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Gutiérrez-Jara JP, Vogt-Geisse K, Correa MCG, Vilches-Ponce K, Pérez LM, Chowell G. Modeling the Impact of Agricultural Mitigation Measures on the Spread of Sharka Disease in Sweet Cherry Orchards. PLANTS (BASEL, SWITZERLAND) 2023; 12:3442. [PMID: 37836182 PMCID: PMC10575084 DOI: 10.3390/plants12193442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
Sharka is a disease affecting stone fruit trees. It is caused by the Plum pox virus (PPV), with Myzus persicae being one of the most efficient aphid species in transmitting it within and among Prunus orchards. Other agricultural management strategies are also responsible for the spread of disease among trees, such as grafting and pruning. We present a mathematical model of impulsive differential equations to represent the dynamics of Sharka disease in the tree and vector population. We consider three transmission routes: grafting, pruning, and through aphid vectors. Grafting, pruning, and vector control occur as pulses at specific instants. Within the model, human risk perception towards disease influences these agricultural management strategies. Model results show that grafting with infected biological material has a significant impact on the spread of the disease. In addition, detecting infectious symptomatic and asymptomatic trees in the short term is critical to reduce disease spread. Furthermore, vector control to prevent aphid movement between trees is crucial for disease mitigation, as well as implementing awareness campaigns for Sharka disease in agricultural communities that provide a long-term impact on responsible pruning, grafting, and vector control.
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Affiliation(s)
- Juan Pablo Gutiérrez-Jara
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3480112, Chile;
| | - Katia Vogt-Geisse
- Facultad de Ingeniería y Ciencias, Unidad Adolfo Ibáñez, Diagonal Las Torres 2640, Peñalolén, Santiago 7941169, Chile
| | - Margarita C. G. Correa
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3480112, Chile;
| | - Karina Vilches-Ponce
- Facultad de Ciencias Básicas, Universidad Católica del Maule, Avenida San Miguel 3605, Talca 3480112, Chile;
| | - Laura M. Pérez
- Departamento de Física, Universidad de Tarapacá, Casilla 7D, Arica 1000000, Chile;
| | - Gerardo Chowell
- School of Public Health, Georgia State University, Atlanta, GA 30303, USA;
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2
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Tricon D, Faivre d'Arcier J, Eyquard JP, Liu S, Decroocq S, Chague A, Liu W, Balakishiyeva G, Mammadov A, Turdiev T, Kostritsyna T, Asma BM, Akparov Z, Decroocq V. Allele mining of eukaryotic translation initiation factor genes in Prunus for the identification of new sources of resistance to sharka. Sci Rep 2023; 13:15247. [PMID: 37709842 PMCID: PMC10502034 DOI: 10.1038/s41598-023-42215-w] [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: 06/09/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Members of the eukaryotic translation initiation complex are co-opted in viral infection, leading to susceptibility in many crop species, including stone fruit trees (Prunus spp.). Therefore, modification of one of those eukaryotic translation initiation factors or changes in their gene expression may result in resistance. We searched the crop and wild Prunus germplasm from the Armeniaca and Amygdalus taxonomic sections for allelic variants in the eIF4E and eIFiso4E genes, to identify alleles potentially linked to resistance to Plum pox virus (PPV). Over one thousand stone fruit accessions (1397) were screened for variation in eIF4E and eIFiso4E transcript sequences which are in single copy within the diploid Prunus genome. We identified new alleles for both genes differing from haplotypes associated with PPV susceptible accessions. Overall, analyses showed that eIFiso4E is genetically more constrained since it displayed less polymorphism than eIF4E. We also demonstrated more variations at both loci in the related wild species than in crop species. As the eIFiso4E translation initiation factor was identified as indispensable for PPV infection, a selection of ten different eIFiso4E haplotypes along 13 accessions were tested by infection with PPV and eight of them displayed a range of reduced susceptibility to resistance, indicating new potential sources of resistance to sharka.
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Affiliation(s)
- David Tricon
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
- INRAE Unité de Recherches 1052 GAFL, 67 allee des Chênes, 84143, Montfavet, France
| | - Julie Faivre d'Arcier
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
- INRAE Unité Expérimentale Domaine des Jarres, 33210, Toulenne, France
| | - Jean-Philippe Eyquard
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Shuo Liu
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou, 115009, Liaoning, China
| | - Stéphane Decroocq
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Aurélie Chague
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Weisheng Liu
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou, 115009, Liaoning, China
| | - Gulnara Balakishiyeva
- Institute of Molecular Biology and Biotechnologies, Ministry of Science and Education, 11 Izzat Nabiev Str., 1073, Baku, Azerbaijan
| | - Alamdar Mammadov
- Institute of Molecular Biology and Biotechnologies, Ministry of Science and Education, 11 Izzat Nabiev Str., 1073, Baku, Azerbaijan
| | - Timur Turdiev
- Institute of Plant Biology and Biotechnology, Timiryazev Str. 45, 050040, Almaty, Kazakhstan
| | - Tatiana Kostritsyna
- International Higher School of Medicine, 1F Intergelpo Street, 720054, Bishkek, Kyrgyzstan
| | - Bayram M Asma
- Department of Horticulture, Malatya Turgut Ozal University, Malatya, 44210, Turkey
| | - Zeynal Akparov
- Genetic Resources Institute of ANAS, Azadlig Ave. 155, 1106, Baku, Azerbaijan
| | - Véronique Decroocq
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France.
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3
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Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
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Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583
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4
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Jeger MJ. Tolerance of plant virus disease: Its genetic, physiological, and epidemiological significance. Food Energy Secur 2022. [DOI: 10.1002/fes3.440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Michael John Jeger
- Department of Life Sciences, Silwood Park Imperial College London Ascot UK
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5
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Li Y, Wang A. Biolistic Inoculation of Fruit Trees with Full-Length Infectious cDNA Clones of RNA Viruses. Methods Mol Biol 2022; 2400:207-216. [PMID: 34905204 DOI: 10.1007/978-1-0716-1835-6_20] [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] [Indexed: 06/14/2023]
Abstract
Long life cycle and lack of efficient and robust virus inoculation technique are the major technical challenges for studying virus infection in perennial woody plants such as fruit trees. Biolistic technology also called particle bombardment is a physical approach that can directly introduce virions or viral full-length cDNA infectious clones into target cells and tissues by high velocity microcarrier particles. The flexibility and high efficiency of the biolistic inoculation method facilitate research on fruit tree virology and the screening and identification of fruit tree germplasms resistant to viruses. Here, we describe a detailed protocol for the biolistic inoculation of peach with of a cDNA infectious clone of Plum pox virus (PPV) using the Helios gene gun, a biolistic particle delivery system.
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Affiliation(s)
- Yinzi Li
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.
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6
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Modelling interference between vectors of non-persistently transmitted plant viruses to identify effective control strategies. PLoS Comput Biol 2021; 17:e1009727. [PMID: 34962929 PMCID: PMC8758101 DOI: 10.1371/journal.pcbi.1009727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/13/2022] [Accepted: 12/07/2021] [Indexed: 11/23/2022] Open
Abstract
Aphids are the primary vector of plant viruses. Transient aphids, which probe several plants per day, are considered to be the principal vectors of non-persistently transmitted (NPT) viruses. However, resident aphids, which can complete their life cycle on a single host and are affected by agronomic practices, can transmit NPT viruses as well. Moreover, they can interfere both directly and indirectly with transient aphids, eventually shaping plant disease dynamics. By means of an epidemiological model, originally accounting for ecological principles and agronomic practices, we explore the consequences of fertilization and irrigation, pesticide deployment and roguing of infected plants on the spread of viral diseases in crops. Our results indicate that the spread of NPT viruses can be i) both reduced or increased by fertilization and irrigation, depending on whether the interference is direct or indirect; ii) counter-intuitively increased by pesticide application and iii) reduced by roguing infected plants. We show that a better understanding of vectors’ interactions would enhance our understanding of disease transmission, supporting the development of disease management strategies. A range of both experimental and theoretical studies show that the behaviour and population dynamics of insects depend strongly upon interactions with other insect species. These interactions have the potential to greatly affect the dynamics of insect-vectored plant disease, as transmission of viruses is intimately dependent on the local density of vectors, as well as how they select and move between potential host plants. Surprisingly, the effects of interaction between vector species on epidemics remains little studied and even worse understood, probably because experimentation is costly and difficult. Here, we present a model which permits us to investigate the effect of interaction between a virus, two vector species and the host plant on the spread of viral disease in crops. In this study, our model is used to explore the consequences of common agronomic practices on epidemics. Our study highlights the importance of exploring vectors’ interactions to enhance the understanding of disease transmission, supporting the development of disease management strategies.
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7
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Zhou J, Xing F, Wang H, Li S. Occurrence, Distribution, and Genomic Characteristics of Plum Pox Virus Isolates from Common Apricot ( Prunus armeniaca) and Japanese Apricot ( Prunus mume) in China. PLANT DISEASE 2021; 105:3474-3480. [PMID: 33858186 DOI: 10.1094/pdis-09-20-1936-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Plum pox, or Sharka disease, caused by infection with plum pox virus (PPV), results in enormous economic losses to the stone fruit industry. However, the frequency and distribution of PPV remain unclear in China, the world's largest stone fruit producer. Systemic visual surveys were performed on stone fruit trees in China from 2008 to 2018, and the results suggest that plum pox disease is widely distributed on common apricots (Prunus armeniaca) and Japanese apricots (Prunus mume), with an average symptoms incidence rate >30% in the latter. In samples collected from Beijing, Nanjing, Shanghai, Wuhan, Wuxi, and Yuncheng, PPV was detected in 77% (85 of 110) of collected samples by immunochromatographic (IC) strip tests and reverse transcription PCR, and 96% (67 of 70) of samples showing Sharka symptoms were PPV positive. Transmission electron microscopy revealed filamentous particles of ∼640 × 12.5 nm (n = 19) in size and pinwheel inclusions in symptomatic plants but not in the asymptomatic and PPV-negative plants. Full-length genomes were determined for four isolates (three from Japanese apricot and one from common apricot), and phylogenetic analyses indicated that all four isolates belong to a clade PPV-D, despite slight differences in genome size. These findings not only highlight the widespread occurrence and distribution of PPV in China but also provide detailed information about the genomic characteristics and evolutionary position of PPV isolates in China.
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Affiliation(s)
- Jun Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
| | - Fei Xing
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongqing Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
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8
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Singh K, Callahan AM, Smith BJ, Malinowski T, Scorza R, Jarošová J, Beoni E, Polák J, Kundu JK, Dardick C. Long-Term Efficacy and Safety of RNAi-Mediated Virus Resistance in 'HoneySweet' Plum. FRONTIERS IN PLANT SCIENCE 2021; 12:726881. [PMID: 34712254 PMCID: PMC8546108 DOI: 10.3389/fpls.2021.726881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Interfering RNA technology has been established as an effective strategy to protect plants against viral infection. Despite this success, interfering RNA (RNAi) has rarely been applied due to the regulatory barriers that confront genetically engineered plants and concerns over possible environmental and health risks posed by non-endogenous small RNAs. 'HoneySweet' was developed as a virus-resistant plum variety that is protected by an RNAi-mediated process against Sharka disease caused by the plum pox virus. 'HoneySweet' has been approved for cultivation in the United States but not in countries where the plum pox virus is endemic. In this study, we evaluated the long-term efficacy of virus resistance in 'HoneySweet,' the nature and stability of its sRNA profile, and the potential health risks of consuming 'HoneySweet' plums. Graft-challenged 'HoneySweet' trees carrying large non-transgenic infected limbs remained virus-free after more than 10 years in the field, and the viral sequences from the non-transgenic infected limbs showed no evidence of adaptation to the RNAi-based resistance. Small RNA profiling revealed that transgene-derived sRNA levels were stable across different environments and, on average, were more than 10 times lower than those present in symptom-less fruits from virus-infected trees. Comprehensive 90-day mouse feeding studies showed no adverse health impacts in mice, and there was no evidence for potential siRNA off-target pathologies predicted by comparisons of the most abundant transgene-derived sRNAs to the mouse genome. Collectively, the data confirmed that RNAi provides a highly effective, stable, and safe strategy to combat virus diseases in crop plants.
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Affiliation(s)
- Khushwant Singh
- Innovative Fruit Production, Improvement and Protection, Appalachian Fruit Research Station, Agricultural Research Service (USDA), Kearneysville, WV, United States
- Division of Crop Protection and Plant Health, Crop Research Institute, Prague, Czech Republic
| | - Ann M. Callahan
- Innovative Fruit Production, Improvement and Protection, Appalachian Fruit Research Station, Agricultural Research Service (USDA), Kearneysville, WV, United States
| | - Brenda J. Smith
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Tadeusz Malinowski
- Innovative Fruit Production, Improvement and Protection, Appalachian Fruit Research Station, Agricultural Research Service (USDA), Kearneysville, WV, United States
- The National Research Institute of Horticulture, Skierniewice, Poland
| | - Ralph Scorza
- Innovative Fruit Production, Improvement and Protection, Appalachian Fruit Research Station, Agricultural Research Service (USDA), Kearneysville, WV, United States
| | - Jana Jarošová
- Division of Crop Protection and Plant Health, Crop Research Institute, Prague, Czech Republic
| | - Eva Beoni
- Division of Crop Protection and Plant Health, Crop Research Institute, Prague, Czech Republic
| | - Jaroslav Polák
- Division of Crop Protection and Plant Health, Crop Research Institute, Prague, Czech Republic
| | - Jiban Kumar Kundu
- Division of Crop Protection and Plant Health, Crop Research Institute, Prague, Czech Republic
| | - Chris Dardick
- Innovative Fruit Production, Improvement and Protection, Appalachian Fruit Research Station, Agricultural Research Service (USDA), Kearneysville, WV, United States
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9
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Yang X, Li Y, Wang A. Research Advances in Potyviruses: From the Laboratory Bench to the Field. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:1-29. [PMID: 33891829 DOI: 10.1146/annurev-phyto-020620-114550] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Potyviruses (viruses in the genus Potyvirus, family Potyviridae) constitute the largest group of known plant-infecting RNA viruses and include many agriculturally important viruses that cause devastating epidemics and significant yield losses in many crops worldwide. Several potyviruses are recognized as the most economically important viral pathogens. Therefore, potyviruses are more studied than other groups of plant viruses. In the past decade, a large amount of knowledge has been generated to better understand potyviruses and their infection process. In this review, we list the top 10 economically important potyviruses and present a brief profile of each. We highlight recent exciting findings on the novel genome expression strategy and the biological functions of potyviral proteins and discuss recent advances in molecular plant-potyvirus interactions, particularly regarding the coevolutionary arms race. Finally, we summarize current disease control strategies, with a focus on biotechnology-based genetic resistance, and point out future research directions.
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Affiliation(s)
- Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3, Canada;
| | - Yinzi Li
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3, Canada;
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3, Canada;
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10
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Espinoza C, Bascou B, Calvayrac C, Bertrand C. Deciphering Prunus Responses to PPV Infection: A Way toward the Use of Metabolomics Approach for the Diagnostic of Sharka Disease. Metabolites 2021; 11:metabo11070465. [PMID: 34357359 PMCID: PMC8307365 DOI: 10.3390/metabo11070465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/09/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Sharka disease, caused by Plum pox virus (PPV), induces several changes in Prunus. In leaf tissues, the infection may cause oxidative stress and disrupt the photosynthetic process. Moreover, several defense responses can be activated after PPV infection and have been detected at the phytohormonal, transcriptomic, proteomic, and even translatome levels. As proposed in this review, some responses may be systemic and earlier to the onset of symptoms. Nevertheless, these changes are highly dependent among species, variety, sensitivity, and tissue type. In the case of fruit tissues, PPV infection can modify the ripening process, induced by an alteration of the primary metabolism, including sugars and organic acids, and secondary metabolism, including phenolic compounds. Interestingly, metabolomics is an emerging tool to better understand Prunus–PPV interactions mainly in primary and secondary metabolisms. Moreover, through untargeted metabolomics analyses, specific and early candidate biomarkers of PPV infection can be detected. Nevertheless, these candidate biomarkers need to be validated before being selected for a diagnostic or prognosis by targeted analyses. The development of a new method for early detection of PPV-infected trees would be crucial for better management of the outbreak, especially since there is no curative treatment.
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Affiliation(s)
- Christian Espinoza
- PSL Université de Paris EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, CEDEX, 66860 Perpignan, France; (C.E.); (B.B.)
- S.A.S. AkiNaO, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Benoît Bascou
- PSL Université de Paris EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, CEDEX, 66860 Perpignan, France; (C.E.); (B.B.)
| | - Christophe Calvayrac
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, CEDEX, 66860 Perpignan, France;
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UMPC) Paris 6 et CNRS, Observatoire Océanologique, Banyuls-sur-Mer, CEDEX, 75005 Paris, France
| | - Cédric Bertrand
- PSL Université de Paris EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, CEDEX, 66860 Perpignan, France; (C.E.); (B.B.)
- S.A.S. AkiNaO, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, CEDEX, 66860 Perpignan, France
- Correspondence: ; Tel.: +33-(0)4-6866-2258
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11
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Cai Z, Ouyang F, Zhang X, Chen J, Xiao Y, Ge F, Zhang J. Biological Control of Aphis spiraecola (Hemiptera: Aphididae) Using Three Different Flowering Plants in Apple Orchards. JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:1128-1137. [PMID: 33834196 DOI: 10.1093/jee/toab064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Indexed: 06/12/2023]
Abstract
Increasing the biodiversity of agroecosystems can increase populations of natural enemies that are useful for pest control. Orchards often have a low diversity of plant species, which is not conducive to maintaining ecosystem functions and services. However, additional flowering plants could provide natural enemies with beneficial resources. To assess the ability of flowering plants to attract predators and increase the biological control of Aphis spiraecola Patch, we established individual plots of three different flowering plant species with sequential bloom periods between the rows of apple orchard. These plants attracted predators such as Coccinellidae, Syrphidae, and Chrysopidae when flowering. The density of predators on trees in the three flowering plant plots was significantly higher than that in the control, whereas the density of aphids on trees in Orychophragmus violaceus (L.) O. E. Schulz (Rhoeadales: Brassicaceae) and Cnidium monnieri (Linn.) Cuss. (Apiales: Apiaceae) plots were significantly lower than that in control. The density of aphids on trees in Calendula officinalis L. (Asterales: Asteraceae) plots was significantly lower than in other plots at second peak period. There was a significant negative correlation between the population of aphids and predators on trees at peak of aphids. Cage exclusion tests showed that the biocontrol services index (BSI) of O. violaceus was highest (32.7%) on 24 May, and the BSI of C. monnieri was highest (47.6%) on 7 June. Our results suggest that the temporal combination of different flowering plants could provide useful effective biocontrol to management pest in orchard.
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Affiliation(s)
- Zhiping Cai
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fang Ouyang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xingrui Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jing Chen
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, China
| | - Yunli Xiao
- Plant Protection Station of Shandong Province, Jinan, China
| | - Feng Ge
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jianping Zhang
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, China
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Jones RAC. Global Plant Virus Disease Pandemics and Epidemics. PLANTS (BASEL, SWITZERLAND) 2021; 10:233. [PMID: 33504044 PMCID: PMC7911862 DOI: 10.3390/plants10020233] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
The world's staple food crops, and other food crops that optimize human nutrition, suffer from global virus disease pandemics and epidemics that greatly diminish their yields and/or produce quality. This situation is becoming increasingly serious because of the human population's growing food requirements and increasing difficulties in managing virus diseases effectively arising from global warming. This review provides historical and recent information about virus disease pandemics and major epidemics that originated within different world regions, spread to other continents, and now have very wide distributions. Because they threaten food security, all are cause for considerable concern for humanity. The pandemic disease examples described are six (maize lethal necrosis, rice tungro, sweet potato virus, banana bunchy top, citrus tristeza, plum pox). The major epidemic disease examples described are seven (wheat yellow dwarf, wheat streak mosaic, potato tuber necrotic ringspot, faba bean necrotic yellows, pepino mosaic, tomato brown rugose fruit, and cucumber green mottle mosaic). Most examples involve long-distance virus dispersal, albeit inadvertent, by international trade in seed or planting material. With every example, the factors responsible for its development, geographical distribution and global importance are explained. Finally, an overall explanation is given of how to manage global virus disease pandemics and epidemics effectively.
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Affiliation(s)
- Roger A C Jones
- The UWA Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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13
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Hou W, Li S, Massart S. Is There a "Biological Desert" With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses. Front Microbiol 2020; 11:592816. [PMID: 33329473 PMCID: PMC7710903 DOI: 10.3389/fmicb.2020.592816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
High throughput sequencing technologies accelerated the pace of discovery and identification of new viral species. Nevertheless, biological characterization of a new virus is a complex and long process, which can hardly follow the current pace of virus discovery. This review has analyzed 78 publications of new viruses and viroids discovered from 32 fruit tree species since 2011. The scientific biological information useful for a pest risk assessment and published together with the discovery of a new fruit tree virus or viroid has been analyzed. In addition, the 933 publications citing at least one of these original publications were reviewed, focusing on the biology-related information provided. In the original publications, the scientific information provided was the development of a detection test (94%), whole-genome sequence including UTRs (92%), local and large-scale epidemiological surveys (68%), infectivity and indicators experiments (50%), association with symptoms (25%), host range infection (23%), and natural vector identification (8%). The publication of a new virus is cited 2.8 times per year on average. Only 18% of the citations reported information on the biology or geographical repartition of the new viruses. These citing publications improved the new virus characterization by identifying the virus in a new country or continent, determining a new host, developing a new diagnostic test, studying genome or gene diversity, or by studying the transmission. Based on the gathered scientific information on the virus biology, the fulfillment of a recently proposed framework has been evaluated. A baseline prioritization approach for publishing a new plant virus is proposed for proper assessment of the potential risks caused by a newly identified fruit tree virus.
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Affiliation(s)
- Wanying Hou
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Institute of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao, China
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shifang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Maejima K, Hashimoto M, Hagiwara‐Komoda Y, Miyazaki A, Nishikawa M, Tokuda R, Kumita K, Maruyama N, Namba S, Yamaji Y. Intra-strain biological and epidemiological characterization of plum pox virus. MOLECULAR PLANT PATHOLOGY 2020; 21:475-488. [PMID: 31978272 PMCID: PMC7060144 DOI: 10.1111/mpp.12908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 05/21/2023]
Abstract
Plum pox virus (PPV) is one of the most important plant viruses causing serious economic losses. Thus far, strain typing based on the definition of 10 monophyletic strains with partially differentiable biological properties has been the sole approach used for epidemiological characterization of PPV. However, elucidating the genetic determinants underlying intra-strain biological variation among populations or isolates remains a relevant but unexamined aspect of the epidemiology of the virus. In this study, based on complete nucleotide sequence information of 210 Japanese and 47 non-Japanese isolates of the PPV-Dideron (D) strain, we identified five positively selected sites in the PPV-D genome. Among them, molecular studies showed that amino acid substitutions at position 2,635 in viral replicase correlate with viral titre and competitiveness at the systemic level, suggesting that amino acid position 2,635 is involved in aphid transmission efficiency and symptom severity. Estimation of ancestral genome sequences indicated that substitutions at amino acid position 2,635 were reversible and peculiar to one of two genetically distinct PPV-D populations in Japan. The reversible amino acid evolution probably contributes to the dissemination of the virus population. This study provides the first genomic insight into the evolutionary epidemiology of PPV based on intra-strain biological variation ascribed to positive selection.
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Affiliation(s)
- Kensaku Maejima
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Masayoshi Hashimoto
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yuka Hagiwara‐Komoda
- Department of Sustainable AgricultureCollege of Agriculture, Food and Environment SciencesRakuno Gakuen UniversityEbetsuHokkaidoJapan
| | - Akio Miyazaki
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Masanobu Nishikawa
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Ryosuke Tokuda
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Kohei Kumita
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Noriko Maruyama
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Shigetou Namba
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
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15
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Rodamilans B, Valli A, García JA. Molecular Plant-Plum Pox Virus Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:6-17. [PMID: 31454296 DOI: 10.1094/mpmi-07-19-0189-fi] [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] [Indexed: 06/10/2023]
Abstract
Plum pox virus, the agent that causes sharka disease, is among the most important plant viral pathogens, affecting Prunus trees across the globe. The fabric of interactions that the virus is able to establish with the plant regulates its life cycle, including RNA uncoating, translation, replication, virion assembly, and movement. In addition, plant-virus interactions are strongly conditioned by host specificities, which determine infection outcomes, including resistance. This review attempts to summarize the latest knowledge regarding Plum pox virus-host interactions, giving a comprehensive overview of their relevance for viral infection and plant survival, including the latest advances in genetic engineering of resistant species.
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Affiliation(s)
- Bernardo Rodamilans
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Adrián Valli
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan Antonio García
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
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16
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De Mori G, Falchi R, Testolin R, Bassi D, Savazzini F, Dondini L, Tartarini S, Palmisano F, Minafra A, Spadotto A, Scalabrin S, Geuna F. Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of 'Lito' Chromosome 1 and Analysis of Candidate Genes. FRONTIERS IN PLANT SCIENCE 2019; 10:1576. [PMID: 31867032 PMCID: PMC6905379 DOI: 10.3389/fpls.2019.01576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
Sharka, a common disease among most stone fruit crops, is caused by the Plum Pox Virus (PPV). Resistant genotypes have been found in apricot (Prunus armeniaca L.), one of which-the cultivar 'Lito' heterozygous for the resistance-has been used to map a major quantitative trait locus (QTL) on linkage group 1, following a pseudo-test-cross mating design with 231 individuals. In addition, 19 SNP markers were selected from among the hundreds previously developed, which allowed the region to be limited to 236 kb on chromosome 1. A 'Lito' bacterial artificial chromosome (BAC) library was produced, screened with markers of the region, and positive BAC clones were sequenced. Resistant (R) and susceptible (S) haplotypes were assembled independently. To refine the assembly, the whole genome of 'Lito' was sequenced to high coverage (98×) using PacBio technology, enabling the development of a detailed assembly of the region that was able to predict and annotate the genes in the QTL region. The selected cultivar 'Lito' allowed not only to discriminate structural variants between the two haplotypic regions but also to distinguish specific allele expression, contributing towards mining the PPVres locus. In light of these findings, genes previously indicated (i.e., MATHd genes) to have a possible role in PPV resistance were further analyzed, and new candidates were discussed. Although the results are not conclusive, the accurate and independent assembly of R and S haplotypes of 'Lito' is a valuable resource to predict and test alternative transcription and regulation mechanisms underpinning PPV resistance.
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Affiliation(s)
- Gloria De Mori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Rachele Falchi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
| | - Federica Savazzini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Locorotondo, Italy
| | - Angelantonio Minafra
- National Research Council, Institute for Sustainable Plant Protection, Bari, Italy
| | | | - Simone Scalabrin
- IGA Technology Services, Science and Technology Park, ZIU, Udine, Italy
| | - Filippo Geuna
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
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Hajizadeh M, Gibbs AJ, Amirnia F, Glasa M. The global phylogeny o f Plum pox virus is emerging. J Gen Virol 2019; 100:1457-1468. [PMID: 31418674 DOI: 10.1099/jgv.0.001308] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The 206 complete genomic sequences of Plum pox virus in GenBank (January 2019) were downloaded. Their main open reading frames (ORF)s were compared by phylogenetic and population genetic methods. All fell into the nine previously recognized strain clusters; the PPV-Rec and PPV-T strain ORFs were all recombinants, whereas most of those in the PPV-C, PPV-CR, PPV-CV, PPV-D, PPV-EA, PPV-M and PPV-W strain clusters were not. The strain clusters ranged in size from 2 (PPV-CV and PPV-EA) to 74 (PPV-D). The isolates of eight of the nine strains came solely from Europe and the Levant (with an exception resulting from a quarantine breach), but many PPV-D strain isolates also came from east and south Asia and the Americas. The estimated time to the most recent common ancestor (TMRCA) of all 134 non-recombinant ORFs was 820 (865-775) BCE. Most strain populations were only a few decades old, and had small intra-strain, but large inter-strain, differences; strain PPV-W was the oldest. Eurasia is clearly the 'centre of emergence' of PPV and the several PPV-D strain populations found elsewhere only show evidence of gene flow with Europe, so have come from separate introductions from Europe. All ORFs and their individual genes show evidence of strong negative selection, except the positively selected pipo gene of the recently migrant populations. The possible ancient origins of PPV are discussed.
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Affiliation(s)
- Mohammad Hajizadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Adrian J Gibbs
- Emeritus Faculty Australian National University, Canberra, Australia
| | - Fahimeh Amirnia
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia
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18
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Rimbaud L, Dallot S, Bruchou C, Thoyer S, Jacquot E, Soubeyrand S, Thébaud G. Improving Management Strategies of Plant Diseases Using Sequential Sensitivity Analyses. PHYTOPATHOLOGY 2019; 109:1184-1197. [PMID: 30844325 DOI: 10.1094/phyto-06-18-0196-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Improvement of management strategies of epidemics is often hampered by constraints on experiments at large spatiotemporal scales. A promising approach consists of modeling the biological epidemic process and human interventions, which both impact disease spread. However, few methods enable the simultaneous optimization of the numerous parameters of sophisticated control strategies. To do so, we propose a heuristic approach (i.e., a practical improvement method approximating an optimal solution) based on sequential sensitivity analyses. In addition, we use an economic improvement criterion based on the net present value, accounting for both the cost of the different control measures and the benefit generated by disease suppression. This work is motivated by sharka (caused by Plum pox virus), a vector-borne disease of prunus trees (especially apricot, peach, and plum), the management of which in orchards is mainly based on surveillance and tree removal. We identified the key parameters of a spatiotemporal model simulating sharka spread and control and approximated optimal values for these parameters. The results indicate that the current French management of sharka efficiently controls the disease, but it can be economically improved using alternative strategies that are identified and discussed. The general approach should help policy makers to design sustainable and cost-effective strategies for disease management.
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Affiliation(s)
- Loup Rimbaud
- 1 BGPI, INRA, Montpellier SupAgro, University of Montpellier, CIRAD, TA A-54/K, 34398 Montpellier Cedex 5, France
| | - Sylvie Dallot
- 1 BGPI, INRA, Montpellier SupAgro, University of Montpellier, CIRAD, TA A-54/K, 34398 Montpellier Cedex 5, France
| | | | - Sophie Thoyer
- 3 CEE-M, Montpellier SupAgro, INRA, CNRS, University of Montpellier, Montpellier, France
| | - Emmanuel Jacquot
- 1 BGPI, INRA, Montpellier SupAgro, University of Montpellier, CIRAD, TA A-54/K, 34398 Montpellier Cedex 5, France
| | | | - Gaël Thébaud
- 1 BGPI, INRA, Montpellier SupAgro, University of Montpellier, CIRAD, TA A-54/K, 34398 Montpellier Cedex 5, France
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19
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Picard C, Soubeyrand S, Jacquot E, Thébaud G. Analyzing the Influence of Landscape Aggregation on Disease Spread to Improve Management Strategies. PHYTOPATHOLOGY 2019; 109:1198-1207. [PMID: 31166155 DOI: 10.1094/phyto-05-18-0165-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Epidemiological models are increasingly used to predict epidemics and improve management strategies. However, they rarely consider landscape characteristics although such characteristics can influence the epidemic dynamics and, thus, the effectiveness of disease management strategies. Here, we present a generic in silico approach which assesses the influence of landscape aggregation on the costs associated with an epidemic and on improved management strategies. We apply this approach to sharka, one of the most damaging diseases of Prunus trees, for which a management strategy is already applied in France. Epidemic simulations were carried out with a spatiotemporal stochastic model under various management strategies in landscapes differing in patch aggregation. Using sensitivity analyses, we highlight the impact of management parameters on the economic output of the model. We also show that the sensitivity analysis can be exploited to identify several strategies that are, according to the model, more profitable than the current French strategy. Some of these strategies are specific to a given aggregation level, which shows that management strategies should generally be tailored to each specific landscape. However, we also identified a strategy that is efficient for all levels of landscape aggregation. This one-size-fits-all strategy has important practical implications because of its simple applicability at a large scale.
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Affiliation(s)
- Coralie Picard
- 1 BGPI, INRA, Montpellier SupAgro, Univ Montpellier, Cirad, TA A-54/K, 34398, Montpellier Cedex 5, France
| | | | - Emmanuel Jacquot
- 1 BGPI, INRA, Montpellier SupAgro, Univ Montpellier, Cirad, TA A-54/K, 34398, Montpellier Cedex 5, France
| | - Gaël Thébaud
- 1 BGPI, INRA, Montpellier SupAgro, Univ Montpellier, Cirad, TA A-54/K, 34398, Montpellier Cedex 5, France
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20
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Sidorova T, Mikhailov R, Pushin A, Miroshnichenko D, Dolgov S. Agrobacterium-Mediated Transformation of Russian Commercial Plum cv. "Startovaya" ( Prunus domestica L.) With Virus-Derived Hairpin RNA Construct Confers Durable Resistance to PPV Infection in Mature Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:286. [PMID: 30915093 PMCID: PMC6423057 DOI: 10.3389/fpls.2019.00286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/20/2019] [Indexed: 05/19/2023]
Abstract
In modern horticulture Plum pox virus (PPV) imposes serious threats to commercial plantations of a wide range of fruit species belonging to genera Prunus. Given the lack of natural genetic resources, which display reliable resistance to PPV infection, there has been considerable interest in using genetic engineering methods for targeted genome modification of stone fruit trees to control Sharka disease caused by PPV. Among the many virus defense mechanisms, RNA interference is shown to be the most promising transgenic disease-control strategy in plant biotechnology. The present study describes the production of transgenic PPV resistant European plum "Startovaya" (P. domestica L.) through the Agrobacterium-mediated transformation of in vitro leaf explants. Due to organogenesis from leaves, the established protocol allows the genetic engineering of the plum genome without losing clonal fidelity of original cultivar. Seven independent transgenic plum lines containing the self-complementary fragments of PPV-CP gene sequence separated by a PDK intron were generated using hpt as a selective gene and uidA as a reporter gene. The transformation was verified through the histochemical staining for β-glucuronidase activity, PCR amplification of appropriate vector products from isolated genomic DNA and Southern blot analysis of hairpin PPV-CP gene fragments. To clarify the virus resistance, plum buds infected by PPV-M strain were grafted onto 1-year-old transgenic plants, which further were grown into mature trees in the greenhouse. As evaluated by RT-PCR, DAS-ELISA, Western blot, ImmunoStrip test, and visual observations, GM plum trees remained uninfected over 9 years. Infected branches that developed from grafted buds displayed obvious symptoms of Sharka disease over the years and maintained the high level of virus accumulation, whereby host transgenic trees had been constantly challenged with the pathogen. Since the virus was unable to spread to transgenic tissues, the stable expression of PPV-derived gene construct encoding intron-spliced hairpin RNAs provided a highly effective protection of plum trees against permanent viral infection. At the same time, this observation indicates the lack of the systemic spread of resistance from GM tissues to an infected plum graft even after years of joint growth.
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Affiliation(s)
- Tatiana Sidorova
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Puschino, Russia
- Nikita Botanical Gardens – National Scientific Centre, Russian Academy of Sciences, Yalta, Russia
| | - Roman Mikhailov
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Puschino, Russia
| | - Alexander Pushin
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Puschino, Russia
- Nikita Botanical Gardens – National Scientific Centre, Russian Academy of Sciences, Yalta, Russia
| | - Dmitry Miroshnichenko
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Puschino, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Science, Moscow, Russia
| | - Sergey Dolgov
- Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Puschino, Russia
- Nikita Botanical Gardens – National Scientific Centre, Russian Academy of Sciences, Yalta, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Science, Moscow, Russia
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21
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Alonso Chavez V, Gilligan CA, van den Bosch F. Variability in commercial demand for tree saplings affects the probability of introducing exotic forest diseases. J Appl Ecol 2019; 56:180-189. [PMID: 30686839 PMCID: PMC6334522 DOI: 10.1111/1365-2664.13242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/18/2018] [Indexed: 11/28/2022]
Abstract
Several devastating forest pathogens are suspected or known to have entered the UK through imported planting material. The nursery industry is a key business of the tree trade network. Variability in demand for trees makes it difficult for nursery owners to predict how many trees to produce in their nursery. When in any given year, the demand for trees is larger than the production, nursery owners buy trees from foreign sources to match market demand. These imports may introduce exotic diseases. We have developed a model of the dynamics of plant production linked to an economic model. We have used this to quantify the effect of demand variability on the risk of introducing an exotic disease. We find that: (a) When the cost of producing a tree in a UK nursery is considerably smaller than the cost of importing a tree (in the example presented, less than half the importing cost), the risk of introducing an exotic disease is hardly affected by an increase in demand variability. (b) When the cost of producing a tree in the nursery is smaller than, but not very different from the cost of importing a tree, the risk of importing exotic diseases increases with increasing demand variability. Synthesis and applications. Our model and results demonstrate how a balanced management of demand variability and costs can reduce the risk of importing an exotic forest disease according to the management strategy adopted. For example, a management strategy that can reduce the demand variability, the ratio of production to import cost or both, optimizes the nursery gross margin when mainly own‐produced trees are commercialized. This can also translate into a reduction of the risk of introducing exotic forest diseases due to the small number of imported trees for sale.
Our model and results demonstrate how a balanced management of demand variability and costs can reduce the risk of importing an exotic forest disease according to the management strategy adopted. For example, a management strategy that can reduce the demand variability, the ratio of production to import cost or both, optimizes the nursery gross margin when mainly own‐produced trees are commercialized. This can also translate into a reduction of the risk of introducing exotic forest diseases due to the small number of imported trees for sale.
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Affiliation(s)
- Vasthi Alonso Chavez
- Department of Biointeractions and Crop Protection Rothamsted Research Harpenden UK
| | | | - Frank van den Bosch
- Department of Biointeractions and Crop Protection Rothamsted Research Harpenden UK
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22
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Development of one-tube real-time RT-qPCR for the universal detection and quantification of Plum pox virus (PPV). J Virol Methods 2019; 263:10-13. [DOI: 10.1016/j.jviromet.2018.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/30/2018] [Accepted: 10/12/2018] [Indexed: 12/22/2022]
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23
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Bernal-Vicente A, Cantabella D, Hernández JA, Diaz-Vivancos P. The effect of mandelonitrile, a recently described salicylic acid precursor, on peach plant response against abiotic and biotic stresses. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:986-994. [PMID: 30098127 DOI: 10.1111/plb.12894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/05/2018] [Indexed: 06/08/2023]
Abstract
In a previous work, we observed that mandelonitrile (MD), which controls cyanogenic glycoside turnover, is involved in salicylic acid (SA) biosynthesis in peach plants. In order to gain knowledge about the possible roles of this SA biosynthetic pathway, this current study looks at the effect of MD and phenylalanine (Phe; MD precursor) treatments on peach plant performance from an agronomic point of view. Abiotic (2 g·l-1 NaCl) and biotic (Plum pox virus, PPV) stresses were assayed. We recorded the following chlorophyll fluorescence parameters: quantum yield of photochemical energy conversion in PSII [Y(II)], photochemical quenching (qP) and quantum yield of regulated non-photochemical energy loss in PSII and its coefficient [Y(NPQ) and qN]. In addition, considering that environmental stresses lead to nutritional disorders, we determined the soluble K+ , Ca2+ , Na+ and Cl- concentrations in NaCl-stressed seedlings. In PPV-infected seedlings, we recorded the Ca2+ level, which has been suggested to play critical roles in regulating SA-related plant defence responses against pathogens. The MD treatment lessened the effect of both stresses on plant development. In addition, an increase in non-photochemical quenching parameters was observed in MD-treated seedlings, suggesting a safer dissipation of excess energy under stress conditions. In NaCl-stressed peach seedlings both treatments stimulated the accumulation of phytotoxic ions in roots, whereas in PPV-infected seedlings MD increased Ca2+ content. Our results suggest that MD and Phe influence the response of peach seedlings to the deleterious effects of salt and PPV infection stresses.
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Affiliation(s)
- A Bernal-Vicente
- Department of Plant Breeding, Group of Fruit Tree Biotechnology, CEBAS-CSIC, Murcia, Spain
| | - D Cantabella
- Department of Plant Breeding, Group of Fruit Tree Biotechnology, CEBAS-CSIC, Murcia, Spain
| | - J A Hernández
- Department of Plant Breeding, Group of Fruit Tree Biotechnology, CEBAS-CSIC, Murcia, Spain
| | - P Diaz-Vivancos
- Department of Plant Breeding, Group of Fruit Tree Biotechnology, CEBAS-CSIC, Murcia, Spain
- Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
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Zhu X, Zhao J, Abbas HMK, Liu Y, Cheng M, Huang J, Cheng W, Wang B, Bai C, Wang G, Dong W. Pyramiding of nine transgenes in maize generates high-level resistance against necrotrophic maize pathogens. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2145-2156. [PMID: 30006836 DOI: 10.1007/s00122-018-3143-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/06/2018] [Indexed: 05/25/2023]
Abstract
Key message Nine transgenes from different categories, viz. plant defense response genes and anti-apoptosis genes, played combined roles in maize to inhibit the necrotrophic pathogens Rhizoctonia solani and Bipolaris maydis. Maize sheath blight and southern corn leaf blight are major global threats to maize production. The management of these necrotrophic pathogens has encountered limited success due to the characteristics of their lifestyle. Here, we presented a transgenic pyramiding breeding strategy to achieve nine different resistance genes integrated in one transgenic maize line to combat different aspects of necrotrophic pathogens. These nine genes, selected from two different categories, plant defense response genes (Chi, Glu, Ace-AMP1, Tlp, Rs-AFP2, ZmPROPEP1 and Pti4), and anti-apoptosis genes (Iap and p35), were successfully transferred into maize and further implicated in resistance against the necrotrophic pathogens Rhizoctonia solani and Bipolaris maydis. Furthermore, the transgenic maize line 910, with high expression levels of the nine integrated genes, was selected from 49 lines. Under greenhouse and field trial conditions, line 910 showed significant resistance against maize sheath blight and southern corn leaf blight diseases. Higher-level resistance was obtained after the pyramiding of more resistance transgenes from different categories that function via different mechanisms. The present study provides a successful strategy for the management of necrotrophic pathogens.
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Affiliation(s)
- Xiang Zhu
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jinfeng Zhao
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, Shanxi Province, China
| | - Hafiz Muhammad Khalid Abbas
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Yunjun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, South Street of Zhongguancun 12, Beijing, 100081, China
| | - Menglan Cheng
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jue Huang
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Wenjuan Cheng
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Beibei Wang
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Cuiying Bai
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, South Street of Zhongguancun 12, Beijing, 100081, China
| | - Wubei Dong
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.
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25
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Sheveleva A, Ivanov P, Gasanova T, Osipov G, Chirkov S. Sequence Analysis of Plum pox virus Strain C Isolates from Russia Revealed Prevalence of the D96E Mutation in the Universal Epitope and Interstrain Recombination Events. Viruses 2018; 10:E450. [PMID: 30142962 PMCID: PMC6164383 DOI: 10.3390/v10090450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/13/2018] [Accepted: 08/22/2018] [Indexed: 12/01/2022] Open
Abstract
The understanding of genetic diversity, geographic distribution, and antigenic properties of Plum pox virus (PPV) is a prerequisite to improve control of sharka, the most detrimental viral disease of stone fruit crops worldwide. Forty new PPV strain C isolates were detected in sour cherry (Prunus cerasus) from three geographically distant (700⁻1100 km) regions of European Russia. Analysis of their 3'-terminal genomic sequences showed that nineteen isolates (47.5%) bear the D96E mutation in the universal epitope of the coat protein. Almost all of them cannot be detected by the monoclonal antibody 5B in triple antibody sandwich enzyme-linked immunosorbent assayand Western blot analysis that may potentially compromise serological PPV detection in cherries. Full-length genomes of seven PPV-C isolates were determined employing next-generation sequencing. Using the Recombination Detection Program (RDP4), the recombination event covering the region from (Cter)P1 to the middle of the HcPro gene was predicted in all the available PPV-C complete genomes. The isolates Tat-4, belonging to the strain CV, and RU-17sc (PPV-CR) were inferred as major and minor parents, respectively, suggesting possible pathways of evolution of the cherry-adapted strains. Downy cherry (P. tomentosa) was identified as the natural PPV-C host for the first time.
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Affiliation(s)
- Anna Sheveleva
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
| | - Peter Ivanov
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
| | - Tatiana Gasanova
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
| | - Gennady Osipov
- Tatar Research Institute of Agriculture, Kazan 420059, Russia.
| | - Sergei Chirkov
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
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26
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Jeger MJ, Madden LV, van den Bosch F. Plant Virus Epidemiology: Applications and Prospects for Mathematical Modeling and Analysis to Improve Understanding and Disease Control. PLANT DISEASE 2018; 102:837-854. [PMID: 30673389 DOI: 10.1094/pdis-04-17-0612-fe] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In recent years, mathematical modeling has increasingly been used to complement experimental and observational studies of biological phenomena across different levels of organization. In this article, we consider the contribution of mathematical models developed using a wide range of techniques and uses to the study of plant virus disease epidemics. Our emphasis is on the extent to which models have contributed to answering biological questions and indeed raised questions related to the epidemiology and ecology of plant viruses and the diseases caused. In some cases, models have led to direct applications in disease control, but arguably their impact is better judged through their influence in guiding research direction and improving understanding across the characteristic spatiotemporal scales of plant virus epidemics. We restrict this article to plant virus diseases for reasons of length and to maintain focus even though we recognize that modeling has played a major and perhaps greater part in the epidemiology of other plant pathogen taxa, including vector-borne bacteria and phytoplasmas.
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Affiliation(s)
- M J Jeger
- Centre for Environmental Policy, Imperial College London, Silwood Park, Ascot SL5 7PY, United Kingdom
| | - L V Madden
- Department of Plant Pathology, Ohio State University, Wooster, OH 44691
| | - F van den Bosch
- Computational and Systems Biology, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
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27
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Pleydell DRJ, Soubeyrand S, Dallot S, Labonne G, Chadœuf J, Jacquot E, Thébaud G. Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape. PLoS Comput Biol 2018; 14:e1006085. [PMID: 29708968 PMCID: PMC5945227 DOI: 10.1371/journal.pcbi.1006085] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/10/2018] [Accepted: 03/03/2018] [Indexed: 01/29/2023] Open
Abstract
Characterising the spatio-temporal dynamics of pathogens in natura is key to ensuring their efficient prevention and control. However, it is notoriously difficult to estimate dispersal parameters at scales that are relevant to real epidemics. Epidemiological surveys can provide informative data, but parameter estimation can be hampered when the timing of the epidemiological events is uncertain, and in the presence of interactions between disease spread, surveillance, and control. Further complications arise from imperfect detection of disease and from the huge number of data on individual hosts arising from landscape-level surveys. Here, we present a Bayesian framework that overcomes these barriers by integrating over associated uncertainties in a model explicitly combining the processes of disease dispersal, surveillance and control. Using a novel computationally efficient approach to account for patch geometry, we demonstrate that disease dispersal distances can be estimated accurately in a patchy (i.e. fragmented) landscape when disease control is ongoing. Applying this model to data for an aphid-borne virus (Plum pox virus) surveyed for 15 years in 605 orchards, we obtain the first estimate of the distribution of flight distances of infectious aphids at the landscape scale. About 50% of aphid flights terminate beyond 90 m, which implies that most infectious aphids leaving a tree land outside the bounds of a 1-ha orchard. Moreover, long-distance flights are not rare-10% of flights exceed 1 km. By their impact on our quantitative understanding of winged aphid dispersal, these results can inform the design of management strategies for plant viruses, which are mainly aphid-borne.
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Affiliation(s)
- David R. J. Pleydell
- BGPI, INRA, Montpellier SupAgro, Univ. Montpellier, Cirad, TA A-54/K, Campus de Baillarguet, 34398, Montpellier cedex 5, France
- ASTRE, INRA, CIRAD, Univ. Montpellier, Montpellier, France
| | | | - Sylvie Dallot
- BGPI, INRA, Montpellier SupAgro, Univ. Montpellier, Cirad, TA A-54/K, Campus de Baillarguet, 34398, Montpellier cedex 5, France
| | - Gérard Labonne
- BGPI, INRA, Montpellier SupAgro, Univ. Montpellier, Cirad, TA A-54/K, Campus de Baillarguet, 34398, Montpellier cedex 5, France
| | | | - Emmanuel Jacquot
- BGPI, INRA, Montpellier SupAgro, Univ. Montpellier, Cirad, TA A-54/K, Campus de Baillarguet, 34398, Montpellier cedex 5, France
| | - Gaël Thébaud
- BGPI, INRA, Montpellier SupAgro, Univ. Montpellier, Cirad, TA A-54/K, Campus de Baillarguet, 34398, Montpellier cedex 5, France
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28
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Chirkov S, Sheveleva A, Ivanov P, Zakubanskiy A. Analysis of Genetic Diversity of Russian Sour Cherry Plum pox virus Isolates Provides Evidence of a New Strain. PLANT DISEASE 2018; 102:569-575. [PMID: 30673474 DOI: 10.1094/pdis-07-17-1104-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plum pox virus (PPV) exists as a complex of nine strains adapted to different Prunus hosts. Unusual PPV isolates that do not belong to the known cherry-adapted strains were discovered on sour cherry in Russia. Here, two complete genomes of isolates Tat-2 and Tat-4 were determined by sequencing on the Illumina HiSeq 2500 platform. Both were composed of 9,792 nucleotides, excluding the poly(A) tail, with the organization typical of PPV and had 99.4 and 99.7% identity between each other at the nucleotide and amino acid levels. The sequence identities between Tat-2/Tat-4 and known PPV strains ranged from 77.6 to 83.3% for genomic RNA and from 80.0 to 93.8% for polyprotein. Phylogenetic analysis placed Tat-2 and Tat-4 in a separate clade, distinct from the C and CR strains. Three more Tat-2/Tat-4-like isolates were detected in local cherry plantings using the newly developed, specific RT-PCR assay. Based on the phylogenetic analysis, sequence identities, and environmental distribution, Tat-2, Tat-4, and related isolates represent a new cherry-adapted PPV strain for which the name PPV-CV (Cherry Volga) is proposed.
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Affiliation(s)
- Sergei Chirkov
- Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Anna Sheveleva
- Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Peter Ivanov
- Lomonosov Moscow State University, 119234 Moscow, Russia
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29
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Rimbaud L, Bruchou C, Dallot S, Pleydell DRJ, Jacquot E, Soubeyrand S, Thébaud G. Using sensitivity analysis to identify key factors for the propagation of a plant epidemic. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171435. [PMID: 29410846 PMCID: PMC5792923 DOI: 10.1098/rsos.171435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/01/2017] [Indexed: 05/15/2023]
Abstract
Identifying the key factors underlying the spread of a disease is an essential but challenging prerequisite to design management strategies. To tackle this issue, we propose an approach based on sensitivity analyses of a spatiotemporal stochastic model simulating the spread of a plant epidemic. This work is motivated by the spread of sharka, caused by plum pox virus, in a real landscape. We first carried out a broad-range sensitivity analysis, ignoring any prior information on six epidemiological parameters, to assess their intrinsic influence on model behaviour. A second analysis benefited from the available knowledge on sharka epidemiology and was thus restricted to more realistic values. The broad-range analysis revealed that the mean duration of the latent period is the most influential parameter of the model, whereas the sharka-specific analysis uncovered the strong impact of the connectivity of the first infected orchard. In addition to demonstrating the interest of sensitivity analyses for a stochastic model, this study highlights the impact of variation ranges of target parameters on the outcome of a sensitivity analysis. With regard to sharka management, our results suggest that sharka surveillance may benefit from paying closer attention to highly connected patches whose infection could trigger serious epidemics.
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Affiliation(s)
- Loup Rimbaud
- BGPI, INRA, Montpellier SupAgro, University of Montpellier, CIRAD, TA A-54/K, Campus de Baillarguet, Montpellier Cedex 5, 34398, France
| | | | - Sylvie Dallot
- BGPI, INRA, Montpellier SupAgro, University of Montpellier, CIRAD, TA A-54/K, Campus de Baillarguet, Montpellier Cedex 5, 34398, France
| | - David R. J. Pleydell
- BGPI, INRA, Montpellier SupAgro, University of Montpellier, CIRAD, TA A-54/K, Campus de Baillarguet, Montpellier Cedex 5, 34398, France
| | - Emmanuel Jacquot
- BGPI, INRA, Montpellier SupAgro, University of Montpellier, CIRAD, TA A-54/K, Campus de Baillarguet, Montpellier Cedex 5, 34398, France
| | | | - Gaël Thébaud
- BGPI, INRA, Montpellier SupAgro, University of Montpellier, CIRAD, TA A-54/K, Campus de Baillarguet, Montpellier Cedex 5, 34398, France
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30
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Cirilli M, Rossini L, Geuna F, Palmisano F, Minafra A, Castrignanò T, Gattolin S, Ciacciulli A, Babini AR, Liverani A, Bassi D. Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch). BMC PLANT BIOLOGY 2017; 17:192. [PMID: 29100531 PMCID: PMC5670703 DOI: 10.1186/s12870-017-1117-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/09/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Plum pox virus (PPV), agent of Sharka disease, is the most important quarantine pathogen of peach (P. persica L. Batsch). Extensive evaluation of peach germplasm has highlighted the lack of resistant sources, while suggesting the presence of a quantitative disease resistance, expressed as reduction in the intensity of symptoms. Unravelling the genetic architecture of peach response to PPV infection is essential for pyramiding resistant genes and for developing more tolerant varieties. For this purpose, a genome-wide association (GWA) approach was applied in a panel of accessions phenotyped for virus susceptibility and genotyped with the IPSC peach 9 K SNP Array, and coupled with an high-coverage resequencing of the tolerant accession 'Kamarat'. RESULTS Genome-wide association identified three highly significant associated loci on chromosome 2 and 3, accounting for most of the reduction in PPV-M susceptibility within the analysed peach population. The exploration of associated intervals through whole-genome comparison of the tolerant accession 'Kamarat' and other susceptible accessions, including the PPV-resistant wild-related species P. davidiana, allow the identification of allelic variants in promising candidate genes, including an RTM2-like gene already characterized in A. thaliana. CONCLUSIONS The present study is the first effort to identify genetic factors involved in Sharka disease in peach germplasm through a GWA approach. We provide evidence of the presence of quantitative resistant loci in a collection of peach accessions, identifying major loci and highly informative SNPs that could be useful for marker assisted selection. These results could serve as reference bases for future research aimed at the comprehension of genetic mechanism regulating the complex peach-PPV interaction.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
- Parco Tecnologico Padano, via Einstein, Loc. C.na Codazza, Lodi, Italy
| | - Filippo Geuna
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura Basile-Caramia (CRSFA), via Cisternino, 281 Locorotondo, Bari, Italy
| | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), via Amendola 122/D, Bari, Italy
| | - Tiziana Castrignanò
- CINECA, SCAI Super Computing Applications and Innovation, via dei Tizii 6, Rome, Italy
| | - Stefano Gattolin
- Parco Tecnologico Padano, via Einstein, Loc. C.na Codazza, Lodi, Italy
| | - Angelo Ciacciulli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | | | - Alessandro Liverani
- CREA, Research Centre for Olive, Citrus and Tree Fruit, via La Canapona 1 bis, Forlì, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
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31
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Nicaise V, Candresse T. Plum pox virus capsid protein suppresses plant pathogen-associated molecular pattern (PAMP)-triggered immunity. MOLECULAR PLANT PATHOLOGY 2017; 18:878-886. [PMID: 27301551 PMCID: PMC6638313 DOI: 10.1111/mpp.12447] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 06/01/2016] [Accepted: 06/10/2016] [Indexed: 05/20/2023]
Abstract
The perception of pathogen-associated molecular patterns (PAMPs) by immune receptors launches defence mechanisms referred to as PAMP-triggered immunity (PTI). Successful pathogens must suppress PTI pathways via the action of effectors to efficiently colonize their hosts. So far, plant PTI has been reported to be active against most classes of pathogens, except viruses, although this defence layer has been hypothesized recently as an active part of antiviral immunity which needs to be suppressed by viruses for infection success. Here, we report that Arabidopsis PTI genes are regulated upon infection by viruses and contribute to plant resistance to Plum pox virus (PPV). Our experiments further show that PPV suppresses two early PTI responses, the oxidative burst and marker gene expression, during Arabidopsis infection. In planta expression of PPV capsid protein (CP) was found to strongly impair these responses in Nicotiana benthamiana and Arabidopsis, revealing its PTI suppressor activity. In summary, we provide the first clear evidence that plant viruses acquired the ability to suppress PTI mechanisms via the action of effectors, highlighting a novel strategy employed by viruses to escape plant defences.
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Affiliation(s)
- Valerie Nicaise
- INRA, UMR 1332 BFP, CS 20032Villenave d'Ornon cedex33882France
- University of Bordeaux, UMR 1332 BFP, CS 20032Villenave d'Ornon cedex33882France
| | - Thierry Candresse
- INRA, UMR 1332 BFP, CS 20032Villenave d'Ornon cedex33882France
- University of Bordeaux, UMR 1332 BFP, CS 20032Villenave d'Ornon cedex33882France
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32
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Cui H, Wang A. An efficient viral vector for functional genomic studies of Prunus fruit trees and its induced resistance to Plum pox virus via silencing of a host factor gene. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:344-356. [PMID: 27565765 PMCID: PMC5316922 DOI: 10.1111/pbi.12629] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/23/2016] [Accepted: 08/22/2016] [Indexed: 05/17/2023]
Abstract
RNA silencing is a powerful technology for molecular characterization of gene functions in plants. A commonly used approach to the induction of RNA silencing is through genetic transformation. A potent alternative is to use a modified viral vector for virus-induced gene silencing (VIGS) to degrade RNA molecules sharing similar nucleotide sequence. Unfortunately, genomic studies in many allogamous woody perennials such as peach are severely hindered because they have a long juvenile period and are recalcitrant to genetic transformation. Here, we report the development of a viral vector derived from Prunus necrotic ringspot virus (PNRSV), a widespread fruit tree virus that is endemic in all Prunus fruit production countries and regions in the world. We show that the modified PNRSV vector, harbouring the sense-orientated target gene sequence of 100-200 bp in length in genomic RNA3, could efficiently trigger the silencing of a transgene or an endogenous gene in the model plant Nicotiana benthamiana. We further demonstrate that the PNRSV-based vector could be manipulated to silence endogenous genes in peach such as eukaryotic translation initiation factor 4E isoform (eIF(iso)4E), a host factor of many potyviruses including Plum pox virus (PPV). Moreover, the eIF(iso)4E-knocked down peach plants were resistant to PPV. This work opens a potential avenue for the control of virus diseases in perennial trees via viral vector-mediated silencing of host factors, and the PNRSV vector may serve as a powerful molecular tool for functional genomic studies of Prunus fruit trees.
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Affiliation(s)
- Hongguang Cui
- London Research and Development CentreAgriculture and Agri‐Food Canada (AAFC)LondonONCanada
| | - Aiming Wang
- London Research and Development CentreAgriculture and Agri‐Food Canada (AAFC)LondonONCanada
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33
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Decroocq S, Cornille A, Tricon D, Babayeva S, Chague A, Eyquard JP, Karychev R, Dolgikh S, Kostritsyna T, Liu S, Liu W, Geng W, Liao K, Asma BM, Akparov Z, Giraud T, Decroocq V. New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance. Mol Ecol 2016; 25:4712-29. [PMID: 27480465 DOI: 10.1111/mec.13772] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 07/14/2016] [Accepted: 07/25/2016] [Indexed: 12/01/2022]
Abstract
Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.
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Affiliation(s)
- Stéphane Decroocq
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Amandine Cornille
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala, Sweden
| | - David Tricon
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Sevda Babayeva
- Genetic Resources Institute of ANAS, Azadlig ave. 155, AZ1106, Baku, Azerbaijan
| | - Aurélie Chague
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Jean-Philippe Eyquard
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Raul Karychev
- Kazakh Research Institute of Horticulture and Viticulture, 238-a Gagarin Avenue, 480060, Almaty, Kazakhstan
| | - Svetlana Dolgikh
- Kazakh Research Institute of Horticulture and Viticulture, 238-a Gagarin Avenue, 480060, Almaty, Kazakhstan
| | - Tatiana Kostritsyna
- Botanical Garden of National Academy of Sciences, Akhunbaeva street 1a, 720064, Bishkek, Kyrgyzstan
| | - Shuo Liu
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France.,Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou City, Liaoning, 115009, China
| | - Weisheng Liu
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou City, Liaoning, 115009, China
| | - Wenjuan Geng
- College of Horticulture & Forestry Sciences, Xinjiang Agricultural University, 311 NongDaDong Road, 830052, Urumqi City, Xinjiang, China
| | - Kang Liao
- College of Horticulture & Forestry Sciences, Xinjiang Agricultural University, 311 NongDaDong Road, 830052, Urumqi City, Xinjiang, China
| | - Bayram M Asma
- Department of Horticulture, Inonu University, Malatya, 44210, Turkey
| | - Zeynal Akparov
- Genetic Resources Institute of ANAS, Azadlig ave. 155, AZ1106, Baku, Azerbaijan
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France.
| | - Véronique Decroocq
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France. .,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France.
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Cirilli M, Geuna F, Babini AR, Bozhkova V, Catalano L, Cavagna B, Dallot S, Decroocq V, Dondini L, Foschi S, Ilardi V, Liverani A, Mezzetti B, Minafra A, Pancaldi M, Pandolfini T, Pascal T, Savino VN, Scorza R, Verde I, Bassi D. Fighting Sharka in Peach: Current Limitations and Future Perspectives. FRONTIERS IN PLANT SCIENCE 2016; 7:1290. [PMID: 27625664 PMCID: PMC5004351 DOI: 10.3389/fpls.2016.01290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/12/2016] [Indexed: 05/05/2023]
Abstract
Sharka, caused by Plum Pox Virus (PPV), is by far the most important infectious disease of peach [P. persica (L.) Batsch] and other Prunus species. The progressive spread of the virus in many important growing areas throughout Europe poses serious issues to the economic sustainability of stone fruit crops, peach in particular. The adoption of internationally agreed-upon rules for diagnostic tests, strain-specific monitoring schemes and spatial-temporal modeling of virus spread, are all essential for a more effective sharka containment. The EU regulations on nursery activity should be modified based on the zone delimitation of PPV presence, limiting open-field production of propagation materials only to virus-free areas. Increasing the efficiency of preventive measures should be augmented by the short-term development of resistant cultivars. Putative sources of resistance/tolerance have been recently identified in peach germplasm, although the majority of novel resistant sources to PPV-M have been found in almond. However, the complexity of introgression from related-species imposes the search for alternative strategies. The use of genetic engineering, particularly RNA interference (RNAi)-based approaches, appears as one of the most promising perspectives to introduce a durable resistance to PPV in peach germplasm, notwithstanding the well-known difficulties of in vitro plant regeneration in this species. In this regard, rootstock transformation to induce RNAi-mediated systemic resistance would avoid the transformation of numerous commercial cultivars, and may alleviate consumer resistance to the use of GM plants.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences (DISAA), University of MilanMilan, Italy
| | - Filippo Geuna
- Department of Agricultural and Environmental Sciences (DISAA), University of MilanMilan, Italy
| | - Anna R. Babini
- Phytosanitary Service, Regione Emilia-RomagnaBologna, Italy
| | - Valentina Bozhkova
- Department of Breeding, Genetic Resources and Biotechnology, Fruit-Growing InstitutePlovdiv, Bulgaria
| | - Luigi Catalano
- Centro Interprofessionale per le Attività VivaisticheRoma, Italy
| | | | | | - Véronique Decroocq
- INRA, Université de Bordeaux, UMR 1332 Biologie du Fruit et PathologieVillenave d’Ornon, France
| | - Luca Dondini
- Dipartimento di Scienze Agrarie, University of BolognaBologna, Italy
| | | | - Vincenza Ilardi
- Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Centro di Ricerca per la Patologia VegetaleRome, Italy
| | - Alessandro Liverani
- Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Unità di Ricerca per la Frutticoltura di ForlìForlì, Italy
| | - Bruno Mezzetti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle MarcheAncona, Italy
| | | | | | | | | | - Vito N. Savino
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (DiSSPA), Università degli Studi di Bari Aldo MoroBari, Italy
| | - Ralph Scorza
- Appalachian Fruit Research Station, United States Department of Agriculture-Agricultural Research Service, KearneysvilleWV, USA
| | - Ignazio Verde
- Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Centro di Ricerca per la FrutticolturaRome, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of MilanMilan, Italy
- *Correspondence: Daniele Bassi,
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