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Maria Amelia Gava Ferrao - One of the best experts on this subject based on the ideXlab platform.
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Accurate genomic prediction of Coffea Canephora in multiple environments using whole-genome statistical models
Heredity, 2019Co-Authors: Luís Felipe Ventorim Ferrão, Maria Amelia Gava Ferrao, Romario Gava Ferrao, Aymbiré Fonseca, Peter Carbonetto, Matthew Stephens, Antonio Augusto Franco GarciaAbstract:Genomic selection has been proposed as the standard method to predict breeding values in animal and plant breeding. Although some crops have benefited from this methodology, studies in Coffea are still emerging. To date, there have been no studies describing how well genomic prediction models work across populations and environments for different complex traits in coffee. Considering that predictive models are based on biological and statistical assumptions, it is expected that their performance vary depending on how well these assumptions align with the true genetic architecture of the phenotype. To investigate this, we used data from two recurrent selection populations of Coffea Canephora , evaluated in two locations, and single nucleotide polymorphisms identified by Genotyping-by-Sequencing. In particular, we evaluated the performance of 13 statistical approaches to predict three important traits in the coffee—production of coffee beans, leaf rust incidence and yield of green beans. Analyses were performed for predictions within-environment, across locations and across populations to assess the reliability of genomic selection. Overall, differences in the prediction accuracy of the competing models were small, although the Bayesian methods showed a modest improvement over other methods, at the cost of more computation time. As expected, predictive accuracy for within-environment analysis, on average, were higher than predictions across locations and across populations. Our results support the potential of genomic selection to reshape traditional plant breeding schemes. In practice, we expect to increase the genetic gain per unit of time by reducing the length cycle of recurrent selection in coffee.
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A mixed model to multiple harvest-location trials applied to genomic prediction in Coffea Canephora
Tree Genetics & Genomes, 2017Co-Authors: Luís Felipe Ventorim Ferrão, Maria Amelia Gava Ferrao, Romário Gava Ferrão, Aymbiré Francisco, Antonio Augusto Franco GarciaAbstract:Genomic selection (GS) has been studied in several crops to increase the rates of genetic gain and reduce the length of breeding cycles. Despite its relevance, there are only a modest number of reports applied to the genus Coffea . Effective implementation depends on the ability to consider genomic models, which correctly represent breeding scenario in which the species are inserted. Coffee experimentation, in general, is represented by evaluations in multiple locations and harvests to understand the interaction and predict the performance of untested genotypes. Therefore, the main objective of this study was to investigate GS models suitable for use in Coffea Canephora . An expansion of traditional GBLUP was considered and genomic analysis was performed using a genotyping-by-sequencing (GBS) approach, showed good potential to be used in coffee breeding programs. Interactions were modeled using the multiplicative mixed model theory, which is commonly used in multi-environment trials (MET) analysis in perennial crops. The effectiveness of the method used was compared with other genetic models in terms of goodness-of-fit statistics and prediction accuracy. Different scenarios that mimic coffee breeding were used in the cross-validation process. The method used had the lowest AIC and BIC values and, consequently, the best fit. In terms of predictive ability, the incorporation of the MET modeling showed higher accuracy (on average 10–17% higher) and lower prediction errors than traditional GBLUP. The results may be used as basis for additional studies into the genus Coffea and can be expanded for similar perennial crops.
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the multi resistant reaction of drought tolerant coffee conilon clone 14 to meloidogyne spp and late hypersensitive like response in Coffea Canephora
Phytopathology, 2015Co-Authors: Edriana Araujo De Lima, Maria Amelia Gava Ferrao, Cleber Furlanetto, Michel Nicole, Ana Cristina M M Gomes, Maria Ritta A Almeida, Aldemiro Jorgejunior, Valdir R Correa, Sonia M L Salgado, Regina M D G CarneiroAbstract:Root-knot nematodes (RKN), Meloidogyne spp., have major economic impact on coffee production in Central and South America. Genetic control of RKN constitutes an essential part for integrated pest management strategy. The objective of this study was to evaluate the resistance of Coffea Canephora genotypes (clones) to Meloidogyne spp. Sensitive and drought-tolerant coffee genotypes were used to infer their resistance using nematode reproduction factor and histopathology. Eight clonal genotypes were highly resistant to M. paranaensis. ‘Clone 14’ (drought-tolerant) and ‘ESN2010-04’ were the only genotypes highly resistant and moderately resistant, respectively, to both M. incognita races 3 and 1. Several clones were highly resistant to both avirulent and virulent M. exigua. Clone 14 and ESN2010-04 showed multiple resistance to major RKNs tested. Roots of ‘clone 14’ (resistant) and ‘clone 22’ (susceptible) were histologically studied against infection by M. incognita race 3 and M. paranaensis. Reduction of juv...
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different molecular mechanisms account for drought tolerance in Coffea Canephora var conilon
Tropical Plant Biology, 2013Co-Authors: Natalia Gomes Vieira, Fábio M. Damatta, Fernanda A Carneiro, Patricia Sanae Sujii, Jean Carlos Alekcevetch, Luciana Pereira Freire, Felipe Vinecky, Sonia Elbelt, Vânia Aparecida Silva, Maria Amelia Gava FerraoAbstract:The effects of water deficit on photochemical parameters and expression of several candidate genes were investigated in drought-tolerant clone 73 of Coffea Canephora submitted to slowly imposed water limitation. Under irriga- tion, this clone showed low values of stomatal conductance (gs) and of CO2 assimilation rates (A )s uggesting that it had a great efficiency in controlling stomatal closure and transpira- tion. After water withdrawal, this clone reached a −3.0 MPa after 15days without irrigation and showeda slow decrease in the pre-dawn leaf water potential. Under drought, the suppres- sion of Awas accompanied by maintenance of photochemical quenching (qP) and internal to ambient CO2 concentration (Ci/Ca) ratios as well as by a decrease of non-photochemical quenching (qN). This is confirmed by the transport rate/CO2 assimilation (ETR/A) rates that suggested the participation of an alternative electron sink protecting the photosynthetic apparatus against photoinhibition. At the transcriptomic level, high up-regulation of genes encoding for a dehydrin (CcDH3), an ascorbate peroxidase (CcAPX1), a prephenate-dehydrogenase like protein (CcPDH1) and a non-symbiotic haemoglobin (CcNSH1) was also observed upon drought suggesting a strong induction of antioxidant and osmoprotection systems in this clone. High expression levels of gene-encoding ABA receptors (CcPYL3 and CcPYL7) under water limitation were also ob- served suggesting the involvement of the ABA signaling path- way in response to drought. All these results where compared to those previously obtained for drought-tolerant clones 14 and 120. Our results demonstrated the existence of different mecha- nisms amongst the drought-tolerant coffee clones regarding water deficit.
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evaluation of the initial development of conilon coffee clones Coffea Canephora
Scientia agraria, 2010Co-Authors: Cristiano Cezana Contarato, Fabricio Moreira Sobreira, Marcelo Antonio Tomaz, Aymbire Francisco Almeida Da Fonseca, Maria Amelia Gava Ferrao, Romario Gava FerraoAbstract:The �Vitoria Incaper 8142� variety of conilon coffee (Coffea Canephora), presents superior productivity in relation to the others released so far. It consists of thirteen elite clones, whose cultivation is performed in lines. This work aimed to quantify the initial development of the clones which compose �Vitoria Incaper 8142� variety. The experiment was conducted in greenhouse, under a completely randomized design, with 13 treatments (clones) and seven repetitions. The plants were cultivated in vases and evaluated by 210 days after plantation. The 1V, 2V, 8V, 11V and 13V clones presented superior development in relation to the others concerning leaf number, plant height, plagiothropic branch emission, stem dry matter, root dry matter, air part dry matter and total dry matter. In general, this cultivar presents two groups of clones concerning the development by 210 days of plantation. The data indicates that the management can be different among the clones since the initial stage and that studies involving different environments are necessary in order to confirm these results.
Paulo Cezar Cavatti - One of the best experts on this subject based on the ideXlab platform.
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seasonal vegetative growth in genotypes of Coffea Canephora as related to climatic factors
The Journal of Agricultural Science, 2013Co-Authors: Fabio Luiz Partelli, Henrique Duarte Vieira, Wellington Braida Marre, Antelmo Ralph Falqueto, Paulo Cezar CavattiAbstract:Knowledge about the seasonality of different genotypes of Coffea Canephora is an important tool for this crop management, particularly with regard to irrigation and fertilisation issues. This study was conducted in Espirito Santo, Brazil and aimed at to evaluate the seasonal vegetative growth in genotypes of C. Canephora , as related to climatic factors, based on the growth of groups of orthotropic and plagiotropic branches with different ages. Three groups of plagiotropic branches and one group of orthotropic branches of 14 genotypes (Ipiranga and 13 that belonged to the variety Vitoria) were selected and marked to followed along the one-year experiment. Three-year-old plants were cultivated under full-sun conditions, with a spacing of 3 m between rows and 1 m between plants. The growth rates of the orthotropic and plagiotropic branches differed among the genotypes and underwent seasonal variation during the entire year, with high correlations to the air temperature. Under the natural experimental conditions, the growth rate of the branches decreased when the minimum air temperatures were below 17.2oC for most of the genotypes studied. The plagiotropic branches presented lower vegetative growth, mainly for the coffee berries, compared to the younger branches. Presumably, the genotypes of C. Canephora demanded more nutrients for growth between mid-September and the second week of May.
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seasonal vegetative growth in genotypes of Coffea Canephora as related to climatic factors
The Journal of Agricultural Science, 2013Co-Authors: Fabio Luiz Partelli, Henrique Duarte Vieira, Wellington Braida Marre, Antelmo Ralph Falqueto, Paulo Cezar CavattiAbstract:Knowledge about the seasonality of different genotypes of Coffea Canephora is an important tool for this crop management, particularly with regard to irrigation and fertilisation issues. This study was conducted in Espirito Santo, Brazil and aimed at to evaluate the seasonal vegetative growth in genotypes of C. Canephora , as related to climatic factors, based on the growth of groups of orthotropic and plagiotropic branches with different ages. Three groups of plagiotropic branches and one group of orthotropic branches of 14 genotypes (Ipiranga and 13 that belonged to the variety Vitoria) were selected and marked to followed along the one-year experiment. Three-year-old plants were cultivated under full-sun conditions, with a spacing of 3 m between rows and 1 m between plants. The growth rates of the orthotropic and plagiotropic branches differed among the genotypes and underwent seasonal variation during the entire year, with high correlations to the air temperature. Under the natural experimental conditions, the growth rate of the branches decreased when the minimum air temperatures were below 17.2oC for most of the genotypes studied. The plagiotropic branches presented lower vegetative growth, mainly for the coffee berries, compared to the younger branches. Presumably, the genotypes of C. Canephora demanded more nutrients for growth between mid-September and the second week of May.
Christophe Montagnon - One of the best experts on this subject based on the ideXlab platform.
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identification by the dartseq method of the genetic origin of the Coffea Canephora cultivated in vietnam and mexico
BMC Plant Biology, 2016Co-Authors: Andrea Garavito, Christophe Montagnon, Romain Guyot, Benoit BertrandAbstract:The coffee species Coffea Canephora is commercially identified as “Conilon” when produced in Brazil, or “Robusta” when produced elsewhere in the world. It represents approximately 40 % of coffee production worldwide. While the genetic diversity of wild C. Canephora has been well studied in the past, only few studies have addressed the genetic diversity of currently cultivated varieties around the globe. Vietnam is the largest Robusta producer in the world, while Mexico is the only Latin American country, besides Brazil, that has a significant Robusta production. Knowledge of the genetic origin of Robusta cultivated varieties in countries as important as Vietnam and Mexico is therefore of high interest. Through the use of Sequencing-based diversity array technology-DArTseq method-on a collection of C. Canephora composed of known accessions and accessions cultivated in Vietnam and Mexico, 4,021 polymorphic SNPs were identified. We used a multivariate analysis using SNP data from reference accessions in order to confirm and further fine-tune the genetic diversity of C. Canephora. Also, by interpolating the data obtained for the varieties from Vietnam and Mexico, we determined that they are closely related to each other, and identified that their genetic origin is the Robusta Congo – Uganda group. The genetic characterization based on SNP markers of the varieties grown throughout the world, increased our knowledge on the genetic diversity of C. Canephora, and contributed to the understanding of the genetic background of varieties from very important coffee producers. Given the common genetic origin of the Robusta varieties cultivated in Vietnam, Mexico and Uganda, and the similar characteristics of climatic areas and relatively high altitude where they are grown, we can state that the Vietnamese and the Mexican Robusta have the same genetic potential to produce good cup quality.
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amelioration genetique du cafeier Coffea Canephora pierre connaissances acquises strategies et perspectives
Cahiers Agricultures, 2012Co-Authors: Christophe Montagnon, Philippe Cubry, Thierry LeroyAbstract:L’amelioration varietale de Coffea Canephora represente un grand defi pour augmenter la productivite de cette espece et assurer un meilleur revenu aux planteurs. Les opportunites sont nombreuses : la diversite genetique de cette espece est bien documentee, les parametres genetiques sont relativement bien etablis pour les principaux caracteres d’interet et les ressources genomiques disponibles s’accumulent. Toutefois, des contraintes sont egalement a considerer : en particulier, l’histoire specifique de la mise en culture et de la selection a conduit a une inegalite des selectionneurs a travers le monde pour l’acces a l’ensemble de la diversite genetique de l’espece. Ainsi, la selection recurrente reciproque (SRR) qui represente une innovation majeure en termes d’utilisation raisonnee des ressources genetiques n’a pu etre menee qu’en Cote d’Ivoire qui seule dispose d’un ensemble complet et reference des ressources genetiques de base de C. Canephora. Cette strategie est adaptee a une sortie varietale sous la forme de semences hybrides, plus adaptees a une diffusion de masse que les boutures clonales. En dehors de la Cote d’Ivoire, une selection massale clonale sur des populations en recombinaison plus ou moins bien decrites reste souvent l’axe des programmes de creation varietale. Par ailleurs, le genome de C. Canephora est sur le point d’etre sequence et les ressources genomiques sont maintenant suffisantes pour venir en appui des programmes de selection. Les choix strategiques qui permettront d’utiliser au mieux ces ressources au service de l’amelioration genetique doivent etre l’objet d’une reflexion approfondie, tenant compte de l’experience acquise pour d’autres plantes : les cles de ces choix sont discutees.
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yield stability in clones of Coffea Canephora in the short and medium term longitudinal data analyses and measures of stability over time
Tree Genetics & Genomes, 2011Co-Authors: Christian Cilas, Christophe Montagnon, Avner BarhenAbstract:In perennial crops like coffee, genetic improvement efficiency is limited by several factors. These include determining the acceptable minimum observation period for yield traits, and also variation of the traits over time, in order to develop breeding objectives that incorporate stability and persistence of the desired traits. Yield data from a trial comparing 20 Coffea Canephora clones in Ivory Coast, monitored over nine production years, were analyzed by two different methods. (1) After studying genetic correlations between yields in successive years, longitudinal data analyses were applied to understand relationships between years. Several models were tested and the Compound Symmetry model, with heterogeneous variances (CSH model), best described the data structure. For instance, at tree level, correlations between yields of the different years were moderately stable, which revealed a major tree effect within clones. (2) Subsequently, derived index traits were considered, characterizing yield distribution over the different years. The traits involved were earliness, alternation, and the intensity of variations between years. Despite a marked tendency towards biennial cropping, especially in the early years, the estimated genetic correlations between years, and between individual years and cumulative yield were generally high. The intensity of the relative differences between yields in successive years was heritable only in the second production cycle. Despite some clonal differences in yield-stability variables, clonal yields in single years or groups of years evidently reflected both cumulative yields and comparative yield stability.
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improving the quality of african robustas qtls for yield and quality related traits in Coffea Canephora
Tree Genetics & Genomes, 2011Co-Authors: Thierry Leroy, Christophe Montagnon, Luiz Filipe Protasio Pereira, Fabien De Bellis, Hyacinthe Legnate, Edmund Kananura, Gustavo Gonzales, Alan Carvalho Andrade, Pierre Charmetant, Philippe CubryAbstract: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.
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Definition of Architectural Ideotypes for Good Yield Capacity in Coffea Canephora
Annals of Botany, 2006Co-Authors: Christian Cilas, Christophe Montagnon, Avner Bar-hen, Christophe GodinAbstract:Background :Yield capacity is a target trait for selection of agronomically desirable lines; it is preferred to simple yields recorded over different harvests. Yield capacity is derived using certain architectural parameters used to measure the components of yield capacity. Methods: Observation protocols for describing architecture and yield capacity were applied to six clones of coffee trees (Coffea Canephora) in a comparative trial. The observations were used to establish architectural databases, which were explored using AMAPmod, a software dedicated to the analyses of plant architecture data. The traits extracted from the database were used to identify architectural parameters for predicting the yield of the plant material studied. Conclusions: Architectural traits are highly heritable and some display strong genetic correlations with cumulated yield. In particular, the proportion of fruiting nodes at plagiotropic level 15 counting from the top of the tree proved to be a good predictor of yield over two fruiting cycles.
Fabio Luiz Partelli - One of the best experts on this subject based on the ideXlab platform.
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microclimate and development of Coffea Canephora cv conilon under different shading levels promoted by australian cedar toona ciliata m roem var australis
Australian Journal of Crop Science, 2016Co-Authors: Gleison Oliosi, Joao Antonio Dutra Giles, Weverton Pereira Rodrigues, Jose C Ramalho, Fabio Luiz PartelliAbstract:Coffee growers are searching for more sustainable production systems. Shaded cultivation is presented as a management option to attenuate coffee environmental stresses. This work aims at to evaluate the microclimate and coffee plant (Coffea Canephora cv. Conilon Clone 02) development under different shading levels promoted by the intercropping with Australian cedar (Toona ciliata M. Roem. var. Australis) or under unshaded conditions. Australian cedar and Conilon coffee were planted in 15 × 2m and 3 x 1.2 m spacing, respectively, resulting in five rows of coffee to one row of Australian cedar. The closer the coffee rows were in relation to the Australian cedar trees the higher shade level was obtained. Climatic variables (temperature, irradiance and relative humidity) and leaf areas were evaluated over four seasons, and the internode lengths of plagiotropic and orthotropic branches were evaluated monthly. The 2013yield was also measured. There was a decrease in both the irradiance and temperature and an increase in the relative humidity at all times under shaded cultivation (closer to the Australian cedar row). The highest growth of plagiotropic and orthotropic branches and leaf expansion were found under shaded cultivation; however, the number of nodes per branch and the yields were similar among treatments. Growing Conilon coffee intercropped with Australian cedar showed a good yield potential.
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seasonal vegetative growth in genotypes of Coffea Canephora as related to climatic factors
The Journal of Agricultural Science, 2013Co-Authors: Fabio Luiz Partelli, Henrique Duarte Vieira, Wellington Braida Marre, Antelmo Ralph Falqueto, Paulo Cezar CavattiAbstract:Knowledge about the seasonality of different genotypes of Coffea Canephora is an important tool for this crop management, particularly with regard to irrigation and fertilisation issues. This study was conducted in Espirito Santo, Brazil and aimed at to evaluate the seasonal vegetative growth in genotypes of C. Canephora , as related to climatic factors, based on the growth of groups of orthotropic and plagiotropic branches with different ages. Three groups of plagiotropic branches and one group of orthotropic branches of 14 genotypes (Ipiranga and 13 that belonged to the variety Vitoria) were selected and marked to followed along the one-year experiment. Three-year-old plants were cultivated under full-sun conditions, with a spacing of 3 m between rows and 1 m between plants. The growth rates of the orthotropic and plagiotropic branches differed among the genotypes and underwent seasonal variation during the entire year, with high correlations to the air temperature. Under the natural experimental conditions, the growth rate of the branches decreased when the minimum air temperatures were below 17.2oC for most of the genotypes studied. The plagiotropic branches presented lower vegetative growth, mainly for the coffee berries, compared to the younger branches. Presumably, the genotypes of C. Canephora demanded more nutrients for growth between mid-September and the second week of May.
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seasonal vegetative growth in genotypes of Coffea Canephora as related to climatic factors
The Journal of Agricultural Science, 2013Co-Authors: Fabio Luiz Partelli, Henrique Duarte Vieira, Wellington Braida Marre, Antelmo Ralph Falqueto, Paulo Cezar CavattiAbstract:Knowledge about the seasonality of different genotypes of Coffea Canephora is an important tool for this crop management, particularly with regard to irrigation and fertilisation issues. This study was conducted in Espirito Santo, Brazil and aimed at to evaluate the seasonal vegetative growth in genotypes of C. Canephora , as related to climatic factors, based on the growth of groups of orthotropic and plagiotropic branches with different ages. Three groups of plagiotropic branches and one group of orthotropic branches of 14 genotypes (Ipiranga and 13 that belonged to the variety Vitoria) were selected and marked to followed along the one-year experiment. Three-year-old plants were cultivated under full-sun conditions, with a spacing of 3 m between rows and 1 m between plants. The growth rates of the orthotropic and plagiotropic branches differed among the genotypes and underwent seasonal variation during the entire year, with high correlations to the air temperature. Under the natural experimental conditions, the growth rate of the branches decreased when the minimum air temperatures were below 17.2oC for most of the genotypes studied. The plagiotropic branches presented lower vegetative growth, mainly for the coffee berries, compared to the younger branches. Presumably, the genotypes of C. Canephora demanded more nutrients for growth between mid-September and the second week of May.
Massimo E Maffei - One of the best experts on this subject based on the ideXlab platform.
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chemical partitioning and antioxidant capacity of green coffee Coffea arabica and Coffea Canephora of different geographical origin
Phytochemistry, 2016Co-Authors: Oxana Babova, Andrea Occhipinti, Massimo E MaffeiAbstract:Green coffee beans of Coffea arabica and Coffea Canephora accessions from different geographical origin (Brazil, Colombia, Ethiopia, Honduras, Kenya, Mexico, Peru, Uganda and Vietnam) were extracted and the extracts analyzed by HPLC-ESI-MS/MS for the identification and quantification of chlorogenic acids and caffeine content. Principal component and cluster analyses were used to identify chemical patterns separating the different species and accessions based on their geographical origin. C. Canephora showed always a higher caffeine content with respect to C. arabica, whereas the C. arabica accessions from Kenya showed a higher chlorogenic acids and a lower caffeine content. The antioxidant capacity of green coffee extracts was assayed by the reducing power and DPPH assays. The antioxidant capacity correlated with the chlorogenic acids content. The results show that the C. arabica from Kenya possesses the highest chlorogenic acids/caffeine ratio and, among the C. arabica accessions, the highest antioxidant capacity. Therefore, the C. arabica from Kenya is the most suitable green coffee source for nutraceutical applications because of its high antioxidant capacity and low caffeine content.