike Arabidopsis, tomato has a nearly perfect gene-for-gene match with coffee. These results are consistent with the facts that coffee and tomato have a similar genome size, chromosome karyotype (tomato, n=12; coffee n=11) and chromosome architecture. Moreover, both belong to the Asterid I clade of dicot plant families. Thus, the biology of coffee (family Rubiacaeae) and tomato (family Solanaceae) may be united into one common network of shared discoveries, resources and information.
The genetic bases of the molecular, cellular and developmental responses to drought involve many gene functions regulated by water availability. Genomics-based approaches provide access to agronomically desirable alleles present at quantitative trait loci (QTLs) that affect such responses, thus enabling us to improve the drought tolerance and yield of crops under water-limited conditions more effectively. Marker-assisted selection is already helping breeders improve drought-related traits. Analysis of sequence data and gene products should facilitate the identification and cloning of genes at target QTLs. Based on such premises, we envision a quick broadening of our understanding of the genetic and functional basis of drought tolerance. Novel opportunities will be generated for tailoring new genotypes "by design". Harnessing the full potential of genomics-assisted breeding will require a multidisciplinary approach and an integrated knowledge of the molecular and physiological processes influencing tolerance to drought.
Sucrose metabolism and the role of sucrose synthase were investigated in the fruit tissues (pericarp, perisperm, and endosperm) of Coffea arabica during development. Acid invertase, sucrose phosphate synthase, and sucrose synthase activities were monitored and compared with the levels of sucrose and reducing sugars. Among these enzymes, sucrose synthase showed the highest activities during the last stage of endosperm and pericarp development and this activity paralleled closely the accumulation of sucrose in these tissues at this stage. Carbon partitioning in fruits was studied by pulse-chase experiments with (14)C-sugars and revealed high rates of sucrose turnover in perisperm and endosperm tissues. Additional feeding experiments with (14)CO(2) showed that leaf photosynthesis contributed more to seed development than the pericarp in terms of photosynthate supply to the endosperm. Sugar analysis, feeding experiments, and histological studies indicated that the perisperm plays an important role in this downloading process. It was observed that the perisperm presents a transient accumulation of starch which is degraded as the seed develops. Two full-length cDNAs (CaSUS1 and CaSUS2) and the complete gene sequence of the latter were also isolated. They encode sucrose synthase isoforms that are phylogenetically distinct, indicating their involvement in different physiological functions during cherry development. Contrasting expression patterns were observed for CaSUS1 and CaSUS2 in perisperm, endosperm, and pericarp tissues: CaSUS1 mRNAs accumulated mainly during the early development of perisperm and endosperm, as well as during pericarp growing phases, whereas those of CaSUS2 paralleled sucrose synthase activity in the last weeks of pericarp and endosperm development. Taken together, these results indicate that sucrose synthase plays an important role in sugar metabolism during sucrose accumulation in the coffee fruit.
Of the 103 accepted Coffea species, 70% are threatened with extinction but only a few of them have been studied. A set of 40 polymorphic microsatellite markers was developed using a GA/GT-enriched Coffea canephora genomic library. Amplification of these markers was tested in accessions of C. heterocalyx (a Critically Endangered species) and C. pseudozanguebariae (a Vulnerable species) belonging to different African geographical clades. All microsatellites were polymorphic in C. canephora, with a mean allele number per polymorphic locus of more than 3 (at least 9 genotypes were tested). Observed and expected heterozygosities calculated for C. canephora and C. pseudozanguebariae varied from 0.10 to 0.91 and from 0.20 to 0.77, respectively. In total, 38 primer pairs (95%) were amplified in C. heterocalyx and C. pseudozanguebariae, indicating their high level of transferability across the genus Coffea. This large marker set will be useful for more extensive genetic studies of threatened Coffea species.
The present study shows transferability of microsatellite markers developed in the two cultivated coffee species (Coffea arabica L. and C. canephora Pierre ex Froehn.) to 15 species representing the previously identified main groups of the genus Coffea. Evaluation of the genetic diversity and available resources within Coffea and development of molecular markers transferable across species are important steps for breeding of the two cultivated species. We worked on 15 species with 60 microsatellite markers developed using different strategies (SSR-enriched libraries, BAC libraries, gene sequences). We focused our analysis on 4 species used for commercial or breeding purposes. Our results establish the high transferability of microsatellite markers within Coffea. We show the large amount of diversity available within wild species for breeding applications. Finally we discuss the consequences for future comparative mapping studies and breeding of the two cultivated species.
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.