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Pereira CM, Bautz KR, Rodríguez MDCH, Saavedra-Tobar LM, Kapeua-Ndacnou M, Belachew-Bekele K, Elliot SL, Evans HC, Barreto RW. Cordyceps cateniannulata: An endophyte of coffee, a parasite of coffee leaf rust and a pathogen of coffee pests. Fungal Biol 2024; 128:1917-1932. [PMID: 39059847 DOI: 10.1016/j.funbio.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 07/28/2024]
Abstract
Here, we report on a Cordyceps species entering into a multi-trophic, multi-kingdom association. Cordyceps cateniannulata, isolated from the stem of wild Coffea arabica in Ethiopia, is shown to function as an endophyte, a mycoparasite and an entomopathogen. A detailed polyphasic taxonomic study, including a multilocus phylogenetic analysis, confirmed its identity. An emended description of C. cateniannulata is provided herein. Previously, this species was known as a pathogen of various insect hosts in both the Old and New World. The endophytic status of C. cateniannulata was confirmed by re-isolating it from inoculated coffee plants. Inoculation studies have further shown that C. cateniannulata is a mycoparasite of Hemileia vastatrix, as well as an entomopathogen of major coffee pests; infecting and killing Hypothenemus hampei and Leucoptera coffeella. This is the first record of C. cateniannulata from Africa, as well as an endophyte and a mycoparasite. The implications for its use as a biocontrol agent are discussed.
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Affiliation(s)
- Caio M Pereira
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Keminy R Bautz
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | | | - Laura M Saavedra-Tobar
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Miraine Kapeua-Ndacnou
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; Institute of Agricultural Research for Development, Regional Biocontrol and Applied Microbiology Laboratory, PO Box 2067, Yaoundé, Cameroon
| | | | - Simon L Elliot
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Harry C Evans
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; CAB International, Bakeham Lane, Egham, Surrey, TW20 9TY, UK
| | - Robert W Barreto
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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Manzoor S, Nabi SU, Rather TR, Gani G, Mir ZA, Wani AW, Ali S, Tyagi A, Manzar N. Advancing crop disease resistance through genome editing: a promising approach for enhancing agricultural production. Front Genome Ed 2024; 6:1399051. [PMID: 38988891 PMCID: PMC11234172 DOI: 10.3389/fgeed.2024.1399051] [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: 03/11/2024] [Accepted: 04/22/2024] [Indexed: 07/12/2024] Open
Abstract
Modern agriculture has encountered several challenges in achieving constant yield stability especially due to disease outbreaks and lack of long-term disease-resistant crop cultivars. In the past, disease outbreaks in economically important crops had a major impact on food security and the economy. On the other hand climate-driven emergence of new pathovars or changes in their host specificity further poses a serious threat to sustainable agriculture. At present, chemical-based control strategies are frequently used to control microbial pathogens and pests, but they have detrimental impact on the environment and also resulted in the development of resistant phyto-pathogens. As a replacement, cultivating engineered disease-resistant crops can help to minimize the negative impact of regular pesticides on agriculture and the environment. Although traditional breeding and genetic engineering have been instrumental in crop disease improvement but they have certain limitations such as labour intensity, time consumption, and low efficiency. In this regard, genome editing has emerged as one of the potential tools for improving disease resistance in crops by targeting multiple traits with more accuracy and efficiency. For instance, genome editing techniques, such as CRISPR/Cas9, CRISPR/Cas13, base editing, TALENs, ZFNs, and meganucleases, have proved successful in improving disease resistance in crops through targeted mutagenesis, gene knockouts, knockdowns, modifications, and activation of target genes. CRISPR/Cas9 is unique among these techniques because of its remarkable efficacy, low risk of off-target repercussions, and ease of use. Some primary targets for developing CRISPR-mediated disease-resistant crops are host-susceptibility genes (the S gene method), resistance genes (R genes) and pathogen genetic material that prevents their development, broad-spectrum disease resistance. The use of genome editing methods has the potential to notably ameliorate crop disease resistance and transform agricultural practices in the future. This review highlights the impact of phyto-pathogens on agricultural productivity. Next, we discussed the tools for improving disease resistance while focusing on genome editing. We provided an update on the accomplishments of genome editing, and its potential to improve crop disease resistance against bacterial, fungal and viral pathogens in different crop systems. Finally, we highlighted the future challenges of genome editing in different crop systems for enhancing disease resistance.
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Affiliation(s)
- Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, Srinagar, India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, India
| | | | - Gousia Gani
- Division of Basic Science and Humanities, FOA-SKUAST-K, Wadura, Srinagar, India
| | - Zahoor Ahmad Mir
- Department of Plant Science and Agriculture, University of Manitoba, Winnipeg, MB, Canada
| | - Ab Waheed Wani
- Department of Horticulture, LPU, Jalander, Punjab, India
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Nazia Manzar
- Plant Pathology Lab, ICAR-National Bureau of Agriculturally Important Microorganism, Mau, Uttar Pradesh, India
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Saubin M, Tellier A, Stoeckel S, Andrieux A, Halkett F. Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population. Mol Ecol 2024; 33:e16965. [PMID: 37150947 DOI: 10.1111/mec.16965] [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: 11/07/2022] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023]
Abstract
Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual-based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering a dense versus sparse sampling. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetic changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent-based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.
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Affiliation(s)
- Méline Saubin
- Université de Lorraine, INRAE, IAM, Nancy, France
- Department for Life Science Systems, Technical University of Munich, Freising, Germany
| | - Aurélien Tellier
- Department for Life Science Systems, Technical University of Munich, Freising, Germany
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
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Poma-Angamarca RA, Rojas JR, Sánchez-Rodríguez A, Ruiz-González MX. Diversity of Leaf Fungal Endophytes from Two Coffea arabica Varieties and Antagonism towards Coffee Leaf Rust. PLANTS (BASEL, SWITZERLAND) 2024; 13:814. [PMID: 38592839 PMCID: PMC11154406 DOI: 10.3390/plants13060814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Coffee has immense value as a worldwide-appreciated commodity. However, its production faces the effects of climate change and the spread of severe diseases such as coffee leaf rust (CLR). The exploration of fungal endophytes associated with Coffea sp. has already found the existence of nearly 600 fungal species, but their role in the plants remains practically unknown. We have researched the diversity of leaf fungal endophytes in two Coffea arabica varieties: one susceptible and one resistant to CLR. Then, we conducted cross-infection essays with four common endophyte species (three Colletotrichum sp. and Xylaria sp. 1) and Hemileia vastatrix (CLR) in leaf discs, to investigate the interaction of the endophytes on CLR colonisation success and severity of infection. Two Colletotrichum sp., when inoculated 72 h before H. vastatrix, prevented the colonisation of the leaf disc by the latter. Moreover, the presence of endophytes prior to the arrival of H. vastatrix ameliorated the severity of CLR. Our work highlights both the importance of characterising the hidden biodiversity of endophytes and investigating their potential roles in the plant-endophyte interaction.
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Affiliation(s)
- Ruth A. Poma-Angamarca
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador; (R.A.P.-A.); (J.R.R.); (A.S.-R.)
| | - Jacqueline R. Rojas
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador; (R.A.P.-A.); (J.R.R.); (A.S.-R.)
| | - Aminael Sánchez-Rodríguez
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador; (R.A.P.-A.); (J.R.R.); (A.S.-R.)
| | - Mario X. Ruiz-González
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador; (R.A.P.-A.); (J.R.R.); (A.S.-R.)
- SENESCYT is the Secretaría de Educación Superior, Ciencia, Tecnología e Innovación from the Government of Ecuador, Proyecto Prometeo SENESCYT, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador
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5
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Martins NF, Viana MJA, Maigret B. Fungi Tryptophan Synthases: What Is the Role of the Linker Connecting the α and β Structural Domains in Hemileia vastatrix TRPS? A Molecular Dynamics Investigation. Molecules 2024; 29:756. [PMID: 38398508 PMCID: PMC10893352 DOI: 10.3390/molecules29040756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Tryptophan synthase (TRPS) is a complex enzyme responsible for tryptophan biosynthesis. It occurs in bacteria, plants, and fungi as an αββα heterotetramer. Although encoded by independent genes in bacteria and plants, in fungi, TRPS is generated by a single gene that concurrently expresses the α and β entities, which are linked by an elongated peculiar segment. We conducted 1 µs all-atom molecular dynamics simulations on Hemileia vastatrix TRPS to address two questions: (i) the role of the linker segment and (ii) the comparative mode of action. Since there is not an experimental structure, we started our simulations with homology modeling. Based on the results, it seems that TRPS makes use of an already-existing tunnel that can spontaneously move the indole moiety from the α catalytic pocket to the β one. Such behavior was completely disrupted in the simulation without the linker. In light of these results and the αβ dimer's low stability, the full-working TRPS single genes might be the result of a particular evolution. Considering the significant losses that Hemileia vastatrix causes to coffee plantations, our next course of action will be to use the TRPS to look for substances that can block tryptophan production and therefore control the disease.
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Affiliation(s)
- Natália F Martins
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Marcos J A Viana
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Bernard Maigret
- LORIA, UMR 7504 CNRS, Université de Lorraine, 54000 Vandoeuvre les Nancy, France
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de Fátima Pereira Silva P, de Resende MLV, Reichel T, de Lima Santos M, Dos Santos Botelho DM, Ferreira EB, Freitas NC. Potassium Phosphite Activates Components Associated with Constitutive Defense Responses in Coffea arabica Cultivars. Mol Biotechnol 2023; 65:1777-1795. [PMID: 36790658 DOI: 10.1007/s12033-023-00683-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023]
Abstract
Phosphites have been used as inducers of resistance, activating the defense of plants and increasing its ability to respond to the invasion of the pathogen. However, the mode of action of phosphites in defense responses has not yet been fully elucidated. The objective of this study was to evaluate the effect of potassium phosphite (KPhi) in coffee cultivars with different levels of resistance to rust to clarify the mechanism by which KPhi activates the constitutive defense of plants. To this end, we studied the expression of genes and the activity of enzymes involved in the defense pathway of salicylic acid (SA) and reactive oxygen species (ROS), in addition to the levels of total soluble phenolic compounds and soluble lignin. Treatment with KPhi induced constitutive defense responses in cultivars resistant and susceptible to rust. The results suggest that KPhi acts in two parallel defense pathways, SA and ROS, which are essential for the induction of systemic acquired resistance (SAR) when activated simultaneously. The activation of the mechanisms associated with defense routes demonstrates that KPhi is a potential inducer of resistance in coffee plants.
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Affiliation(s)
- Priscilla de Fátima Pereira Silva
- Department of Phytopathology, Federal University of Lavras, Trevo Rotatório Professor Edmir Sá Santos, Lavras, Minas Gerais, CEP 37203-202, Brazil
| | - Mário Lúcio Vilela de Resende
- Department of Phytopathology, Federal University of Lavras, Trevo Rotatório Professor Edmir Sá Santos, Lavras, Minas Gerais, CEP 37203-202, Brazil.
| | - Tharyn Reichel
- Department of Phytopathology, Federal University of Lavras, Trevo Rotatório Professor Edmir Sá Santos, Lavras, Minas Gerais, CEP 37203-202, Brazil
| | - Mariana de Lima Santos
- Graduate Program in Plant Biotechnology, Federal University of Lavras, Trevo Rotatório Professor Edmir Sá Santos, Lavras, Minas Gerais, CEP 37203-202, Brazil
| | - Deila Magna Dos Santos Botelho
- Department of Phytopathology, Federal University of Lavras, Trevo Rotatório Professor Edmir Sá Santos, Lavras, Minas Gerais, CEP 37203-202, Brazil
| | - Eric Batista Ferreira
- Department of Statistics, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, Centro, Alfenas, Minas Gerais, CEP 37130-001, Brazil
| | - Natália Chagas Freitas
- Department of Phytopathology, Federal University of Lavras, Trevo Rotatório Professor Edmir Sá Santos, Lavras, Minas Gerais, CEP 37203-202, Brazil
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Santiago-Santiago M, Sánchez-Viveros G, Hernández-Adame L, Chiquito-Contreras CJ, Salinas-Castro A, Chiquito-Contreras RG, Hernández-Montiel LG. Essential Oils and Antagonistic Microorganisms as Eco-Friendly Alternatives for Coffee Leaf Rust Control. PLANTS (BASEL, SWITZERLAND) 2023; 12:3519. [PMID: 37895983 PMCID: PMC10609872 DOI: 10.3390/plants12203519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023]
Abstract
Coffee leaf rust (CLR) is caused by the biotrophic fungus Hemileia vastatrix Berk. & Br., a disease of economic importance, reducing coffee yield up to 60%. Currently, CLR epidemics have negatively impacted food security. Therefore, the objective of the present research study is to show a current framework of this disease and its effects on diverse areas, as well as the biological systems used for its control, mode of action, and effectiveness. The use of essential plant oils and antagonistic microorganisms to H. vastatrix are highlighted. Terpenes, terpenoids, and aromatic compounds are the main constituents of these oils, which alter the cell wall and membrane composition and modify the basic cell functions. Beneficial microorganisms inhibit urediniospore germination and reduce disease incidence and severity. The antagonistic microorganisms and essential oils of some aromatic plants have great potential in agriculture. These biological systems may have more than one mechanism of action, which reduces the possibility of the emergence of resistant strains of H. vastatrix.
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Affiliation(s)
| | - Gabriela Sánchez-Viveros
- Facultad de Ciencias Agrícolas, Universidad Veracruzana, Xalapa 91090, Mexico; (G.S.-V.); (C.J.C.-C.)
| | - Luis Hernández-Adame
- CONAHCYT-Centro de Investigaciones Biológicas del Noroeste, La Paz 23096, Mexico;
- Nanotechnology & Microbial Biocontrol Group, Centro de Investigaciones Biológicas del Noroeste, La Paz 23096, Mexico
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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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Rojas-Orduña E, Hernández-Carrión M, Gómez-Franco JD, Narváez-Cuenca CE, Sánchez-Camargo ADP. Utilization of red and yellow Coffea arabica var. Caturra pulp: macronutrient analysis, carotenoid extraction, and encapsulation for dairy product enrichment. Front Nutr 2023; 10:1231049. [PMID: 37720375 PMCID: PMC10501141 DOI: 10.3389/fnut.2023.1231049] [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: 05/30/2023] [Accepted: 08/14/2023] [Indexed: 09/19/2023] Open
Abstract
This study aimed to investigate the macronutrient and carotenoid content of red and yellow Coffea arabica var. Caturra pulp, a by-product of coffee processing in Colombia. The study employed ultra-sound-assisted extraction (UAE) to extract carotenoids, and a 23 factorial design was used to evaluate the effects of pulp color, biomass-solvent ratio, and solvent mixture composition on carotenoid content and extraction yield. The condition that provided the highest carotenoid extraction was further encapsulated by spray drying and added to a dairy product. The results showed that coffee pulp has significant dietary fiber content and high levels of carotenoids, with yellow pulp having a higher content than red pulp. Lutein isomers and lutein esters were the most abundant carotenoids found in both red and yellow coffee pulp. The highest carotenoid extraction was achieved using a 1:40 (g/mL) biomass:solvent ratio and a 20:80% v/v Ethanol:Ethyl Acetate solvent mixture for the yellow pulp. The carotenoid extract also demonstrated high encapsulation efficiency (46.57 ± 4.03%) and was found to be stable when added to a fermented milk product. This study presents an alternative solution for utilizing coffee by-products in Colombia, which could positively impact the families of over half a million Colombian coffee producers.
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Affiliation(s)
- Elkin Rojas-Orduña
- Group of Product and Process Design, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - María Hernández-Carrión
- Group of Product and Process Design, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Juan David Gómez-Franco
- Food Chemistry Research Group, Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Carlos-Eduardo Narváez-Cuenca
- Food Chemistry Research Group, Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
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10
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Asad S, Priyashantha AKH, Tibpromma S, Luo Y, Zhang J, Fan Z, Zhao L, Shen K, Niu C, Lu L, Promputtha I, Karunarathna SC. Coffee-Associated Endophytes: Plant Growth Promotion and Crop Protection. BIOLOGY 2023; 12:911. [PMID: 37508343 PMCID: PMC10376224 DOI: 10.3390/biology12070911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023]
Abstract
Endophytic microbes are a ubiquitous group of plant-associated communities that colonize the intercellular or intracellular host tissues while providing numerous beneficial effects to the plants. All the plant species are thought to be associated with endophytes, majorly constituted with bacteria and fungi. During the last two decades, there has been a considerable movement toward the study of endophytes associated with coffee plants. In this review, the main consideration is given to address the coffee-associated endophytic bacteria and fungi, particularly their action on plant growth promotion and the biocontrol of pests. In addition, we sought to identify and analyze the gaps in the available research. Additionally, the potential of endophytes to improve the quality of coffee seeds is briefly discussed. Even though there are limited studies on the subject, the potentiality of coffee endophytes in plant growth promotion through enhancing nitrogen fixation, availability of minerals, nutrient absorption, secretion of phytohormones, and other bioactive metabolites has been well recognized. Further, the antagonistic effect against various coffee pathogenic bacteria, fungi, nematodes, and also insect pests leads to the protection of the crop. Furthermore, it is recognized that endophytes enhance the sensory characteristics of coffee as a new field of study.
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Affiliation(s)
- Suhail Asad
- School of Biology and Chemistry, Pu'er University, Pu'er 665000, China
| | | | - Saowaluck Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Yinling Luo
- School of Biology and Chemistry, Pu'er University, Pu'er 665000, China
| | - Jianqiang Zhang
- School of Biology and Chemistry, Pu'er University, Pu'er 665000, China
| | - Zhuqing Fan
- School of Biology and Chemistry, Pu'er University, Pu'er 665000, China
| | - Likun Zhao
- School of Biology and Chemistry, Pu'er University, Pu'er 665000, China
| | - Ke Shen
- School of Biology and Chemistry, Pu'er University, Pu'er 665000, China
| | - Chen Niu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou 570100, China
| | - Li Lu
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Samantha C Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- National Institute of Fundamental Studies (NIFS), Hantana Road, Kandy 20000, Sri Lanka
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11
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Assessing the Biocontrol Potential of Clonostachys Species Isolated as Endophytes from Coffea Species and as Mycoparasites of Hemileia Rusts of Coffee in Africa. J Fungi (Basel) 2023; 9:jof9020248. [PMID: 36836362 PMCID: PMC9962503 DOI: 10.3390/jof9020248] [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: 12/24/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
During surveys conducted in South America and Africa to identify natural fungal enemies of coffee leaf rust (CLR), Hemileia vastatrix, over 1500 strains were isolated, either as endophytes from healthy tissues of Coffea species or as mycoparasites growing on rust pustules. Based on morphological data, eight isolates-three isolated from wild or semiwild coffee and five from Hemileia species on coffee, all from Africa-were provisionally assigned to the genus Clonostachys. A polyphasic study of their morphological, cultural and molecular characteristics-including the Tef1 (translation elongation factor 1 alpha), RPB1 (largest subunit of RNA polymerase II), TUB (β-tubulin) and ACL1 (ATP citrate lyase) regions-confirmed these isolates as belonging to three species of the genus Clonostachys: namely C. byssicola, C. rhizophaga and C. rosea f. rosea. Preliminary assays were also conducted to test the potential of the Clonostachys isolates to reduce CLR severity on coffee under greenhouse conditions. Foliar and soil applications indicated that seven of the isolates had a significant effect (p < 0.05) in reducing CLR severity. In parallel, in vitro tests that involved conidia suspensions of each of the isolates together with urediniospores of H. vastatrix resulted in high levels of inhibition of urediniospore germination. All eight isolates showed their ability to establish as endophytes in C. arabica during this study, and some proved to be mycoparasites of H. vastatrix. In addition to reporting the first records of Clonostachys associated with healthy coffee tissues and with Hemileia rusts of coffee, this work provides the first evidence that Clonostachys isolates have potential as biological control agents against CLR.
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Saavedra LM, Caixeta ET, Barka GD, Borém A, Zambolim L, Nascimento M, Cruz CD, de Oliveira ACB, Pereira AA. Marker-Assisted Recurrent Selection for Pyramiding Leaf Rust and Coffee Berry Disease Resistance Alleles in Coffea arabica L. Genes (Basel) 2023; 14:189. [PMID: 36672930 PMCID: PMC9858729 DOI: 10.3390/genes14010189] [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: 10/28/2022] [Revised: 11/23/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
In this study, marker-assisted recurrent selection was evaluated for pyramiding resistance gene alleles against coffee leaf rust (CLR) and coffee berry diseases (CBD) in Coffea arabica. A total of 144 genotypes corresponding to 12 hybrid populations from crosses between eight parent plants with desired morphological and agronomic traits were evaluated. Molecular data were used for cross-certification, diversity study and resistance allele marker-assisted selection (MAS) against the causal agent of coffee leaf rust (Hemileia vastatrix) and coffee berry disease (Colletotrichum kahawae). In addition, nine morphological and agronomic traits were evaluated to determine the components of variance, select superior hybrids, and estimate genetic gain. From the genotypes evaluated, 134 were confirmed as hybrids. The genetic diversity between and within populations was 75.5% and 24.5%, respectively, and the cluster analysis revealed three primary groups. Pyramiding of CLR and CBD resistance genes was conducted in 11 genotypes using MAS. A selection intensity of 30% resulted in a gain of over 50% compared to the original population. Selected hybrids with increased gain also showed greater genetic divergence in addition to the pyramided resistance alleles. The strategies used were, therefore, efficient to select superior coffee hybrids for recurrent selection programs and could be used as a source of resistance in various crosses.
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Affiliation(s)
- Laura Maritza Saavedra
- Instituto de Biotecnologia Aplicada à Agropecuária-Bioagro, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Eveline Teixeira Caixeta
- Instituto de Biotecnologia Aplicada à Agropecuária-Bioagro, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Coffee, Brasília 70770-901, DF, Brazil
| | - Geleta Dugassa Barka
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama 1888, Ethiopia
| | - Aluízio Borém
- Departamento de Agronomia, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Laércio Zambolim
- Instituto de Biotecnologia Aplicada à Agropecuária-Bioagro, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Moysés Nascimento
- Departamento de Estatística, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Cosme Damião Cruz
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil
| | - Antonio Carlos Baião de Oliveira
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Coffee, Brasília 70770-901, DF, Brazil
- Empresa de Pesquisa Agropecuária de Minas Gerais-Epamig, Viçosa 36570-000, MG, Brazil
| | - Antonio Alves Pereira
- Empresa de Pesquisa Agropecuária de Minas Gerais-Epamig, Viçosa 36570-000, MG, Brazil
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13
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Dispersal and plant arrangement condition the timing and magnitude of coffee rust infection. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2022.110206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Gagliardi S, Avelino J, Martin AR, Cadotte M, Virginio Filho EDM, Isaac ME. Leaf functional traits and pathogens: Linking coffee leaf rust with intraspecific trait variation in diversified agroecosystems. PLoS One 2023; 18:e0284203. [PMID: 37053244 PMCID: PMC10101423 DOI: 10.1371/journal.pone.0284203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
Research has demonstrated that intraspecific functional trait variation underpins plant responses to environmental variability. However, few studies have evaluated how trait variation shifts in response to plant pathogens, even though pathogens are a major driver of plant demography and diversity, and despite evidence of plants expressing distinct strategies in response to pathogen pressures. Understanding trait-pathogen relationships can provide a more realistic understanding of global patterns of functional trait variation. We examined leaf intraspecific trait variability (ITV) in response to foliar disease severity, using Coffea arabica cv. Caturra as a model species. We quantified coffee leaf rust (CLR) severity-a fungal disease prominent in coffee systems-and measured key coffee leaf functional traits under contrasting, but widespread, management conditions in an agroforestry system. We found that coffee plants express significant ITV, which is largely related to shade tree treatment and leaf position within coffee canopy strata. Yet within a single plant canopy stratum, CLR severity increased with increasing resource conserving trait values. However, coffee leaves with visible signs of disease expressed overall greater resource acquiring trait values, as compared to plants without visible signs of disease. We provide among the first evidence that leaf traits are correlated with foliar disease severity in coffee, and that functional trait relationships and syndromes shift in response to increased disease prevalence in this plant-pathogen system. In doing so, we address a vital gap in our understanding of global patterns of functional trait variation and highlight the need to further explore the potential role of pathogens within established global trait relationships and spectra.
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Affiliation(s)
- Stephanie Gagliardi
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Jacques Avelino
- CIRAD, UMR PHIM, Montpellier, France
- Institute Agro, PHIM, University Montpellier, CIRAD, INRAE, IRD, Montpellier, France
| | - Adam R Martin
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Marc Cadotte
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | | | - Marney E Isaac
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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15
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Enzyme activity of three mycoparasite isolates and their effect on Coffee Leaf Rust (Hemileia vastatrix Berk. & Br.). Symbiosis 2022. [DOI: 10.1007/s13199-022-00885-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Daba G, Berecha G, Lievens B, Hundera K, Helsen K, Honnay O. Contrasting coffee leaf rust epidemics between forest coffee and semi-forest coffee agroforestry systems in SW-Ethiopia. Heliyon 2022; 8:e11892. [PMID: 36506396 PMCID: PMC9730127 DOI: 10.1016/j.heliyon.2022.e11892] [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: 05/05/2022] [Revised: 08/30/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022] Open
Abstract
Ethiopian Arabica coffee is produced in different agroforestry systems which differ in forest management intensity. In forest coffee systems (FC), coffee shrubs grow naturally in the understory of Afromontane forests with little human intervention, whereas in semi-forest coffee systems (SFC) thinning of the canopy and removal of the understory is applied. Coffee leaf rust (CLR) disease is a growing concern for coffee agroforestry, but to what extent infection pressure is affected by management intensity is poorly known. Here we assessed CLR infection through time across FC and SFC systems in SW-Ethiopia. CLR infection was significantly higher for SFC, with a gradual reduction of this difference during the beginning of dry season (November) through main rainy season of (July). Our findings also demonstrated that CLR infections were significantly lower in the FC system as compared to SFC system in both years 2015/16 and 2020/21. The higher CLR infection was partly explained by lower crown cover and higher human impact. We expect that reduced wind speed and droplet penetration under closed canopies and reduced human-facilitated spore dispersal are the dominating mechanisms behind lower CLR infection in FC systems, yet lower coffee density in FC may also play a role. Overall, our results indicate that although higher management intensity still generally results in higher total yields per hectare, proportionally larger losses due to CLR infection can be expected. Therefore, introducing more coffee genetic diversity, screening resistant coffee varieties and increasing canopy cover in the SFC will mitigate the CLR disease pressure and guarantee the sustainability of higher yields of the system in the future. Also, lower yields in the FC will be rewarded through providing price premiums so that farmers instantly get a higher price for their lower yield, guaranteeing livelihoods.
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Affiliation(s)
- Gerba Daba
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium,College of Agriculture and Veterinary Medicine, Department of Horticulture and Plant Sciences, Jimma University, PO Box 307, Jimma, Ethiopia,Corresponding author.
| | - Gezahegn Berecha
- College of Agriculture and Veterinary Medicine, Department of Horticulture and Plant Sciences, Jimma University, PO Box 307, Jimma, Ethiopia
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Campus De Nayer, Fortsesteenweg 30A, 2860 Sint-Katelijne-Waver, Belgium
| | - Kitessa Hundera
- Department of Biology, Jimma University, PO Box 378, Jimma, Ethiopia
| | - Kenny Helsen
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Olivier Honnay
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
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17
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Rabello AS, Rubinger MMM, da Silva LF, de Oliveira AH, Serrão JE, Albuini-Oliveira NM, Tavares EDC, Vidigal AEC, de Oliveira MRL, Zambolim L, Souza RAC, Guilardi S, Ellena J. Zinc-dithiocarbimates for the control of Hemileia vastatrix: a versatile alternative. PEST MANAGEMENT SCIENCE 2022; 78:4741-4752. [PMID: 35871604 DOI: 10.1002/ps.7094] [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: 11/29/2021] [Revised: 07/20/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The purpose of this work was to investigate the potential use of zinc-dithiocarbimate salts to control Hemileia vastatrix, the causal agent of the coffee leaf rust disease, and to evaluate their toxicity towards Apis mellifera, one of the most important coffee plant pollinators. RESULTS Zinc-dithiocarbimate salts were prepared and fully characterized by infrared, proton (1 H) and carbon-13 (13 C) nuclear magnetic resonance and elemental analyses of carbon (C), hydrogen (H), nitrogen (N) and zinc (Zn). X-ray diffraction technique studies confirmed the proposed structures. The salts inhibited the germination of H. vastatrix spores in vitro, with a 50% inhibitory concentration (IC50 ) from 12 to 18 μmol.L-1 and a 90% inhibitory concentration (IC90 ) from 23 to 26 μmol.L-1 . Zinc-dithiocarbimate salts with the best in vitro results were selected for in vivo experiments with Coffea arabica var Caturra and with the pollinator A. mellifera. The results were similar to those of Mancozeb, a broad-spectrum contact fungicide, with a good control of the disease and low toxicity to the honeybee. CONCLUSION The zinc-dithiocarbimate complex salts have potential to control coffee leaf rust, with low toxicity to the pollinator insect. © 2022 Society of Chemical Industry.
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Affiliation(s)
| | | | | | | | - José Eduardo Serrão
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | | | | | - Laércio Zambolim
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Silvana Guilardi
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Javier Ellena
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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18
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Budzinski IGF, Camargo PO, Lemos SMC, Guyot R, Calzado NF, Ivamoto-Suzuki ST, Domingues DS. Transcriptomic alterations in roots of two contrasting Coffea arabica cultivars after hexanoic acid priming. Front Genet 2022; 13:925811. [PMID: 36386801 PMCID: PMC9651915 DOI: 10.3389/fgene.2022.925811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/13/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ilara G. F. Budzinski
- Group of Genomics and Transcriptomes in Plants, Department of Biodiversity, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil
| | - Paula O. Camargo
- Group of Genomics and Transcriptomes in Plants, Department of Biodiversity, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil
| | - Samara M. C. Lemos
- Group of Genomics and Transcriptomes in Plants, Department of Biodiversity, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil
- Graduate Program in Biological Sciences (Genetics), Institute of Biosciences, São Paulo State University, UNESP, Botucatu, Brazil
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), Université Montpellier, Montpellier, France
| | - Natália F. Calzado
- Group of Genomics and Transcriptomes in Plants, Department of Biodiversity, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil
| | - Suzana T. Ivamoto-Suzuki
- Group of Genomics and Transcriptomes in Plants, Department of Biodiversity, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil
| | - Douglas S. Domingues
- Group of Genomics and Transcriptomes in Plants, Department of Biodiversity, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, Brazil
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, ESALQ/USP, Piracicaba, Brazil
- *Correspondence: Douglas S. Domingues,
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19
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Castillo NET, Acosta YA, Parra-Arroyo L, Martínez-Prado MA, Rivas-Galindo VM, Iqbal HMN, Bonaccorso AD, Melchor-Martínez EM, Parra-Saldívar R. Towards an Eco-Friendly Coffee Rust Control: Compilation of Natural Alternatives from a Nutritional and Antifungal Perspective. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202745. [PMID: 36297767 PMCID: PMC9609732 DOI: 10.3390/plants11202745] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 05/28/2023]
Abstract
Hemileia vastatrix (HV) is the pathogen responsible for the coffee leaf rust (CLR) disease that has spread globally. CLR causes losses of up to a billion dollars annually and affects all types of crops regardless of their production regime (organic or inorganic). Additionally, smallholders produce approximately 80% of coffee in developing countries. The condition causes losses of up to a billion dollars annually. It affects all types of crops regardless of their production regime (organic or inorganic). Approximately 80% of coffee is produced by smallholders in developing countries. Until the 90s, shaded-production systems and native varieties were encouraged; however, the rapid spread of CLR has forced farmers to migrate towards inorganic schemes, mainly due to a lack of knowledge about natural alternatives to pesticides that can be implemented to control HV. Therefore, the purpose of this article is to compile the currently existing options, emphasizing two key factors that guarantee efficient rust control: selective fungicidal activity against HV and the nutrition of coffee crops. Thus, by comprehending how these natural compounds (such as plant, bacteria, fungi, animals, or algae metabolites) impact coffee rust proliferation. Furthermore, since a various range of biochar effects contributes to the control of foliar fungal pathogens through modification of root exudates, soil properties, and nutrient availability, which influence the growth of antagonist microorganisms, we present a review of the pathogen-suppressive effects of biochar, and new control strategies suitable for organic schemes can be developed.
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Affiliation(s)
| | - Yovanina Aguilera Acosta
- Department of Chemical and Biochemical Engineering, Tecnologico Nacional de México-Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote, Durango 34080, Mexico
| | - Lizeth Parra-Arroyo
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey 64849, Mexico
| | - María Adriana Martínez-Prado
- Department of Chemical and Biochemical Engineering, Tecnologico Nacional de México-Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote, Durango 34080, Mexico
| | - Verónica M. Rivas-Galindo
- Departamento de Química Analítica, Facultad de Medicina, Universidad Autonoma de Nuevo Leon, Monterrey 66455, Mexico
| | - Hafiz M. N. Iqbal
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey 64849, Mexico
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Mexico
| | | | - Elda M. Melchor-Martínez
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey 64849, Mexico
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Mexico
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Roberto Parra-Saldívar
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey 64849, Mexico
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Mexico
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20
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Wani AK, Akhtar N, Singh R, Chopra C, Kakade P, Borde M, Al-Khayri JM, Suprasanna P, Zimare SB. Prospects of advanced metagenomics and meta-omics in the investigation of phytomicrobiome to forecast beneficial and pathogenic response. Mol Biol Rep 2022; 49:12165-12179. [PMID: 36169892 DOI: 10.1007/s11033-022-07936-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/19/2022] [Accepted: 09/08/2022] [Indexed: 12/01/2022]
Abstract
Microorganisms dwell in diverse plant niches as non-axenic biotic components that are beneficial as well pathogenic for the host. They improve nutrients-uptake, stress tolerance, phytohormone synthesis, and strengthening the defense system through phyllosphere, rhizosphere, and endosphere. The negative consequences of the microbial communities are largely in the form of diseases characterized by certain symptoms such as gall, cankers, rots etc. Uncultivable and unspecified nature of different phytomicrobiomes communities is a challenge in the management of plant disease, a leading cause for the loss of the plant products. Metagenomics has opened a new gateway for the exploration of microorganisms that are hitherto unknown, enables investigation of the functional aspect of microbial gene products through metatranscriptomics and metabolomics. Metagenomics offers advantages of characterizing previously unknown microorganisms from extreme environments like hot springs, glaciers, deep seas, animal gut etc. besides bioprospecting gene products such as Taq polymerase, bor encoded indolotryptoline, hydrolases, and polyketides. This review provides a detailed account of the phytomicrobiome networks and highlights the importance and limitations of metagenomics and other meta-omics approaches for the understanding of plant microbial diversity with special focus on the disease control and its management.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Prachi Kakade
- Department of Botany, Amdar Shashikant Shinde Mahavidyalay, 415012, Medha, Satara, India
| | - Mahesh Borde
- Department of Botany, Savitribai Phule Pune University, 411007, Pune, India
| | - Jameel M Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, 31982, Al- Ahsa, Saudi Arabia
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, 400094, Mumbai, India
| | - Saurabha B Zimare
- Department of Botany, Amdar Shashikant Shinde Mahavidyalay, 415012, Medha, Satara, India. .,Department of Botany, D. P. Bhosale College, Koregaon, , Satara, 415501, Maharashtra, India.
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21
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Moncada MM, Elvir MA, Lopez JR, Ortiz AS. Predicción bioinformática de proteínas NBS-LRR en el genoma de Coffea arabica. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.03.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Gracias al acceso al genoma completo de Coffea arabica y el Desarrollo de multiples herramientas de bioinformartica que permite la búsqueda de genes de resistencia de plantas (R-genes), ha sido posible implementar estas estrategias en programas de mejora genética. En las plantas, los R-genes codifican proteínas involucradas en mecanismos de defensa contra patógenos. Los genes con dominios tipo Nucleotide-Binding-Site Leucine-Rich-Repeat (NBS-LRR) forman la familia de R-genes de plantas más grande. El objetivo de este estudio fue identificar genes de proteínas NBS-LRR en el genoma de C. arabica utilizando un enfoque bioinformático. Identificamos motivos conservados de R-genes de C. arabica relacionados con genes similares encontrados en Coffea canephora y Coffea eugenoides, dos especies evolutivas relacionadas con C. arabica. Los resultados de estos análisis revelaron proteínas con origen evolutivo provenientes de dicotiledóneo ancestrales, así como proteínas de resistencia específicas del género Coffea. Además, todas las secuencias de los R-genes de C. arabica mostraron una gran similitud con proteína CNL de Arabidopsis thaliana. Finalmente, la presencia de motivos altamente conservados, la distribución cromosómica y las relaciones filogenéticas de los R-genes de C. arabica muestran procesos de coevolución con patógenos adaptados, demostrando de esta manera la importancia del estudio de estos genes en la inmunidad del café.
Palabras clave: Café, NBS-LRR, Proteínas de Resistencia, Bioinformática.
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Affiliation(s)
| | | | | | - Andrés S. Ortiz
- Universidad Nacional Autónoma de Honduras Instituto de Investigaciones en Microbiología
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22
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Rodrigues ASB, Silva DN, Várzea V, Paulo OS, Batista D. Worldwide Population Structure of the Coffee Rust Fungus Hemileia vastatrix Is Strongly Shaped by Local Adaptation and Breeding History. PHYTOPATHOLOGY 2022; 112:1998-2011. [PMID: 35322716 DOI: 10.1094/phyto-09-21-0376-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The devastating disease coffee leaf rust, caused by Hemileia vastatrix, has been a major constraint to worldwide coffee production. Recently, H. vastatrix populations were shown to be structured into three divergent genetic lineages with marked host specialization (C1, C2, and C3). However, there is yet no overall understanding of the population dynamics and adaptation of the most widespread and epidemiological relevant H. vastatrix group (C3). We used restriction site-associated DNA sequencing to generate 13,804 single nucleotide polymorphisms (SNPs) across a worldwide collection of 99 H. vastatrix isolates. Phylogenetic analyses uncovered a well-supported structuring within C3, with three main subgroups (SGs; SGI, SGII, and SGIII), which seem to reflect the historical distribution, breeding, and exchange of coffee cultivars. SGI shows a ladder-like diversification pattern and occurs across all four continents sampled, SGII is mainly restricted to Africa, and SGIII is observed only in Timor, revealing a higher genetic differentiation. Outlier and association tests globally identified 112 SNPs under putative positive selection, which impacted population structure. In particular, 29 overlapping SNPs per se seemed to have an extremely strong effect on H. vastatrix population divergence. We also found exclusive and fixed alleles associated with the SGs supporting local adaptation. Functional annotation revealed that transposable elements may play a role in host adaptation. Our study provides a higher-resolution perspective on the evolutionary history of H. vastatrix on cultivated coffee, showing its strong ability to adapt and the strength of the selective force imposed by coffee hosts, which should be taken into account when designing strategies for pathogen dissemination control and selective breeding.
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Affiliation(s)
- Ana Sofia B Rodrigues
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Diogo Nuno Silva
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Vitor Várzea
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Dora Batista
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
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Xia C, Qiu A, Wang M, Liu T, Chen W, Chen X. Current Status and Future Perspectives of Genomics Research in the Rust Fungi. Int J Mol Sci 2022; 23:ijms23179629. [PMID: 36077025 PMCID: PMC9456177 DOI: 10.3390/ijms23179629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of the devastating rust fungi has generated unprecedented insights into various aspects of rust biology. In this review, we first present a summary of the main findings in the genomics of rust fungi related to variations in genome size and gene composition between and within species. Then we show how the genomics of rust fungi has promoted our understanding of the pathogen virulence and population dynamics. Even with great progress, many questions still need to be answered. Therefore, we introduce important perspectives with emphasis on the genome evolution and host adaptation of rust fungi. We believe that the comparative genomics and population genomics of rust fungi will provide a further understanding of the rapid evolution of virulence and will contribute to monitoring the population dynamics for disease management.
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Affiliation(s)
- Chongjing Xia
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (C.X.); (X.C.); Tel.: +86-13880134318 (C.X.); +1-509-335-8086 (X.C.)
| | - Age Qiu
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430, USA
- Correspondence: (C.X.); (X.C.); Tel.: +86-13880134318 (C.X.); +1-509-335-8086 (X.C.)
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24
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Velásquez S, Banchón C. Influence of pre-and post-harvest factors on the organoleptic and physicochemical quality of coffee: a short review. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2022; 60:1-13. [PMID: 35993003 PMCID: PMC9376573 DOI: 10.1007/s13197-022-05569-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/16/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022]
Abstract
The coffee quality is affected by 40% pre-harvest, 40% post-harvest, and 20% export handling. Besides, future risks for the coffee industry are related with climate change and increased pathogens. Considering the importance of the aroma profile and unique flavor of Arabica coffee, most literature focuses on this variety because of the high market share; however, nowadays, Robusta coffee stands out for its increasing industrial value and resistance to drought. In this review, both species are emphasized, highlighting sensory aspects of possible new products mixed with a higher proportion of Robusta given market trends for bitter beverages. In the present work, a systematic search of peer-reviewed literature evaluates how the coffee cup quality and physicochemical characteristics of Robusta and Arabica are influenced by environmental, agronomic, and further processing factors.
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Affiliation(s)
- Sofía Velásquez
- Escuela Superior Politécnica Agropecuaria de Manabí, ESPAM-MFL, 130602 Calceta, Ecuador
- Universidad de Córdoba, Campus de Rabanales, Madrid-Cádiz Km. 396, 14014 Córdoba, Spain
| | - Carlos Banchón
- Escuela Superior Politécnica Agropecuaria de Manabí, ESPAM-MFL, 130602 Calceta, Ecuador
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Bai X, Zheng H, Huang X, Li J, Guo T, Luo Q, Zhang Z, Wu W, Yi K. The complete chloroplast genome of Coffea liberica (Gentianales: Rubiaceae). Mitochondrial DNA B Resour 2022; 7:1454-1456. [PMID: 35965645 PMCID: PMC9364704 DOI: 10.1080/23802359.2022.2107459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Coffee is one of the most popular beverages around the world. As one of the best-known coffee species, Liberian coffee (Coffea liberica Bull ex Hiern 1876) has a high resistance to leaf rust, a devasting disease caused by Hemileia vastatrix. However, there are few reports on the systematic position and phylogenetic relationship of C. liberica at the chloroplast (cp) genome level. Thus, we successfully assembled its cp genome. The full length is 154,799 bp with a GC content of 37.48%. We have further annotated the cp genome and predicted 85 protein-coding genes together with 8 rRNAs and 37 tRNAs. Furthermore, a large single copy region (LSC), a small single copy region (SSC), an inverted repeat region a (IRa) and an inverted repeat region b (IRb) are identified with lengths of 84,868 bp, 18,121 bp, 25,905 bp and 25,905 bp, respectively. The phylogenetic tree indicates that C. liberica is closely related to C. canephora, which is consistent with a previous result obtained from genotyping‐by‐sequencing.
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Affiliation(s)
- Xuehui Bai
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili, PR China
| | - Hongyu Zheng
- China State Farms Economic Development Center, Beijing, PR China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Jinhong Li
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili, PR China
| | - Tieying Guo
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili, PR China
| | - Qin Luo
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili, PR China
| | - Zhirun Zhang
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili, PR China
| | - Weihuai Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou, PR China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou, PR China
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26
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Le CTM, Okane I, Ono Y, Tsuda Y, Yamaoka Y. Incidence of Coffee Leaf Rust in Vietnam, Possible Original Sources and Subsequent Pathways of Migration. FRONTIERS IN PLANT SCIENCE 2022; 13:872877. [PMID: 35449887 PMCID: PMC9016365 DOI: 10.3389/fpls.2022.872877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/08/2022] [Indexed: 05/30/2023]
Abstract
This research focused on the incidence and population genetics of coffee leaf rust (CLR) fungus, Hemileia vastatrix, to estimate the possible original source(s) and subsequent migration pathways of wind-borne and human-aided spores in three main coffee production regions (Northwest, Central Highlands, and Southeast) in Vietnam. In southern Vietnam (Central Highlands and Southeast), Coffea canephora covers the majority area, while Catimor lines of C. arabica accounts for 95% of the coffee plantations in northwestern Vietnam. Field surveys conducted at eighty-five plantations, show coffee leaf samples infected by the rust fungus across forty-one plantations. Catimor varieties exhibited high levels of susceptibility with severe rust symptoms, while robusta varieties had varying degrees of susceptibility. We analyzed 863-869 base pairs of internal transcribed spacer (ITS) region from 83 samples (41 sequences from Vietnam, 2 from Thailand, and the remaining 40 from American countries); and fifty-two haplotypes consisting of 123 polymorphic sites were detected. Although the analysis of molecular variance (AMOVA) indicates significant genetic differentiation in the H. vastatrix populations in Vietnam, there was no clear genetic structure with respect to the three geographic areas surveyed. Based on the haplotype network, NeighborNet analysis, and geographical distribution patterns of the haplotypes, five haplotypes were identified as early established, from which most other haplotypes in Vietnam were derived. The early established haplotypes were found in the highest frequency in Northwest Vietnam. This finding corresponds to the earliest record of CLR in Vietnam. The phylogenetic network analysis also illustrated that H. vastatrix had expanded from the northwest to southern Vietnam. Pairwise genetic distance analysis and the geophylogenetic tree also suggests that CLR was first established in the Northwest. In addition, some scattered individuals on the principal coordinate analysis (PCoA) diagram and several separated haplotypes in the phylogenetic networks indicated that other branches of CLR in Vietnam were initiated in the Central Highlands. Hemileia vastatrix from these branches have been spreading in southern Vietnam.
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Affiliation(s)
- Cham Thi Mai Le
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Division of Microbial Technology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Izumi Okane
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoshitaka Ono
- College of Education, Ibaraki University, Mito, Japan
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Ueda, Japan
| | - Yuichi Yamaoka
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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27
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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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28
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Comprehensive Review of Fungi on Coffee. Pathogens 2022; 11:pathogens11040411. [PMID: 35456086 PMCID: PMC9024902 DOI: 10.3390/pathogens11040411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Coffee is grown in more than 80 countries as a cash crop and consumed worldwide as a beverage and food additive. It is susceptible to fungal infection during growth, processing and storage. Fungal infections, in particular, can seriously affect the quality of coffee and threaten human health. The data for this comprehensive review were collected from the United States Department of Agriculture, Agricultural Research Service (USDA ARS) website and published papers. This review lists the fungal species reported on coffee based on taxonomy, life mode, host, affected plant part and region. Five major fungal diseases and mycotoxin-producing species (post-harvest diseases of coffee) are also discussed. Furthermore, we address why coffee yield and quality are affected by fungi and propose methods to control fungal infections to increase coffee yield and improve quality. Endophytic fungi and their potential as biological control agents of coffee disease are also discussed.
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Ramírez-Camejo LA, Eamvijarn A, Díaz-Valderrama JR, Karlsen-Ayala E, Koch RA, Johnson E, Pruvot-Woehl S, Mejía LC, Montagnon C, Maldonado-Fuentes C, Aime MC. Global Analysis of Hemileia vastatrix Populations Shows Clonal Reproduction for the Coffee Leaf Rust Pathogen Throughout Most of Its Range. PHYTOPATHOLOGY 2022; 112:643-652. [PMID: 34428920 DOI: 10.1094/phyto-06-21-0255-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hemileia vastatrix is the most important fungal pathogen of coffee and the causal agent of recurrent disease epidemics that have invaded nearly every coffee growing region in the world. The development of coffee varieties resistant to H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown, and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of H. vastatrix to infer the reproductive mode of the fungus across most of its geographic range, including Central Africa, Southeast Asia, the Caribbean, and South and Central America. The population structure of H. vastatrix was determined via eight simple sequence repeat markers developed for this study. The analyses of the standardized index of association, Hardy-Weinberg equilibrium, and clonal richness all strongly support asexual reproduction of H. vastatrix in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled H. vastatrix populations. These findings may have profound implications for resistance breeding and management programs against H. vastatrix.
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Affiliation(s)
- Luis A Ramírez-Camejo
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Ancón, Republic of Panama
- Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton, Panama, Republic of Panama
| | - Amnat Eamvijarn
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- Department of Agriculture, Chatuchak, Bangkok, Thailand
| | - Jorge R Díaz-Valderrama
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
| | - Elena Karlsen-Ayala
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- University of Florida, Department of Plant Pathology, Gainesville, FL, U.S.A
| | - Rachel A Koch
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
| | - Elizabeth Johnson
- Inter-American Institute for Cooperation on Agriculture, Hope Gardens, Kingston, Jamaica
| | | | - Luis C Mejía
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Ancón, Republic of Panama
| | | | | | - M Catherine Aime
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
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30
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Santos MDL, de Resende MLV, dos Santos Ciscon BA, Freitas NC, Pereira MHDB, Reichel T, Mathioni SM. LysM receptors in Coffea arabica: Identification, characterization, and gene expression in response to Hemileia vastatrix. PLoS One 2022; 17:e0258838. [PMID: 35143519 PMCID: PMC8830669 DOI: 10.1371/journal.pone.0258838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/28/2022] [Indexed: 11/24/2022] Open
Abstract
Pathogen‐associated molecular patterns (PAMPs) are recognized by pattern recognition receptors (PRRs) localized on the host plasma membrane. These receptors activate a broad-spectrum and durable defense, which are desired characteristics for disease resistance in plant breeding programs. In this study, candidate sequences for PRRs with lysin motifs (LysM) were investigated in the Coffea arabica genome. For this, approaches based on the principle of sequence similarity, conservation of motifs and domains, phylogenetic analysis, and modulation of gene expression in response to Hemileia vastatrix were used. The candidate sequences for PRRs in C. arabica (Ca1-LYP, Ca2-LYP, Ca1-CERK1, Ca2-CERK1, Ca-LYK4, Ca1-LYK5 and Ca2-LYK5) showed high similarity with the reference PRRs used: Os-CEBiP, At-CERK1, At-LYK4 and At-LYK5. Moreover, the ectodomains of these sequences showed high identity or similarity with the reference sequences, indicating structural and functional conservation. The studied sequences are also phylogenetically related to the reference PRRs described in Arabidopsis, rice, and other plant species. All candidates for receptors had their expression induced after the inoculation with H. vastatrix, since the first time of sampling at 6 hours post‐inoculation (hpi). At 24 hpi, there was a significant increase in expression, for most of the receptors evaluated, and at 48 hpi, a suppression. The results showed that the candidate sequences for PRRs in the C. arabica genome display high homology with fungal PRRs already described in the literature. Besides, they respond to pathogen inoculation and seem to be involved in the perception or signaling of fungal chitin, acting as receptors or co-receptors of this molecule. These findings represent an advance in the understanding of the basal immunity of this species.
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Affiliation(s)
- Mariana de Lima Santos
- Programa de Pós-graduação em Biotecnologia Vegetal, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
- * E-mail: (MLS); (MLVR)
| | | | | | - Natália Chagas Freitas
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | | | - Tharyn Reichel
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Sandra Marisa Mathioni
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
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31
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Portilla M, Follett PA, Armstrong JW, Leesch JG, Tebbets JS, Smilanick J, McHugh TH, Olsen CW, Whitehand L, Cavaletto C, Bittenbender HCS, Bustillo AE, Peña JE. Risk Assessment of Ozone Fumigation Under Vacuum to Control Potential Infestation of Coffee Berry Borer and Coffee Leaf Rust in Green Coffee Beans Imported Into Hawaii. JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:2277-2289. [PMID: 34447985 DOI: 10.1093/jee/toab165] [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: 04/30/2021] [Indexed: 06/13/2023]
Abstract
Studies were conducted with ozone gas fumigation under vacuum as a methyl bromide alternative against life stages of coffee berry borer (CBB) Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae: Scolytinae), and the urediniospores of coffee leaf rust (CLR), Hemileia vastatrix Berkeley & Broome (Basidiomycota: Pucciniales) in green coffee, Coffea spp. L. Fumigation with 10,000 ppm O3 gas under -25.4 mm Hg vacuum1 at 13.0 ± 3.0°C for 6.0 h killed all CBB larvae, pupae, and adults, but did not kill all CBB eggs (~15% survival). Mortality of CLR urediniospores was 100% within the first hour of the 6-h fumigation. Ozone fumigation had no adverse effects on coffee quality. Results indicated that CBB adult hitchhikers may be the only target life stage of quarantine concern, and additional studies focused on this stage. CBB adult survival and reproduction decreased significantly at moisture contents ≤20%, and F1 generation survival did not occur in green coffee at moisture contents ≤15%. As the international standard for green coffee moisture content is 9-12%, adult CBB should not survive or reproduce in exported dry green coffee. Standard industry processing of harvested coffee cherries to the green coffee stage using either mechanical- or sun-drying eliminated CBB infestations from the field. A systems approach is recommended for exporting green coffee to control CBB and CLR that includes eliminating CBB life stages with standard processing methods, reducing moisture content to 9-12% to prevent egg deposition, survival or reproduction, and O3 fumigation to ensure quarantine security against potential CBB adult hitchhikers.
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Affiliation(s)
- M Portilla
- USDA-ARS-Southern Insect Management Research Unit, Stoneville, MS, USA
| | - P A Follett
- Tropical Crop and Commodity Protection Research, USDA-ARS, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - J W Armstrong
- Tropical Crop and Commodity Protection Research, USDA-ARS, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - J G Leesch
- USDA-ARS-Posts-harvest Pest Control Unit, Parlier, CA, USA
| | - J S Tebbets
- USDA-ARS-Posts-harvest Pest Control Unit, Parlier, CA, USA
| | - J Smilanick
- USDA-ARS-Posts-harvest Pest Control Unit, Parlier, CA, USA
| | - T H McHugh
- Healthy Processed Foods Research Unit, USDA-ARS-Western Regional Research Center, Albany, CA, USA
| | - C W Olsen
- Healthy Processed Foods Research Unit, USDA-ARS-Western Regional Research Center, Albany, CA, USA
| | - L Whitehand
- Healthy Processed Foods Research Unit, USDA-ARS-Western Regional Research Center, Albany, CA, USA
| | - C Cavaletto
- Department of Tropical Plant and Soil Science, University of Hawaii at Manoa, College of Tropical Agriculture and Human Resources, Honolulu, HI, USA
| | - H C S Bittenbender
- Department of Tropical Plant and Soil Science, University of Hawaii at Manoa, College of Tropical Agriculture and Human Resources, Honolulu, HI, USA
| | - A E Bustillo
- Department of Entomology, FEDERACAFE-Centro Nacional de Investigaciones del Café. Sede Planalto, Kilometre 4 via Chinchina-Manizales, Colombia
| | - J E Peña
- Department of Entomology and Nematology, University of Florida, TREC-IFAS, Homestead, FL, USA
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Li L, Várzea VMP, Xia Q, Xiang W, Tang T, Zhu M, He C, Pereira AP, Lavado da Silva MDCM, Wu W, Yi K. First Report of Hemileia vastatrix (Coffee Leaf Rust) Physiological Races Emergent in Coffee Germplasm Collections in the Coffee-Cropping Regions of China. PLANT DISEASE 2021; 105:4162. [PMID: 34184552 DOI: 10.1094/pdis-04-21-0796-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Le Li
- NHC Key Laboratory of Tropical Disease Control/Key Laboratory of Tropical Translational Medicine of Ministry of Education/School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou City, Hainan Province, P.R. China
| | - Vítor Manuel Pinto Várzea
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, Oeiras 2784-505, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisbon 1349-017, Portugal
| | - Qianfeng Xia
- NHC Key Laboratory of Tropical Disease Control/Key Laboratory of Tropical Translational Medicine of Ministry of Education/School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou City, Hainan Province, P.R. China
| | - Wei Xiang
- NHC Key Laboratory of Tropical Disease Control/Key Laboratory of Tropical Translational Medicine of Ministry of Education/School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou City, Hainan Province, P.R. China
| | - Tianle Tang
- NHC Key Laboratory of Tropical Disease Control/Key Laboratory of Tropical Translational Medicine of Ministry of Education/School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou City, Hainan Province, P.R. China
| | - Mengfeng Zhu
- Key Laboratory of Tropical Agriculture Pest Monitoring and Control, Hainan Province/Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, P.R. China
| | - Chunping He
- Key Laboratory of Tropical Agriculture Pest Monitoring and Control, Hainan Province/Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, P.R. China
| | - Ana Paula Pereira
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, Oeiras 2784-505, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisbon 1349-017, Portugal
| | - Maria do Céu Machado Lavado da Silva
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Quinta do Marquês, Oeiras 2784-505, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisbon 1349-017, Portugal
| | - Weihuai Wu
- Key Laboratory of Tropical Agriculture Pest Monitoring and Control, Hainan Province/Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, P.R. China
| | - Kexian Yi
- Key Laboratory of Tropical Agriculture Pest Monitoring and Control, Hainan Province/Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, P.R. China
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Constitutive Defense Strategy of Coffee Under Field Conditions: A Comparative Assessment of Resistant and Susceptible Cultivars to Rust. Mol Biotechnol 2021; 64:263-277. [PMID: 34595725 DOI: 10.1007/s12033-021-00405-9] [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: 04/14/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Coffea arabica is the most economically important coffee species worldwide. However, its production is severely limited by diseases such as rust. The mechanisms underlying constitutive defense responses in coffee are still poorly understood, compared with induced defense mechanisms. We aimed to characterize constitutive defense responses of thirteen cultivars of C. arabica. Cultivars were classified under field conditions according to the level of resistance to rust: resistant (R), moderately resistant (MR), and susceptible (S). Based on this classification, the stability of eight reference genes (RGs) was evaluated. The most stable RGs were EF1α, APT1, and 24S. We also evaluated the expression of CaWRKY1, CaPAL1, CaCAD1, and CaPOX1, and activities of PAL, CAD, and POX, which are involved in lignin biosynthesis, and leaf content of total phenolic compounds and lignin. Gene expression and enzymatic activity were not correlated with defense metabolites in the R cultivar group but showed a negative correlation with phenolic compounds in MR cultivars. Cultivar S showed positive correlations of gene expression and enzyme activity with phenolic compounds. These results may assist coffee breeding programs regarding selection of genotypes and in optimization of rust resistance.
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Girón EJ, Corrales DC, Sesmero MP, Iglesias JA, Corrales JC. Synthetic samples generator (SYSGEN), an approach to increase the size of incidence samples in coffee leaf rust modelling. EVOLVING SYSTEMS 2021. [DOI: 10.1007/s12530-021-09395-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Manawasinghe IS, Phillips AJL, Xu J, Balasuriya A, Hyde KD, Stępień Ł, Harischandra DL, Karunarathna A, Yan J, Weerasinghe J, Luo M, Dong Z, Cheewangkoon R. Defining a species in fungal plant pathology: beyond the species level. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00481-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
In this perspective, we draw on recent scientific research on the coffee leaf rust (CLR) epidemic that severely impacted several countries across Latin America and the Caribbean over the last decade, to explore how the socioeconomic impacts from COVID-19 could lead to the reemergence of another rust epidemic. We describe how past CLR outbreaks have been linked to reduced crop care and investment in coffee farms, as evidenced in the years following the 2008 global financial crisis. We discuss relationships between CLR incidence, farmer-scale agricultural practices, and economic signals transferred through global and local effects. We contextualize how current COVID-19 impacts on labor, unemployment, stay-at-home orders, and international border policies could affect farmer investments in coffee plants and in turn create conditions favorable for future shocks. We conclude by arguing that COVID-19's socioeconomic disruptions are likely to drive the coffee industry into another severe production crisis. While this argument illustrates the vulnerabilities that come from a globalized coffee system, it also highlights the necessity of ensuring the well-being of all. By increasing investments in coffee institutions and paying smallholders more, we can create a fairer and healthier system that is more resilient to future social-ecological shocks.
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Quispe-Apaza C, Mansilla-Samaniego R, Espejo-Joya R, Bernacchia G, Yabar-Larios M, López-Bonilla C. Spatial and Temporal Genetic Diversity and Population Structure of Hemileia vastatrix from Peruvian Coffee Plantations. THE PLANT PATHOLOGY JOURNAL 2021; 37:280-290. [PMID: 34111917 PMCID: PMC8200579 DOI: 10.5423/ppj.oa.10.2020.0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/23/2021] [Accepted: 05/05/2021] [Indexed: 06/01/2023]
Abstract
Population genetic studies of Hemileia vastatrix have been conducted in order to describe the evolutionary dynamics of the pathogen and the disease epidemiology as consequence of changes in disease management and host distribution occurred in Peru after the 2013 epidemic. These analyses were performed by sequencing the internal transcribed spacers of the nuclear ribosomal DNA (rDNA-ITS) of H. vastatrix collected from two coffee growing areas in 2014 and 2018. H. vastatrix population showed high haplotype diversity (Hd = 0.9373 ± 0.0115) with a low nucleotide diversity (π = 0.00322 ± 0.00018). Likewise, AMOVA indicated that fungus population has behaved as a large population without structuring by geographical origin and sampling years (FST = 0.00180, P = 0.20053 and FST = 0.00241, P = 0.19693, respectively). Additionally, the haplotype network based on intraspecific phylogenetic analysis of H. vastatrix using Peruvian and NCBI sequences revealed that Peruvian ancestral haplotypes, which were maintained in time and space, would correspond to the reported sequences of the races II and XXII. This result suggests that no substantial changes have occurred through time in Peruvian Hemileia vastatrix population.
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Affiliation(s)
- Cinthia Quispe-Apaza
- Universidad Nacional Agraria La Molina, Av. La Molina s/n, La Molina, 15024 Lima, Perú
| | | | - Rosa Espejo-Joya
- Universidad Nacional Agraria La Molina, Av. La Molina s/n, La Molina, 15024 Lima, Perú
| | - Giovanni Bernacchia
- Università degli Studi di Ferrara, Dip Scienze della Vita e Biotecnologie, Via Borsari 46, 44121 Ferrara, Italy
| | - Marisela Yabar-Larios
- Servicio Nacional de Sanidad Agraria, Av. La Molina 1915, La Molina, 15024 Lima, Perú
| | - César López-Bonilla
- Universidad Nacional Agraria La Molina, Av. La Molina s/n, La Molina, 15024 Lima, Perú
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Mattoon ER, Casadevall A, Cordero RJB. Beat the heat: correlates, compounds, and mechanisms involved in fungal thermotolerance. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Salcedo-Sarmiento S, Aucique-Pérez CE, Silveira PR, Colmán AA, Silva AL, Corrêa Mansur PS, Rodrigues FÁ, Evans HC, Barreto RW. Elucidating the interactions between the rust Hemileia vastatrix and a Calonectria mycoparasite and the coffee plant. iScience 2021; 24:102352. [PMID: 33870142 PMCID: PMC8044427 DOI: 10.1016/j.isci.2021.102352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 11/21/2022] Open
Abstract
Calonectria hemileiae, a fungus associated with pustules of the coffee leaf rust (CLR, Hemileia vastatrix) in Brazil, was tested in vitro and in planta to assess its biocontrol potential. The fungus inhibited the germination of rust spores by over 80%. CLR severity was reduced by 93% when Calonectria was applied to coffee leaf discs inoculated with H. vastatrix, whilst a reduction of 70-90% was obtained for in planta experiments. Mycoparasitism was demonstrated through the fulfillment of Koch's postulates. Elucidation of the biochemical interaction between Calonectria and Hemileia on coffee plants indicated that the mycoparasite was able to increase plant resistance to rust infection. Coffee plants sprayed with Calonectria alone showed greater levels of chitinase, β-1,3-glucanase, ascorbate peroxidase and peroxidase. Although effective in controlling the rust, fungicide applications damaged coffee photosynthesis, whereas no harm was caused by Calonectria. We conclude that C. hemileiae shows promise as a biocontrol agent of CLR.
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Affiliation(s)
| | | | - Patrícia R. Silveira
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Adans A. Colmán
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - André L. Silva
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | | | | | - Harry C. Evans
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
- CAB International, UK Centre, Egham, Surrey, UK
| | - Robert W. Barreto
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
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Chaves AFA, Xander P, Romera LMD, Fonseca FLA, Batista WL. What is the elephant in the room when considering new therapies for fungal diseases? Crit Rev Microbiol 2021; 47:275-289. [PMID: 33513315 DOI: 10.1080/1040841x.2021.1876632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The global scenario of antimicrobial resistance is alarming, and the development of new drugs has not appeared to make substantial progress. The constraints on drug discovery are due to difficulties in finding new targets for therapy, the high cost of development, and the mismatch between the time of drug introduction in a clinic and microorganism adaptation to a drug. Policies to address neglected diseases miss the broad spectrum of mycosis. Society is not aware of the actual threat represented by fungi to human health, food security, and biodiversity. The evidence discussed here is critical for warning governments to establish effective surveillance policies for fungi.HIGHLIGHTSFungal diseases are ignored even among neglected disease classifications.There are few options to treat mycoses, which is an increasing concern regarding fungal resistance to drugs, as evidenced by the spread of Candida auris.Fungal diseases represent a real threat to human health and food security.Investment in research to investigate the potential of repurposing drugs already in use could obtain results in the short term.
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Affiliation(s)
| | - Patricia Xander
- Department of Pharmaceutical Sciences, Federal University of São Paulo, São Paulo, Brazil
| | | | | | - Wagner Luiz Batista
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Brazil.,Department of Pharmaceutical Sciences, Federal University of São Paulo, São Paulo, Brazil
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Colmán AA, Evans HC, Salcedo-Sarmiento SS, Braun U, Belachew-Bekele K, Barreto RW. A fungus-eat-fungus world: Digitopodium, with particular reference to mycoparasites of the coffee leaf rust, Hemileia vastatrix. IMA Fungus 2021; 12:1. [PMID: 33402223 PMCID: PMC7784264 DOI: 10.1186/s43008-020-00052-w] [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: 09/10/2019] [Accepted: 12/15/2020] [Indexed: 11/25/2022] Open
Abstract
Digitopodium hemileiae was described originally in 1930 as Cladosporium hemileiae; growing as a mycoparasite of the coffee leaf rust (CLR), Hemileia vastatrix, in a sample of diseased leaves of Coffea canephora collected in the Democratic Republic of Congo. No cultures from this material exist. More recently, the type material was re-examined and, based on morphological features, considered to be incorrectly placed in Cladosporium. The new genus Digitopodium was erected to accommodate this species. Interest in fungal antagonists of H. vastarix, as potential biocontrol agents of CLR, led to comprehensive surveys for mycoparasites, both in the African centre of origin of the rust, as well as in its South American exotic range. Among the rust specimens from Ethiopia, one was found to be colonized by a fungus congeneric with, and similar to, D. hemileiae. Pure cultures obtained from the Ethiopian material enabled a molecular study and for its phylogenetic position to be elucidated, based on DNA sequence data from the ITS and LSU regions. Molecular data showed that two members of the recently erected genus Hyalocladosporiella (Herpotrichiellaceae: Chaetothyriales) are congeneric with Digitopodium from Ethiopia and morphologically similar to both D. hemileiae and the two Ethiopian isolates. These isolates were found to be morphologically and genetically identical to H. tectonae, described previously from Brazil. Thus, species of Hyalocladosporiella are re-allocated to Digitopodium here; including D. tectonae, and a novel species, D. canescens, recently found in Brazil growing as a mycoparasite of Puccinia thaliae. The potential use of D. hemileiae and D. tectonae for classical biological control of CLR is discussed.
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Affiliation(s)
- Adans A Colmán
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Harry C Evans
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- CAB International, UK Centre, Egham, Surrey, TW20 9TY, UK
| | | | - Uwe Braun
- Martin Luther University Halle, Institute of Biology, Department of Geobotany and Botanical Garden, Herbarium, Neuwerk 21, 06099, Halle (Saale), Germany
| | | | - Robert W Barreto
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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Hessenauer P, Feau N, Gill U, Schwessinger B, Brar GS, Hamelin RC. Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene. PHYTOPATHOLOGY 2021; 111:49-67. [PMID: 33200962 DOI: 10.1094/phyto-08-20-0358-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.
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Affiliation(s)
- Pauline Hessenauer
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
| | - Nicolas Feau
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Upinder Gill
- College of Agriculture, Food Systems, and Natural Resources, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Richard C Hamelin
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
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Guido Z, Knudson C, Rhiney K. Will COVID-19 be one shock too many for smallholder coffee livelihoods? WORLD DEVELOPMENT 2020; 136:105172. [PMID: 32921878 PMCID: PMC7474699 DOI: 10.1016/j.worlddev.2020.105172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Coffee supports the livelihoods of millions of smallholder farmers in more than 52 countries, and generates billions of dollars in revenue. The threats that COVID-19 pose to the global coffee sector is daunting with profound implications for coffee production. The financial impacts will be long-lived and uneven, and smallholders will be among the hardest hit. We argue that the impacts are rooted in the systemic vulnerability of the coffee production system and the unequal ways the sector is organized: Large revenues from the sale of coffee in the Global North are made possible by mostly impoverished smallholders in the Global South. COVID-19 will accentuate the existing vulnerabilities and create new ones, forcing many smallholders into alternative livelihoods. This outcome, however, is not inevitable. COVID-19 presents an opportunity to rebalance the system that currently creates large profits on one end of the supply chain and great vulnerability on the other.
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Affiliation(s)
- Zack Guido
- Arizona Institutes for Resilience, University of Arizona, 1064 E. Lowell Street, Tucson, AZ 85719, USA
- School of Natural Resources and Environment, University of Arizona, 1064 E Lowell Street, Tucson, AZ 85719, USA
| | - Chris Knudson
- Department of Geography and Environmental Science, University of Hawaii at Hilo, USA
| | - Kevon Rhiney
- Department of Geography, Rutgers University, 54 Joyce Kilmer Ave, Piscataway, NJ 08854, USA
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Torres Castillo NE, Melchor-Martínez EM, Ochoa Sierra JS, Ramirez-Mendoza RA, Parra-Saldívar R, Iqbal HMN. Impact of climate change and early development of coffee rust - An overview of control strategies to preserve organic cultivars in Mexico. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:140225. [PMID: 32806380 DOI: 10.1016/j.scitotenv.2020.140225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 02/08/2023]
Abstract
Coffee is one of the most important commercial traded commodities in the international market, as well as the most popular beverage around the world. In Mexico, organic coffee cultivation (specifically, Arabica coffee crops) is a highly demanded that generates up to 500,000 employments in 14 federal entities. Among various coffee producers, Chiapas, Veracruz, and Oaxaca are responsible of 80% of the total coffee production in the country. Currently, Mexico is the leading producer of organic coffee in the world. However, there have been a slow recovery due to the large production losses since 2012, caused by earlier and highly aggressive outbreaks of coffee leaf rust (CLR), in the country, where the infectious agent is known as Hemileia vastatrix (HV). This phenomenon is becoming frequent, and climate change effects could be the main contributors. This spontaneous proliferation was generated in Mexico, due to the precipitation and temperature variability, during the last decade. As result, in Mexico, the biological interaction between coffee crops and their environment has been harmed and crucial characteristics, as crop yield and quality, are particularly being affected, directly by the negative effects of the greenhouse phenomenon, and indirectly, through diseases as CLR. Therefore, this review discusses the contribution of climate change effects in the early development of CLR in Mexico. The focus is also given on possible schemes and actions taken around the world as control measures to adapt the vulnerable coffee varieties to tackle this challenging issue.
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Affiliation(s)
- Nora E Torres Castillo
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. CP 64849, Mexico
| | - Elda M Melchor-Martínez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. CP 64849, Mexico
| | - Jhosseph S Ochoa Sierra
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. CP 64849, Mexico
| | - Ricardo A Ramirez-Mendoza
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. CP 64849, Mexico
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. CP 64849, Mexico.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. CP 64849, Mexico.
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Serrato-Diaz LM, Mariño YA, Bayman P. Pathogens Causing Anthracnose and Fruit Rots of Coffee Associated with the Coffee Berry Borer and the Entomopathogenic Fungus Beauveria bassiana in Puerto Rico. PHYTOPATHOLOGY 2020; 110:1541-1552. [PMID: 32343616 DOI: 10.1094/phyto-02-20-0057-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fruit rots reduce coffee production worldwide. Eight Colletotrichum species have been reported to cause coffee fruit rots; the most important is C. kahawae, the cause of coffee berry disease (CBD) in Africa. It is unknown whether these fruit rot pathogens can be dispersed by the coffee berry borer (CBB, Hypothenemus hampei) or whether Beauveria bassiana (a natural enemy of CBB) might reduce coffee fruit rots. We identified pathogens causing coffee fruits rots in Puerto Rico and evaluated whether B. bassiana reduced fruit rot and whether CBB could disperse pathogens. A total of 2,333 coffee fruit with CBB damage were collected; of these, 1,197 had visible growth of B. bassiana. C. fructicola, C. siamense, C. theobromicola, and C. tropicale were isolated and identified from the fruit using morphological traits and phylogeny of three nuclear genes. All four species caused internal and external rot after inoculation of healthy green coffee fruit. Coffee fruit treated with B. bassiana had significantly less fruit rot than untreated fruit, suggesting B. bassiana can protect against fruit rot. To test whether B. bassiana had a protective effect, B. bassiana and Colletotrichum were coinoculated on coffee fruit. Fruit inoculated with both B. bassiana and Colletotrichum had significantly less rot than fruit inoculated with Colletotrichum alone. To test if CBBs dispersed the pathogens, CBBs were exposed to Colletotrichum conidia and placed on green fruit, which resulted in fruit rot. This study identifies new pathogens causing coffee fruit rot, shows that C. kahawae is not the only Colletotrichum that attacks green fruits, suggests a role for B. bassiana in disease management and demonstrates CBB can disperse the pathogens.
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Affiliation(s)
- Luz M Serrato-Diaz
- Department of Biology, University of Puerto Rico-Río Piedras, P.O. Box 23360, San Juan, PR 00931-3360, U.S.A
- U.S. Department of Agriculture-Agriculture Research Service-Tropical Agriculture Research Station (TARS), 2200 P.A. Campos Ave., Ste. 201, Mayagüez, PR 00680-5470, U.S.A
| | - Yobana A Mariño
- Department of Biology, University of Puerto Rico-Río Piedras, P.O. Box 23360, San Juan, PR 00931-3360, U.S.A
| | - Paul Bayman
- Department of Biology, University of Puerto Rico-Río Piedras, P.O. Box 23360, San Juan, PR 00931-3360, U.S.A
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An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population. mSphere 2020; 5:5/3/e00128-20. [PMID: 32554716 PMCID: PMC7300351 DOI: 10.1128/msphere.00128-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe (yellow) rust, is an obligate, biotrophic fungus. It was difficult to study the genetics of the pathogen due to the lack of sexual reproduction. The recent discovery of alternate hosts for P. striiformis f. sp. tritici makes it possible to study inheritance and map genes involved in its interaction with plant hosts. To identify avirulence (Avr) genes in P. striiformis f. sp. tritici, we developed a segregating population by selfing isolate 12-368 on barberry (Berberis vulgaris) plants under controlled conditions. The dikaryotic sexual population segregated for avirulent/virulent phenotypes on nine Yr single-gene lines. The parental and progeny isolates were whole-genome sequenced at >30× coverage using Illumina HiSeq PE150 technology. A total of 2,637 high-quality markers were discovered by mapping the whole-genome sequencing (WGS) reads to the reference genome of strain 93-210 and used to construct a genetic map, consisting of 41 linkage groups, spanning 7,715.0 centimorgans (cM) and covering 68 Mb of the reference genome. The recombination rate was estimated to be 1.81 ± 2.32 cM/10 kb. Quantitative trait locus analysis mapped six Avr gene loci to the genetic map, including an Avr cluster harboring four Avr genes, AvYr7, AvYr43, AvYr44, and AvYrExp2 Aligning the genetic map to the reference genome identified Avr candidates and narrowed them to a small genomic region (<200 kb). The discovery of the Avr gene cluster is useful for understanding pathogen evolution, and the identification of candidate genes is an important step toward cloning Avr genes for studying molecular mechanisms of pathogen-host interactions.IMPORTANCE Stripe rust is a destructive disease of wheat worldwide. Growing resistant cultivars is the most effective, easy-to-use, economical, and environmentally friendly strategy for the control of the disease. However, P. striiformis f. sp. tritici can produce new virulent races that may circumvent race-specific resistance. Therefore, understanding the genetic basis of the interactions between wheat genes for resistance and P. striiformis f. sp. tritici genes for avirulence is useful for improving cultivar resistance for more effective control of the disease. This study developed a high-quality map that facilitates genomic and genetic studies of important traits related to pathogen pathogenicity and adaptation to different environments and crop cultivars carrying different resistance genes. The information on avirulence/virulence genes identified in this study can be used for guiding breeding programs to select combinations of genes for developing new cultivars with effective resistance to mitigate this devastating disease.
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Ramos M, Carvalho R, Soares da Silva E, Ramos AP, Talhinhas P. Pathological and Epidemiological Characterization of First Outbreak of Daylily Rust in Europe and Evaluation of Puccinia hemerocallidis Resistance in Hemerocallis Cultivars. PLANTS 2020; 9:plants9040427. [PMID: 32244437 PMCID: PMC7238211 DOI: 10.3390/plants9040427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/21/2020] [Accepted: 03/27/2020] [Indexed: 01/25/2023]
Abstract
Daylily rust—caused by Puccinia hemerocallidis—was confined to Eastern Asia until the disease was reported in Oceania, Africa, the Americas and Portugal in the 21st century. Although information on rust resistance of American cultivars is available, little is known about the resistance of European bred cultivars, threating the ornamental sector if the fungus spreads to other European countries. Aiming to provide tools to address this, we analyzed the Portuguese pathogens and characterized rust resistance in a selection of cultivars, while optimizing disease rating scales. Morphologic, genetic and cytogenomic characterization of four isolates reveals narrow diversity and raises the question whether the pathogen may have originated in North- or Central America. Daily records of multiple symptomatologic parameters enabled a detailed disease progress analysis, discriminating cultivars according to their resistance levels and revealing susceptibility as the most common state. Among the tested cultivars, 12 out of 17 began to show symptoms between 6–8 dai and were classified as susceptible. Cultivars ‘Stella d’Oro’, ‘Bitsy’ and ‘Cherry Tiger’ behaved as moderately resistant although the occurrence of late sporulation on leaves suggests incomplete resistance and challenges common rating scales. The identification of resistance sources in European breeding lines is crucial for the sustainable future of daylilies.
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Affiliation(s)
- Madalena Ramos
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (M.R.); (E.S.d.S.); (A.P.R.); (P.T.)
| | - Rita Carvalho
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (M.R.); (E.S.d.S.); (A.P.R.); (P.T.)
- Correspondence: ; Tel.: +351-21-365-31-00
| | - Elsa Soares da Silva
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (M.R.); (E.S.d.S.); (A.P.R.); (P.T.)
| | - Ana Paula Ramos
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (M.R.); (E.S.d.S.); (A.P.R.); (P.T.)
- LPVVA, Laboratório de Patologia Vegetal “Veríssimo de Almeida”, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Pedro Talhinhas
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (M.R.); (E.S.d.S.); (A.P.R.); (P.T.)
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Hollingsworth RG, Aristizábal LF, Shriner S, Mascarin GM, Moral RDA, Arthurs SP. Incorporating Beauveria bassiana Into an Integrated Pest Management Plan for Coffee Berry Borer in Hawaii. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00022] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Among the thousands of rust species described, many are known for their devastating effects on their hosts, which include major agriculture crops and trees. Hence, for over a century, these basidiomycete pathogenic fungi have been researched and experimented with. However, due to their biotrophic nature, they are challenging organisms to work with and, needing their hosts for propagation, represent pathosystems that are not easily experimentally accessible. Indeed, efforts to perform genetics have been few and far apart for the rust fungi, though one study performed in the 1940s was famously instrumental in formulating the gene-for-gene hypothesis describing pathogen-host interactions. By taking full advantage of the molecular genetic tools developed in the 1980s, research on many plant pathogenic microbes thrived, yet similar work on the rusts remained very challenging though not without some successes. However, the genomics era brought real breakthrough research for the biotrophic fungi and with innovative experimentation and the use of heterologous systems, molecular genetic analyses over the last 2 decades have significantly advanced our insight into the function of many rust fungus genes and their role in the interaction with their hosts. This has allowed optimizing efforts for resistance breeding and the design and testing of various novel strategies to reduce the devastating diseases they cause.
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Affiliation(s)
- Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research & Development Centre, 4200 Hwy 97, Summerland, BC, Canada V0H 1Z0
| | - Les J Szabo
- U.S. Department of Agriculture-Agriculture Research Service, Cereal Disease Laboratory and University of Minnesota, 1551 Lindig Street, St. Paul, MN 55108, U.S.A
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