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Cuevas-Zuviria B, Fraile A, García-Arenal F. An Agent-Based Model Shows How Mixed Infections Drive Multiyear Pathotype Dynamics in a Plant-Virus System. PHYTOPATHOLOGY 2024; 114:1276-1288. [PMID: 38330173 DOI: 10.1094/phyto-06-23-0214-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Mathematical models are widely used to understand the evolution and epidemiology of plant pathogens under a variety of scenarios. Here, we used this approach to analyze the effects of different traits intrinsic and extrinsic to plant-virus interactions on the dynamics of virus pathotypes in genetically heterogeneous plant-virus systems. For this, we propose an agent-based epidemiological model that includes epidemiologically significant pathogen life-history traits related to virulence, transmission, and survival in the environment and allows for integrating long- and short-distance transmission, primary and secondary infections, and within-host pathogen competition in mixed infections. The study focuses on the tobamovirus-pepper pathosystem. Model simulations allowed us to integrate pleiotropic effects of resistance-breaking mutations on different virus life-history traits into the net costs of resistance breaking, allowing for predictions on multiyear pathotype dynamics. We also explored the effects of two control measures, the use of host resistance and roguing of symptomatic plants, that modify epidemiological attributes of the pathogens to understand how their populations will respond to evolutionary pressures. One major conclusion points to the importance of pathogen competition within mixed-infected hosts as a component of the overall fitness of each pathogen that, thus, drives their multiyear dynamics.
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Affiliation(s)
- Bruno Cuevas-Zuviria
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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Jeger M, Hamelin F, Cunniffe N. Emerging Themes and Approaches in Plant Virus Epidemiology. PHYTOPATHOLOGY 2023; 113:1630-1646. [PMID: 36647183 DOI: 10.1094/phyto-10-22-0378-v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plant diseases caused by viruses share many common features with those caused by other pathogen taxa in terms of the host-pathogen interaction, but there are also distinctive features in epidemiology, most apparent where transmission is by vectors. Consequently, the host-virus-vector-environment interaction presents a continuing challenge in attempts to understand and predict the course of plant virus epidemics. Theoretical concepts, based on the underlying biology, can be expressed in mathematical models and tested through quantitative assessments of epidemics in the field; this remains a goal in understanding why plant virus epidemics occur and how they can be controlled. To this end, this review identifies recent emerging themes and approaches to fill in knowledge gaps in plant virus epidemiology. We review quantitative work on the impact of climatic fluctuations and change on plants, viruses, and vectors under different scenarios where impacts on the individual components of the plant-virus-vector interaction may vary disproportionately; there is a continuing, sometimes discordant, debate on host resistance and tolerance as plant defense mechanisms, including aspects of farmer behavior and attitudes toward disease management that may affect deployment in crops; disentangling host-virus-vector-environment interactions, as these contribute to temporal and spatial disease progress in field populations; computational techniques for estimating epidemiological parameters from field observations; and the use of optimal control analysis to assess disease control options. We end by proposing new challenges and questions in plant virus epidemiology.
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Affiliation(s)
- Mike Jeger
- Department of Life Sciences, Imperial College London, Silwood Park, U.K
| | - Fred Hamelin
- IGEPP INRAE, University of Rennes, Rennes, France
| | - Nik Cunniffe
- Department of Plant Sciences, University of Cambridge, Cambridge, U.K
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Clin P, Grognard F, Andrivon D, Mailleret L, Hamelin FM. The proportion of resistant hosts in mixtures should be biased towards the resistance with the lowest breaking cost. PLoS Comput Biol 2023; 19:e1011146. [PMID: 37228168 DOI: 10.1371/journal.pcbi.1011146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Current agricultural practices facilitate emergence and spread of plant diseases through the wide use of monocultures. Host mixtures are a promising alternative for sustainable plant disease control. Their effectiveness can be partly explained by priming-induced cross-protection among plants. Priming occurs when plants are challenged with non-infective pathogen genotypes, resulting in increased resistance to subsequent infections by infective pathogen genotypes. We developed an epidemiological model to explore how mixing two distinct resistant varieties can reduce disease prevalence. We considered a pathogen population composed of three genotypes infecting either one or both varieties. We found that host mixtures should not contain an equal proportion of resistant plants, but a biased ratio (e.g. 80 : 20) to minimize disease prevalence. Counter-intuitively, the optimal ratio of resistant varieties should contain a lower proportion of the costliest resistance for the pathogen to break. This benefit is amplified by priming. This strategy also prevents the invasion of pathogens breaking all resistances.
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Affiliation(s)
- Pauline Clin
- Institut Agro, Univ Rennes, INRAE, IGEPP, Rennes, France
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia-Antipolis, France
| | - Frédéric Grognard
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, Sophia-Antipolis, France
| | | | - Ludovic Mailleret
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia-Antipolis, France
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, Sophia-Antipolis, France
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Karisto P, Suffert F, Mikaberidze A. Spatially explicit ecological modeling improves empirical characterization of plant pathogen dispersal. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2023; 4:86-96. [PMID: 37288164 PMCID: PMC10243544 DOI: 10.1002/pei3.10104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/09/2023]
Abstract
Dispersal is a key ecological process, but it remains difficult to measure. By recording numbers of dispersed individuals at different distances from the source, one acquires a dispersal gradient. Dispersal gradients contain information on dispersal, but they are influenced by the spatial extent of the source. How can we separate the two contributions to extract knowledge about dispersal? One could use a small, point-like source for which a dispersal gradient represents a dispersal kernel, which quantifies the probability of an individual dispersal event from a source to a destination. However, the validity of this approximation cannot be established before conducting measurements. This represents a key challenge hindering progress in characterization of dispersal. To overcome it, we formulated a theory that incorporates the spatial extent of sources to estimate dispersal kernels from dispersal gradients. Using this theory, we re-analyzed published dispersal gradients for three major plant pathogens. We demonstrated that the three pathogens disperse over substantially shorter distances compared to conventional estimates. This method will allow the researchers to re-analyze a vast number of existing dispersal gradients to improve our knowledge about dispersal. The improved knowledge has potential to advance our understanding of species' range expansions and shifts, and inform management of weeds and diseases in crops.
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Affiliation(s)
- Petteri Karisto
- Plant Pathology Group, Institute of Integrative BiologyETH ZurichZurichSwitzerland
- Plant HealthNatural Resources Institute FinlandJokioinenFinland
| | - Frédéric Suffert
- Université Paris‐Saclay, INRAE, AgroParisTech, UMR BIOGER78850Thiverval‐GrignonFrance
| | - Alexey Mikaberidze
- Plant Pathology Group, Institute of Integrative BiologyETH ZurichZurichSwitzerland
- School of Agriculture, Policy and DevelopmentUniversity of ReadingWhiteknightsReadingUK
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Newton AC, Skelsey P. Understanding the effect of component proportions on disease control in two-component cultivar cereal mixtures using a pathogen dispersal scaling hypothesis. Sci Rep 2023; 13:4091. [PMID: 36906626 PMCID: PMC10008548 DOI: 10.1038/s41598-023-31032-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
A field experiment was carried out to determine the importance of component cultivar proportions to spring barley mixture efficacy against rhynchosporium or scald symptoms caused by the splash-dispersed pathogen Rhynchosporium commune. A larger effect than expected was observed of small amounts of one component on another for reducing disease overall, but relative insensitivity to proportion as amounts of each component become more similar. An established theoretical framework, the 'Dispersal scaling hypothesis', was used to model the expected effect of mixing proportions on the spatiotemporal spread of disease. The model captured the unequal effect of mixing different proportions on disease spread and there was good agreement between predictions and observations. The dispersal scaling hypothesis therefore provides a conceptual framework to explain the observed phenomenon, and a tool to predict the proportion of mixing at which mixture performance is maximized.
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Affiliation(s)
- Adrian C Newton
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK.
| | - Peter Skelsey
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
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Murray-Watson RE, Cunniffe NJ. How the epidemiology of disease-resistant and disease-tolerant varieties affects grower behaviour. J R Soc Interface 2022; 19:20220517. [PMID: 36259173 PMCID: PMC9579772 DOI: 10.1098/rsif.2022.0517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/29/2022] [Indexed: 11/12/2022] Open
Abstract
Population-scale effects of resistant or tolerant crop varieties have received little consideration from epidemiologists. When growers deploy tolerant crop, population-scale disease pressures are often unaffected. This only benefits growers using tolerant varieties, selfishly decreasing yields for others. However, resistant crop can reduce disease pressure for all. We coupled an epidemiological model with game theory to understand how this affects uptake of control. Each time a grower plants a new crop, they must decide whether to use an improved (i.e. tolerant/resistant) or unimproved variety. This decision is based on strategic-adaptive expectations in our model, with growers comparing last season's profit with an estimate of what is expected from the alternative crop. Despite the positive feedback loop promoting use of a tolerant variety whenever it is available, a mixed unimproved- and tolerant-crop equilibrium can persist. Tolerant crop can also induce bistability between a scenario in which all growers use tolerant crop and the disease-free equilibrium, where no growers do. However, due to 'free-riding' by growers of unimproved crop, resistant crop nearly always exists in a mixed equilibrium. This work highlights how growers respond to contrasting incentives caused by tolerant and resistant varieties, and the distinct effects on yields and population-scale deployment.
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Affiliation(s)
| | - Nik J. Cunniffe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 1TN, UK
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Jiang C, Lei M, Luan H, Pan Y, Zhang L, Zhou S, Cai Y, Xu X, Shen H, Xu R, Feng Z, Zhang J, Yang P. Genomic and Pathogenic Diversity of Barley Yellow Mosaic Virus and Barley Mild Mosaic Virus Isolates in Fields of China and Their Compatibility with Resistance Genes of Cultivated Barley. PLANT DISEASE 2022; 106:2201-2210. [PMID: 35077235 DOI: 10.1094/pdis-11-21-2473-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant viruses transmitted by the soilborne plasmodiophorid Polymyxa graminis constantly threaten global production of cereal crops. Although the yellow mosaic virus disease of barley has been known to be present for a long time in China, the understanding of the diversity of the viral pathogens and their interactions with host resistance remains limited. In this study, we conducted a nationwide survey of P. graminis and the barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV) it transmits, followed by genomic and pathogenic diversity analyses of both viruses. BaYMV and BaMMV were found exclusively in the region downstream of the Yangtze River, despite the national distribution of its transmission vector P. graminis. Analysis of the genomic variations of BaYMV and BaMMV revealed an elevated rate of nonsynonymous substitutions in the viral genome-linked protein (VPg), in which most substitutions were located in its interaction surface with the host eukaryotic translation initiation factor 4E (eIF4E). VPg sequence diversity was associated with the divergence in virus pathogenicity that was identified through multiple field trials. The majority of the resistance genes, including the widely applied rym4 and rym5 (alleles of eIF4E), as well as the combination of rym1/11 and rym5, are not sufficient to protect cultivated barley against viruses in China. Collectively, these results provide insights into virulence specificity and interaction mode with host resistance in cultivated barley, which has significant implications in breeding for the broad-spectrum resistance barley varieties.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Miaomiao Lei
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Haiye Luan
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng 224002, China
| | - Yuhan Pan
- College of Agronomy, Yangzhou University, Yangzhou 225009, China
| | - Li Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shenghui Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Cai
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiao Xu
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng 224002, China
| | - Huiquan Shen
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng 224002, China
| | - Rugen Xu
- College of Agronomy, Yangzhou University, Yangzhou 225009, China
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ping Yang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Saubin M, Louet C, Bousset L, Fabre F, Frey P, Fudal I, Grognard F, Hamelin F, Mailleret L, Stoeckel S, Touzeau S, Petre B, Halkett F. Improving sustainable crop protection using population genetics concepts. Mol Ecol 2022; 32:2461-2471. [PMID: 35906846 DOI: 10.1111/mec.16634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 10/16/2022]
Abstract
Growing genetically resistant plants allows pathogen populations to be controlled and reduces the use of pesticides. However, pathogens can quickly overcome such resistance. In this context, how can we achieve sustainable crop protection? This crucial question has remained largely unanswered despite decades of intense debate and research effort. In this study, we used a bibliographic analysis to show that the research field of resistance durability has evolved into three subfields: (i) 'plant breeding' (generating new genetic material), (ii) 'molecular interactions' (exploring the molecular dialogue governing plant-pathogen interactions) and (iii) 'epidemiology and evolution' (explaining and forecasting of pathogen population dynamics resulting from selection pressure(s) exerted by resistant plants). We argue that this triple split of the field impedes integrated research progress and ultimately compromises the sustainable management of genetic resistance. After identifying a gap among the three subfields, we argue that the theoretical framework of population genetics could bridge this gap. Indeed, population genetics formally explains the evolution of all heritable traits, and allows genetic changes to be tracked along with variation in population dynamics. This provides an integrated view of pathogen adaptation, in particular via evolutionary-epidemiological feedbacks. In this Opinion Note, we detail examples illustrating how such a framework can better inform best practices for developing and managing genetically resistant cultivars.
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Affiliation(s)
| | - Clémentine Louet
- Université de Lorraine, INRAE, IAM, Nancy, France.,Université Paris Saclay, INRAE, BIOGER, Thiverval-Grignon, France
| | - Lydia Bousset
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, F-33882 Villenave d'Ornon, France
| | - Pascal Frey
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Isabelle Fudal
- Université Paris Saclay, INRAE, BIOGER, Thiverval-Grignon, France
| | - Frédéric Grognard
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France
| | - Frédéric Hamelin
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Ludovic Mailleret
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France.,Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Suzanne Touzeau
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France
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Host Diversification May Split Epidemic Spread into Two Successive Fronts Advancing at Different Speeds. Bull Math Biol 2022; 84:68. [DOI: 10.1007/s11538-022-01023-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/13/2022] [Indexed: 11/02/2022]
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Kwon SJ, Cho YE, Byun HS, Kwak HR, Seo JK. A multiplex RT-PCR assay for detection of emergent pepper Tsw resistance-breaking variants of tomato spotted wilt virus in South Korea. Mol Cell Probes 2022; 61:101792. [PMID: 35041994 DOI: 10.1016/j.mcp.2022.101792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/03/2021] [Accepted: 01/13/2022] [Indexed: 11/27/2022]
Abstract
Tomato spotted wilt virus (TSWV) is a highly destructive virus for pepper. Introgression of the resistance gene Tsw in pepper is used to manage TSWV worldwide; however, the occurrence of Tsw resistance-breaking (RB) variants threatens the pepper industry. Here, we developed a multiplex reverse-transcription PCR assay for detection of recently emerged Tsw RB variants in South Korea with high specificity and sensitivity.
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Affiliation(s)
- Sun-Jung Kwon
- Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Young-Eun Cho
- Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Hee-Seong Byun
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Hae-Ryun Kwak
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jang-Kyun Seo
- Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea; Department of International Agricultural Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea.
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Hinterberger V, Douchkov D, Lück S, Kale S, Mascher M, Stein N, Reif JC, Schulthess AW. Mining for New Sources of Resistance to Powdery Mildew in Genetic Resources of Winter Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:836723. [PMID: 35300015 PMCID: PMC8922026 DOI: 10.3389/fpls.2022.836723] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 05/02/2023]
Abstract
Genetic pathogen control is an economical and sustainable alternative to the use of chemicals. In order to breed resistant varieties, information about potentially unused genetic resistance mechanisms is of high value. We phenotyped 8,316 genotypes of the winter wheat collection of the German Federal ex situ gene bank for Agricultural and Horticultural Crops, Germany, for resistance to powdery mildew (PM), Blumeria graminis f. sp. tritici, one of the most important biotrophic pathogens in wheat. To achieve this, we used a semi-automatic phenotyping facility to perform high-throughput detached leaf assays. This data set, combined with genotyping-by-sequencing (GBS) marker data, was used to perform a genome-wide association study (GWAS). Alleles of significantly associated markers were compared with SNP profiles of 171 widely grown wheat varieties in Germany to identify currently unexploited resistance conferring genes. We also used the Chinese Spring reference genome annotation and various domain prediction algorithms to perform a domain enrichment analysis and produced a list of candidate genes for further investigation. We identified 51 significantly associated regions. In most of these, the susceptible allele was fixed in the tested commonly grown wheat varieties. Eleven of these were located on chromosomes for which no resistance conferring genes have been previously reported. In addition to enrichment of leucine-rich repeats (LRR), we saw enrichment of several domain types so far not reported as relevant to PM resistance, thus, indicating potentially novel candidate genes for the disease resistance research and prebreeding in wheat.
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Affiliation(s)
| | - Dimitar Douchkov
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Stefanie Lück
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sandip Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- *Correspondence: Albert W. Schulthess
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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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Impact of Host Resistance to Tomato Spotted Wilt Orthotospovirus in Peanut Cultivars on Virus Population Genetics and Thrips Fitness. Pathogens 2021; 10:pathogens10111418. [PMID: 34832574 PMCID: PMC8625697 DOI: 10.3390/pathogens10111418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 11/25/2022] Open
Abstract
Thrips-transmitted tomato spotted wilt orthotospovirus (TSWV) is a major constraint to peanut production in the southeastern United States. Peanut cultivars with resistance to TSWV have been widely used for over twenty years. Intensive usage of resistant cultivars has raised concerns about possible selection pressure against TSWV and a likelihood of resistance breakdown. Population genetics of TSWV isolates collected from cultivars with varying levels of TSWV resistance was investigated using five TSWV genes. Phylogenetic trees of genes did not indicate host resistance-based clustering of TSWV isolates. Genetic variation in TSWV isolates and neutrality tests suggested recent population expansion. Mutation and purifying selection seem to be the major forces driving TSWV evolution. Positive selection was found in N and RdRp genes but was not influenced by TSWV resistance. Population differentiation occurred between isolates collected from 1998 and 2010 and from 2016 to 2019 but not between isolates from susceptible and resistant cultivars. Evaluated TSWV-resistant cultivars differed, albeit not substantially, in their susceptibility to thrips. Thrips oviposition was reduced, and development was delayed in some cultivars. Overall, no evidence was found to support exertion of selection pressure on TSWV by host resistance in peanut cultivars, and some cultivars differentially affected thrips fitness than others.
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Agaoua A, Bendahmane A, Moquet F, Dogimont C. Membrane Trafficking Proteins: A New Target to Identify Resistance to Viruses in Plants. PLANTS 2021; 10:plants10102139. [PMID: 34685948 PMCID: PMC8541145 DOI: 10.3390/plants10102139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022]
Abstract
Replication cycles from most simple-stranded positive RNA viruses infecting plants involve endomembrane deformations. Recent published data revealed several interactions between viral proteins and plant proteins associated with vesicle formation and movement. These plant proteins belong to the COPI/II, SNARE, clathrin and ESCRT endomembrane trafficking mechanisms. In a few cases, variations of these plant proteins leading to virus resistance have been identified. In this review, we summarize all known interactions between these plant cell mechanisms and viruses and highlight strategies allowing fast identification of variant alleles for membrane-associated proteins.
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Affiliation(s)
- Aimeric Agaoua
- INRAE Génétique et Amélioration des Fruits et Légumes (GAFL), 84140 Montfavet, France;
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences-Paris-Saclay (IPS2), Université Paris-Saclay, INRAE, CNRS, Univ Evry, 91405 Orsay, France;
| | | | - Catherine Dogimont
- INRAE Génétique et Amélioration des Fruits et Légumes (GAFL), 84140 Montfavet, France;
- Correspondence:
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15
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Rimbaud L, Fabre F, Papaïx J, Moury B, Lannou C, Barrett LG, Thrall PH. Models of Plant Resistance Deployment. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:125-152. [PMID: 33929880 DOI: 10.1146/annurev-phyto-020620-122134] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Owing to their evolutionary potential, plant pathogens are able to rapidly adapt to genetically controlled plant resistance, often resulting in resistance breakdown and major epidemics in agricultural crops. Various deployment strategies have been proposed to improve resistance management. Globally, these rely on careful selection of resistance sources and their combination at various spatiotemporal scales (e.g., via gene pyramiding, crop rotations and mixtures, landscape mosaics). However, testing and optimizing these strategies using controlled experiments at large spatiotemporal scales are logistically challenging. Mathematical models provide an alternative investigative tool, and many have been developed to explore resistance deployment strategies under various contexts. This review analyzes 69 modeling studies in light of specific model structures (e.g., demographic or demogenetic, spatial or not), underlying assumptions (e.g., whether preadapted pathogens are present before resistance deployment), and evaluation criteria (e.g., resistance durability, disease control, cost-effectiveness). It highlights major research findings and discusses challenges for future modeling efforts.
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Affiliation(s)
- Loup Rimbaud
- INRAE, Pathologie Végétale, 84140 Montfavet, France; ,
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; ,
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, 33882 Villenave d'Ornon, France;
| | | | - Benoît Moury
- INRAE, Pathologie Végétale, 84140 Montfavet, France; ,
| | | | - Luke G Barrett
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; ,
| | - Peter H Thrall
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; ,
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16
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Clin P, Grognard F, Mailleret L, Val F, Andrivon D, Hamelin FM. Taking Advantage of Pathogen Diversity and Immune Priming to Minimize Disease Prevalence in Host Mixtures: A Model. PHYTOPATHOLOGY 2021; 111:1219-1227. [PMID: 33297731 DOI: 10.1094/phyto-09-20-0429-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Host mixtures are a promising method for agroecological plant disease control. Plant immunity is key to the success of host mixtures against polymorphic pathogen populations. This immunity results from priming-induced cross-protection, whereby plants able to resist infection by specific pathogen genotypes become more resistant to other pathogen genotypes. Strikingly, this phenomenon was absent from mathematical models aiming at designing host mixtures. We developed a model to specifically explore how priming affects the coexistence of two pathogen genotypes in host mixtures composed of two host genotypes and how it affects disease prevalence. The main effect of priming is to reduce the coexistence region in the parameter space (due to the cross-protection) and to generate a singular mixture of resistant and susceptible hosts corresponding to the maximal reduction disease prevalence (in absence of priming, a resistant pure stand is optimal). The epidemiological advantage of host mixtures over a resistant pure stand thus appears as a direct consequence of immune priming. We also showed that there is indirect cross-protection between host genotypes in a mixture. Moreover, the optimal mix prevents the emergence of a resistance-breaking pathogen genotype. Our results highlight the importance of considering immune priming to design optimal and sustainable host mixtures.
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Affiliation(s)
- Pauline Clin
- IGEPP, INRAE, Institut Agro, Université Rennes, 35000 Rennes, France
- Université Côte d'Azur, INRAE, CNRS, ISA, France
| | - Frédéric Grognard
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, France
| | - Ludovic Mailleret
- Université Côte d'Azur, INRAE, CNRS, ISA, France
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, France
| | - Florence Val
- IGEPP, INRAE, Institut Agro, Université Rennes, 35000 Rennes, France
| | - Didier Andrivon
- IGEPP, INRAE, Institut Agro, Université Rennes, 35000 Rennes, France
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17
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Jeanneret P, Aviron S, Alignier A, Lavigne C, Helfenstein J, Herzog F, Kay S, Petit S. Agroecology landscapes. LANDSCAPE ECOLOGY 2021; 36:2235-2257. [PMID: 34219965 PMCID: PMC8233588 DOI: 10.1007/s10980-021-01248-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 04/10/2021] [Indexed: 05/19/2023]
Abstract
Context Agroecology combines agronomic and ecological concepts. It relies on the enhancement of biodiversity and related ecosystem services to support agricultural production. It is dependent on biological interactions for the design and management of agricultural systems in agricultural landscapes. Objectives We review the role of landscape ecology to understand and promote biodiversity, pest regulation and crop pollination for the designing of "agroecology landscapes". We illustrate the use of landscape ecological methods for supporting agroforestry systems as an example of agroecological development, and we propose pathways to implement agroecology at landscape scale. Methods The state of the art of how landscape ecology contributes to agroecology development is summarized based on a literature review. Results Agroecology requires thinking beyond the field scale to consider the positioning, quality and connectivity of fields and semi-natural habitats at larger spatial scales. The spatial and temporal organisation of semi-natural elements and the crop mosaic interact. Understanding this interaction is the pre-requisite for promoting patterns and mechanisms that foster biodiversity and ecosystem service provision. Promoting agroecological practices beyond individual farm borders can be rooted in a bottom-up approach from agroecological lighthouse farms to farm networks to amplify agroecology adoption at the landscape scale. Conclusions Achieving agricultural landscapes composed of fields and farms following agroecological management requires understanding of biodiversity patterns, biological interactions and mechanisms that determine and boost ecosystem functioning to improve services at landscape scale, involving farmers in a bottom-up and context-specific approach.
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Affiliation(s)
- Ph. Jeanneret
- Department of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - S. Aviron
- UMR BAGAP, INRAE - Institut Agro-Agrocampus Ouest - ESA, 35042 Rennes, France
| | - A. Alignier
- UMR BAGAP, INRAE - Institut Agro-Agrocampus Ouest - ESA, 35042 Rennes, France
| | | | - J. Helfenstein
- Department of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - F. Herzog
- Department of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - S. Kay
- Department of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - S. Petit
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
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18
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Petit S, Deytieux V, Cordeau S. Landscape-scale approaches for enhancing biological pest control in agricultural systems. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:75. [PMID: 33988768 DOI: 10.1007/s10661-020-08812-2] [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] [Received: 12/23/2018] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Over the last decades, land management options have been investigated that aim at enhancing services to agriculture delivered by biodiversity and its associated biotic interactions. Such services can be promoted through land management strategies ranging from in-field single agricultural practices, long-term strategies compiling these agricultural practices at the crop rotation scale, to management strategies at the landscape scale. In this paper, we provide an overview of the land management options that can be implemented at multiple scales, with a specific focus on the provision of one service that is key in agriculture, i.e. pest control. We present existing knowledge and highlight current gaps and limitations in our understanding of pest control response to land management. Based on this analysis, we propose two promising and complementary research approaches that could help filling existing knowledge gaps and provide guidelines for designing landscapes for agroecological services: (1) landscape monitoring networks (LMN), based on long-term monitoring of ecological and managerial processes within sets of landscapes located in contrasted production contexts; (2) agroecological system experiments (ASE), which design and assess combinations of land management options at multiple embedded spatial scales.
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Affiliation(s)
- Sandrine Petit
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France.
| | - Violaine Deytieux
- INRAE, UE115 Domaine Expérimental d'Epoisses, F-21000, Dijon, France
| | - Stéphane Cordeau
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
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19
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Choe S, Choi B, Kang J, Seo J. Tolerance to tomato yellow leaf curl virus in transgenic tomato overexpressing a cellulose synthase-like gene. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:657-659. [PMID: 33378588 PMCID: PMC8051598 DOI: 10.1111/pbi.13539] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/23/2020] [Indexed: 06/01/2023]
Affiliation(s)
- Siwon Choe
- Department of International Agricultural TechnologySeoul National UniversityPyeongchangKorea
| | - Boram Choi
- Institutes of Green Bio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Jin‐Ho Kang
- Department of International Agricultural TechnologySeoul National UniversityPyeongchangKorea
- Institutes of Green Bio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Jang‐Kyun Seo
- Department of International Agricultural TechnologySeoul National UniversityPyeongchangKorea
- Institutes of Green Bio Science and TechnologySeoul National UniversityPyeongchangKorea
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20
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Watkinson-Powell B, Gilligan CA, Cunniffe NJ. When Does Spatial Diversification Usefully Maximize the Durability of Crop Disease Resistance? PHYTOPATHOLOGY 2020; 110:1808-1820. [PMID: 32500812 DOI: 10.1094/phyto-07-19-0261-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Maximizing the durability of crop disease resistance genes in the face of pathogen evolution is a major challenge in modern agricultural epidemiology. Spatial diversification in the deployment of resistance genes, where susceptible and resistant fields are more closely intermixed, is predicted to drive lower epidemic intensities over evolutionary timescales. This is due to an increase in the strength of dilution effects, caused by pathogen inoculum challenging host tissue to which it is not well-specialized. The factors that interact with and determine the magnitude of this spatial suppressive effect are not currently well understood, however, leading to uncertainty over the pathosystems where such a strategy is most likely to be cost-effective. We model the effect on landscape scale disease dynamics of spatial heterogeneity in the arrangement of fields planted with either susceptible or resistant cultivars, and the way in which this effect depends on the parameters governing the pathosystem of interest. Our multiseason semidiscrete epidemiological model tracks spatial spread of wild-type and resistance-breaking pathogen strains, and incorporates a localized reservoir of inoculum, as well as the effects of within and between field transmission. The pathogen dispersal characteristics, any fitness cost(s) of the resistance-breaking trait, the efficacy of host resistance, and the length of the timeframe of interest all influence the strength of the spatial diversification effect. A key result is that spatial diversification has the strongest beneficial effect at intermediate fitness costs of the resistance-breaking trait, an effect driven by a complex set of nonlinear interactions. On the other hand, however, if the resistance-breaking strain is not fit enough to invade the landscape, then a partially effective resistance gene can result in spatial diversification actually worsening the epidemic. These results allow us to make general predictions of the types of system for which spatial diversification is most likely to be cost-effective, paving the way for potential economic modeling and pathosystem specific evaluation. These results highlight the importance of studying the effect of genetics on landscape scale spatial dynamics within host-pathogen disease systems.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Benjamin Watkinson-Powell
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, United Kingdom
| | - Christopher A Gilligan
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, United Kingdom
| | - Nik J Cunniffe
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, United Kingdom
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21
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Nilusmas S, Mercat M, Perrot T, Djian‐Caporalino C, Castagnone‐Sereno P, Touzeau S, Calcagno V, Mailleret L. Multi-seasonal modelling of plant-nematode interactions reveals efficient plant resistance deployment strategies. Evol Appl 2020; 13:2206-2221. [PMID: 33005219 PMCID: PMC7513734 DOI: 10.1111/eva.12989] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023] Open
Abstract
Root-knot nematodes, Meloidogyne spp., are soil-borne polyphagous pests with major impact on crop yield worldwide. Resistant crops efficiently control avirulent root-knot nematodes, but favour the emergence of virulent forms. Since virulence is associated with fitness costs, susceptible crops counter-select virulent root-knot nematodes. In this study, we identify optimal rotation strategies between susceptible and resistant crops to control root-knot nematodes and maximize crop yield. We developed an epidemiological model describing the within-season dynamics of avirulent and virulent root-knot nematodes on susceptible or resistant plant root-systems, and their between-season survival. The model was fitted to experimental data and used to predict yield-maximizing rotation strategies, with special attention to the impact of epidemic severity and genetic parameters. Crop rotations were found to be efficient under realistic parameter ranges. They were characterized by low ratios of resistant plants and were robust to parameter uncertainty. Rotations provide significant gain over resistant-only strategies, especially under intermediate fitness costs and severe epidemic contexts. Switching from the current general deployment of resistant crops to custom rotation strategies could not only maintain or increase crop yield, but also preserve the few and valuable R-genes available.
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Affiliation(s)
- Samuel Nilusmas
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
| | - Mathilde Mercat
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
| | - Thomas Perrot
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
| | | | | | - Suzanne Touzeau
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
| | | | - Ludovic Mailleret
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
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22
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Peláez A, McLeish MJ, Paswan RR, Dubay B, Fraile A, García-Arenal F. Ecological fitting is the forerunner to diversification in a plant virus with broad host range. J Evol Biol 2020; 34:1917-1931. [PMID: 32618008 DOI: 10.1111/jeb.13672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/23/2020] [Accepted: 06/24/2020] [Indexed: 11/29/2022]
Abstract
The evolution and diversification of ssRNA plant viruses are often examined under reductionist conditions that ignore potentially much wider biotic interactions. The host range of a plant virus is central to interactions at higher levels that are organized by both fitness and ecological criteria. Here we employ a strategy to minimize sampling biases across distinct plant communities and combine it with a high-throughput sequencing approach to examine the influence of four habitats on the evolution of Watermelon mosaic virus (WMV). Local, regional and global levels of genetic diversity that correspond to spatial and temporal extents are used to infer haplotype relationships using network and phylogenetic approaches. We find that the incidence and genetic diversity of WMV were structured significantly by host species and habitat type. A single haplotype that infected 11 host species of a total of 24 showed that few constraints on host species use exist in the crop communities. When the evolution of WMV was examined at broader levels of organization, we found variation in genetic diversity and contrasting host use footprints that broadly corresponded to habitat effects. The findings demonstrated that nondeterministic ecological factors structured the genetic diversity of WMV. Habitat-driven constraints underlie host use preferences.
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Affiliation(s)
- Adrián Peláez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
| | - Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
| | - Ricky R Paswan
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
| | - Bhumika Dubay
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, Madrid, Spain
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Rousseau E, Bonneault M, Fabre F, Moury B, Mailleret L, Grognard F. Virus epidemics, plant-controlled population bottlenecks and the durability of plant resistance. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180263. [PMID: 31056046 DOI: 10.1098/rstb.2018.0263] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plant qualitative resistances to viruses are natural exhaustible resources that can be impaired by the emergence of resistance-breaking (RB) virus variants. Mathematical modelling can help determine optimal strategies for resistance durability by a rational deployment of resistance in agroecosystems. Here, we propose an innovative approach, built up from our previous empirical studies, based on plant cultivars combining qualitative resistance with quantitative resistance narrowing population bottlenecks exerted on viruses during host-to-host transmission and/or within-host infection. Narrow bottlenecks are expected to slow down virus adaptation to plant qualitative resistance. To study the effect of bottleneck size on yield, we developed a stochastic epidemic model with mixtures of susceptible and resistant plants, relying on continuous-time Markov chain processes. Overall, narrow bottlenecks are beneficial when the fitness cost of RB virus variants in susceptible plants is intermediate. In such cases, they could provide up to 95 additional percentage points of yield compared with deploying a qualitative resistance alone. As we have shown in previous works that virus population bottlenecks are at least partly heritable plant traits, our results suggest that breeding and deploying plant varieties exposing virus populations to narrowed bottlenecks will increase yield and delay the emergence of RB variants. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.
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Affiliation(s)
- Elsa Rousseau
- 1 Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne Université, Biocore team , Sophia Antipolis , France.,2 Université Côte d'Azur, INRA, CNRS, ISA , France.,3 Pathologie Végétale, INRA , F-84140 Montfavet , France
| | - Mélanie Bonneault
- 1 Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne Université, Biocore team , Sophia Antipolis , France
| | - Frédéric Fabre
- 4 UMR 1065 SAVE, INRA , Bordeaux Sciences Agro, F-33882, Villenave d'Ornon , France
| | - Benoît Moury
- 3 Pathologie Végétale, INRA , F-84140 Montfavet , France
| | - Ludovic Mailleret
- 1 Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne Université, Biocore team , Sophia Antipolis , France.,2 Université Côte d'Azur, INRA, CNRS, ISA , France
| | - Frédéric Grognard
- 1 Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne Université, Biocore team , Sophia Antipolis , France
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Moury B, Desbiez C. Host Range Evolution of Potyviruses: A Global Phylogenetic Analysis. Viruses 2020; 12:v12010111. [PMID: 31963241 PMCID: PMC7020010 DOI: 10.3390/v12010111] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/28/2022] Open
Abstract
Virus host range, i.e., the number and diversity of host species of viruses, is an important determinant of disease emergence and of the efficiency of disease control strategies. However, for plant viruses, little is known about the genetic or ecological factors involved in the evolution of host range. Using available genome sequences and host range data, we performed a phylogenetic analysis of host range evolution in the genus Potyvirus, a large group of plant RNA viruses that has undergone a radiative evolution circa 7000 years ago, contemporaneously with agriculture intensification in mid Holocene. Maximum likelihood inference based on a set of 59 potyviruses and 38 plant species showed frequent host range changes during potyvirus evolution, with 4.6 changes per plant species on average, including 3.1 host gains and 1.5 host loss. These changes were quite recent, 74% of them being inferred on the terminal branches of the potyvirus tree. The most striking result was the high frequency of correlated host gains occurring repeatedly in different branches of the potyvirus tree, which raises the question of the dependence of the molecular and/or ecological mechanisms involved in adaptation to different plant species.
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25
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Marchant WG, Gautam S, Hutton SF, Srinivasan R. Tomato Yellow Leaf Curl Virus-Resistant and -Susceptible Tomato Genotypes Similarly Impact the Virus Population Genetics. FRONTIERS IN PLANT SCIENCE 2020; 11:599697. [PMID: 33365041 PMCID: PMC7750400 DOI: 10.3389/fpls.2020.599697] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/13/2020] [Indexed: 05/14/2023]
Abstract
Tomato yellow leaf curl virus is a species in the genus Begomovirus and family Geminiviridae. Tomato yellow leaf curl virus (TYLCV) infection induces severe symptoms on tomato plants and causes serious yield losses worldwide. TYLCV is persistently transmitted by the sweetpotato whitefly, Bemisia tabaci (Gennadius). Cultivars and hybrids with a single or few genes conferring resistance against TYLCV are often planted to mitigate TYLCV-induced losses. These resistant genotypes (cultivars or hybrids) are not immune to TYLCV. They typically develop systemic infection, display mild symptoms, and produce more marketable tomatoes than susceptible genotypes under TYLCV pressure. In several pathosystems, extensive use of resistant cultivars with single dominant resistance-conferring gene has led to intense selection pressure on the virus, development of highly virulent strains, and resistance breakdown. This study assessed differences in TYLCV genomes isolated from susceptible and resistant genotypes in Florida and Georgia. Phylogenetic analyses indicated that Florida and Georgia isolates were distinct from each other. Population genetics analyses with genomes field-collected from resistant and susceptible genotypes from Florida and/or Georgia provided no evidence of a genetic structure between the resistant and susceptible genotypes. No codons in TYLCV genomes from TYLCV-resistant or susceptible genotypes were under positive selection, suggesting that highly virulent or resistance-breaking TYLCV strains might not be common in tomato farmscapes in Florida and Georgia. With TYLCV-resistant genotypes usage increasing recently and multiple tomato crops being planted during a calendar year, host resistance-induced selection pressure on the virus remains a critical issue. To address the same, a greenhouse selection experiment with one TYLCV-resistant and susceptible genotype was conducted. Each genotype was challenged with TYLCV through whitefly-mediated transmission serially 10 times (T1-T10). Population genetics parameters at the genome level were assessed at T1, T5, and T10. Results indicated that genomes from resistant and susceptible genotypes did not differentiate with increasing transmission number, no specific mutations were repeatedly observed, and no positive selection was detected. These results reiterate that resistance in tomato might not be exerting selection pressure against TYLCV to facilitate development of resistance-breaking strains. TYLCV populations rather seem to be shaped by purifying selection and/or population expansion.
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Affiliation(s)
- Wendy G. Marchant
- Department of Entomology, University of Georgia, Tifton, GA, United States
| | - Saurabh Gautam
- Department of Entomology, University of Georgia, Griffin, GA, United States
| | - Samuel F. Hutton
- Horticulture Sciences Department, University of Florida, Wimauma, FL, United States
| | - Rajagopalbabu Srinivasan
- Department of Entomology, University of Georgia, Griffin, GA, United States
- *Correspondence: Rajagopalbabu Srinivasan
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26
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Boëte C, Seston M, Legros M. Strategies of host resistance to pathogens in spatially structured populations: An agent-based evaluation. Theor Popul Biol 2019; 130:170-181. [PMID: 31394115 DOI: 10.1016/j.tpb.2019.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/23/2019] [Accepted: 07/29/2019] [Indexed: 12/23/2022]
Abstract
There is growing theoretical evidence that spatial structure can affect the ecological and evolutionary outcomes of host-parasite interactions. Locally restricted interactions have been shown in particular to affect host resistance and tolerance. In this study we investigate the evolution of several types of host disease resistance strategies, alone or in combination, in spatially structured populations. We construct a spatially explicit, individual-based stochastic model where hosts and parasites interact with each other in a spatial lattice, and interactions are restricted to a given neighbourhood of varying size. We investigate several host resistance strategies, including constitutive (expressed in all resistant hosts), induced (expressed only upon infection), and combinations thereof. We show that a costly constitutive resistance cannot reach fixation, whereas an inducible resistance strategy may become fixed in the population if the cost remains low, particularly if it impacts host recovery. We also demonstrate that mixed strategies can be maintained in the host population, and that a higher investment in a recovery-boosting inducible resistance allows for a higher investment in a constitutive response. Our simulations reveal that the spatial structure of the population impacts the selection for resistance in a complex fashion. While single strategies of resistance are generally favoured in less structured populations, mixed strategies can sometimes prevail only in highly structured environments, e.g. when combining constitutive and transmission-blocking induced responses Overall these results shed new light on the dynamics of disease resistance in a spatially-structured host-pathogen system, and advance our theoretical understanding of the evolutionary dynamics of disease resistance, a necessary step to elaborate more efficient and sustainable strategies for disease management.
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Affiliation(s)
- Christophe Boëte
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.
| | - Morgan Seston
- Unite des Virus Emergents (UVE: Aix-Marseille Univ- IRD 190 - INSERM 1207 - IHU Mediterranée Infection), Marseille, France
| | - Mathieu Legros
- ETH Zürich, Institut für Integrative Biologie, Universitätstrasse 16, 8092 Zürich, Switzerland; CSIRO Agriculture & Food, Canberra, ACT 2601, Australia
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Monci F, García-Andrés S, Sánchez-Campos S, Fernández-Muñoz R, Díaz-Pendón JA, Moriones E. Use of Systemic Acquired Resistance and Whitefly Optical Barriers to Reduce Tomato Yellow Leaf Curl Disease Damage to Tomato Crops. PLANT DISEASE 2019; 103:1181-1188. [PMID: 30908127 DOI: 10.1094/pdis-06-18-1069-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Epidemics of tomato yellow leaf curl disease (TYLCD) caused by tomato yellow leaf curl-like begomoviruses (genus Begomovirus, family Geminiviridae) severely damage open field and protected tomato crops worldwide. Intensive application of insecticides against the whitefly vector Bemisia tabaci is generally used as control strategy to reduce TYLCD impact. This practice, however, is frequently ineffective and has a negative impact on the environment and human health. TYLCD-resistant varieties are commercially available, but cultivation of susceptible traditional tasting ones is also requested if possible. For susceptible tomatoes, here we show that using whitefly optical barriers by means of UV-blocking plastics in protected crops can contribute to reducing TYLCD damage and increasing commercial fruit yield. Moreover, induction of systemic acquired resistance by application of the elicitor of plant defense acibenzolar-S-methyl was effective to reduce yield losses when viral pressure was moderate. Interestingly, combining both practices in protected tomato crops can result in a significant TYLCD control. Therefore, these control practices are proposed to be used commercially as management alternatives to include in integrated management of TYLCD.
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Affiliation(s)
- Francisco Monci
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
| | - Susana García-Andrés
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
| | - Sonia Sánchez-Campos
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
| | - Rafael Fernández-Muñoz
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
| | - Juan Antonio Díaz-Pendón
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
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28
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Rousseau E, Tamisier L, Fabre F, Simon V, Szadkowski M, Bouchez O, Zanchetta C, Girardot G, Mailleret L, Grognard F, Palloix A, Moury B. Impact of genetic drift, selection and accumulation level on virus adaptation to its host plants. MOLECULAR PLANT PATHOLOGY 2018; 19:2575-2589. [PMID: 30074299 PMCID: PMC6638063 DOI: 10.1111/mpp.12730] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The efficiency of plant major resistance genes is limited by the emergence and spread of resistance-breaking mutants. Modulation of the evolutionary forces acting on pathogen populations constitutes a promising way to increase the durability of these genes. We studied the effect of four plant traits affecting these evolutionary forces on the rate of resistance breakdown (RB) by a virus. Two of these traits correspond to virus effective population sizes (Ne ) at either plant inoculation or during infection. The third trait corresponds to differential selection exerted by the plant on the virus population. Finally, the fourth trait corresponds to within-plant virus accumulation (VA). These traits were measured experimentally on Potato virus Y (PVY) inoculated to a set of 84 pepper doubled-haploid lines, all carrying the same pvr23 resistance gene, but having contrasting genetic backgrounds. The lines showed extensive variation for the rate of pvr23 RB by PVY and for the four other traits of interest. A generalized linear model showed that three of these four traits, with the exception of Ne at inoculation, and several pairwise interactions between them had significant effects on RB. RB increased with increasing values of Ne during plant infection or VA. The effect of differential selection was more complex because of a strong interaction with VA. When VA was high, RB increased as the differential selection increased. An opposite relationship between RB and differential selection was observed when VA was low. This study provides a framework to select plants with appropriate virus evolution-related traits to avoid or delay RB.
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Affiliation(s)
- Elsa Rousseau
- Pathologie VégétaleINRA84140MontfavetFrance
- Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne UniversitéBiocore TeamSophia AntipolisFrance
- Université Côte d'Azur, INRA, CNRS, ISAFrance
- Present address:
IBM Almaden Research CenterSan Jose, CA 95120–6099USA
| | - Lucie Tamisier
- Pathologie VégétaleINRA84140MontfavetFrance
- GAFL, INRA84140MontfavetFrance
- Present address:
Université de Liège, Terra‐Gembloux Agro-Bio Tech, PlantPathology Laboratory, Passage des Déportés2, GemblouxBelgium, 5030
| | | | - Vincent Simon
- Pathologie VégétaleINRA84140MontfavetFrance
- UMR BFPINRA33882Villenave d'OrnonFrance
| | | | - Olivier Bouchez
- INRAGeT‐PlaGe, US 1426, Genotoul, 31326 Castanet‐TolosanFrance
| | | | | | - Ludovic Mailleret
- Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne UniversitéBiocore TeamSophia AntipolisFrance
- Université Côte d'Azur, INRA, CNRS, ISAFrance
| | - Frederic Grognard
- Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne UniversitéBiocore TeamSophia AntipolisFrance
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Rimbaud L, Papaïx J, Barrett LG, Burdon JJ, Thrall PH. Mosaics, mixtures, rotations or pyramiding: What is the optimal strategy to deploy major gene resistance? Evol Appl 2018; 11:1791-1810. [PMID: 30459830 PMCID: PMC6231482 DOI: 10.1111/eva.12681] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/14/2018] [Accepted: 07/06/2018] [Indexed: 01/08/2023] Open
Abstract
Once deployed uniformly in the field, genetically controlled plant resistance is often quickly overcome by pathogens, resulting in dramatic losses. Several strategies have been proposed to constrain the evolutionary potential of pathogens and thus increase resistance durability. These strategies can be classified into four categories, depending on whether resistance sources are varied across time (rotations) or combined in space in the same cultivar (pyramiding), in different cultivars within a field (cultivar mixtures) or among fields (mosaics). Despite their potential to differentially affect both pathogen epidemiology and evolution, to date the four categories of deployment strategies have never been directly compared together within a single theoretical or experimental framework, with regard to efficiency (ability to reduce disease impact) and durability (ability to limit pathogen evolution and delay resistance breakdown). Here, we used a spatially explicit stochastic demogenetic model, implemented in the R package landsepi, to assess the epidemiological and evolutionary outcomes of these deployment strategies when two major resistance genes are present. We varied parameters related to pathogen evolutionary potential (mutation probability and associated fitness costs) and landscape organization (mostly the relative proportion of each cultivar in the landscape and levels of spatial or temporal aggregation). Our results, broadly focused on qualitative resistance to rust fungi of cereal crops, show that evolutionary and epidemiological control are not necessarily correlated and that no deployment strategy is universally optimal. Pyramiding two major genes offered the highest durability, but at high mutation probabilities, mosaics, mixtures and rotations can perform better in delaying the establishment of a universally infective superpathogen. All strategies offered the same short-term epidemiological control, whereas rotations provided the best long-term option, after all sources of resistance had broken down. This study also highlights the significant impact of landscape organization and pathogen evolutionary ability in considering the optimal design of a deployment strategy.
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Affiliation(s)
- Loup Rimbaud
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | | | - Luke G. Barrett
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | - Jeremy J. Burdon
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | - Peter H. Thrall
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
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30
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Lasserre-Zuber P, Caffier V, Stievenard R, Lemarquand A, Le Cam B, Durel CE. Pyramiding Quantitative Resistance with a Major Resistance Gene in Apple: From Ephemeral to Enduring Effectiveness in Controlling Scab. PLANT DISEASE 2018; 102:2220-2223. [PMID: 30145950 DOI: 10.1094/pdis-11-17-1759-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Genetic resistance is a useful strategy to control plant disease, but its effectiveness may be reduced over time due to the emergence of pathogens able to circumvent the defenses of the plant. However, the pyramiding of different resistance factors in the same plant can improve the effectiveness and durability of the resistance. To investigate the potential for this approach in apple to control scab disease we surveyed scab incidence in two experimental orchards located at a distance of more than 300 km planted with apple genotypes carrying quantitative resistance and major gene resistance alone or in combination. Our results showed that the effectiveness of pyramiding in controlling scab was dependent on the site and could not be completely explained by the effectiveness level of the resistances alone.
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Affiliation(s)
- Pauline Lasserre-Zuber
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France; present address: INRA, UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France
| | - Valérie Caffier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - René Stievenard
- CRRG, Centre Régional de Ressources Génétiques, Ferme du Héron, Chemin de la ferme de Lenglet, 59650, Villeneuve d'Ascq, France
| | - Arnaud Lemarquand
- UE0449 Unité Expérimentale Horticole, INRA, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Bruno Le Cam
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Charles-Eric Durel
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
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31
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Soubeyrand S, de Jerphanion P, Martin O, Saussac M, Manceau C, Hendrikx P, Lannou C. Inferring pathogen dynamics from temporal count data: the emergence of Xylella fastidiosa in France is probably not recent. THE NEW PHYTOLOGIST 2018; 219:824-836. [PMID: 29689134 PMCID: PMC6032966 DOI: 10.1111/nph.15177] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/16/2018] [Indexed: 05/08/2023]
Abstract
Unravelling the ecological structure of emerging plant pathogens persisting in multi-host systems is challenging. In such systems, observations are often heterogeneous with respect to time, space and host species, and may lead to biases of perception. The biased perception of pathogen ecology may be exacerbated by hidden fractions of the whole host population, which may act as infection reservoirs. We designed a mechanistic-statistical approach to help understand the ecology of emerging pathogens by filtering out some biases of perception. This approach, based on SIR (Susceptible-Infected-Removed) models and a Bayesian framework, disentangles epidemiological and observational processes underlying temporal counting data. We applied our approach to French surveillance data on Xylella fastidiosa, a multi-host pathogenic bacterium recently discovered in Corsica, France. A model selection led to two diverging scenarios: one scenario without a hidden compartment and an introduction around 2001, and the other with a hidden compartment and an introduction around 1985. Thus, Xylella fastidiosa was probably introduced into Corsica much earlier than its discovery, and its control could be arduous under the hidden compartment scenario. From a methodological perspective, our approach provides insights into the dynamics of emerging plant pathogens and, in particular, the potential existence of infection reservoirs.
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Affiliation(s)
| | | | | | - Mathilde Saussac
- Unit of Coordination and Support to SurveillanceANSES69364LyonFrance
| | | | - Pascal Hendrikx
- Unit of Coordination and Support to SurveillanceANSES69364LyonFrance
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32
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Pacilly FC, Hofstede GJ, Lammerts van Bueren ET, Kessel GJ, Groot JC. Simulating crop-disease interactions in agricultural landscapes to analyse the effectiveness of host resistance in disease control: The case of potato late blight. Ecol Modell 2018. [DOI: 10.1016/j.ecolmodel.2018.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Papaïx J, Rimbaud L, Burdon JJ, Zhan J, Thrall PH. Differential impact of landscape-scale strategies for crop cultivar deployment on disease dynamics, resistance durability and long-term evolutionary control. Evol Appl 2018; 11:705-717. [PMID: 29875812 PMCID: PMC5979631 DOI: 10.1111/eva.12570] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 10/23/2017] [Indexed: 01/28/2023] Open
Abstract
A multitude of resistance deployment strategies have been proposed to tackle the evolutionary potential of pathogens to overcome plant resistance. In particular, many landscape-based strategies rely on the deployment of resistant and susceptible cultivars in an agricultural landscape as a mosaic. However, the design of such strategies is not easy as strategies targeting epidemiological or evolutionary outcomes may not be the same. Using a stochastic spatially explicit model, we studied the impact of landscape organization (as defined by the proportion of fields cultivated with a resistant cultivar and their spatial aggregation) and key pathogen life-history traits on three measures of disease control. Our results show that short-term epidemiological dynamics are optimized when landscapes are planted with a high proportion of the resistant cultivar in low aggregation. Importantly, the exact opposite situation is optimal for resistance durability. Finally, well-mixed landscapes (balanced proportions with low aggregation) are optimal for long-term evolutionary equilibrium (defined here as the level of long-term pathogen adaptation). This work offers a perspective on the potential for contrasting effects of landscape organization on different goals of disease management and highlights the role of pathogen life history.
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Affiliation(s)
| | | | | | - Jiasui Zhan
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
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34
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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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35
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Rimbaud L, Papaïx J, Rey JF, Barrett LG, Thrall PH. Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens. PLoS Comput Biol 2018; 14:e1006067. [PMID: 29649208 PMCID: PMC5918245 DOI: 10.1371/journal.pcbi.1006067] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 04/24/2018] [Accepted: 02/27/2018] [Indexed: 11/18/2022] Open
Abstract
Genetically-controlled plant resistance can reduce the damage caused by pathogens. However, pathogens have the ability to evolve and overcome such resistance. This often occurs quickly after resistance is deployed, resulting in significant crop losses and a continuing need to develop new resistant cultivars. To tackle this issue, several strategies have been proposed to constrain the evolution of pathogen populations and thus increase genetic resistance durability. These strategies mainly rely on varying different combinations of resistance sources across time (crop rotations) and space. The spatial scale of deployment can vary from multiple resistance sources occurring in a single cultivar (pyramiding), in different cultivars within the same field (cultivar mixtures) or in different fields (mosaics). However, experimental comparison of the efficiency (i.e. ability to reduce disease impact) and durability (i.e. ability to limit pathogen evolution and delay resistance breakdown) of landscape-scale deployment strategies presents major logistical challenges. Therefore, we developed a spatially explicit stochastic model able to assess the epidemiological and evolutionary outcomes of the four major deployment options described above, including both qualitative resistance (i.e. major genes) and quantitative resistance traits against several components of pathogen aggressiveness: infection rate, latent period duration, propagule production rate, and infectious period duration. This model, implemented in the R package landsepi, provides a new and useful tool to assess the performance of a wide range of deployment options, and helps investigate the effect of landscape, epidemiological and evolutionary parameters. This article describes the model and its parameterisation for rust diseases of cereal crops, caused by fungi of the genus Puccinia. To illustrate the model, we use it to assess the epidemiological and evolutionary potential of the combination of a major gene and different traits of quantitative resistance. The comparison of the four major deployment strategies described above will be the objective of future studies. There are many recent examples which demonstrate the evolutionary potential of plant pathogens to overcome the resistances deployed in agricultural landscapes to protect our crops. Increasingly, it is recognised that how resistance is deployed spatially and temporally can impact on rates of pathogen evolution and resistance breakdown. Such deployment strategies are mainly based on the combination of several sources of resistance at different spatiotemporal scales. However, comparison of these strategies in a predictive sense is not an easy task, owing to the logistical difficulties associated with experiments involving the spread of a pathogen at large spatio-temporal scales. Moreover, both the durability of a strategy and the epidemiological protection it provides to crops must be assessed since these evaluation criteria are not necessarily correlated. Surprisingly, no current simulation model allows a thorough comparison of the different options. Here we describe a spatio-temporal model able to simulate a wide range of deployment strategies and resistance sources. This model, implemented in the R package landsepi, facilitates assessment of both epidemiological and evolutionary outcomes across simulated scenarios. In this work, the model is used to investigate the combination of different sources of resistance against fungal diseases such as rusts of cereal crops.
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Affiliation(s)
- Loup Rimbaud
- CSIRO Agriculture and Food, Canberra, ACT, Australia
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36
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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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37
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Rousseau E, Moury B, Mailleret L, Senoussi R, Palloix A, Simon V, Valière S, Grognard F, Fabre F. Estimating virus effective population size and selection without neutral markers. PLoS Pathog 2017; 13:e1006702. [PMID: 29155894 PMCID: PMC5720836 DOI: 10.1371/journal.ppat.1006702] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 12/07/2017] [Accepted: 10/19/2017] [Indexed: 12/04/2022] Open
Abstract
By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and variant frequencies were determined by HTS in eight plants of each pepper line at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers. This method requires variant frequency determination at several time points, in independent hosts. The parameters are the selection coefficients for each PVY variant and four effective population sizes Ne at different time-points of the experiment. Numerical simulations of asexual haploid Wright-Fisher populations subjected to contrasting genetic drift (Ne ∈ [10, 2000]) and selection (|s| ∈ [0, 0.15]) regimes were used to validate the method proposed. The experiment in closely related pepper host genotypes revealed that viruses experienced a considerable diversity of selection and genetic drift regimes. The resulting variant dynamics were accurately described by Wright-Fisher models. The fitness ranks of the variants were almost identical between host genotypes. By contrast, the dynamics of Ne were highly variable, although a bottleneck was often identified during the systemic movement of the virus. We demonstrated that, for a fixed initial PVY population, virus effective population size is a heritable trait in plants. These findings pave the way for the breeding of plant varieties exposing viruses to stronger genetic drift, thereby slowing virus adaptation. A growing number of experimental evolution studies are using an “evolve-and-resequence” approach to observe the within-host dynamics of pathogen variants of biomedical or ecological interest. The resulting data are particularly appropriate for studying the effects of evolutionary forces, such as selection and genetic drift, on the emergence of new pathogen variants. However, it remains challenging to unravel the effects of selection and genetic drift in the absence of neutral markers, a situation frequently encountered for microbes, such as viruses, due to their small constrained genomes. Using such an approach on a plant virus, we observed that the same set of virus variants displayed highly diverse dynamics in closely related plant genotypes. We developed and validated a method that does not require neutral markers, for estimating selection coefficients and effective population sizes from these experimental evolution data. We found that the viruses experienced considerable diversity in genetic drift regimes, depending on host genotype. Importantly, genetic drift experienced by virus populations was shown to be a heritable plant trait. These findings pave the way for the breeding of plant varieties exposing viruses to strong genetic drift, thereby slowing virus adaptation.
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Affiliation(s)
- Elsa Rousseau
- Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France
- Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
- Pathologie Végétale, INRA, 84140 Montfavet, France
- * E-mail: (ER); (FF)
| | - Benoît Moury
- Pathologie Végétale, INRA, 84140 Montfavet, France
| | - Ludovic Mailleret
- Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France
- Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
| | | | | | - Vincent Simon
- Pathologie Végétale, INRA, 84140 Montfavet, France
- UMR BFP, INRA, Villenave d’Ornon, France
| | - Sophie Valière
- GeT-PlaGe, INRA, Genotoul, Castanet-tolosan, France
- UAR DEPT GA, INRA, Castanet-Tolosan, France
| | - Frédéric Grognard
- Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France
| | - Frédéric Fabre
- UMR SAVE, INRA, Villenave d’Ornon, France
- * E-mail: (ER); (FF)
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Wininger K, Rank N. Evolutionary dynamics of interactions between plants and their enemies: comparison of herbivorous insects and pathogens. Ann N Y Acad Sci 2017; 1408:46-60. [PMID: 29125186 DOI: 10.1111/nyas.13541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 09/29/2017] [Accepted: 10/04/2017] [Indexed: 01/21/2023]
Abstract
Plants colonized land over 400 million years ago. Shortly thereafter, organisms began to consume terrestrial plant tissue as a nutritional resource. Most plant enemies are plant pathogens or herbivores, and they impose natural selection for plants to evolve defenses. These traits generate selection pressures on enemies. Coevolution between terrestrial plants and their enemies is an important element of the evolutionary history of both groups. However, coevolutionary studies of plant-pathogen interactions have tended to focus on different research topics than plant-herbivore interactions. Specifically, studies of plant-pathogen interactions often adopt a "gene-for-gene" conceptual framework. In contrast, studies of plants and herbivores often investigate escalation or elaboration of plant defense and herbivore adaptations to overcome it. The main exceptions to the general pattern are studies that focus on small, sessile herbivores that share many features with plant pathogens, studies that incorporate both herbivores and pathogens into a single investigation, and studies that test aspects of Thompson's geographic mosaic theory for coevolution. We discuss the implications of these findings for future research.
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Affiliation(s)
- Kerry Wininger
- Department of Biology, Sonoma State University, Rohnert Park, California
| | - Nathan Rank
- Department of Biology, Sonoma State University, Rohnert Park, California
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Nelson R, Wiesner-Hanks T, Wisser R, Balint-Kurti P. Navigating complexity to breed disease-resistant crops. Nat Rev Genet 2017; 19:21-33. [PMID: 29109524 DOI: 10.1038/nrg.2017.82] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plant diseases are responsible for substantial crop losses each year and pose a threat to global food security and agricultural sustainability. Improving crop resistance to pathogens through breeding is an environmentally sound method for managing disease and minimizing these losses. However, it is challenging to breed varieties with resistance that is effective, stable and broad-spectrum. Recent advances in genetic and genomic technologies have contributed to a better understanding of the complexity of host-pathogen interactions and have identified some of the genes and mechanisms that underlie resistance. This new knowledge is benefiting crop improvement through better-informed breeding strategies that utilize diverse forms of resistance at different scales, from the genome of a single plant to the plant varieties deployed across a region.
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Affiliation(s)
- Rebecca Nelson
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Tyr Wiesner-Hanks
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Randall Wisser
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716, USA
| | - Peter Balint-Kurti
- United States Department of Agriculture Agricultural Research Service (USDA-ARS), Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695-7616, USA
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40
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Nilusmas S, Mercat M, Perrot T, Touzeau S, Calcagno V, Djian Caporalino C, Castagnone-Sereno P, Mailleret L. A multi-seasonal model of plant-nematode interactions and its use to identify durable plant resistance deployment strategies. ACTA ACUST UNITED AC 2017. [DOI: 10.17660/actahortic.2017.1182.25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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41
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Vyska M, Cunniffe N, Gilligan C. Trade-off between disease resistance and crop yield: a landscape-scale mathematical modelling perspective. J R Soc Interface 2017; 13:rsif.2016.0451. [PMID: 27707906 DOI: 10.1098/rsif.2016.0451] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/06/2016] [Indexed: 11/12/2022] Open
Abstract
The deployment of crop varieties that are partially resistant to plant pathogens is an important method of disease control. However, a trade-off may occur between the benefits of planting the resistant variety and a yield penalty, whereby the standard susceptible variety outyields the resistant one in the absence of disease. This presents a dilemma: deploying the resistant variety is advisable only if the disease occurs and is sufficient for the resistant variety to outyield the infected standard variety. Additionally, planting the resistant variety carries with it a further advantage in that the resistant variety reduces the probability of disease invading. Therefore, viewed from the perspective of a grower community, there is likely to be an optimal trade-off and thus an optimal cropping density for the resistant variety. We introduce a simple stochastic, epidemiological model to investigate the trade-off and the consequences for crop yield. Focusing on susceptible-infected-removed epidemic dynamics, we use the final size equation to calculate the surviving host population in order to analyse the yield, an approach suitable for rapid epidemics in agricultural crops. We identify a single compound parameter, which we call the efficacy of resistance and which incorporates the changes in susceptibility, infectivity and durability of the resistant variety. We use the compound parameter to inform policy plots that can be used to identify the optimal strategy for given parameter values when an outbreak is certain. When the outbreak is uncertain, we show that for some parameter values planting the resistant variety is optimal even when it would not be during the outbreak. This is because the resistant variety reduces the probability of an outbreak occurring.
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Affiliation(s)
- Martin Vyska
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, UK
| | - Nik Cunniffe
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, UK
| | - Christopher Gilligan
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, UK
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Djidjou-Demasse R, Moury B, Fabre F. Mosaics often outperform pyramids: insights from a model comparing strategies for the deployment of plant resistance genes against viruses in agricultural landscapes. THE NEW PHYTOLOGIST 2017; 216:239-253. [PMID: 28776688 DOI: 10.1111/nph.14701] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/13/2017] [Indexed: 06/07/2023]
Abstract
The breakdown of plant virus resistance genes is a major issue in agriculture. We investigated whether a set of resistance genes would last longer when stacked into a single plant cultivar (pyramiding) or when deployed individually in regional mosaics (mosaic strategy). We modeled the genetic and epidemiological processes shaping the demogenetic dynamics of viruses under a multilocus gene-for-gene system, from the plant to landscape scales. The landscape consisted of many fields, was subject to seasonality, and of a reservoir hosting viruses year-round. Strategy performance depended principally on the fitness costs of adaptive mutations, epidemic intensity before resistance deployment and landscape connectivity. Mosaics were at least as good as pyramiding strategies in most production situations tested. Pyramiding strategies performed better only with slowly changing virus reservoir dynamics. Mosaics are more versatile than pyramiding strategies, and we found that deploying a mosaic of three to five resistance genes generally provided effective disease control, unless the epidemics were driven mostly by within-field infections. We considered the epidemiological and evolutionary mechanisms underlying the greater versatility of mosaics in our case study, with a view to providing breeders and growers with guidance as to the most appropriate deployment strategy.
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Affiliation(s)
| | - Benoît Moury
- UR 407, Pathologie Végétale, INRA, Montfavet, F-84140, France
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Pinel-Galzi A, Dubreuil-Tranchant C, Hébrard E, Mariac C, Ghesquière A, Albar L. Mutations in Rice yellow mottle virus Polyprotein P2a Involved in RYMV2 Gene Resistance Breakdown. FRONTIERS IN PLANT SCIENCE 2016; 7:1779. [PMID: 27965688 PMCID: PMC5125353 DOI: 10.3389/fpls.2016.01779] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/11/2016] [Indexed: 05/09/2023]
Abstract
Rice yellow mottle virus (RYMV) is one of the major diseases of rice in Africa. The high resistance of the Oryza glaberrima Tog7291 accession involves a null allele of the RYMV2 gene, whose ortholog in Arabidopsis, CPR5, is a transmembrane nucleoporin involved in effector-triggered immunity. To optimize field deployment of the RYMV2 gene and improve its durability, which is often a weak point in varietal resistance, we analyzed its efficiency toward RYMV isolates representing the genetic diversity of the virus and the molecular basis of resistance breakdown. Tog7291 resistance efficiency was highly variable depending on the isolate used, with infection rates ranging from 0 to 98% of plants. Back-inoculation experiments indicated that infection cases were not due to an incomplete resistance phenotype but to the emergence of resistance-breaking (RB) variants. Interestingly, the capacity of the virus to overcome Tog7291 resistance is associated with a polymorphism at amino-acid 49 of the VPg protein which also affects capacity to overcome the previously studied RYMV1 resistance gene. This polymorphism appeared to be a main determinant of the emergence of RB variants. It acts independently of the resistance gene and rather reflects inter-species adaptation with potential consequences for the durability of resistance. RB mutations were identified by full-length or partial sequencing of the RYMV genome in infected Tog7291 plants and were validated by directed mutagenesis of an infectious viral clone. We found that Tog7291 resistance breakdown involved mutations in the putative membrane anchor domain of the polyprotein P2a. Although the precise effect of these mutations on rice/RYMV interaction is still unknown, our results offer a new perspective for the understanding of RYMV2 mediated resistance mechanisms. Interestingly, in the susceptible IR64 variety, RB variants showed low infectivity and frequent reversion to the wild-type genotype, suggesting that Tog7291 resistance breakdown is associated with a major loss of viral fitness in normally susceptible O. sativa varieties. Despite the high frequency of resistance breakdown in controlled conditions, this loss of fitness is an encouraging element with regards to RYMV2 resistance durability.
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Affiliation(s)
- Agnès Pinel-Galzi
- Interactions Plantes Microorganismes Environnement, Institut de Recherche pour le Développement – Centre de Coopération Internationale en Recherche Agronomique pour le Développement – Université de MontpellierMontpellier, France
| | - Christine Dubreuil-Tranchant
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
| | - Eugénie Hébrard
- Interactions Plantes Microorganismes Environnement, Institut de Recherche pour le Développement – Centre de Coopération Internationale en Recherche Agronomique pour le Développement – Université de MontpellierMontpellier, France
| | - Cédric Mariac
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
| | - Alain Ghesquière
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
| | - Laurence Albar
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
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44
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Burdon JJ, Zhan J, Barrett LG, Papaïx J, Thrall PH. Addressing the Challenges of Pathogen Evolution on the World's Arable Crops. PHYTOPATHOLOGY 2016; 106:1117-1127. [PMID: 27584868 DOI: 10.1094/phyto-01-16-0036-fi] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Advances in genomic and molecular technologies coupled with an increasing understanding of the fine structure of many resistance and infectivity genes, have opened up a new era of hope in controlling the many plant pathogens that continue to be a major source of loss in arable crops. Some new approaches are under consideration including the use of nonhost resistance and the targeting of critical developmental constraints. However, the major thrust of these genomic and molecular approaches is to enhance the identification of resistance genes, to increase their ease of manipulation through marker and gene editing technologies and to lock a range of resistance genes together in simply manipulable resistance gene cassettes. All these approaches essentially continue a strategy that assumes the ability to construct genetic-based resistance barriers that are insurmountable to target pathogens. Here we show how the recent advances in knowledge and marker technologies can be used to generate more durable disease resistance strategies that are based on broad evolutionary principles aimed at presenting pathogens with a shifting, landscape of fluctuating directional selection.
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Affiliation(s)
- Jeremy J Burdon
- First and second authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology; Fujian Agriculture and Forestry University, Fuzhou, China; first, third, and fifth authors: CSIRO Agriculture, PO Box 1600, Canberra, A.C.T. 2601, Australia; and fourth author: INRA Biostatistics and Spatial Processes, Domaine Saint-Paul AgroParc, 84914 Avignon, France
| | - Jiasui Zhan
- First and second authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology; Fujian Agriculture and Forestry University, Fuzhou, China; first, third, and fifth authors: CSIRO Agriculture, PO Box 1600, Canberra, A.C.T. 2601, Australia; and fourth author: INRA Biostatistics and Spatial Processes, Domaine Saint-Paul AgroParc, 84914 Avignon, France
| | - Luke G Barrett
- First and second authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology; Fujian Agriculture and Forestry University, Fuzhou, China; first, third, and fifth authors: CSIRO Agriculture, PO Box 1600, Canberra, A.C.T. 2601, Australia; and fourth author: INRA Biostatistics and Spatial Processes, Domaine Saint-Paul AgroParc, 84914 Avignon, France
| | - Julien Papaïx
- First and second authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology; Fujian Agriculture and Forestry University, Fuzhou, China; first, third, and fifth authors: CSIRO Agriculture, PO Box 1600, Canberra, A.C.T. 2601, Australia; and fourth author: INRA Biostatistics and Spatial Processes, Domaine Saint-Paul AgroParc, 84914 Avignon, France
| | - Peter H Thrall
- First and second authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology; Fujian Agriculture and Forestry University, Fuzhou, China; first, third, and fifth authors: CSIRO Agriculture, PO Box 1600, Canberra, A.C.T. 2601, Australia; and fourth author: INRA Biostatistics and Spatial Processes, Domaine Saint-Paul AgroParc, 84914 Avignon, France
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45
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Hamelin FM, Allen LJS, Prendeville HR, Hajimorad MR, Jeger MJ. The evolution of plant virus transmission pathways. J Theor Biol 2016; 396:75-89. [PMID: 26908348 DOI: 10.1016/j.jtbi.2016.02.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/30/2015] [Accepted: 02/12/2016] [Indexed: 01/12/2023]
Abstract
The evolution of plant virus transmission pathways is studied through transmission via seed, pollen, or a vector. We address the questions: under what circumstances does vector transmission make pollen transmission redundant? Can evolution lead to the coexistence of multiple virus transmission pathways? We restrict the analysis to an annual plant population in which reproduction through seed is obligatory. A semi-discrete model with pollen, seed, and vector transmission is formulated to investigate these questions. We assume vector and pollen transmission rates are frequency-dependent and density-dependent, respectively. An ecological stability analysis is performed for the semi-discrete model and used to inform an evolutionary study of trade-offs between pollen and seed versus vector transmission. Evolutionary dynamics critically depend on the shape of the trade-off functions. Assuming a trade-off between pollen and vector transmission, evolution either leads to an evolutionarily stable mix of pollen and vector transmission (concave trade-off) or there is evolutionary bi-stability (convex trade-off); the presence of pollen transmission may prevent evolution of vector transmission. Considering a trade-off between seed and vector transmission, evolutionary branching and the subsequent coexistence of pollen-borne and vector-borne strains is possible. This study contributes to the theory behind the diversity of plant-virus transmission patterns observed in nature.
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Affiliation(s)
- Frédéric M Hamelin
- Department of Ecology, Agrocampus Ouest, UMR1349 IGEPP, F-35042 Rennes, France.
| | - Linda J S Allen
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, TX 79409-1042, USA
| | - Holly R Prendeville
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR 97331, USA
| | - M Reza Hajimorad
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996-4560, USA
| | - Michael J Jeger
- Division of Ecology and Evolution, Centre for Environmental Policy, Imperial College London, SL5 7PY, UK
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46
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Fabre F, Rousseau E, Mailleret L, Moury B. Epidemiological and evolutionary management of plant resistance: optimizing the deployment of cultivar mixtures in time and space in agricultural landscapes. Evol Appl 2015; 8:919-32. [PMID: 26640518 PMCID: PMC4662345 DOI: 10.1111/eva.12304] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 08/05/2015] [Indexed: 12/11/2022] Open
Abstract
The management of genes conferring resistance to plant–pathogens should make it possible to control epidemics (epidemiological perspective) and preserve resistance durability (evolutionary perspective). Resistant and susceptible cultivars must be strategically associated according to the principles of cultivar mixture (within a season) and rotation (between seasons). We explored these questions by modeling the evolutionary and epidemiological processes shaping the dynamics of a pathogen population in a landscape composed of a seasonal cultivated compartment and a reservoir compartment hosting pathogen year-round. Optimal deployment strategies depended mostly on the molecular basis of plant–pathogen interactions and on the agro-ecological context before resistance deployment, particularly epidemic intensity and landscape connectivity. Mixtures were much more efficient in landscapes in which between-field infections and infections originating from the reservoir were more prevalent than within-field infections. Resistance genes requiring two mutations of the pathogen avirulence gene to be broken down, rather than one, were particularly useful when infections from the reservoir predominated. Combining mixture and rotation principles were better than the use of the same mixture each season as (i) they controlled epidemics more effectively in situations in which within-field infections or infections from the reservoir were frequent and (ii) they fulfilled the epidemiological and evolutionary perspectives.
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Affiliation(s)
- Frédéric Fabre
- UMR 1065 Unité Santé et Agroécologie du Vignoble, INRA Villenave d'Ornon Cedex, France
| | - Elsa Rousseau
- Biocore Team, INRIA Sophia Antipolis, France ; UMR 1355 Institut Sophia Agrobiotech, INRA Sophia Antipolis, France ; UMR 7254 Institut Sophia Agrobiotech, Université Nice Sophia Antipolis Sophia Antipolis, France ; UMR 7254 Institut Sophia Agrobiotech, CNRS Sophia Antipolis, France ; UR 407 Pathologie Végétale, INRA Montfavet, France
| | - Ludovic Mailleret
- Biocore Team, INRIA Sophia Antipolis, France ; UMR 1355 Institut Sophia Agrobiotech, INRA Sophia Antipolis, France ; UMR 7254 Institut Sophia Agrobiotech, Université Nice Sophia Antipolis Sophia Antipolis, France ; UMR 7254 Institut Sophia Agrobiotech, CNRS Sophia Antipolis, France
| | - Benoît Moury
- UR 407 Pathologie Végétale, INRA Montfavet, France
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47
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Papaïx J, Burdon JJ, Zhan J, Thrall PH. Crop pathogen emergence and evolution in agro-ecological landscapes. Evol Appl 2015; 8:385-402. [PMID: 25926883 PMCID: PMC4408149 DOI: 10.1111/eva.12251] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/25/2015] [Indexed: 12/22/2022] Open
Abstract
Remnant areas hosting natural vegetation in agricultural landscapes can impact the disease epidemiology and evolutionary dynamics of crop pathogens. However, the potential consequences for crop diseases of the composition, the spatial configuration and the persistence time of the agro-ecological interface - the area where crops and remnant vegetation are in contact - have been poorly studied. Here, we develop a demographic-genetic simulation model to study how the spatial and temporal distribution of remnant wild vegetation patches embedded in an agricultural landscape can drive the emergence of a crop pathogen and its subsequent specialization on the crop host. We found that landscape structures that promoted larger pathogen populations on the wild host facilitated the emergence of a crop pathogen, but such landscape structures also reduced the potential for the pathogen population to adapt to the crop. In addition, the evolutionary trajectory of the pathogen population was determined by interactions between the factors describing the landscape structure and those describing the pathogen life histories. Our study contributes to a better understanding of how the shift of land-use patterns in agricultural landscapes might influence crop diseases to provide predictive tools to evaluate management practices.
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Affiliation(s)
- Julien Papaïx
- UMR 1290 BIOGER, INRAThiverval-Grignon, France
- UR 341 MIA, INRAJouy-en-Josas, France
- UR 546 BioSP, INRAAvignon, France
- CSIRO Agriculture FlagshipCanberra, ACT, Australia
| | | | - Jiasui Zhan
- Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry UniversityFuzhou, China
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Rimbaud L, Dallot S, Gottwald T, Decroocq V, Jacquot E, Soubeyrand S, Thébaud G. Sharka epidemiology and worldwide management strategies: learning lessons to optimize disease control in perennial plants. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:357-78. [PMID: 26047559 DOI: 10.1146/annurev-phyto-080614-120140] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Many plant epidemics that cause major economic losses cannot be controlled with pesticides. Among them, sharka epidemics severely affect prunus trees worldwide. Its causal agent, Plum pox virus (PPV; genus Potyvirus), has been classified as a quarantine pathogen in numerous countries. As a result, various management strategies have been implemented in different regions of the world, depending on the epidemiological context and on the objective (i.e., eradication, suppression, containment, or resilience). These strategies have exploited virus-free planting material, varietal improvement, surveillance and removal of trees in orchards, and statistical models. Variations on these management options lead to contrasted outcomes, from successful eradication to widespread presence of PPV in orchards. Here, we present management strategies in the light of sharka epidemiology to gain insights from this worldwide experience. Although focused on sharka, this review highlights more general levers and promising approaches to optimize disease control in perennial plants.
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Affiliation(s)
- Loup Rimbaud
- Montpellier SupAgro, UMR 385 BGPI (Biology and Genetics of Plant-Pathogen Interactions), 34398 Montpellier Cedex 5, France;
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49
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Nicaise V. Crop immunity against viruses: outcomes and future challenges. FRONTIERS IN PLANT SCIENCE 2014; 5:660. [PMID: 25484888 PMCID: PMC4240047 DOI: 10.3389/fpls.2014.00660] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/04/2014] [Indexed: 05/02/2023]
Abstract
Viruses cause epidemics on all major cultures of agronomic importance, representing a serious threat to global food security. As strict intracellular pathogens, they cannot be controlled chemically and prophylactic measures consist mainly in the destruction of infected plants and excessive pesticide applications to limit the population of vector organisms. A powerful alternative frequently employed in agriculture relies on the use of crop genetic resistances, approach that depends on mechanisms governing plant-virus interactions. Hence, knowledge related to the molecular bases of viral infections and crop resistances is key to face viral attacks in fields. Over the past 80 years, great advances have been made on our understanding of plant immunity against viruses. Although most of the known natural resistance genes have long been dominant R genes (encoding NBS-LRR proteins), a vast number of crop recessive resistance genes were cloned in the last decade, emphasizing another evolutive strategy to block viruses. In addition, the discovery of RNA interference pathways highlighted a very efficient antiviral system targeting the infectious agent at the nucleic acid level. Insidiously, plant viruses evolve and often acquire the ability to overcome the resistances employed by breeders. The development of efficient and durable resistances able to withstand the extreme genetic plasticity of viruses therefore represents a major challenge for the coming years. This review aims at describing some of the most devastating diseases caused by viruses on crops and summarizes current knowledge about plant-virus interactions, focusing on resistance mechanisms that prevent or limit viral infection in plants. In addition, I will discuss the current outcomes of the actions employed to control viral diseases in fields and the future investigations that need to be undertaken to develop sustainable broad-spectrum crop resistances against viruses.
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Affiliation(s)
- Valérie Nicaise
- Fruit Biology and Pathology, Virology Laboratory, Institut National de la Recherche Agronomique, University of BordeauxUMR 1332, Villenave d’Ornon, France
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50
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Janzac B, Tribodet M, Lacroix C, Moury B, Verrier JL, Jacquot E. Evolutionary Pathways to Break Down the Resistance of Allelic Versions of the PVY Resistance Gene va. PLANT DISEASE 2014; 98:1521-1529. [PMID: 30699784 DOI: 10.1094/pdis-11-13-1126-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Emergence of viral genotypes can make control strategies based on resistance genes ineffective. A few years after the deployment of tobacco genotypes carrying alleles of the Potato virus Y (PVY) recessive resistance gene va, virulent PVY isolates have been reported, suggesting the low durability of va. To have a broader view of the evolutionary processes involved in PVY adaptation to va, we studied mutational pathways leading to the emergence of PVY resistance-breaking populations. The viral genome-linked protein (VPg) has been described to be potentially involved in va adaptation. Analyses of the VPg sequence of PVY isolates sampled from susceptible and resistant tobacco allowed us to identify mutations in the central part of the VPg. Analysis of the virulence of wild-type isolates with known VPg sequences and of mutated versions of PVY infectious clones allowed us to (i) validate VPg as the PVY virulence factor corresponding to va, (ii) highlight the fact that virulence gain in PVY occurs rapidly and preferentially by substitution at position AA105 in the VPg, and (iii) show that the 101G substitution in the VPg of a PVYC isolate is responsible for cross-virulence toward two resistance sources. Moreover, it appears that the evolutionary pathway of PVY adaptation to va depends on both virus and host genetic backgrounds.
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Affiliation(s)
- B Janzac
- INRA-Agrocampus Ouest-Université Rennes 1, UMR 1349 IGEPP, F-35653 Le Rheu, France; Imperial Tobacco Group, SEITA, Institut du Tabac, Domaine de la Tour, F-24100 Bergerac France; and INRA-Cirad Montpellier SupAgro, UMR 385 BGPI, Cirad TA A-54K, Campus International de Baillarguet, F-34398 Montpellier, France
| | - M Tribodet
- INRA-Agrocampus Ouest-Université Rennes 1
| | - C Lacroix
- INRA-Agrocampus Ouest-Université Rennes 1 and Imperial Tobacco Group, SEITA, Institut du Tabac
| | - B Moury
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, BP94, F-84140 Montfavet, France
| | - J L Verrier
- Imperial Tobacco Group, SEITA, Institut du Tabac
| | - E Jacquot
- INRA-Agrocampus Ouest-Université Rennes 1 and INRA-Cirad Montpellier SupAgro
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