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Verleysen L, Depecker J, Bollen R, Asimonyio J, Hatangi Y, Kambale JL, Mwanga Mwanga I, Ebele T, Dhed'a B, Stoffelen P, Ruttink T, Vandelook F, Honnay O. Crop-to-wild gene flow in wild coffee species: the case of Coffea canephora in the Democratic Republic of the Congo. ANNALS OF BOTANY 2024; 133:917-930. [PMID: 38441303 PMCID: PMC11089259 DOI: 10.1093/aob/mcae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/01/2024] [Indexed: 05/14/2024]
Abstract
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 hybridization with their nearby cultivated crops. This might be a particular 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 focused 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 hybridization 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 them using genotyping-by-sequencing (GBS). We compared the 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 probable 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 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 hybridization, our results indicate that the overall impact in terms of risk of introgression remains limited so far.
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Affiliation(s)
- Lauren Verleysen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Jonas Depecker
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
| | - Robrecht Bollen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Justin Asimonyio
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, DR Congo
| | - Yves Hatangi
- Meise Botanic Garden, Meise, Belgium
- Université de Kisangani, Kisangani, DR Congo
- Liège University, Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Jean-Léon Kambale
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, DR Congo
| | | | - Thsimi Ebele
- Institut National des Etudes et Recherches Agronomique, Yangambi, DR Congo
| | | | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Filip Vandelook
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Olivier Honnay
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
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Marie L, Breitler JC, Bamogo PKA, Bordeaux M, Lacombe S, Rios M, Lebrun M, Boulanger R, Lefort E, Nakamura S, Motoyoshi Y, Mieulet D, Campa C, Legendre L, Bertrand B. Combined sensory, volatilome and transcriptome analyses identify a limonene terpene synthase as a major contributor to the characteristic aroma of a Coffea arabica L. specialty coffee. BMC PLANT BIOLOGY 2024; 24:238. [PMID: 38566027 PMCID: PMC10988958 DOI: 10.1186/s12870-024-04890-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND The fruity aromatic bouquet of coffee has attracted recent interest to differentiate high value market produce as specialty coffee. Although the volatile compounds present in green and roasted coffee beans have been extensively described, no study has yet linked varietal molecular differences to the greater abundance of specific substances and support the aroma specificity of specialty coffees. RESULTS This study compared four Arabica genotypes including one, Geisha Especial, suggested to generate specialty coffee. Formal sensory evaluations of coffee beverages stressed the importance of coffee genotype in aroma perception and that Geisha Especial-made coffee stood out by having fine fruity, and floral, aromas and a more balanced acidity. Comparative SPME-GC-MS analyses of green and roasted bean volatile compounds indicated that those of Geisha Especial differed by having greater amounts of limonene and 3-methylbutanoic acid in agreement with the coffee cup aroma perception. A search for gene ontology differences of ripening beans transcriptomes of the four varieties revealed that they differed by metabolic processes linked to terpene biosynthesis due to the greater gene expression of prenyl-pyrophosphate biosynthetic genes and terpene synthases. Only one terpene synthase (CaTPS10-like) had an expression pattern that paralleled limonene loss during the final stage of berry ripening and limonene content in the studied four varieties beans. Its functional expression in tobacco leaves confirmed its functioning as a limonene synthase. CONCLUSIONS Taken together, these data indicate that coffee variety genotypic specificities may influence ripe berry chemotype and final coffee aroma unicity. For the specialty coffee variety Geisha Especial, greater expression of terpene biosynthetic genes including CaTPS10-like, a limonene synthase, resulted in the greater abundance of limonene in green beans, roasted beans and a unique citrus note of the coffee drink.
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Affiliation(s)
- Lison Marie
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR DIADE, Montpellier, F-34398, France.
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France.
| | - Jean-Christophe Breitler
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR DIADE, Montpellier, F-34398, France
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France
| | - Pingdwende Kader Aziz Bamogo
- PHIM (Plant Health Institute of Montpellier), University of Montpellier, CIRAD, IRD, INRAE, Institut Agro, Montpellier, F-34398, France
| | | | - Séverine Lacombe
- PHIM (Plant Health Institute of Montpellier), University of Montpellier, CIRAD, IRD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Maëlle Rios
- PHIM (Plant Health Institute of Montpellier), University of Montpellier, CIRAD, IRD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Marc Lebrun
- CIRAD, UMR QualiSud, Montpellier, F-34398, France
- QualiSud, University of Montpellier, CIRAD, IRD, INRAE, Institut Agro, University of La Réunion, University of Avignon, Montpellier, F-34398, France
| | - Renaud Boulanger
- CIRAD, UMR QualiSud, Montpellier, F-34398, France
- QualiSud, University of Montpellier, CIRAD, IRD, INRAE, Institut Agro, University of La Réunion, University of Avignon, Montpellier, F-34398, France
| | - Eveline Lefort
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR DIADE, Montpellier, F-34398, France
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France
| | - Sunao Nakamura
- Research Institute, Suntory Global Innovation Center Limited, 8-1-1, Seika-dai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
| | - Yudai Motoyoshi
- Research Institute, Suntory Global Innovation Center Limited, 8-1-1, Seika-dai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
| | - Delphine Mieulet
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR DIADE, Montpellier, F-34398, France
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France
| | - Claudine Campa
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France
| | - Laurent Legendre
- INRAE, UR 1115 Plantes et Systèmes de Culture Horticoles, Site Agroparc, Avignon, 84914, France
| | - Benoît Bertrand
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR DIADE, Montpellier, F-34398, France
- DIADE (Diversity, Adaptation, Development of Plants), University of Montpellier, CIRAD, IRD, Montpellier, F-34398, France
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Cherubino Ribeiro TH, Baldrich P, de Oliveira RR, Fernandes-Brum CN, Mathioni SM, de Sousa Cardoso TC, de Souza Gomes M, do Amaral LR, Pimenta de Oliveira KK, Dos Reis GL, Meyers BC, Chalfun-Junior A. The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38488203 DOI: 10.1111/tpj.16713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/05/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Noncoding and coding RNAs are key regulators of plant growth, development, and stress responses. To investigate the types of transcripts accumulated during the vegetative to reproductive transition and floral development in the Coffea arabica L., we sequenced small RNA libraries from eight developmental stages, up to anthesis. We combined these data with messenger RNA and PARE sequencing of two important development stages that marks the transition of an apparent latent to a rapid growth stage. In addition, we took advantage of multiple in silico tools to characterize genomic loci producing small RNAs such as phasiRNAs, miRNAs, and tRFs. Our differential and co-expression analysis showed that some types of small RNAs such as tRNAs, snoRNAs, snRNAs, and phasiRNAs preferentially accumulate in a stage-specific manner. Members of the miR482/miR2118 superfamily and their 21-nucleotide phasiRNAs originating from resistance genes show a robust co-expression pattern that is maintained across all the evaluated developmental stages. Finally, the majority of miRNAs accumulate in a family stage-specific manner, related to modulated hormonal responses and transcription factor expression.
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Affiliation(s)
- Thales Henrique Cherubino Ribeiro
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | | | - Raphael Ricon de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | - Christiane Noronha Fernandes-Brum
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | | | - Thaís Cunha de Sousa Cardoso
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, Lavras, 38700-128, MG, Brazil
| | - Matheus de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, Lavras, 38700-128, MG, Brazil
| | - Laurence Rodrigues do Amaral
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, Lavras, 38700-128, MG, Brazil
| | - Kellen Kauanne Pimenta de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | - Gabriel Lasmar Dos Reis
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | - Blake C Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
- Division of Plant Sciences and Technology, University of Missouri-Columbia, Columbia, MI, 65211, USA
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
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Rodrigues AP, Pais IP, Leitão AE, Dubberstein D, Lidon FC, Marques I, Semedo JN, Rakocevic M, Scotti-Campos P, Campostrini E, Rodrigues WP, Simões-Costa MC, Reboredo FH, Partelli FL, DaMatta FM, Ribeiro-Barros AI, Ramalho JC. Uncovering the wide protective responses in Coffea spp. leaves to single and superimposed exposure of warming and severe water deficit. FRONTIERS IN PLANT SCIENCE 2024; 14:1320552. [PMID: 38259931 PMCID: PMC10801242 DOI: 10.3389/fpls.2023.1320552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024]
Abstract
Climate changes boosted the frequency and severity of drought and heat events, with aggravated when these stresses occur simultaneously, turning crucial to unveil the plant response mechanisms to such harsh conditions. Therefore, plant responses/resilience to single and combined exposure to severe water deficit (SWD) and heat were assessed in two cultivars of the main coffee-producing species: Coffea arabica cv. Icatu and C. canephora cv. Conilon Clone 153 (CL153). Well-watered plants (WW) were exposed to SWD under an adequate temperature of 25/20°C (day/night), and thereafter submitted to a gradual increase up to 42/30°C, and a 14-d recovery period (Rec14). Greater protective response was found to single SWD than to single 37/28°C and/or 42/30°C (except for HSP70) in both cultivars, but CL153-SWD plants showed the larger variations of leaf thermal imaging crop water stress index (CWSI, 85% rise at 37/28°C) and stomatal conductance index (IG, 66% decline at 25/20°C). Both cultivars revealed great resilience to SWD and/or 37/28°C, but a tolerance limit was surpassed at 42/30°C. Under stress combination, Icatu usually displayed lower impacts on membrane permeability, and PSII function, likely associated with various responses, usually mostly driven by drought (but often kept or even strengthened under SWD and 42/30°C). These included the photoprotective zeaxanthin and lutein, antioxidant enzymes (superoxide dismutase, Cu,Zn-SOD; ascorbate peroxidase, APX), HSP70, arabinose and mannitol (involving de novo sugar synthesis), contributing to constrain lipoperoxidation. Also, only Icatu showed a strong reinforcement of glutathione reductase activity under stress combination. In general, the activities of antioxidative enzymes declined at 42/30°C (except Cu,Zn-SOD in Icatu and CAT in CL153), but HSP70 and raffinose were maintained higher in Icatu, whereas mannitol and arabinose markedly increased in CL153. Overall, a great leaf plasticity was found, especially in Icatu that revealed greater responsiveness of coordinated protection under all experimental conditions, justifying low PIChr and absence of lipoperoxidation increase at 42/30°C. Despite a clear recovery by Rec14, some aftereffects persisted especially in SWD plants (e.g., membranes), relevant in terms of repeated stress exposure and full plant recovery to stresses.
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Affiliation(s)
- Ana P. Rodrigues
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
| | - Isabel P. Pais
- Unidade de Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - António E. Leitão
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Danielly Dubberstein
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), São Mateus, ES, Brazil
- Assistência Técnica e Gerencial em Cafeicultura - Serviço Nacional de Aprendizagem Rural (SENAR), Porto Velho, RO, Brazil
| | - Fernando C. Lidon
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Isabel Marques
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
| | - José N. Semedo
- Unidade de Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Miroslava Rakocevic
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), São Mateus, ES, Brazil
| | - Paula Scotti-Campos
- Unidade de Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Eliemar Campostrini
- Setor de Fisiologia Vegetal, Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Rio de Janeiro, Brazil
| | - Weverton P. Rodrigues
- Setor de Fisiologia Vegetal, Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Rio de Janeiro, Brazil
- Centro de Ciências Agrárias, Naturais e Letras, Universidade Estadual da Região Tocantina do Maranhão, Maranhão, Brazil
| | - Maria Cristina Simões-Costa
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
| | - Fernando H. Reboredo
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Fábio L. Partelli
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), São Mateus, ES, Brazil
| | - Fábio M. DaMatta
- Departamento de Biologia Vegetal, Universidade Federal Viçosa (UFV), Viçosa, MG, Brazil
| | - Ana I. Ribeiro-Barros
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - José C. Ramalho
- Laboratório de Interações Planta-Ambiente e Biodiversidade (PlantStress & Biodiversity), Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Oeiras, Lisboa, Portugal
- Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, (ISA/ULisboa), Lisboa, Portugal
- Unidade de GeoBiociências, GeoEngenharias e GeoTecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
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5
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Aisala H, Kärkkäinen E, Jokinen I, Seppänen-Laakso T, Rischer H. Proof of Concept for Cell Culture-Based Coffee. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18478-18488. [PMID: 37972222 PMCID: PMC10690795 DOI: 10.1021/acs.jafc.3c04503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
The global coffee production is facing serious challenges including land use, climate change, and sustainability while demand is rising. Cellular agriculture is a promising alternative to produce plant-based commodities such as coffee, which are conventionally produced by farming. In this study, the complex process of drying and roasting was adapted for bioreactor-grown coffee cells to generate a coffee-like aroma and flavor. The brews resulting from different roasting regimes were characterized with chemical and sensory evaluation-based approaches and compared to conventional coffee. Roasting clearly influenced the aroma profile. In contrast to conventional coffee, the dominant odor and flavor attributes were burned sugar-like and smoky but less roasted. The intensities of bitterness and sourness were similar to those of conventional coffee. The present results demonstrate a proof of concept for a cellular agriculture approach as an alternative coffee production platform and guide future optimization work.
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Affiliation(s)
- Heikki Aisala
- VTT Technical Research Centre
of Finland Ltd, P.O. Box 1000, Espoo FI-02044, Finland
| | - Elviira Kärkkäinen
- VTT Technical Research Centre
of Finland Ltd, P.O. Box 1000, Espoo FI-02044, Finland
| | - Iina Jokinen
- VTT Technical Research Centre
of Finland Ltd, P.O. Box 1000, Espoo FI-02044, Finland
| | | | - Heiko Rischer
- VTT Technical Research Centre
of Finland Ltd, P.O. Box 1000, Espoo FI-02044, Finland
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6
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Khemira H, Mahdhi M, Afzal M, Oteef MD, Tounekti T, AL-Faifi Z, Alsolami W. Assessment of genetic diversity and phylogenetic relationship of local coffee populations in southwestern Saudi Arabia using DNA barcoding. PeerJ 2023; 11:e16486. [PMID: 38025745 PMCID: PMC10680449 DOI: 10.7717/peerj.16486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts.
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Affiliation(s)
- Habib Khemira
- Centre for Environmental Research and Studies, Jazan University, Jazan, Saudi Arabia
| | - Mosbah Mahdhi
- Centre for Environmental Research and Studies, Jazan University, Jazan, Saudi Arabia
- Laboratory of Biodiversity and Valorization of Bioresources in Arid Zones, Faculty of Sciences of Gabes, University of Gabes, Gabes, Tunisia
| | - Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed D.Y. Oteef
- Department of Chemistry, College of Science, Jazan University, Jazan, Saudi Arabia
| | - Taieb Tounekti
- Laboratory of Process Engineering & Industrial Systems (LR11ES54), National Engineering School of Gabes, University of Gabes, Gabes, Tunisia
| | - Zarraq AL-Faifi
- Department of Biology, College of Science, Jazan University, Jazan, Saudi Arabia
| | - Wail Alsolami
- Department of Biology, College of Science, Jazan University, Jazan, Saudi Arabia
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7
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Wallen-Russell C, Pearlman N, Wallen-Russell S, Cretoiu D, Thompson DC, Voinea SC. A Catastrophic Biodiversity Loss in the Environment Is Being Replicated on the Skin Microbiome: Is This a Major Contributor to the Chronic Disease Epidemic? Microorganisms 2023; 11:2784. [PMID: 38004795 PMCID: PMC10672968 DOI: 10.3390/microorganisms11112784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
There has been a catastrophic loss of biodiversity in ecosystems across the world. A similar crisis has been observed in the human gut microbiome, which has been linked to "all human diseases affecting westernized countries". This is of great importance because chronic diseases are the leading cause of death worldwide and make up 90% of America's healthcare costs. Disease development is complex and multifactorial, but there is one part of the body's interlinked ecosystem that is often overlooked in discussions about whole-body health, and that is the skin microbiome. This is despite it being a crucial part of the immune, endocrine, and nervous systems and being continuously exposed to environmental stressors. Here we show that a parallel biodiversity loss of 30-84% has occurred on the skin of people in the developed world compared to our ancestors. Research has shown that dysbiosis of the skin microbiome has been linked to many common skin diseases and, more recently, that it could even play an active role in the development of a growing number of whole-body health problems, such as food allergies, asthma, cardiovascular diseases, and Parkinson's, traditionally thought unrelated to the skin. Damaged skin is now known to induce systemic inflammation, which is involved in many chronic diseases. We highlight that biodiversity loss is not only a common finding in dysbiotic ecosystems but also a type of dysbiosis. As a result, we make the case that biodiversity loss in the skin microbiome is a major contributor to the chronic disease epidemic. The link between biodiversity loss and dysbiosis forms the basis of this paper's focus on the subject. The key to understanding why biodiversity loss creates an unhealthy system could be highlighted by complex physics. We introduce entropy to help understand why biodiversity has been linked with ecosystem health and stability. Meanwhile, we also introduce ecosystems as being governed by "non-linear physics" principles-including chaos theory-which suggests that every individual part of any system is intrinsically linked and implies any disruption to a small part of the system (skin) could have a significant and unknown effect on overall system health (whole-body health). Recognizing the link between ecosystem health and human health allows us to understand how crucial it could be to maintain biodiversity across systems everywhere, from the macro-environment we inhabit right down to our body's microbiome. Further, in-depth research is needed so we can aid in the treatment of chronic diseases and potentially change how we think about our health. With millions of people currently suffering, research to help mitigate the crisis is of vital importance.
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Affiliation(s)
| | - Nancy Pearlman
- Ecology Center of Southern California, Los Angeles, CA 90035, USA;
| | | | - Dragos Cretoiu
- Department of Medical Genetics, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, 011062 Bucharest, Romania
| | - Dana Claudia Thompson
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, 011062 Bucharest, Romania
| | - Silviu Cristian Voinea
- Department of Surgical Oncology, Prof. Dr. Al. Trestioreanu Oncology Institute, Carol Davila University of Medicine and Pharmacy, 022328 Bucharest, Romania
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8
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de Oliveira US, de Souza AH, de Andrade MT, Oliveira LA, Gouvea DG, Martins SCV, Ramalho JDC, Cardoso AA, DaMatta FM. Carbon gain is coordinated with enhanced stomatal conductance and hydraulic architecture in coffee plants acclimated to elevated [CO 2]: The interplay with irradiance supply. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108145. [PMID: 37907041 DOI: 10.1016/j.plaphy.2023.108145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/09/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023]
Abstract
We recently demonstrated that, under elevated [CO2] (eCa), coffee (Coffea arabica L.) plants grown at high light (HL), but not at low light (LL), display higher stomatal conductance (gs) than at ambient [CO2] (aCa). We then hypothesized that the enhanced gs at eCa/HL, if sustained at the long-term, would lead to adjustments in hydraulic architecture. To test this hypothesis, potted plants of coffee were grown in open-top chambers for 12 months under HL or LL (ca. 9 or 1 mol photons m-2 day-1, respectively); these light treatments were combined with two [CO2] levels (ca. 437 or 705 μmol mol-1, respectively). Under eCa/HL, increased gs was closely accompanied by increases in branch and leaf hydraulic conductances, suggesting a coordinated response between liquid- and vapor-phase water flows throughout the plant. Still under HL, eCa also resulted in increased Huber value (sapwood area-to-total leaf area), sapwood area-to-stem diameter, and root mass-to-total leaf area, thus further improving the water supply to the leaves. Our results demonstrate that Ca is a central player in coffee physiology increasing carbon gain through a close association between stomatal function and an improved hydraulic architecture under HL conditions.
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Affiliation(s)
- Uéliton S de Oliveira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Antonio H de Souza
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Moab T de Andrade
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Leonardo A Oliveira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Débora G Gouvea
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Samuel C V Martins
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - José D C Ramalho
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. da República, 2784-505, Oeiras, Portugal; Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516, Caparica, Portugal
| | - Amanda A Cardoso
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Fábio M DaMatta
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil.
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9
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Guerra-Guimarães L, Pinheiro C, Oliveira ASF, Mira-Jover A, Valverde J, Guedes FADF, Azevedo H, Várzea V, Muñoz Pajares AJ. The chloroplast protein HCF164 is predicted to be associated with Coffea S H9 resistance factor against Hemileia vastatrix. Sci Rep 2023; 13:16019. [PMID: 37749157 PMCID: PMC10520047 DOI: 10.1038/s41598-023-41950-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid "Híbrido de Timor". Individual reads were also aligned on the C. arabica reference genome to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.
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Affiliation(s)
- Leonor Guerra-Guimarães
- CIFC - Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal.
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal.
| | - Carla Pinheiro
- UCIBIO Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- Associate Laboratory i4HB Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| | - Ana Sofia F Oliveira
- Center for Computational Chemistry, School of Chemistry, University of Bristol, University Walk, Bristol, BS8 1TS, UK
| | - Andrea Mira-Jover
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain
- Área de Ecología, Departamento de Biología Aplicada, Universidad Miguel Hernández, Elche, Spain
| | - Javier Valverde
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 26, 41092, Sevilla, Spain
| | - Fernanda A de F Guedes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Herlander Azevedo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade Do Porto, 4099-002, Porto, Portugal
| | - Vitor Várzea
- CIFC - Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal
| | - Antonio Jesús Muñoz Pajares
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- Research Unit Modeling Nature, Universidad de Granada, 18071, Granada, Spain.
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10
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Tapaça IDPE, Mavuque L, Corti R, Pedrazzani S, Maquia ISA, Tongai C, Partelli FL, Ramalho JC, Marques I, Ribeiro-Barros AI. Genomic Evaluation of Coffea arabica and Its Wild Relative Coffea racemosa in Mozambique: Settling Resilience Keys for the Coffee Crop in the Context of Climate Change. PLANTS (BASEL, SWITZERLAND) 2023; 12:2044. [PMID: 37653961 PMCID: PMC10220690 DOI: 10.3390/plants12102044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/27/2023] [Accepted: 05/16/2023] [Indexed: 09/02/2023]
Abstract
Climate change is negatively affecting the coffee value chain, with a direct effect on approximately 100 million people from 80 countries. This has been attributed to the high vulnerability of the two-mainstream species, Coffea arabica and Coffea canephora, to extreme weather events, with notable uneven increases in market prices. Taking into account the narrow genetic plasticity of the commercial coffee cultivars, wild-relatives and underutilized Coffea species are valuable genetic resources. In this work, we have assessed the occurrence of Coffea species in to understand the degree of genetic relationships between Coffea species in the country, as well as the patterns of genetic diversity, differentiation, and genetic structure. Only one wild species was found, C. racemosa, which showed a high level of genetic separation with C. arabica, based on plastid, as well as SSR and SNP analysis. C. arabica presented low levels of diversity likely related to their autogamous nature, while the allogamous C. racemosa presented higher levels of diversity and heterozygosity. The analysis of the functional pathways based on SNPs suggests that the stress signaling pathways are more robust in this species. This novel approach shows that it is vital to introduce more resilient species and increase genomic diversity in climate-smart practices.
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Affiliation(s)
- Inocência da Piedade Ernesto Tapaça
- Forest Research Center (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa (UL), Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.d.P.E.T.); (L.M.); (R.C.); (S.P.); (I.S.A.M.); (C.T.); (J.C.R.)
- Mozambique Agricultural Research Institute (IIAM), Avenida das FPLM 2698, Mavalane B, Maputo P.O. Box 3658, Mozambique
| | - Lopes Mavuque
- Forest Research Center (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa (UL), Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.d.P.E.T.); (L.M.); (R.C.); (S.P.); (I.S.A.M.); (C.T.); (J.C.R.)
- Unilurio, Faculty of Agricultural Sciences Campus de Unang, EN733 Km 42, Unango P.O. Box 3003, Mozambique
| | - Riccardo Corti
- Forest Research Center (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa (UL), Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.d.P.E.T.); (L.M.); (R.C.); (S.P.); (I.S.A.M.); (C.T.); (J.C.R.)
- Facoltà di Agraria, Università degli studi di Firenze, Piazzale delle Cascine 18, 50144 Firenze, Italy
| | - Samuele Pedrazzani
- Forest Research Center (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa (UL), Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.d.P.E.T.); (L.M.); (R.C.); (S.P.); (I.S.A.M.); (C.T.); (J.C.R.)
- Facoltà di Agraria, Università degli studi di Firenze, Piazzale delle Cascine 18, 50144 Firenze, Italy
| | - Ivete S. A. Maquia
- Forest Research Center (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa (UL), Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.d.P.E.T.); (L.M.); (R.C.); (S.P.); (I.S.A.M.); (C.T.); (J.C.R.)
- Biotechnology Center, Eduardo Mondlane University, Km 1.5, Maputo P.O. Box 3453, Mozambique
| | - Castigo Tongai
- Forest Research Center (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa (UL), Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.d.P.E.T.); (L.M.); (R.C.); (S.P.); (I.S.A.M.); (C.T.); (J.C.R.)
- Department of Scientific Services, Gorongosa National Park, Gorongosa P.O. Box 1983, Mozambique
| | - Fábio Luiz Partelli
- Centro Universitário do Norte do Espírito Santo (CEUNES), Departmento Ciências Agrárias e Biológicas (DCAB), Universidade Federal Espírito Santo (UFES), Rodovia BR 101 Norte, Km 60, Bairro Litorâneo, São Mateus 29932-540, ES, Brazil;
| | - José C. Ramalho
- Forest Research Center (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa (UL), Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.d.P.E.T.); (L.M.); (R.C.); (S.P.); (I.S.A.M.); (C.T.); (J.C.R.)
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516 Caparica, Portugal
| | - Isabel Marques
- Forest Research Center (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa (UL), Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.d.P.E.T.); (L.M.); (R.C.); (S.P.); (I.S.A.M.); (C.T.); (J.C.R.)
| | - Ana I. Ribeiro-Barros
- Forest Research Center (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa (UL), Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.d.P.E.T.); (L.M.); (R.C.); (S.P.); (I.S.A.M.); (C.T.); (J.C.R.)
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516 Caparica, Portugal
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11
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Bertrand B, Davis AP, Maraval I, Forestier N, Mieulet D. Potential beverage quality of three wild coffee species (Coffea brevipes, C. congensis and C. stenophylla) and consideration of their agronomic use. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:3602-3612. [PMID: 36418192 DOI: 10.1002/jsfa.12347] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Of the 130 known coffee (Coffea) species, very few have been properly evaluated for their beverage quality. The diversity of wild coffee species is considered critical to the long-term sustainability of the coffee sector, particularly under climate change. The challenge is finding coffee crops that satisfy agronomic criteria, now and under the altered climatic conditions of the future, as well as consumer requirements for flavour. We evaluated the sensory characteristics of three wild coffee species with four independent sensory panels, and the key environmental/agronomic requirements of these wild species based on a literature review. RESULTS Coffea congensis and C. stenophylla have a lower unroasted seed weight compared to C. arabica and C. canephora, while C. brevipes has the largest. Sensory analysis showed that the main differences between species was for the fruitiness attribute. Coffea stenophylla was the fruitiest wild species, and was considered an Arabica-like coffee. The flavour profile range of C. stenophylla covers herb-like, vegetal, floral and fruit; C. brevipes resembles C. stenophylla in some respects. Opinions concerning C. congensis were contradictory and several judges considered the industry-standard coffee flavour wheel not suitable for the beverage produced from this species. CONCLUSION The three wild species have the required sensory qualities for commercialization. According to published data, C. stenophylla has agronomic potential, especially in warmer climates than Arabica areas. Coffea brevipes and C. congensis have the potential to be easily crossed with C. canephora to form interspecific hybrids capable of adapting to different climatic and agronomic conditions. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Benoît Bertrand
- CIRAD, UMR DIADE, Montpellier, France
- DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France
| | | | - Isabelle Maraval
- CIRAD, UMR Qualisud, Montpellier, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Nelly Forestier
- CIRAD, UMR Qualisud, Montpellier, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Delphine Mieulet
- CIRAD, UMR DIADE, Montpellier, France
- DIADE, Univ Montpellier, IRD, CIRAD, Montpellier, France
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12
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Muñoz-Pajares AJ, Várzea V, Silva MDC. The story of coffee: legend and truth. TRENDS IN PLANT SCIENCE 2023; 28:501-504. [PMID: 36925356 DOI: 10.1016/j.tplants.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 05/22/2023]
Abstract
When we think about coffee, exotic tropical countries such as Colombia, Brazil, and Ethiopia first come to mind. However, the crucial contribution of Portugal and its scientists to each cup of coffee we drink remains either poorly known or overlooked.
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Affiliation(s)
- A J Muñoz-Pajares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Genética, Universidad de Granada, Campus Fuentenueva, 18071 Granada, Spain; Research Unit Modeling Nature, Universidad de Granada, Granada, Spain.
| | - Vitor Várzea
- CIFC - Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal; LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Maria do Céu Silva
- CIFC - Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal; LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
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13
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Tafesse B, Bekele T, Demissew S, Dullo BW, Nemomissa S, Chala D. Conservation implications of mapping the potential distribution of an Ethiopian endemic versatile medicinal plant, Echinops kebericho Mesfin. Ecol Evol 2023; 13:e10061. [PMID: 37168986 PMCID: PMC10164648 DOI: 10.1002/ece3.10061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/08/2023] [Accepted: 04/22/2023] [Indexed: 05/13/2023] Open
Abstract
Echinops kebericho is a narrow-range multipurpose medicinal plant confined to Ethiopia. Intense land use change and overharvesting for traditional medicine have resulted in narrow distributions of its populations. It is a threatened species with a decreasing population trend. This study aims to map its potential distribution, which is key to guide conservation efforts and sustainable use. We modeled the potential distribution of E. kebercho using the maximum entropy model (MaxEnt) employing 11 less correlated predictor variables by calibrating the model at two complexity levels and replicating each model 10 times using a cross validation technique. We projected the models into the whole of Ethiopia and produced binary presence-absence maps by classifying the average map from both complexity levels applying three threshold criteria and ensembling the resulting maps into one for the final result. We mapped suitable habitat predicted with high certainty and identified local districts where E. kebericho can be cultivated or introduced to enhance its conservation. We estimated that E.kebercho has about 137,925 km2 of suitable habitat, mainly concentrated in the western highlands of the Ethiopian mountains. Our models at both complexity levels had high average performances, AUC values of 0.925 for the complex model and 0.907 for the simpler model. The variations in performance among the 10 model replicates were not remarkable, an AUC standard deviation of 0.040 for complex and 0.046 for simple model. Although E. kebericho is locally confined, our models predicted that it has a remarkably wider potential distribution area. We recommend introducing E. kebericho to these areas to improve its conservation status and tap its multiple benefits on a sustainable basis. Locally confined threatened plants and animals likely have wider potential distributions than their actual distributions and thus similar methodology can be applied for their conservation.
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Affiliation(s)
- Bedilu Tafesse
- Department of Plant Biology and Biodiversity Management, College of Natural SciencesAddis Ababa UniversityAddis AbabaEthiopia
| | - Tamrat Bekele
- Department of Plant Biology and Biodiversity Management, College of Natural SciencesAddis Ababa UniversityAddis AbabaEthiopia
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, College of Natural SciencesAddis Ababa UniversityAddis AbabaEthiopia
| | - Bikila Warkineh Dullo
- Department of Plant Biology and Biodiversity Management, College of Natural SciencesAddis Ababa UniversityAddis AbabaEthiopia
| | - Sileshi Nemomissa
- Department of Plant Biology and Biodiversity Management, College of Natural SciencesAddis Ababa UniversityAddis AbabaEthiopia
| | - Desalegn Chala
- Natural History MuseumUniversity of OsloOsloNorway
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityAarhus CDenmark
- Section for Ecoinformatics and Biodiversity, Department of BiologyAarhus UniversityAarhus CDenmark
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14
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Max AC, Loram-Lourenço L, Silva FG, de Souza LHM, Dias JRM, Espíndula MC, Farnese FS, Hammond W, Torres-Ruiz JM, Cochard H, Menezes-Silva PE. A bitter future for coffee production? Physiological traits associated with yield reveal high vulnerability to hydraulic failure in Coffea canephora. PLANT, CELL & ENVIRONMENT 2023; 46:764-779. [PMID: 36517464 DOI: 10.1111/pce.14514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The increase in frequency and intensity of drought events have hampered coffee production in the already threatened Amazon region, yet little is known about key aspects underlying the variability in yield potential across genotypes, nor to what extent higher productivity is linked to reduced drought tolerance. Here we explored how variations in morphoanatomical and physiological leaf traits can explain differences in yield and vulnerability to embolism in 11 Coffea canephora genotypes cultivated in the Western Amazon. The remarkable variation in coffee yield across genotypes was tightly related to differences in their carbon assimilation and water transport capacities, revealing a diffusive limitation to photosynthesis linked by hydraulic constraints. Although a clear trade-off between water transport efficiency and safety was not detected, all the studied genotypes operated in a narrow and/or negative hydraulic safety margin, suggesting a high vulnerability to leaf hydraulic failure (HF), especially on the most productive genotypes. Modelling exercises revealed that variations in HF across genotypes were mainly associated with differences in leaf water vapour leakage when stomata are closed, reflecting contrasting growth strategies. Overall, our results provide a new perspective on the challenges of sustaining coffee production in the Amazon region under a drier and warmer climate.
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Affiliation(s)
- Aldo Custódio Max
- Federal Institute of Education, Science and Technology of Rondônia, Vilhena, Brazil
| | - Lucas Loram-Lourenço
- Laboratory of Applied Studies in Plant Physiology, Federal Institute of Education, Science and Technology Goiano, Rio Verde Campus, Rio Verde, Brazil
| | - Fabiano Guimarães Silva
- Laboratory of Applied Studies in Plant Physiology, Federal Institute of Education, Science and Technology Goiano, Rio Verde Campus, Rio Verde, Brazil
| | | | | | | | - Fernanda S Farnese
- Laboratory of Applied Studies in Plant Physiology, Federal Institute of Education, Science and Technology Goiano, Rio Verde Campus, Rio Verde, Brazil
| | - William Hammond
- Department of Agronomy, University of Florida, Gainesville, Florida, USA
| | | | - Hervé Cochard
- INRAE, PIAF, Université Clermont-Auvergne, Clermont-Ferrand, France
| | - Paulo Eduardo Menezes-Silva
- Laboratory of Applied Studies in Plant Physiology, Federal Institute of Education, Science and Technology Goiano, Rio Verde Campus, Rio Verde, Brazil
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15
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Davis AP, Kiwuka C, Faruk A, Mulumba J, Kalema J. A review of the indigenous coffee resources of Uganda and their potential for coffee sector sustainability and development. FRONTIERS IN PLANT SCIENCE 2023; 13:1057317. [PMID: 36874918 PMCID: PMC9982753 DOI: 10.3389/fpls.2022.1057317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/01/2022] [Indexed: 06/18/2023]
Abstract
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.
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Affiliation(s)
- Aaron P. Davis
- Crops & Global Change, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Catherine Kiwuka
- Plant Genetic Resources Centre, National Agricultural Research Organization, Entebbe, Uganda
| | - Aisyah Faruk
- Partnerships (Conservation), Millennium Seed Bank (Royal Botanic Gardens, Kew), Wakehurst, Sussex, United Kingdom
| | - John Mulumba
- Plant Genetic Resources Centre, National Agricultural Research Organization, Entebbe, Uganda
| | - James Kalema
- Department of Plant Sciences, Microbiology and Biotechnology, College of Natural Sciences, Makerere University, Kampala, Uganda
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16
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Kath J, Byrareddy VM, Reardon-Smith K, Mushtaq S. Early flowering changes robusta coffee yield responses to climate stress and management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158836. [PMID: 36122728 DOI: 10.1016/j.scitotenv.2022.158836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
A shift towards earlier flowering is a widely noted consequence of climate change for the world's plants. However, whether early flowering changes the way in which plants respond to climate stress, and in turn plant yield, remains largely unexplored. Using 10 years of flowering time and yield observations (Total N = 5580) from 558 robusta coffee (Coffea canephora) farms across Vietnam we used structural equation modelling (SEM) to examine the drivers of flowering day anomalies and the consequent effects of this on coffee climate stress sensitivity and management responses (i.e. irrigation and fertilization). SEM allowed us to model the cascading and interacting effects of differences in flowering time, growing season length and climate stress. Warm nights were the main driver of early flowering (i.e. flowering day anomalies <0), which in turn corresponded to longer growing seasons. Early flowering was linked to greater sensitivity of yield to temperature during flowering (i.e. early in the season). In contrast, when late flowering occurred yield was most sensitive to temperature and rainfall later in the growing season, after flowering and fruit development. The positive effects of tree age and fertilizer on yield, apparent under late flowering conditions, were absent when flowering occurred early. Late flowering models predicted yields under early flowering conditions poorly (a 50 % reduction in cross-validated R2 of 0.54 to 0.27). Likewise, models based on early flowering were unable to predict yields well under late flowering conditions (a 75 % reduction in cross-validated R2, from 0.58 to 0.14). Our results show that early flowering changes the sensitivity of coffee production to climate stress and management and in turn our ability to predict yield. Our results indicate that changes in plant phenology need to be taken into account in order to more accurately assess climate risk and management impacts on plant performance and crop yield.
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Affiliation(s)
- Jarrod Kath
- Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia; School of Agriculture and Environmental Science, University of Southern Queensland, Toowoomba, Queensland, Australia.
| | - Vivekananda Mittahalli Byrareddy
- Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia; Future Drought Fund Hub (Research), University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Kathryn Reardon-Smith
- Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia; School of Agriculture and Environmental Science, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Shahbaz Mushtaq
- Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
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17
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Bilen C, El Chami D, Mereu V, Trabucco A, Marras S, Spano D. A Systematic Review on the Impacts of Climate Change on Coffee Agrosystems. PLANTS (BASEL, SWITZERLAND) 2022; 12:102. [PMID: 36616231 PMCID: PMC9824350 DOI: 10.3390/plants12010102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Coffee production is fragile, and the Intergovernmental Panel on Climate Change (IPCC) reports indicate that climate change (CC) will reduce worldwide yields on average and decrease coffee-suitable land by 2050. This article adopted the systematic review approach to provide an update of the literature available on the impacts of climate change on coffee production and other ecosystem services following the framework proposed by the Millenium Ecosystem Assessment. The review identified 148 records from literature considering the effects of climate change and climate variability on coffee production, covering countries mostly from three continents (America, Africa, and Asia). The current literature evaluates and analyses various climate change impacts on single services using qualitative and quantitative methodologies. Impacts have been classified and described according to different impact groups. However, available research products lacked important analytical functions on the precise relationships between the potential risks of CC on coffee farming systems and associated ecosystem services. Consequently, the manuscript recommends further work on ecosystem services and their interrelation to assess the impacts of climate change on coffee following the ecosystem services framework.
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Affiliation(s)
- Christine Bilen
- Department of Soil, Plant and Food Sciences, University of Bari ‘Aldo Moro’, 70126 Bari, BA, Italy
| | | | - Valentina Mereu
- Impacts on Agriculture, Forestry and Ecosystem Services (IAFES) Division, Euro-Mediterranean Center on Climate Changes (CMCC), 07100 Sassari, SS, Italy
| | - Antonio Trabucco
- Impacts on Agriculture, Forestry and Ecosystem Services (IAFES) Division, Euro-Mediterranean Center on Climate Changes (CMCC), 07100 Sassari, SS, Italy
| | - Serena Marras
- Impacts on Agriculture, Forestry and Ecosystem Services (IAFES) Division, Euro-Mediterranean Center on Climate Changes (CMCC), 07100 Sassari, SS, Italy
- Department of Agricultural Sciences, University of Sassari, 07100 Sassari, SS, Italy
| | - Donatella Spano
- Impacts on Agriculture, Forestry and Ecosystem Services (IAFES) Division, Euro-Mediterranean Center on Climate Changes (CMCC), 07100 Sassari, SS, Italy
- Department of Agricultural Sciences, University of Sassari, 07100 Sassari, SS, Italy
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18
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Antonelli A, Smith RJ, Perrigo AL, Crottini A, Hackel J, Testo W, Farooq H, Torres Jiménez MF, Andela N, Andermann T, Andriamanohera AM, Andriambololonera S, Bachman SP, Bacon CD, Baker WJ, Belluardo F, Birkinshaw C, Borrell JS, Cable S, Canales NA, Carrillo JD, Clegg R, Clubbe C, Cooke RSC, Damasco G, Dhanda S, Edler D, Faurby S, de Lima Ferreira P, Fisher BL, Forest F, Gardiner LM, Goodman SM, Grace OM, Guedes TB, Henniges MC, Hill R, Lehmann CER, Lowry PP, Marline L, Matos-Maraví P, Moat J, Neves B, Nogueira MGC, Onstein RE, Papadopulos AST, Perez-Escobar OA, Phelps LN, Phillipson PB, Pironon S, Przelomska NAS, Rabarimanarivo M, Rabehevitra D, Raharimampionona J, Rajaonah MT, Rajaonary F, Rajaovelona LR, Rakotoarinivo M, Rakotoarisoa AA, Rakotoarisoa SE, Rakotomalala HN, Rakotonasolo F, Ralaiveloarisoa BA, Ramirez-Herranz M, Randriamamonjy JEN, Randriamboavonjy T, Randrianasolo V, Rasolohery A, Ratsifandrihamanana AN, Ravololomanana N, Razafiniary V, Razanajatovo H, Razanatsoa E, Rivers M, Sayol F, Silvestro D, Vorontsova MS, Walker K, Walker BE, Wilkin P, Williams J, Ziegler T, Zizka A, Ralimanana H. Madagascar’s extraordinary biodiversity: Evolution, distribution, and use. Science 2022; 378:eabf0869. [DOI: 10.1126/science.abf0869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique “living laboratory” for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth’s biodiversity.
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Affiliation(s)
- Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Oxford, Oxford, UK
| | - Rhian J. Smith
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Allison L. Perrigo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Weston Testo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Field Museum of Natural History, Chicago, Illinois, USA
| | - Harith Farooq
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Faculty of Natural Sciences, Lúrio University, Pemba, Cabo Delgado Province, Mozambique
| | - Maria F. Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Institute of Biosciences, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Niels Andela
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, UK
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | | | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | | | - Francesco Belluardo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Chris Birkinshaw
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
- Missouri Botanical Garden, St. Louis, Missouri, USA
| | | | - Stuart Cable
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Nataly A. Canales
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Juan D. Carrillo
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- CR2P, Muséum National d’Histoire Naturelle, Paris, France
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Rosie Clegg
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Geography, University of Exeter, Exeter, Devon, UK
| | - Colin Clubbe
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Robert S. C. Cooke
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- UK Centre for Ecology and Hydrology, Wallingford, UK
| | - Gabriel Damasco
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Sonia Dhanda
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Daniel Edler
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Paola de Lima Ferreira
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Brian L. Fisher
- California Academy of Sciences, San Francisco, California, USA
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Lauren M. Gardiner
- Cambridge University Herbarium, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Steven M. Goodman
- Field Museum of Natural History, Chicago, Illinois, USA
- Association Vahatra, Antananarivo, Madagascar
| | | | - Thaís B. Guedes
- Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, Campinas, São Paulo, Brazil
| | - Marie C. Henniges
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rowena Hill
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Caroline E. R. Lehmann
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, Missouri, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Lovanomenjanahary Marline
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
- Association Vahatra, Antananarivo, Madagascar
| | - Pável Matos-Maraví
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Justin Moat
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Beatriz Neves
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matheus G. C. Nogueira
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renske E. Onstein
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR Leiden, the Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Leanne N. Phelps
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Peter B. Phillipson
- Missouri Botanical Garden, St. Louis, Missouri, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, UK
| | - Natalia A. S. Przelomska
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Anthropology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | | | - David Rabehevitra
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Mamy Tiana Rajaonah
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Fano Rajaonary
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
| | - Landy R. Rajaovelona
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Mijoro Rakotoarinivo
- Department of Plant Biology and Ecology, University of Antananarivo, Antananarivo, Madagascar
| | - Amédée A. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Solofo E. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Herizo N. Rakotomalala
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Franck Rakotonasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Myriam Ramirez-Herranz
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Instituto de Ecología y Biodiversidad, University of La Serena, La Serena, Chile
- Programa de Doctorado en Biología y Ecología Aplicada, Universidad Católica del Norte, Universidad de La Serena, La Serena, Chile
| | | | | | - Vonona Randrianasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | | | | | - Velosoa Razafiniary
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Henintsoa Razanajatovo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Estelle Razanatsoa
- Plant Conservation Unit, Department of Biological Sciences, University of Cape Town, South Africa
| | - Malin Rivers
- Botanic Gardens Conservation International, Kew, Richmond, Surrey, UK
| | - Ferran Sayol
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | | | - Kim Walker
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Royal Holloway, University of London, Egham, Surrey, UK
| | | | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | | | - Thomas Ziegler
- Cologne Zoo, Cologne, Germany
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Hélène Ralimanana
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
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19
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Cardon CH, de Oliveira RR, Lesy V, Ribeiro THC, Fust C, Pereira LP, Colasanti J, Chalfun-Junior A. Expression of coffee florigen CaFT1 reveals a sustained floral induction window associated with asynchronous flowering in tropical perennials. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111479. [PMID: 36181945 DOI: 10.1016/j.plantsci.2022.111479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
The behavior of florigen(s) and environment-influenced regulatory pathways that control floral initiation in tropical perennials species with complex phenological cycles is poorly understood. Understanding the mechanisms underlying this process is important for food production in the face of climate change, thus, we used Coffea sp. L. (Rubiaceae) as a model to explore this issue. Homologs of FLOWERING LOCUS T (CaFT1) and environment-related regulators CONSTANS (CaCO), PHYTOCHROME INTERACTING FACTOR 4 (CaPIF4) and FLOWERING LOCUS C (CaFLC) were retrieved from coffee genomes and identified through phylogenetic analysis. Overexpression of CaFT1 in Arabidopsis caused early-flowering phenotype and yeast two hybrid studies indicated CaFT1 binding to bZIP floral regulator FD, which suggests that CaFT1 is a coffee florigen. Expression of CaFT1 and other floral regulators, together with carbohydrate analysis, were evaluated over one year using three contrasting genotypes, two C. arabica cultivars and C. canephora. All genotypes showed active and variable CaFT1 transcription from February until October, indicating the potential window for floral induction that reached a maximum in the cold period of June. CaCO expression, as expected, varied over a 24-hour day period and monthly with day length, whereas expression of temperature-responsive homologs, CaFLC and CaPIF4, did not correlate with temperature changes nor CaFT1 expression, suggesting alternative FT regulatory pathways in coffee. Based on our results, we suggest a continuum of floral induction that allows different starting points for floral activation, which explains developmental asynchronicity and prolonged anthesis events in tropical perennial species.
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Affiliation(s)
- Carlos Henrique Cardon
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Minas Gerais, Brazil; Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Raphael Ricon de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Minas Gerais, Brazil.
| | - Victoria Lesy
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Thales Henrique Cherubino Ribeiro
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Minas Gerais, Brazil.
| | - Catherine Fust
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Luísa Peloso Pereira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Minas Gerais, Brazil.
| | - Joseph Colasanti
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Minas Gerais, Brazil.
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20
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Davis AP, Kiwuka C, Faruk A, Walubiri MJ, Kalema J. The re-emergence of Liberica coffee as a major crop plant. NATURE PLANTS 2022; 8:1322-1328. [PMID: 36522448 DOI: 10.1038/s41477-022-01309-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
| | | | - Aisyah Faruk
- Millennium Seed Bank (Royal Botanic Gardens, Kew), Wakehurst, UK
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21
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Incorporating evolutionary and threat processes into crop wild relatives conservation. Nat Commun 2022; 13:6254. [PMID: 36271075 PMCID: PMC9587227 DOI: 10.1038/s41467-022-33703-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/28/2022] [Indexed: 12/25/2022] Open
Abstract
Crop wild relatives (CWR) intra- and interspecific diversity is essential for crop breeding and food security. However, intraspecific genetic diversity, which is central given the idiosyncratic threats to species in landscapes, is usually not considered in planning frameworks. Here, we introduce an approach to develop proxies of genetic differentiation to identify conservation areas, applying systematic conservation planning tools that produce hierarchical prioritizations of the landscape. It accounts for: (i) evolutionary processes, including historical and environmental drivers of genetic diversity, and (ii) threat processes, considering taxa-specific tolerance to human-modified habitats, and their extinction risk status. Our analyses can be used as inputs for developing national action plans for the conservation and use of CWR. Our results also inform public policy to mitigate threat processes to CWR (like crops living modified organisms or agriculture subsidies), and could advise future research (e.g. for potential germplasm collecting). Although we focus on Mesoamerican CWR within Mexico, our methodology offers opportunities to effectively guide conservation and monitoring strategies to safeguard the evolutionary resilience of any taxa, including in regions of complex evolutionary histories and mosaic landscapes.
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22
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Kath J, Craparo A, Fong Y, Byrareddy V, Davis AP, King R, Nguyen-Huy T, van Asten PJA, Marcussen T, Mushtaq S, Stone R, Power S. Vapour pressure deficit determines critical thresholds for global coffee production under climate change. NATURE FOOD 2022; 3:871-880. [PMID: 37117886 DOI: 10.1038/s43016-022-00614-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022]
Abstract
Our understanding of the impact of climate change on global coffee production is largely based on studies focusing on temperature and precipitation, but other climate indicators could trigger critical threshold changes in productivity. Here, using generalized additive models and threshold regression, we investigate temperature, precipitation, soil moisture and vapour pressure deficit (VPD) effects on global Arabica coffee productivity. We show that VPD during fruit development is a key indicator of global coffee productivity, with yield declining rapidly above 0.82 kPa. The risk of exceeding this threshold rises sharply for most countries we assess, if global warming exceeds 2 °C. At 2.9 °C, countries making up 90% of global supply are more likely than not to exceed the VPD threshold. The inclusion of VPD and the identification of thresholds appear critical for understanding climate change impacts on coffee and for the design of adaptation strategies.
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23
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Huded AKC, Jingade P, Mishra MK, Ercisli S, Ilhan G, Marc RA, Vodnar D. Comparative genomic analysis and phylogeny of NAC25 gene from cultivated and wild Coffea species. FRONTIERS IN PLANT SCIENCE 2022; 13:1009733. [PMID: 36186041 PMCID: PMC9523601 DOI: 10.3389/fpls.2022.1009733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Coffee is a high value agricultural commodity grown in about 80 countries. Sustainable coffee cultivation is hampered by multiple biotic and abiotic stress conditions predominantly driven by climate change. The NAC proteins are plants specific transcription factors associated with various physiological functions in plants which include cell division, secondary wall formation, formation of shoot apical meristem, leaf senescence, flowering embryo and seed development. Besides, they are also involved in biotic and abiotic stress regulation. Due to their ubiquitous influence, studies on NAC transcription factors have gained momentum in different crop plant species. In the present study, NAC25 like transcription factor was isolated and characterized from two cultivated coffee species, Coffea arabica and Coffea canephora and five Indian wild coffee species for the first time. The full-length NAC25 gene varied from 2,456 bp in Coffea jenkinsii to 2,493 bp in C. arabica. In all the seven coffee species, sequencing of the NAC25 gene revealed 3 exons and 2 introns. The NAC25 gene is characterized by a highly conserved 377 bp NAM domain (N-terminus) and a highly variable C terminus region. The sequence analysis revealed an average of one SNP per every 40.92 bp in the coding region and 37.7 bp in the intronic region. Further, the non-synonymous SNPs are 8-11 fold higher compared to synonymous SNPs in the non-coding and coding region of the NAC25 gene, respectively. The expression of NAC25 gene was studied in six different tissue types in C. canephora and higher expression levels were observed in leaf and flower tissues. Further, the relative expression of NAC25 in comparison with the GAPDH gene revealed four folds and eight folds increase in expression levels in green fruit and ripen fruit, respectively. The evolutionary relationship revealed the independent evolution of the NAC25 gene in coffee.
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Affiliation(s)
- Arun Kumar C. Huded
- Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Mysore, Karnataka, India
| | - Pavankumar Jingade
- Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Mysore, Karnataka, India
| | - Manoj Kumar Mishra
- Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Mysore, Karnataka, India
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Erzurum, Turkey
| | - Gulce Ilhan
- Department of Horticulture, Faculty of Agriculture, Erzurum, Turkey
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Dan Vodnar
- Institute of Life Sciences, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
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24
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Description of an Arabica Coffee Ideotype for Agroforestry Cropping Systems: A Guideline for Breeding More Resilient New Varieties. PLANTS 2022; 11:plants11162133. [PMID: 36015436 PMCID: PMC9414076 DOI: 10.3390/plants11162133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
Abstract
Climate change (CC) is already impacting Arabica coffee cultivation in the intertropical zone. To deal with this situation, it is no longer possible to manage this crop using industrial agriculture techniques, which has been the main strategy implemented since the Green Revolution. Developing a more sustainable agriculture system that respects people and the environment is essential to guarantee future generations’ access to natural resources. In the case of Arabica coffee, the solution has been found. Agroforestry is proposed as an ecosystem-based strategy to mitigate and adapt to CC. At least 60% of Arabica coffee is produced in agroforestry systems (AFSs), which are the most sustainable way to produce coffee. Nevertheless, AFS coffee cultivation is currently uncompetitive partly because all modern varieties, selected for full-sun intensive cropping systems, have low yields in shaded environments. Here we review the reasons why agroforestry is part of the solution to CC, and why no breeding work has been undertaken for this cropping system. Based on the literature data, for breeding purposes we also define for the first time one possible coffee ideotype required for AFS coffee cultivation. The four main traits are: (1) productivity based on F1 hybrid vigor, tree volume and flowering intensity under shade; (2) beverage quality by using wild Ethiopian accessions as female progenitors and selecting for this criterion using specific biochemical and molecular predictors; (3) plant health to ensure good tolerance to stress, especially biotic; and (4) low fertilization to promote sustainable production. For each of these traits, numerous criteria with threshold values to be achieved per trait were identified. Through this research, an ecosystem-based breeding strategy was defined to help create new F1 hybrid varieties within the next 10 years.
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25
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Akpertey A, Anim-Kwapong E, Adu-Gyamfi PKK, Ofori A. Genetic variability for vigor and yield of robusta coffee ( Coffea canephora) clones in Ghana. Heliyon 2022; 8:e10192. [PMID: 36033278 PMCID: PMC9400079 DOI: 10.1016/j.heliyon.2022.e10192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/21/2022] [Accepted: 07/28/2022] [Indexed: 11/15/2022] Open
Abstract
Effectiveness of plant improvement programs, especially in perennial crops like coffee, may be improved by knowing the level of genetic variation which exist within a breeding population coupled with the knowledge of estimates of genetic parameters for key agronomic traits. Thus, this study was conducted to evaluate C. canephora clones for growth (stem diameter, number of laterals and span) and yield traits; estimate genetic parameters of these traits; and determine the phenotypic and genetic associations between these traits to guide future crop improvement efforts. The productivity of 56 coffee clones was assessed from 2012 to 2020 in a clonal experiment planted in a randomized complete block design with three replicates. Each plot consisted of eight plants spaced at 2 × 3 m at the Cocoa Research Institute of Ghana. There were significant (p < 0.001) differences among clones for all the traits assessed. Broad sense heritability was low-to-moderate for all the traits evaluated with the highest (0.34) observed for cumulative yield (CY). Cumulative yield was genetically correlated (p < 0.001) with span and number of laterals (NOL). For the growth traits, NOL was the most strongly associated with CY (rg = 0.49, p < 0.001). The results revealed that selection based on early years’ yield (MY1) could be as effective as selection based on CY (rg = 0.87, p < 0.001). Our findings indicate that there is significant genetic variation among the test clones for the parameters assessed and presents a good opportunity for future variety development.
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Affiliation(s)
- Abraham Akpertey
- Cocoa Research Institute of Ghana, P. O. Box 8, New Tafo-Akim, ER, Ghana
| | | | | | - Atta Ofori
- Cocoa Research Institute of Ghana, P. O. Box 8, New Tafo-Akim, ER, Ghana
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26
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Tournebize R, Borner L, Manel S, Meynard CN, Vigouroux Y, Crouzillat D, Fournier C, Kassam M, Descombes P, Tranchant-Dubreuil C, Parrinello H, Kiwuka C, Sumirat U, Legnate H, Kambale JL, Sonké B, Mahinga JC, Musoli P, Janssens SB, Stoffelen P, de Kochko A, Poncet V. Ecological and genomic vulnerability to climate change across native populations of Robusta coffee (Coffea canephora). GLOBAL CHANGE BIOLOGY 2022; 28:4124-4142. [PMID: 35527235 DOI: 10.1111/gcb.16191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/11/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
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.
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Affiliation(s)
- Rémi Tournebize
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Leyli Borner
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- INRAE, Le Rheu, France
| | - Stéphanie Manel
- CEFE, CNRS, EPHE-PSL University, IRD, Univ Montpellier, Montpellier, France
| | - Christine N Meynard
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Yves Vigouroux
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
| | | | - Coralie Fournier
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- School of Medicine, University of Geneva, Geneva, Switzerland
| | - Mohamed Kassam
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- Danone Nutricia Research, Singapore
| | - Patrick Descombes
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
| | | | - Hugues Parrinello
- CNRS, INSERM, Univ. Montpellier, Montpellier, France
- Montpellier GenomiX, France Génomique, Montpellier, France
| | | | | | | | - Jean-Léon Kambale
- University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | | | | | - Steven B Janssens
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | | | - Valérie Poncet
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
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27
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Manda L, Idohou R, Assogbadjo AE, Agbangla C. Climate Change Reveals Contractions and Expansions in the Distribution of Suitable Habitats for the Neglected Crop Wild Relatives of the Genus Vigna (Savi) in Benin. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.870041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sustainable conservation of crop wild relatives is one of the pathways to securing global food security amid climate change threats to biodiversity. However, their conservation is partly limited by spatio-temporal distribution knowledge gaps mostly because they are not morphologically charismatic species to attract conservation attention. Therefore, to contribute to the conservation planning of crop wild relatives, this study assessed the present-day distribution and predicted the potential effect of climate change on the distribution of 15 Vigna crop wild relative taxa in Benin under two future climate change scenarios (RCP 4.5 and RCP 8.5) at the 2055-time horizon. MaxEnt model, species occurrence records, and a combination of climate- and soil-related variables were used. The model performed well (AUC, mean = 0.957; TSS, mean = 0.774). The model showed that (i) precipitation of the driest quarter and isothermality were the dominant environmental variables influencing the distribution of the 15 wild Vigna species in Benin; (ii) about half of the total land area of Benin was potentially a suitable habitat of the studied species under the present climate; (iii) nearly one-third of the species may shift their potentially suitable habitat ranges northwards and about half of the species may lose their suitable habitats by 5 to 40% by 2055 due to climate change; and (iv) the existing protected area network in Benin was ineffective in conserving wild Vigna under the current or future climatic conditions, as it covered only about 10% of the total potentially suitable habitat of the studied species. The study concludes that climate change will have both negative and positive effects on the habitat suitability distribution of Vigna crop wild relatives in Benin such that the use of the existing protected areas alone may not be the only best option to conserve the wild Vigna diversity. Integrating multiple in situ and ex situ conservation approaches taking into account “other effective area-based conservation measures” is recommended. This study provides a crucial step towards the development of sustainable conservation strategies for Vigna crop wild relatives in Benin and West Africa.
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28
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Giulia S, Patrizia R, Chiara C, Carlo B, Erica L. Acrylamide in coffee: what is known and what still needs to be explored. A review. Food Chem 2022; 393:133406. [DOI: 10.1016/j.foodchem.2022.133406] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 05/18/2022] [Accepted: 06/03/2022] [Indexed: 12/12/2022]
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29
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Koutouleas A, Sarzynski T, Bordeaux M, Bosselmann AS, Campa C, Etienne H, Turreira-García N, Rigal C, Vaast P, Ramalho JC, Marraccini P, Ræbild A. Shaded-Coffee: A Nature-Based Strategy for Coffee Production Under Climate Change? A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.877476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Coffee is deemed to be a high-risk crop in light of upcoming climate changes. Agroforestry practices have been proposed as a nature-based strategy for coffee farmers to mitigate and adapt to future climates. However, with agroforestry systems comes shade, a highly contentious factor for coffee production in terms of potential yield reduction, as well as additional management needs and interactions between shade trees and pest and disease. In this review, we summarize recent research relating to the effects of shade on (i) farmers' use and perceptions, (ii) the coffee microenvironment, (iii) pest and disease incidence, (iv) carbon assimilation and phenology of coffee plants, (v) coffee quality attributes (evaluated by coffee bean size, biochemical compounds, and cup quality tests), (vi) breeding of new Arabica coffee F1 hybrids and Robusta clones for future agroforestry systems, and (vii) coffee production under climate change. Through this work, we begin to decipher whether shaded systems are a feasible strategy to improve the coffee crop sustainability in anticipation of challenging climate conditions. Further research is proposed for developing new coffee varieties adapted to agroforestry systems (exhibiting traits suitable for climate stressors), refining extension tools by selecting locally-adapted shade trees species and developing policy and economic incentives enabling the adoption of sustainable agroforestry practices.
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30
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Zewdie B, Bawin Y, Tack AJM, Nemomissa S, Tesfaye K, Janssens SB, Van Glabeke S, Roldán-Ruiz I, Ruttink T, Honnay O, Hylander K. Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases. Mol Ecol 2022; 32:2484-2503. [PMID: 35377502 DOI: 10.1111/mec.16458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 11/27/2022]
Abstract
Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.
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Affiliation(s)
- Beyene Zewdie
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Yves Bawin
- Plant Conservation and Population Biology, KU Leuven, Leuven, Belgium.,Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Zwijnaarde, Belgium.,Crop Wild Relatives and Useful Plants, Meise Botanic Garden, Meise, Belgium
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sileshi Nemomissa
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Steven B Janssens
- Crop Wild Relatives and Useful Plants, Meise Botanic Garden, Meise, Belgium.,Department of Biology, KU Leuven, Leuven, Belgium.,Leuven Plant Institute, Heverlee, Belgium
| | - Sabine Van Glabeke
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Zwijnaarde, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Olivier Honnay
- Plant Conservation and Population Biology, KU Leuven, Leuven, Belgium.,Leuven Plant Institute, Heverlee, Belgium
| | - Kristoffer Hylander
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
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31
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de Aquino SO, Kiwuka C, Tournebize R, Gain C, Marraccini P, Mariac C, Bethune K, Couderc M, Cubry P, Andrade AC, Lepelley M, Darracq O, Crouzillat D, Anten N, Musoli P, Vigouroux Y, de Kochko A, Manel S, François O, Poncet V. Adaptive potential of
Coffea canephora
from Uganda in response to climate change. Mol Ecol 2022; 31:1800-1819. [DOI: 10.1111/mec.16360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/12/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Affiliation(s)
| | - Catherine Kiwuka
- NARO Kampala Uganda
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | - Clément Gain
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
| | | | - Cédric Mariac
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Kévin Bethune
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Marie Couderc
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | | | | | | | | | | | - Niels Anten
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | | | | | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD Montpellier France
| | - Olivier François
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
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32
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de Abreu DP, Roda NDM, de Abreu GP, Bernado WDP, Rodrigues WP, Campostrini E, Rakocevic M. Kaolin Film Increases Gas Exchange Parameters of Coffee Seedlings During Transference From Nursery to Full Sunlight. FRONTIERS IN PLANT SCIENCE 2022; 12:784482. [PMID: 35069643 PMCID: PMC8777232 DOI: 10.3389/fpls.2021.784482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Increases in water use efficiency (WUE) and the reduction of negative impacts of high temperatures associated with high solar radiation are being achieved with the application of fine particle film of calcined and purified kaolin (KF) on the leaves and fruits of various plant species. KF was applied on young Coffea arabica and Coffea canephora plants before their transition from nursery to full sunlight during autumn and summer. The effects of KF were evaluated through the responses of leaf temperature (Tleaf), net CO2 assimilation rate (A), stomatal conductance (g s), transpiration (E), WUE, crop water stress index (CWSI), index of relative stomatal conductance (Ig), initial fluorescence (F0), and photosynthetic index (PI) in the first 2-3 weeks after the plant transitions to the full sun. All measurements were performed at midday. In Coffea plants, KF decreased the Tleaf up to 6.7°C/5.6°C and reduced the CWSI. The plants that were not protected with KF showed lower A, g s, E, and Ig than those protected with KF. C. canephora plants protected with KF achieved higher WUE compared with those not protected by 11.23% in autumn and 95.58% in summer. In both Coffea sp., KF application reduced F0, indicating reduced physical dissociation of the PSII reaction centers from the light-harvesting system, which was supported with increased PI. The use of KF can be recommended as a management strategy in the transition of Coffea seedlings from the nursery shade to the full sunlight, to protect leaves against the excessive solar radiation and high temperatures, especially in C. canephora during the summer.
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Affiliation(s)
- Deivisson Pelegrino de Abreu
- Laboratory for Plant Genetic Breeding (LMGV), State University of the North Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
| | - Newton de Matos Roda
- Department of Exact, Environmental and Technological Sciences (CEATEC), Pontifical Catholic University of Campinas, Campinas, Brazil
| | - Gideao Pelegrino de Abreu
- Business School and Polytechnic School, MBA in Business Technology, Data Science and Big Data, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Wallace de Paula Bernado
- Laboratory for Plant Genetic Breeding (LMGV), State University of the North Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
| | - Weverton Pereira Rodrigues
- Laboratory for Plant Genetic Breeding (LMGV), State University of the North Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
- Center of Agricultural, Natural and Literary Sciences, State University of the Tocantina Region of Maranhão (UEMASUL), Estreito, Maranhão, Brazil
| | - Eliemar Campostrini
- Laboratory for Plant Genetic Breeding (LMGV), State University of the North Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
| | - Miroslava Rakocevic
- Laboratory for Plant Genetic Breeding (LMGV), State University of the North Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
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Krishnan S, Pruvot-Woehl S, Davis AP, Schilling T, Moat J, Solano W, Al Hakimi A, Montagnon C. Validating South Sudan as a Center of Origin for Coffea arabica: Implications for Conservation and Coffee Crop Improvement. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.761611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cultivated Arabica coffee outside Ethiopia is plagued by low genetic diversity, compromising disease resistance, climate resiliency and sensory potential. Access to the wider genetic diversity of this species may circumvent some of these problems. In addition to Ethiopia, South Sudan has been postulated as a center of origin for Arabica coffee, but this has never been genetically confirmed. We used simple sequence repeat (SSR) markers to assess the genetic diversity of wild and cultivated populations of Arabica coffee from the Boma Plateau in South Sudan, against farmed accessions (of wild origin) from Ethiopia, Yemen, and global cultivars. Our results not only validate Boma Plateau as part of the natural distribution and as a center of origin for Arabica coffee but also indicate that wild populations in South Sudan are genetically distinct from Ethiopian Arabica. This newly identified genetic diversity within Arabica could have the potential for crop improvement through selection and use in breeding programs. Observations and analyses show that the extent and health of the wild population of Arabica in South Sudan have declined. Urgent action should be taken to conserve (in situ and ex situ) the unique, remaining genetic diversity of wild Arabica populations in South Sudan.
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Davis AP, Gargiulo R, Almeida INDM, Caravela MI, Denison C, Moat J. Hot Coffee: The Identity, Climate Profiles, Agronomy, and Beverage Characteristics of Coffea racemosa and C. zanguebariae. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.740137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Climate change poses a considerable challenge for coffee farming, due to increasing temperatures, worsening weather perturbations, and shifts in the quantity and timing of precipitation. Of the actions required for ensuring climate resilience for coffee, changing the crop itself is paramount, and this may have to include using alternative coffee crop species. In this study we use a multidisciplinary approach to elucidate the identity, distribution, and attributes, of two minor coffee crop species from East Africa: Coffea racemosa and C. zanguebariae. Using DNA sequencing and morphology, we elucidate their phylogenetic relationships and confirm that they represent two distinct but closely related species. Climate profiling is used to understand their basic climatic requirements, which are compared to those of Arabica (C. arabica) and robusta (C. canephora) coffee. Basic agronomic data (including yield) and sensory information are provided and evaluated. Coffea racemosa and C. zanguebariae possess useful traits for coffee crop plant development, particularly heat tolerance, low precipitation requirement, high precipitation seasonality (dry season tolerance) and rapid fruit development (c. 4 months flowering to mature fruit). These attributes would be best accessed via breeding programs, although these species also have niche-market potential, particularly after further pre-farm selection and post-harvest optimization.
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Hung Y, Lee F, Lin C. Classification of coffee bean categories based upon analysis of fatty acid ingredients. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ying‐Che Hung
- Mechatronic Engineering Institute Huafan University New Taipei Taiwan
| | - Fu‐Shin Lee
- Mechatronic Engineering Institute Huafan University New Taipei Taiwan
| | - Chen‐I Lin
- College of Mechanical and Electrical Engineering Wuyi University Wuyishan China
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Rodrigues AM, Jorge T, Osorio S, Pott DM, Lidon FC, DaMatta FM, Marques I, Ribeiro-Barros AI, Ramalho JC, António C. Primary Metabolite Profile Changes in Coffea spp. Promoted by Single and Combined Exposure to Drought and Elevated CO 2 Concentration. Metabolites 2021; 11:metabo11070427. [PMID: 34209624 PMCID: PMC8303404 DOI: 10.3390/metabo11070427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Climate change scenarios pose major threats to many crops worldwide, including coffee. We explored the primary metabolite responses in two Coffea genotypes, C. canephora cv. Conilon Clone 153 and C. arabica cv. Icatu, grown at normal (aCO2) or elevated (eCO2) CO2 concentrations of 380 or 700 ppm, respectively, under well-watered (WW), moderate (MWD), or severe (SWD) water deficit conditions, in order to assess coffee responses to drought and how eCO2 can influence such responses. Primary metabolites were analyzed with a gas chromatography time-of-flight mass spectrometry metabolomics platform (GC-TOF-MS). A total of 48 primary metabolites were identified in both genotypes (23 amino acids and derivatives, 10 organic acids, 11 sugars, and 4 other metabolites), with differences recorded in both genotypes. Increased metabolite levels were observed in CL153 plants under single and combined conditions of aCO2 and drought (MWD and SWD), as opposed to the observed decreased levels under eCO2 in both drought conditions. In contrast, Icatu showed minor differences under MWD, and increased levels (especially amino acids) only under SWD at both CO2 concentration conditions, although with a tendency towards greater increases under eCO2. Altogether, CL153 demonstrated large impact under MWD, and seemed not to benefit from eCO2 in either MWD and SWD, in contrast with Icatu.
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Affiliation(s)
- Ana M. Rodrigues
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; (A.M.R.); (T.J.)
| | - Tiago Jorge
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; (A.M.R.); (T.J.)
| | - Sonia Osorio
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga—Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain; (S.O.); (D.M.P.)
| | - Delphine M. Pott
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga—Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain; (S.O.); (D.M.P.)
| | - Fernando C. Lidon
- GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal;
| | - Fábio M. DaMatta
- Departamento de Biologia Vegetal, Universidade Federal Viçosa (UFV), Viçosa 36570-090, Brazil;
| | - Isabel Marques
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal;
| | - Ana I. Ribeiro-Barros
- GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal;
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal;
- Correspondence: (A.I.R.-B.); (J.C.R.); (C.A.)
| | - José C. Ramalho
- GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal;
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal;
- Correspondence: (A.I.R.-B.); (J.C.R.); (C.A.)
| | - Carla António
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; (A.M.R.); (T.J.)
- Correspondence: (A.I.R.-B.); (J.C.R.); (C.A.)
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Coffee Brews: Are They a Source of Macroelements in Human Nutrition? Foods 2021; 10:foods10061328. [PMID: 34207680 PMCID: PMC8227654 DOI: 10.3390/foods10061328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
Coffee brews, made by pouring water on coffee grounds or brewing in an espresso machine, are among the most popular beverages. The aim of this study was to summarize data on the content of macroelements (sodium, potassium, calcium, magnesium, and phosphorus) in coffee brews prepared with different methods, as well as to review the factors influencing the content of the elements. Studies from 2000 to 2020, published in the PubMed and Google Scholar databases, were reviewed. Taking into account the results presented by the authors, we calculated that one portion of coffee brew can cover 7.5% or 6.4% (for women and men) and 6.6% of the daily requirement for magnesium and potassium, respectively. Coffee provides slightly lower amounts of phosphorus (up to 2.2%), sodium (up to 2.2%), and calcium (up to 0.7% of the daily requirement for women and 0.6% for men). If coffee is drunk in the quantity of three to four cups, it can be an important source of magnesium, considering the risk of magnesium deficiency in modern societies.
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Li Z, Zhang C, Zhang Y, Zeng W, Cesarino I. Coffee cell walls—composition, influence on cup quality and opportunities for coffee improvements. FOOD QUALITY AND SAFETY 2021. [DOI: 10.1093/fqsafe/fyab012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The coffee beverage is the second most consumed drink worldwide after water. In coffee beans, cell wall storage polysaccharides (CWSPs) represent around 50 per cent of the seed dry mass, mainly consisting of galactomannans and arabinogalactans. These highly abundant structural components largely influence the organoleptic properties of the coffee beverage, mainly due to the complex changes they undergo during the roasting process. From a nutritional point of view, coffee CWSPs are soluble dietary fibers shown to provide numerous health benefits in reducing the risk of human diseases. Due to their influence on coffee quality and their health-promoting benefits, CWSPs have been attracting significant research attention. The importance of cell walls to the coffee industry is not restricted to beans used for beverage production, as several coffee by-products also present high concentrations of cell wall components. These by-products include cherry husks, cherry pulps, parchment skin, silver skin, and spent coffee grounds, which are currently used or have the potential to be utilized either as food ingredients or additives, or for the generation of downstream products such as enzymes, pharmaceuticals, and bioethanol. In addition to their functions during plant development, cell walls also play a role in the plant’s resistance to stresses. Here, we review several aspects of coffee cell walls, including chemical composition, biosynthesis, their function in coffee’s responses to stresses, and their influence on coffee quality. We also propose some potential cell wall–related biotechnological strategies envisaged for coffee improvements.
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Affiliation(s)
| | | | | | | | - Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Olechno E, Puścion-Jakubik A, Zujko ME, Socha K. Influence of Various Factors on Caffeine Content in Coffee Brews. Foods 2021; 10:1208. [PMID: 34071879 PMCID: PMC8228209 DOI: 10.3390/foods10061208] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/25/2022] Open
Abstract
Coffee brews are one of the most popular drinks. They are consumed for caffeine and its stimulant properties. The study aimed to summarize data on the influence of various factors on caffeine content in brews prepared with different methods. The study was carried out using a literature review from 2010-2020. PubMed and Google Scholar databases were searched. Data on caffeine content was collected by analyzing the following factors: the influence of species, brewing time, water temperature, pressure, degree of roast, grinding degree, water type, water/coffee ratio as well as other factors (such as geographical origin). To sum up, converting caffeine content to 1 L of the brew, the highest content is that of brews prepared in an espresso machine (portafilter), with the amount of 7.5 g of a coffee blend (95% Robusta + 5% Arabica), and water (the volume of coffee brew was 25 mL) at a temperature of 92 °C and a pressure of 7 bar, but the highest content in one portion was detected in a brew of 50 g of Robusta coffee poured with 500 mL of cold water (25 °C) and boiled.
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Affiliation(s)
- Ewa Olechno
- Department of Food Biotechnology, Faculty of Health Science, Medical University of Białystok, Szpitalna 37 Street, 15-295 Białystok, Poland; (E.O.); (M.E.Z.)
| | - Anna Puścion-Jakubik
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, Mickiewicza 2D Street, 15-222 Białystok, Poland;
| | - Małgorzata Elżbieta Zujko
- Department of Food Biotechnology, Faculty of Health Science, Medical University of Białystok, Szpitalna 37 Street, 15-295 Białystok, Poland; (E.O.); (M.E.Z.)
| | - Katarzyna Socha
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, Mickiewicza 2D Street, 15-222 Białystok, Poland;
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40
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Semedo JN, Rodrigues AP, Lidon FC, Pais IP, Marques I, Gouveia D, Armengaud J, Silva MJ, Martins S, Semedo MC, Dubberstein D, Partelli FL, Reboredo FH, Scotti-Campos P, Ribeiro-Barros AI, DaMatta FM, Ramalho JC. Intrinsic non-stomatal resilience to drought of the photosynthetic apparatus in Coffea spp. is strengthened by elevated air [CO2]. TREE PHYSIOLOGY 2021; 41:708-727. [PMID: 33215189 DOI: 10.1093/treephys/tpaa158] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/11/2020] [Indexed: 05/10/2023]
Abstract
Growing water restrictions associated with climate changes constitute daunting challenges to crop performance. This study unveils the impacts of moderate (MWD) or severe (SWD) water deficit, and their interaction with air [CO2], on the photosynthetic apparatus of Coffea canephora Pierre ex A. Froehner cv. Conilon Clone 153 (CL153) and Coffea arabica L. cv. Icatu. Seven year-old potted plants grown under 380 (aCO2) or 700 μl l -1 (eCO2) [CO2] gradually reached predawn water potentials between -1.6 and -2.1 MPa (MWD), and below -3.5 MPa (SWD). Under drought, stomata closure was chiefly related to abscisic acid (ABA) rise. Increasing drought severity progressively affected gas exchange and fluorescence parameters in both genotypes, with non-stomatal limitations becoming gradually dominating, especially regarding the photochemical and biochemical components of CL153 SWD plants. In contrast, Icatu plants were highly tolerant to SWD, with minor, if any, negative impacts on the potential photosynthetic functioning and components (e.g., Amax, Fv/Fm, electron carriers, photosystems (PSs) and ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO) activities). Besides, drought-stressed Icatu plants displayed increased abundance of a large set of proteins associated with the photosynthetic apparatus (PSs, light-harvesting complexes, cyclic electron flow, RuBisCO activase) regardless of [CO2]. Single eCO2 did not promote stomatal and photosynthetic down-regulation in both genotypes. Instead, eCO2 increased photosynthetic performance, moderately reinforced photochemical (PSs activity, electron carriers) and biochemical (RuBisCO, ribulose-5-phosphate kinase) components, whereas photoprotective mechanisms and protein abundance remained mostly unaffected. In both genotypes, under MWD, eCO2 superimposition delayed stress severity and promoted photosynthetic functioning with lower energy dissipation and PSII impacts, whereas stomatal closure was decoupled from increases in ABA. In SWD plants, most impacts on the photosynthetic performance were reduced by eCO2, especially in the moderately drought affected CL153 genotype, although maintaining RuBisCO as the most sensitive component, deserving special breeder's attention to improve coffee sustainability under future climate scenarios.
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Affiliation(s)
- José N Semedo
- Unidade de Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Qta. Marquês, Av. República, Oeiras 2784-505, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, Caparica 2829-516, Portugal
| | - Ana P Rodrigues
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras 2784-505, Portugal
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, Lisboa 1349-017, Portugal
| | - Fernando C Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, Caparica 2829-516, Portugal
| | - Isabel P Pais
- Unidade de Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Qta. Marquês, Av. República, Oeiras 2784-505, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, Caparica 2829-516, Portugal
| | - Isabel Marques
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras 2784-505, Portugal
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, Lisboa 1349-017, Portugal
| | - Duarte Gouveia
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, Bagnols-sur-Cèze F-F-30200, France
| | - Jean Armengaud
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, Bagnols-sur-Cèze F-F-30200, France
| | - Maria J Silva
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, Caparica 2829-516, Portugal
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras 2784-505, Portugal
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, Lisboa 1349-017, Portugal
| | - Sónia Martins
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, Caparica 2829-516, Portugal
- Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, Lisboa 1959-007, Portugal
| | - Magda C Semedo
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, Caparica 2829-516, Portugal
- Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, Lisboa 1959-007, Portugal
| | - Danielly Dubberstein
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras 2784-505, Portugal
- Departamento de Ciências Agrárias e Biológicas (DCAB), Centro Universitário do Norte do Espírito Santo (CEUNES), Universidade Federal Espírito Santo (UFES), Rod. BR 101 Norte, Km. 60, Bairro Litorâneo, São Mateu-ES, CEP 29932-540, Brazil
| | - Fábio L Partelli
- Departamento de Ciências Agrárias e Biológicas (DCAB), Centro Universitário do Norte do Espírito Santo (CEUNES), Universidade Federal Espírito Santo (UFES), Rod. BR 101 Norte, Km. 60, Bairro Litorâneo, São Mateu-ES, CEP 29932-540, Brazil
| | - Fernando H Reboredo
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, Caparica 2829-516, Portugal
| | - Paula Scotti-Campos
- Unidade de Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Qta. Marquês, Av. República, Oeiras 2784-505, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, Caparica 2829-516, Portugal
| | - Ana I Ribeiro-Barros
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, Caparica 2829-516, Portugal
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras 2784-505, Portugal
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, Lisboa 1349-017, Portugal
| | - Fábio M DaMatta
- Departamento de Biologia Vegetal, Universidade Federal Viçosa, Viçosa, MG 36570-900, Brazil
| | - José C Ramalho
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, Caparica 2829-516, Portugal
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras 2784-505, Portugal
- Plant Stress and Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, Lisboa 1349-017, Portugal
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Raharimalala N, Rombauts S, McCarthy A, Garavito A, Orozco-Arias S, Bellanger L, Morales-Correa AY, Froger S, Michaux S, Berry V, Metairon S, Fournier C, Lepelley M, Mueller L, Couturon E, Hamon P, Rakotomalala JJ, Descombes P, Guyot R, Crouzillat D. The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago. Sci Rep 2021; 11:8119. [PMID: 33854089 PMCID: PMC8046976 DOI: 10.1038/s41598-021-87419-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/23/2021] [Indexed: 02/02/2023] Open
Abstract
Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.
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Affiliation(s)
- Nathalie Raharimalala
- grid.433118.c0000 0001 2302 6762Centre National de Recherche Appliquée au Développement Rural, BP 1444, 101 Ambatobe, Antananarivo Madagascar
| | - Stephane Rombauts
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,grid.11486.3a0000000104788040VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Andrew McCarthy
- grid.418923.50000 0004 0638 528XEuropean Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Andréa Garavito
- grid.7779.e0000 0001 2290 6370Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia ,Centro de Bioinformática y biología computacional de Colombia – BIOS, Ecoparque los Yarumos, Manizales, Caldas, Colombia
| | - Simon Orozco-Arias
- grid.7779.e0000 0001 2290 6370Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia ,grid.441739.c0000 0004 0486 2919Universidad Autónoma de Manizales, Manizales, Colombia
| | - Laurence Bellanger
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Alexa Yadira Morales-Correa
- grid.7779.e0000 0001 2290 6370Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Solène Froger
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Stéphane Michaux
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Victoria Berry
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Sylviane Metairon
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland
| | - Coralie Fournier
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland ,grid.8591.50000 0001 2322 4988Present Address: University of Geneva, CMU-Décanat, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Maud Lepelley
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
| | - Lukas Mueller
- grid.5386.8000000041936877XBoyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
| | - Emmanuel Couturon
- grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Perla Hamon
- grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Jean-Jacques Rakotomalala
- grid.433118.c0000 0001 2302 6762Centre National de Recherche Appliquée au Développement Rural, BP 1444, 101 Ambatobe, Antananarivo Madagascar
| | - Patrick Descombes
- grid.419905.00000 0001 0066 4948Nestle Research, Société des Produits Nestlé SA, 1015 Lausanne, Switzerland
| | - Romain Guyot
- grid.441739.c0000 0004 0486 2919Universidad Autónoma de Manizales, Manizales, Colombia ,grid.121334.60000 0001 2097 0141Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Dominique Crouzillat
- Nestle Research-Plant Science Research Unit, BP 49716, 37097 Tours Cedex 2, France
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Davis AP, Mieulet D, Moat J, Sarmu D, Haggar J. Arabica-like flavour in a heat-tolerant wild coffee species. NATURE PLANTS 2021; 7:413-418. [PMID: 33875832 DOI: 10.1038/s41477-021-00891-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
There are numerous factors to consider when developing climate-resilient coffee crops, including the ability to tolerate altered climatic conditions, meet agronomic and value chain criteria, and satisfy consumer preferences for flavour (aroma and taste). We evaluated the sensory characteristics and key environmental requirements for the enigmatic narrow-leaved coffee (Coffea stenophylla), a wild species from Upper West Africa1. We confirm historical reports of a superior flavour1-3 and uniquely, and remarkably, reveal a sensory profile analogous to high-quality Arabica coffee. We demonstrate that this species grows and crops under the same range of key climatic conditions as (sensorially inferior) robusta and Liberica coffee4-9 and at a mean annual temperature 6.2-6.8 °C higher than Arabica coffee, even under equivalent rainfall conditions. This species substantially broadens the climate envelope for high-quality coffee and could provide an important resource for the development of climate-resilient coffee crop plants.
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Affiliation(s)
| | - Delphine Mieulet
- CIRAD, UMR DIADE, Montpellier, France
- DIADE, Univ. Montpellier, IRD, Montpellier, France
| | | | | | - Jeremy Haggar
- Department of Agriculture, Health and Environment, Natural Resources Institute, University of Greenwich, Medway, UK
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The Unexplored Socio-Cultural Benefits of Coffee Plants: Implications for the Sustainable Management of Ethiopia’s Coffee Forests. SUSTAINABILITY 2021. [DOI: 10.3390/su13073912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Coffee is among the most popular commodity crops around the globe and supports the livelihoods of millions of households along its value chain. Historically, the broader understanding of the roles of coffee has been limited to its commercial value, which largely is derived from coffee, the drink. This study, using in-depth interviews and focus group discussions, explores some of the unrevealed socio-cultural services of coffee of which many people are not aware. The study was conducted in Gomma district, Jimma Zone, Oromia National Regional state, Ethiopia, where arabica coffee was first discovered in its natural habitat. Relying on a case study approach, our study uses ethnographic study methods whereby results are presented from the communities’ perspectives and the subsequent discussions with the communities on how the community perspectives could help to better manage coffee ecosystems. Coffee’s utilities and symbolic functions are numerous—food and drink, commodity crop, religious object, communication medium, heritage and inheritance. Most of the socio-cultural services are not widely known, and hence are not part of the benefits accounting of coffee systems. Understanding and including such socio-cultural benefits into the wider benefits of coffee systems could help in promoting improved management of the Ethiopian coffee forests that are the natural gene pools of this highly valuable crop.
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A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO 2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora. Int J Mol Sci 2021; 22:ijms22063125. [PMID: 33803866 PMCID: PMC8003141 DOI: 10.3390/ijms22063125] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
Understanding the effect of extreme temperatures and elevated air (CO2) is crucial for mitigating the impacts of the coffee industry. In this work, leaf transcriptomic changes were evaluated in the diploid C. canephora and its polyploid C. arabica, grown at 25 °C and at two supra-optimal temperatures (37 °C, 42 °C), under ambient (aCO2) or elevated air CO2 (eCO2). Both species expressed fewer genes as temperature rose, although a high number of differentially expressed genes (DEGs) were observed, especially at 42 °C. An enrichment analysis revealed that the two species reacted differently to the high temperatures but with an overall up-regulation of the photosynthetic machinery until 37 °C. Although eCO2 helped to release stress, 42 °C had a severe impact on both species. A total of 667 photosynthetic and biochemical related-DEGs were altered with high temperatures and eCO2, which may be used as key probe genes in future studies. This was mostly felt in C. arabica, where genes related to ribulose-bisphosphate carboxylase (RuBisCO) activity, chlorophyll a-b binding, and the reaction centres of photosystems I and II were down-regulated, especially under 42°C, regardless of CO2. Transcriptomic changes showed that both species were strongly affected by the highest temperature, although they can endure higher temperatures (37 °C) than previously assumed.
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Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation. PLoS One 2021; 16:e0245965. [PMID: 33556074 PMCID: PMC7870046 DOI: 10.1371/journal.pone.0245965] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 01/12/2021] [Indexed: 11/22/2022] Open
Abstract
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.
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46
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Craparo ACW, Van Asten PJA, Läderach P, Jassogne LTP, Grab SW. Warm nights drive Coffea arabica ripening in Tanzania. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2021; 65:181-192. [PMID: 32929544 DOI: 10.1007/s00484-020-02016-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/30/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Studies have demonstrated that plant phenophases (e.g. budburst, flowering, ripening) are occurring increasingly earlier in the season across diverse ecologies globally. Despite much interest that climate change impacts have on coffee (Coffea arabica), relatively little is known about the driving factors determining its phenophases. Using high-resolution microclimatic data, this study provides initial insights on how climate change is impacting C. arabica phenophases in Tanzania. In particular, we use generalized additive models to show how warming nocturnal temperatures (Tnight), as opposed to day-time or maximum temperatures, have a superseding effect on the ripening of coffee and subsequent timing of harvest. A warm night index (WNI), generated from mean nocturnal temperature, permits accurate prediction of the start of the harvest season, which is superior to existing methods using growing degree days (GDD). The non-linear function indicates that a WNI of 15 °C is associated with the latest ripening coffee cherries (adjusted R2 = 0.95). As the WNI increases past the inflection point of ~ 16 °C, ripening occurs earlier and progresses more or less linearly at a rate of ~ 17 ± 1.95 days for every 1 °C increase in WNI. Using the WNI will thus not only allow farmers to more accurately predict their harvest start date, but also assist with identifying the most suitable adaptation strategies which may reduce harvest-related costs and buffer potential losses in quality and production.
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Affiliation(s)
- A C W Craparo
- International Center for Tropical Agriculture (CIAT), Hanoi, Vietnam.
- School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, P/Bag3, WITS, Johannesburg, 2050, South Africa.
| | | | - P Läderach
- International Center for Tropical Agriculture (CIAT), Rome, Italy
| | - L T P Jassogne
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | - S W Grab
- School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, P/Bag3, WITS, Johannesburg, 2050, South Africa
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Nic Lughadha E, Bachman SP, Leão TCC, Forest F, Halley JM, Moat J, Acedo C, Bacon KL, Brewer RFA, Gâteblé G, Gonçalves SC, Govaerts R, Hollingsworth PM, Krisai‐Greilhuber I, Lirio EJ, Moore PGP, Negrão R, Onana JM, Rajaovelona LR, Razanajatovo H, Reich PB, Richards SL, Rivers MC, Cooper A, Iganci J, Lewis GP, Smidt EC, Antonelli A, Mueller GM, Walker BE. Extinction risk and threats to plants and fungi. PLANTS, PEOPLE, PLANET 2020; 2:389-408. [PMID: 0 DOI: 10.1002/ppp3.10146] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/09/2020] [Indexed: 05/29/2023]
Affiliation(s)
| | - Steven P. Bachman
- Conservation Science Department Royal Botanic Gardens, Kew Richmond UK
| | | | - Félix Forest
- Analytical Methods Royal Botanic Gardens, Kew Richmond UK
| | - John M. Halley
- Laboratory of Ecology Department of Biological Applications & Technology University of Ioannina Ioannina Greece
| | - Justin Moat
- Bioinformatics and Spatial Analysis Department Royal Botanic Gardens, Kew Richmond UK
| | - Carmen Acedo
- Department of Biodiversity and Environment Management Faculty of Biological and Environmental Sciences Campus of Vegazana University of León León Spain
| | - Karen L. Bacon
- Botany & Plant Sciences School of Natural Sciences National University of Ireland Galway Ireland
| | - Ryan F. A. Brewer
- Conservation Science Department Royal Botanic Gardens, Kew Richmond UK
| | - Gildas Gâteblé
- Equipe ARBOREAL Institut Agronomique néo‐Calédonien Mont‐Dore New Caledonia
| | - Susana C. Gonçalves
- Centre for Functional Ecology Department of Life Sciences University of Coimbra Coimbra Portugal
| | - Rafaël Govaerts
- Bioinformatics and Spatial Analysis Department Royal Botanic Gardens, Kew Richmond UK
| | | | - Irmgard Krisai‐Greilhuber
- Mycology Research Group Division of Systematic and Evolutionary Biology Department of Botany and Biodiversity Research University of Vienna Vienna Austria
| | - Elton J. Lirio
- Departamento de Botânica Instituto de Biociências Universidade de São Paulo São Paulo Brazil
| | | | - Raquel Negrão
- Conservation Science Department Royal Botanic Gardens, Kew Richmond UK
| | - Jean Michel Onana
- Systematics, Biodiversity and Conservation of Plants Faculty of Science University of Yaoundé I & National Herbarium of Cameroon Yaoundé Cameroon
| | - Landy R. Rajaovelona
- Conservation Science Department Royal Botanic Gardens, Kew Richmond UK
- Kew Madagascar Conservation Centre Antananarivo Madagascar
| | - Henintsoa Razanajatovo
- Conservation Science Department Royal Botanic Gardens, Kew Richmond UK
- Kew Madagascar Conservation Centre Antananarivo Madagascar
| | - Peter B. Reich
- Department of Forest Resources University of Minnesota St. Paul MN USA
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
| | | | | | - Amanda Cooper
- Bioinformatics and Spatial Analysis Department Royal Botanic Gardens, Kew Richmond UK
- Department of Biological Sciences Royal HollowayUniversity of London Egham UK
| | - João Iganci
- Instituto de Biologia Departamento de Botânica Universidade Federal de Pelotas Pelotas Brazil
- Instituto de Biociências Programa de Pós‐Graduação em Botânica Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology Royal Botanic Gardens, Kew Richmond UK
| | - Eric C. Smidt
- Departamento de Botânica Universidade Federal do Paraná Curitiba Brazil
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew Richmond UK
- Gothenburg Global Biodiversity Centre Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | - Gregory M. Mueller
- Negaunee Institute for Plant Conservation Science and Action Chicago Botanic Garden Chicago IL USA
| | - Barnaby E. Walker
- Conservation Science Department Royal Botanic Gardens, Kew Richmond UK
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Charr JC, Garavito A, Guyeux C, Crouzillat D, Descombes P, Fournier C, Ly SN, Raharimalala EN, Rakotomalala JJ, Stoffelen P, Janssens S, Hamon P, Guyot R. Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee). Mol Phylogenet Evol 2020; 151:106906. [PMID: 32653553 DOI: 10.1016/j.ympev.2020.106906] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022]
Abstract
For decades coffees were associated with the genus Coffea. In 2011, the closely related genus Psilanthus was subsumed into Coffea. However, results obtained in 2017-based on 28,800 nuclear SNPs-indicated that there is not substantial phylogenetic support for this incorporation. In addition, a recent study of 16 plastid full-genome sequences highlighted an incongruous placement of Coffea canephora (Robusta coffee) between maternal and nuclear trees. In this study, similar global features of the plastid genomes of Psilanthus and Coffea are observed. In agreement with morphological and physiological traits, the nuclear phylogenetic tree clearly separates Psilanthus from Coffea (with exception to C. rhamnifolia, closer to Psilanthus than to Coffea). In contrast, the maternal molecular tree was incongruent with both morphological and nuclear differentiation, with four main clades observed, two of which include both Psilanthus and Coffea species, and two with either Psilanthus or Coffea species. Interestingly, Coffea and Psilanthus taxa sampled in West and Central Africa are members of the same group. Several mechanisms such as the retention of ancestral polymorphisms due to incomplete lineage sorting, hybridization leading to homoploidy (without chromosome doubling) and alloploidy (for C. arabica) are involved in the evolutionary history of the coffee species. While sharing similar morphological characteristics, the genetic relationships within C. canephora have shown that some populations are well differentiated and genetically isolated. Given the position of its closely-related species, we may also consider C. canephora to be undergoing a long process of speciation with an intermediate step of (sub-)speciation.
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Affiliation(s)
- Jean-Claude Charr
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, France.
| | - Andrea Garavito
- Departamento de Ciencias biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Christophe Guyeux
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, France.
| | | | | | | | - Serigne N Ly
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France.
| | | | | | - Piet Stoffelen
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium.
| | - Steven Janssens
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium.
| | - Perla Hamon
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France.
| | - Romain Guyot
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France; Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia.
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49
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Dubberstein D, Lidon FC, Rodrigues AP, Semedo JN, Marques I, Rodrigues WP, Gouveia D, Armengaud J, Semedo MC, Martins S, Simões-Costa MC, Moura I, Pais IP, Scotti-Campos P, Partelli FL, Campostrini E, Ribeiro-Barros AI, DaMatta FM, Ramalho JC. Resilient and Sensitive Key Points of the Photosynthetic Machinery of Coffea spp. to the Single and Superimposed Exposure to Severe Drought and Heat Stresses. FRONTIERS IN PLANT SCIENCE 2020; 11:1049. [PMID: 32733525 PMCID: PMC7363965 DOI: 10.3389/fpls.2020.01049] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/25/2020] [Indexed: 05/23/2023]
Abstract
This study unveils the single and combined drought and heat impacts on the photosynthetic performance of Coffea arabica cv. Icatu and C. canephora cv. Conilon Clone 153 (CL153). Well-watered (WW) potted plants were gradually submitted to severe water deficit (SWD) along 20 days under adequate temperature (25/20°C, day/night), and thereafter exposed to a gradual temperature rise up to 42/30°C, followed by a 14-day water and temperature recovery. Single drought affected all gas exchanges (including Amax ) and most fluorescence parameters in both genotypes. However, Icatu maintained Fv/Fm and RuBisCO activity, and reinforced electron transport rates, carrier contents, and proton gradient regulation (PGR5) and chloroplast NADH dehydrogenase-like (NDH) complex proteins abundance. This suggested negligible non-stomatal limitations of photosynthesis that were accompanied by a triggering of protective cyclic electron transport (CEF) involving both photosystems (PSs). These findings contrasted with declines in RuBisCO and PSs activities, and cytochromes (b559 , f, b563 ) contents in CL153. Remarkable heat tolerance in potential photosynthetic functioning was detected in WW plants of both genotypes (up to 37/28°C or 39/30°C), likely associated with CEF in Icatu. Yet, at 42/30°C the tolerance limit was exceeded. Reduced Amax and increased Ci values reflected non-stomatal limitations of photosynthesis, agreeing with impairments in energy capture (F0 rise), PSII photochemical efficiency, and RuBisCO and Ru5PK activities. In contrast to PSs activities and electron carrier contents, enzyme activities were highly heat sensitive. Until 37/28°C, stresses interaction was largely absent, and drought played the major role in constraining photosynthesis functioning. Harsher conditions (SWD, 42/30°C) exacerbated impairments to PSs, enzymes, and electron carriers, but uncontrolled energy dissipation was mitigated by photoprotective mechanisms. Most parameters recovered fully between 4 and 14 days after stress relief in both genotypes, although some aftereffects persisted in SWD plants. Icatu was more drought tolerant, with WW and SWD plants usually showing a faster and/or greater recovery than CL153. Heat affected both genotypes mostly at 42/30°C, especially in SWD and Icatu plants. Overall, photochemical components were highly tolerant to heat and to stress interaction in contrast to enzymes that deserve special attention by breeding programs to increase coffee sustainability in climate change scenarios.
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Affiliation(s)
- Danielly Dubberstein
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), São Mateus, Brazil
| | - Fernando C. Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Ana P. Rodrigues
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
| | - José N. Semedo
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
- Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
| | - Isabel Marques
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
| | - Weverton P. Rodrigues
- Setor Fisiologia Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Univ. Estadual Norte Fluminense (UENF), Darcy Ribeiro, Brazil
- Centro de Ciências Agrárias, Naturais e Letras, Universidade Estadual da Região Tocantina do Maranhão, Estreito, Brazil
| | - Duarte Gouveia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Bagnols-sur-Cèze, France
| | - Magda C. Semedo
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
- Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
| | - Sónia Martins
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
- Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
| | - Maria C. Simões-Costa
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
| | - I. Moura
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
| | - Isabel P. Pais
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
- Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
| | - Paula Scotti-Campos
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
- Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal
| | - Fábio L. Partelli
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), São Mateus, Brazil
| | - Eliemar Campostrini
- Setor Fisiologia Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Univ. Estadual Norte Fluminense (UENF), Darcy Ribeiro, Brazil
| | - Ana I. Ribeiro-Barros
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
| | - Fábio M. DaMatta
- Dept. Biologia Vegetal, Univ. Federal Viçosa (UFV), Viçosa, Brazil
| | - José C. Ramalho
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Caparica, Portugal
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Cheng B, Smyth HE, Furtado A, Henry RJ. Slower development of lower canopy beans produces better coffee. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4201-4214. [PMID: 32206798 PMCID: PMC7337091 DOI: 10.1093/jxb/eraa151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/19/2020] [Indexed: 06/10/2023]
Abstract
The production of high-quality coffee is being challenged by changing climates in coffee-growing regions. The coffee beans from the upper and lower canopy at different development stages of the same plants were analyzed to investigate the impact of the microenvironment on gene expression and coffee quality. Compared with coffee beans from the upper canopy, lower canopy beans displayed more intense aroma with higher caffeine, trigonelline, and sucrose contents, associated with greater gene expression in the representative metabolic pathways. Global gene expression indicated a longer ripening in the lower canopy, resulting from higher expression of genes relating to growth inhibition and suppression of chlorophyll degradation during early bean ripening. Selection of genotypes or environments that enhance expression of the genes slowing bean development may produce higher quality coffee beans, allowing coffee production in a broader range of available future environments.
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Affiliation(s)
- Bing Cheng
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Heather E Smyth
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
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