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1. An epi‐evolutionary model for predicting the adaptation of spore‐producing pathogens to quantitative resistance in heterogeneous environments

Author: Ramsès Djidjou-Demasse, Frédéric Fabre, Sébastien Lion, Arnaud Ducrot, Quentin Richard, Jean-Baptiste Burie, Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques Appliquées du Havre (LMAH), Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Conseil Interprofessionnel du Vin de BordeauxMarie-Curie FP7 COFUND People Programme. Grant Number: FP7-609398, ANR-16-CE35-0012,STEEP,Structuration spatiale, traitements et épidémiologie évolutive des parasites(2016), ANR-18-CE32-0004,ArchiV,Architecture génétique des caractères quantitatifs dans les interactions plante-virus: conséquences pour la gestion des variétés résistantes et/ou tolérantes à l'échelle du paysage.(2018), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, quantitative resistance, Evolution, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Biology, integro-differential equations, 01 natural sciences, 03 medical and health sciences, basic reproduction number, Genetics, QH359-425, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Resistance (ecology), fungi, integro‐differential equations, Original Articles, Spore, adaptive dynamics, Evolutionary biology, spore‐producing pathogens, spore-producing pathogens, Original Article, Adaptation, General Agricultural and Biological Sciences, Basic reproduction number, resistance durability, 010606 plant biology & botany
Abstract: International audience; We have modeled the evolutionary epidemiology of spore-producing plant pathogens in heterogeneous environments sown with several cultivars carrying quantitative resistances. The model explicitly tracks the infection-age structure and genetic composition of the pathogen population. Each strain is characterized by pathogenicity traits determining its infection efficiency and a time-varying sporulation curve taking into account lesion aging. We first derived a general expression of the basic reproduction number urn:x-wiley:17524571:media:eva13328:eva13328-math-0001 for fungal pathogens in heterogeneous environments. We show that the evolutionary attractors of the model coincide with local maxima of urn:x-wiley:17524571:media:eva13328:eva13328-math-0002 only if the infection efficiency is the same on all host types. We then studied the contribution of three basic resistance characteristics (the pathogenicity trait targeted, resistance effectiveness, and adaptation cost), in interaction with the deployment strategy (proportion of fields sown with a resistant cultivar), to (i) pathogen diversification at equilibrium and (ii) the shaping of transient dynamics from evolutionary and epidemiological perspectives. We show that quantitative resistance affecting only the sporulation curve will always lead to a monomorphic population, whereas dimorphism (i.e., pathogen diversification) can occur if resistance alters infection efficiency, notably with high adaptation costs and proportions of the resistant cultivar. Accordingly, the choice of the quantitative resistance genes operated by plant breeders is a driver of pathogen diversification. From an evolutionary perspective, the time to emergence of the evolutionary attractor best adapted to the resistant cultivar tends to be shorter when resistance affects infection efficiency than when it affects sporulation. Conversely, from an epidemiological perspective, epidemiological control is always greater when the resistance affects infection efficiency. This highlights the difficulty of defining deployment strategies for quantitative resistance simultaneously maximizing epidemiological and evolutionary outcomes.
Published: 2022
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2. Models of plant resistance deployment

Author: Frédéric Fabre, Julien Papaïx, Luke G. Barrett, Benoît Moury, Loup Rimbaud, Christian Lannou, Peter H. Thrall, Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CSIRO Agriculture and Food (CSIRO), Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biostatistique et Processus Spatiaux (BioSP), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), GRDC grant CSP00192, AFB Ecophyto II-Leviers Territoriaux Project Médée (2020–2022), INRA-CSIRO linkage program, and ANR-18-CE32-0004,ArchiV,Architecture génétique des caractères quantitatifs dans les interactions plante-virus: conséquences pour la gestion des variétés résistantes et/ou tolérantes à l'échelle du paysage.(2018)
Subjects: Crops, Agricultural, 0106 biological sciences, Plant Science, Computational biology, adaptation, Biology, 01 natural sciences, host–microbe interaction, 03 medical and health sciences, evolution, Disease Resistance, Plant Diseases, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Resistance (ecology), 15. Life on land, simulation, immunity, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Software deployment, durability, Adaptation, 010606 plant biology & botany
Abstract: International audience; 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.
Published: 2021
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3. The quasi-universality of nestedness in the structure of quantitative plant-parasite interactions

Author: Boissot N, Marcel T, Dogimont C, Marie-Laure Pilet-Nayel, Juliette Doumayrou, S. Perrot, Josselin Montarry, Caffier, Chanéac S, Cantet M, Cindy E. Morris, Justafré I, Audergon J, M. Buisson, Paineau M, François Delmotte, Ben Krima S, Frédéric Fabre, Grimault, C. Constant, Omrani M, Sylvain Fournet, Benoît Moury, Losdat D, Baudracco-Arnas S, Ruellan Y, Jaunet T, Bertrand F, Lefebvre, Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Amélioration des Fruits et Légumes (GAFL), Laboratoires ASL, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Bayer seeds SAS, Gautier semences, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Takii France SAS, Sakata Vegetables Europe, Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 0971 Gip Geves SNES Angers, Institut National de la Recherche Agronomique (INRA)-Accueil GEVES (Accueil GEVES)-Groupe d'étude et de controle des variétés et des semences (GEVES)-Gip Geves SNES Angers (Gip Geves SNES Angers), HM. CLAUSE [France], Vilmorin, Rijk Zwaan, Partenaires INRAE, PROGRAILIVE project (grant 808 RBRE160116CR0530019), Institut Carnot PLANT2PRO, Comité Interprofessionnel des Vins de Bordeaux 810 (CIVB), the INRAE departments 'Santé des Plantes et Environnement' (project APÔGÉ and PhD thesis of Safa Ben Krima) and 'Génétique et Amélioration des Plantes', the INRAE métaprogramme SMaCH (Sustainable Management of Crop Health), the French Ministry of Agriculture and Food for projects 'Recherche et mise au point de méthodes pour évaluer des résistances variétales durables à des agents pathogènes' (CTPS project C2008-29), 'Nouvelles sources de résistance à Aphis gossypii chez le melon' (CTPS project C06/02) and 'Caractérisation de la virulence de Podosphaera xanthii, agent causal de l’oïdium du melon, et développement d’un système de codification des races' (CTPS project C-2012-10)., ANR-12-ADAP-0009,GANDALF,Génomique et adaptation des traits de vie des champignons impliqués dans les interactions plante-pathogène(2012), ANR-18-CE32-0004,ArchiV,Architecture génétique des caractères quantitatifs dans les interactions plante-virus: conséquences pour la gestion des variétés résistantes et/ou tolérantes à l'échelle du paysage.(2018), ANR-11-BTBR-0002,PeaMUST,Adaptation multistress et régulations biologiques pour l'amélioration du rendement et de la stabilité du pois protéagineux(2011), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), ANR-05-PADD-0005,CEDRE,Exploitation durable de résistances aux maladies chez les végétaux(2005), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, PROGRAILIVE project (grant RBRE160116CR0530019) funded by the Bretagne region, France, INRAE departments 'Santé des Plantes et Environnement' (project APÔGÉ and PhD thesis of Safa Ben Krima) and 'Génétique et Amélioration des Plantes', INRAE métaprogramme SMaCH (Sustainable Management of Crop Health), French Ministry of Agriculture and Food for projects 'Recherche et mise au point de méthodes pour évaluer des résistances variétales durables à des agents pathogènes' (CTPS project C2008-29), 'Nouvelles sources de résistance à Aphis gossypii chez le melon' (CTPS project C06/02) and 'Caractérisation de la virulence de Podosphaera xanthii, agent causal de l’oïdium du melon, et développement d’un système de codification des races' (CTPS project C-2012-10)., and Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, bipartite network, Plant resistance, pathogenicity, plant parasite, bipartite network, nestedness, modularity, nestedness, Plant Immunity, Plant resistance, Context (language use), Biology, Quantitative trait locus, 01 natural sciences, 03 medical and health sciences, pathogenicity, plant parasite, modularity, 030304 developmental biology, 2. Zero hunger, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Modularity (networks), Resistance (ecology), Host (biology), fungi, food and beverages, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Evolutionary biology, Trait, Nestedness, 010606 plant biology & botany
Abstract: A previous version of this article has been peer-reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100132); International audience; Understanding the relationships between host range and pathogenicity for parasites, and between the efficiency and scope of immunity for hosts are essential to implement efficient disease control strategies. In the case of plant parasites, most studies have focused on describing qualitative interactions and a variety of genetic and evolutionary models has been proposed in this context. Although plant quantitative resistance benefits from advantages in terms of durability, we presently lack models that account for quantitative interactions between plants and their parasites and the evolution of these interactions. Nestedness and modularity are important features to unravel the overall structure of host-parasite interaction matrices. Here, we analysed these two features on 32 matrices of quantitative pathogenicity trait data gathered from 15 plant-parasite pathosystems consisting of either annual or perennial plants along with fungi or oomycetes, bacteria, nematodes, insects and viruses. The performance of several nestedness and modularity algorithms was evaluated through a simulation approach, which helped interpretation of the results. We observed significant modularity in only six of the 32 matrices, with two or three modules detected. For three of these matrices, modules could be related to resistance quantitative trait loci present in the host. In contrast, we found high and significant nestedness in 30 of the 32 matrices. Nestedness was linked to other properties of plant-parasite interactions. First, pathogenicity trait values were explained in majority by a parasite strain effect and a plant accession effect, with no or minor parasite-plant interaction term. Second, correlations between the efficiency and scope of the resistance of plant genotypes, and between the host range breadth and pathogenicity level of parasite strains were overall positive. This latter result questions the efficiency of strategies based on the deployment of several genetically-differentiated cultivars of a given crop species in the case of quantitative plant immunity.
Published: 2021
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4. Impact of genetic drift, selection and accumulation level on virus adaptation to its host plants

Author: Ludovic Mailleret, Elsa Rousseau, Frédéric Fabre, Lucie Tamisier, Olivier Bouchez, Gregory Girardot, Marion Szadkowski, Catherine Zanchetta, Benoît Moury, Frédéric Grognard, Alain Palloix, and Vincent Simon
Subjects: 0106 biological sciences, 0301 basic medicine, 2. Zero hunger, Genetics, education.field_of_study, biology, Population, food and beverages, Soil Science, Plant Science, biology.organism_classification, 01 natural sciences, Virus, 03 medical and health sciences, 030104 developmental biology, Genetic drift, Potato virus Y, Effective population size, Plant virus, Plant breeding, Adaptation, education, Agronomy and Crop Science, Molecular Biology, 010606 plant biology & botany
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.
Published: 2018
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5. Quantitative trait loci in pepper control the effective population size of two RNA viruses at inoculation

Author: Elsa Rousseau, Alain Palloix, Frédéric Grognard, Ludovic Mailleret, Sebastien Barraillé, Marion Szadkowski, Benoît Moury, Lucie Tamisier, Frédéric Fabre, Ghislaine Nemouchi, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Biological control of artificial ecosystems (BIOCORE), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), BAP (Biologie et Amélioration des Plantes) department, SMaCH (Sustainable Management of Crop Health) metaprogramme of INRA, Région Provence-Alpes-Côte d’Azur (PACA), Station de Pathologie Végétale (AVI-PATHO), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité de pathologie végétale (UR 407) INRA Avignon, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Institut des Sciences de la Vigne et du Vin (ISVV)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Capsicum annuum, 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Potyvirus, Population, Quantitative trait locus, Cucumovirus, 01 natural sciences, Virus, Cucumber mosaic virus, 03 medical and health sciences, Virology, virus infection, bottlenecks, Potato virus Y, education, Gene, ComputingMilieux_MISCELLANEOUS, Plant Diseases, Genetics, education.field_of_study, biology, fungi, food and beverages, biology.organism_classification, Plant Leaves, 030104 developmental biology, quantitative trait loci, Capsicum, effective population size, 010606 plant biology & botany
Abstract: We thank the staff of the INRAE Experimental facilities of the Plant Pathology research unit (IEPV, https://doi.org/10.15454/8DGF-QF70) for their involvement in field experiments; International audience; Infection of plants by viruses is a complex process involving several steps: inoculation into plant cells, replication in inoculated cells and plant colonization. The success of the different steps depends, in part, on the viral effective population size (Ne), defined as the number of individuals passing their genes to the next generation. During infection, the virus population will undergo bottlenecks, leading to drastic reductions in Ne and, potentially, to the loss of the fittest variants. Therefore, it is crucial to better understand how plants affect Ne. We aimed to (i) identify the plant genetic factors controlling Ne during inoculation, (ii) understand the mechanisms used by the plant to control Ne and (iii) compare these genetic factors with the genes controlling plant resistance to viruses. Ne was measured in a doubled-haploid population of Capsicum annuum. Plants were inoculated with either a Potato virus Y (PVY) construct expressing the green fluorescent protein or a necrotic variant of Cucumber mosaic virus (CMV). Newas assessed by counting the number of primary infection foci on cotyledons for PVY or the number of necrotic local lesions on leaves for CMV. The number of foci and lesions was correlated (r=0.57) and showed a high heritability (h2=0.93 for PVY and h2=0.98 for CMV). The Ne of the two viruses was controlled by both common quantitative trait loci (QTLs) and virus-specific QTLs, indicating the contribution of general and specific mechanisms. The PVY-specific QTL colocalizes with a QTL that reduces PVY accumulation and the capacity to break down a major-effect resistance gene.
Published: 2017
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6. Virus epidemics, plant-controlled population bottlenecks and the durability of plant resistance

Author: Frédéric Fabre, Frédéric Grognard, Elsa Rousseau, Benoît Moury, Mélanie Bonneault, Ludovic Mailleret, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Santé et agroécologie du vignoble (SAVE), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Université Côte d'Azur (UCA), ANR-13-BSV7-0011,FunFit,Une approche basée sur les traits d'histoire de vie des champignons phytopathogènes pour faire le lien entre fitness individuelle et stratégies écologiques.(2013), Unité de Pathologie Végétale (PV), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Santé et agroécologie du vignoble (UMR SAVE), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), French Agence Nationale de la Recherche (ANR) under grant ANR-13-BSV7-0011 (project FunFit), SMaCH (Sustainable Management of Crop Health) metaprogramme of INRA., Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, quantitative resistance, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Virus, Bottleneck, 03 medical and health sciences, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Cultivar, Plant traits, population bottleneck, Epidemics, yield increase, Disease Resistance, Plant Diseases, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Models, Statistical, business.industry, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Outbreak, food and beverages, Articles, Plants, 15. Life on land, stochastic epidemic model, qualitative resistance, Biotechnology, Plant Breeding, Population bottleneck, Infectious disease (medical specialty), Viruses, General Agricultural and Biological Sciences, Epidemic model, business, resistance durability, Virus Physiological Phenomena, 010606 plant biology & botany
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’.
Published: 2019
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7. An epi-evolutionary model to predict spore-producing pathogens adaptation to quantitative resistance in heterogeneous environments

Author: Ramsès Djidjou-Demasse, Frédéric Fabre, Quentin Richard, Sébastien Lion, Jean-Baptiste Burie, and Arnaud Ducrot
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Resistance (ecology), Host (biology), Strain (biology), Population, Diversification (marketing strategy), Biology, 01 natural sciences, 03 medical and health sciences, Evolutionary biology, Trait, Adaptation, education, Basic reproduction number, 030304 developmental biology, 010606 plant biology & botany
Abstract: We model the evolutionary epidemiology of spore-producing plant pathogens in heterogeneous environments sown with several cultivars carrying quantitative resistances. The model explicitly tracks the infection-age structure and genetic composition of the pathogen population. Each strain is characterized by pathogenicity traits describing its infection efficiency and a time-varying sporulation curve taking into account lesion ageing. We first derive a general expression of the basic reproduction number ℛ0for fungal pathogens in heterogeneous environments. We show that evolutionary attractors of the model coincide with local maxima of ℛ0only if the infection efficiency is the same on all host types. We then study how three basic resistance characteristics (pathogenicity trait targeted, resistance effectiveness, and adaptation cost) in interaction with the deployment strategy (proportion of fields sown with a resistant cultivar) (i) lead to pathogen diversification at equilibrium and (ii) shape the transient dynamics from evolutionary and epidemiological perspectives. We show that quantitative resistance impacting only the sporulation curve will always lead to a monomorphic population, while dimorphism (i.e. pathogen diversification) can occur with resistance altering infection efficiency, notably with high adaptation cost and proportion of R cultivar. Accordingly, the choice of quantitative resistance genes operated by plant breeders is a driver of pathogen diversification. From an evolutionary perspective, the emergence time of the evolutionary attractor best adapted to the R cultivar tends to be shorter when the resistance impacts infection efficiency than when it impacts sporulation. In contrast, from an epidemiological perspective, the epidemiological control is always higher when the resistance impacts infection efficiency. This highlights the difficulty of defining deployment strategies of quantitative resistance maximising at the same time epidemiological and evolutionary outcomes.
Published: 2018
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8. Small Bottleneck Size in a Highly Multipartite Virus during a Complete Infection Cycle

Author: Frédéric Fabre, Yannis Michalakis, Gaël Thébaud, Mircea T. Sofonea, Romain Gallet, Anne Sicard, Stéphane Blanc, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Santé Végétale (SV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Evolution Théorique et Expérimentale (MIVEGEC-ETE), Perturbations, Evolution, Virulence (PEV), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), French national research funding agency (ANR-Nano) : ANR-14-CE02-0014-01, SPE department of INRA, IRD research institute, CNRS research institute, and Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3)
Subjects: 0301 basic medicine, bottleneck, [SDV]Life Sciences [q-bio], Immunology, Biology, Microbiology, Genome, Bottleneck, law.invention, 03 medical and health sciences, Genetic drift, Effective population size, law, Virology, aphid transmission, Animals, Plant Diseases, Aphid, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Host (biology), Nanovirus, food and beverages, FBNSV, biology.organism_classification, Insect Vectors, Vicia faba, Multipartite, 030104 developmental biology, Transmission (mechanics), Genetic Diversity and Evolution, Evolutionary biology, Aphids, Insect Science, DNA, Viral, multipartite virus, effective population size
Abstract: Multipartite viruses package their genomic segments independently and thus incur the risk of being unable to transmit their entire genome during host-to-host transmission if they undergo severe bottlenecks. In this paper, we estimated the bottleneck size during one infection cycle of Faba bean necrotic stunt virus (FBNSV), an octopartite nanovirus whose segments have been previously shown to converge to particular and unequal relative frequencies within host plants and aphid vectors. Two methods were used to derive this estimate, one based on the probability of transmission of the virus and the other based on the temporal evolution of the relative frequency of markers for two genomic segments, one frequent and one rare (segment N and S, respectively), both in plants and vectors. Our results show that FBNSV undergoes severe bottlenecks during aphid transmission. Further, even though the bottlenecks are always narrow under our experimental conditions, they slightly widen with the number of transmitting aphids. In particular, when several aphids are used for transmission, the bottleneck size of the segments is also affected by within-plant processes and, importantly, significantly differs across segments. These results indicate that genetic drift not only must be an important process affecting the evolution of these viruses but also that these effects vary across genomic segments and, thus, across viral genes, a rather unique and intriguing situation. We further discuss the potential consequences of our findings for the transmission of multipartite viruses. IMPORTANCE Multipartite viruses package their genomic segments in independent capsids. The most obvious cost of such genomic structure is the risk of losing at least one segment during host-to-host transmission. A theoretical study has shown that for nanoviruses, composed of 6 to 8 segments, hundreds of copies of each segment need to be transmitted to ensure that at least one copy of each segment was present in the host. These estimations seem to be very high compared to the size of the bottlenecks measured with other viruses. Here, we estimated the bottleneck size during one infection cycle of FBNSV, an octopartite nanovirus. We show that these bottlenecks are always narrow (few viral particles) and slightly widen with the number of transmitting aphids. These results contrast with theoretical predictions and illustrate the fact that a new conceptual framework is probably needed to understand the transmission of highly multipartite viruses.
Published: 2018
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9. Epidemiological and evolutionary management of plant resistance: optimizing the deployment of cultivar mixtures in time and space in agricultural landscapes

Author: Ludovic Mailleret, Benoît Moury, Frédéric Fabre, Elsa Rousseau, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Biological control of artificial ecosystems (BIOCORE), Institut National de la Recherche Agronomique (INRA)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Agence Nationale de la Recherche ('VirAphid' (ANR-10-STRA-0001)), INRA (project 'TakeControl' of the metaprogramme Smach), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), and Fabre, Frédéric
Subjects: agroecosystem, [SDV]Life Sciences [q-bio], prévention des maladies, evolutionary epidemiology, [SPI]Engineering Sciences [physics], durabilité des résistances, landscape epidemiology, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Cultivar, épidémiologie végétale, [MATH]Mathematics [math], pathologie végétale, 2. Zero hunger, résistance variétale, education.field_of_study, mélange de variétés, Ecology, mosaic strategy, disease prevention, rotation des cultures, gène de résistance, agroécosystème, qualitative resistance, Agricultural sciences, heterogeneity of selection, General Agricultural and Biological Sciences, resistance durability, Agricultural landscapes, modèle spatialisé, Landscape epidemiology, Population, Context (language use), Biology, resistance gene, Genetics, education, Ecology, Evolution, Behavior and Systematics, Resistance (ecology), functional connectivity, Original Articles, 15. Life on land, maladie des plantes, Software deployment, rotation strategy, gestion du paysage, évolution génétique des populations, Sciences agricoles, Landscape connectivity, rotation of crops
Abstract: International audience; 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.
Published: 2015
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10. The Number of Target Molecules of the Amplification Step Limits Accuracy and Sensitivity in Ultradeep-Sequencing Viral Population Studies

Author: Stéphane Blanc, Frédéric Fabre, Yannis Michalakis, Romain Gallet, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), Evolution Théorique et Expérimentale (MIVEGEC-ETE), Perturbations, Evolution, Virulence (PEV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), French National Research Funding Agency (ANR) : ANR-14-CE02-0014-01, CNRS, IRD, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD [France-Ouest]), Université de Montpellier (UM), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), and Institut des Sciences de la Vigne et du Vin (ISVV)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Virologie, number of target molecules, Immunology, Population, Computational biology, Microbiology, Genome, DNA sequencing, faba bean, 03 medical and health sciences, FBNSV, Medicago truncatula, next-generation sequencing, rolling-circle amplification, sequencing accuracy, sequencing sensitivity, Virology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, pathologie végétale, education.field_of_study, Genetic diversity, Vegetal Biology, biology, Microbiology and Parasitology, food and beverages, biology.organism_classification, Microbiologie et Parasitologie, Multipartite, 030104 developmental biology, Population bottleneck, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genetic Diversity and Evolution, Rolling circle replication, Insect Science, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Biologie végétale
Abstract: The invention of next-generation sequencing (NGS) techniques marked the coming of a new era in the detection of the genetic diversity of intrahost viral populations. A good understanding of the genetic structure of these populations requires, first, the ability to identify the different isolates or variants and, second, the ability to accurately quantify them. However, the initial amplification step of NGS studies can impose potential quantitative biases, modifying the variant relative frequencies. In particular, the number of target molecules (NTM) used during the amplification step is vastly overlooked although of primary importance, as it sets the limit of the accuracy and sensitivity of the sequencing procedure. In the present article, we investigated quantitative biases in an NGS study of populations of a multipartite single-stranded DNA (ssDNA) virus at different steps of the procedure. We studied 20 independent populations of the ssDNA virus faba bean necrotic stunt virus (FBNSV) in two host plants, Vicia faba and Medicago truncatula . FBNSV is a multipartite virus composed of eight genomic segments, whose specific and host-dependent relative frequencies are defined as the “genome formula.” Our results show a significant distortion of the FBNSV genome formula after the amplification and sequencing steps. We also quantified the genetic bottleneck occurring at the amplification step by documenting the NTM of two genomic segments of FBNSV. We argue that the NTM must be documented and carefully considered when determining the sensitivity and accuracy of data from NGS studies. IMPORTANCE The advent of next-generation sequencing (NGS) techniques now enables study of the genetic diversity of viral populations. A good understanding of the genetic structure of these populations first requires the ability to identify the different isolates or variants and second requires the ability to accurately quantify them. Prior to sequencing, viral genomes need to be amplified, a step that potentially imposes quantitative biases and modifies the viral population structure. In particular, the number of target molecules (NTM) used during the amplification step is of primary importance, as it sets the limit of the accuracy and sensitivity of the sequencing procedure. In this work, we used 20 replicated populations of the multipartite faba bean necrotic stunt virus (FBNSV) to estimate the various limitations of ultradeep-sequencing studies performed on intrahost viral populations. We report quantitative biases during rolling-circle amplification and the NTM of two genomic segments of FBNSV.
Published: 2017
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11. Molecular and biological characterization of two potyviruses infecting lettuce in southeastern France

Author: Brigitte Maisonneuve, Pauline Millot, Frédéric Fabre, Alexandra Schoeny, Karine Berthier, Karine Nozeran, Vincent Simon, Cécile Desbiez, Benoît Moury, Mark Tepfer, Hervé Lecoq, Catherine Wipf-Scheibel, Gregory Girardot, Charlotte Chandeysson, Isabelle Bornard, Eric Verdin, Patrick Gognalons, Hervé Lot, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Génétique et Amélioration des Fruits et Légumes (GAFL), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, SPE department of INRA, Station de Pathologie Végétale (AVI-PATHO), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), and Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE)
Subjects: 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Lactuca spp, sud est france, host range, Lactuca, Plant Science, Horticulture, Asteraceae, culture légumière de plein champ, caractérisation moléculaire, resistance, 03 medical and health sciences, Cichorium endivia, caractérisation biologique, laitue, phytopathogenic virus, potyvirus, Botany, Genetics, aphid transmission, Turnip mosaic virus, Lactuca perennis, transmission par vecteur, pathologie végétale, virus phytopathogène, Lactuca virosa, biology, fungi, Potyvirus, Lactuca serriola, food and beverages, biology.organism_classification, 030112 virology, Lactuca saligna, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, lettuce, résistance génétique, Agronomy and Crop Science
Abstract: International audience; Several potyviruses affect lettuce (Lactuca sativa) and chicory (Cichorium spp.) crops worldwide and are important constraints for production because of the direct losses that they induce and/or because of their seed transmission. Here, the molecular and biological properties are described of two potyviruses that were recently isolated from lettuce plants showing mosaic or strong necrotic symptoms in an experimental field in southeastern France. The first potyvirus belongs to the species Endive necrotic mosaic virus and is present in a large number of wild plant species, especially Tragopogon pratensis. It is unable to infect lettuce cultivars with a resistance to Turnip mosaic virus that is present in many European cultivars and probably conferred by the Tu gene. The second potyvirus belongs to the tentative species lettuce Italian necrotic virus and was not observed in wild plants. It infected all tested lettuce cultivars. Wild accessions of Lactuca serriola, Lactuca saligna, Lactuca virosa and Lactuca perennis were identified as resistant to one or the other potyvirus and could be used for resistance breeding in lettuce. No resistance against these two potyviruses was observed in the tested Cichorium endivia cultivars. In contrast, all tested Cichorium intybus cultivars or accessions were resistant.
Published: 2017
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12. Vectors as motors (of virus evolution)

Author: Benoît Moury, Frédéric Fabre, Fabre, Frédéric, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), and Unité de Pathologie Végétale (PV)
Subjects: 0301 basic medicine, moustique, Biodiversité et Ecologie, Virologie, selection, virus, Biology, Dengue virus, medicine.disease_cause, Virus, Biodiversity and Ecology, 03 medical and health sciences, Genetic drift, Virology, Genotype, evolution, medicine, évolution des populations, Vector (molecular biology), Selection (genetic algorithm), vecteur de virus, Genetics, Genetic diversity, 030102 biochemistry & molecular biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], dengue, humanities, 3. Good health, 030104 developmental biology, Viral evolution, genetic drift, revue d'article, parameter estimation, effective population size
Abstract: International audience; A recommendation of: Lequime S, Fontaine A, Gouilh MA, Moltini-Conclois I and Lambrechts L. 2016. Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes. PloS Genetics 12: e1006111 doi: 10.1371/journal.pgen.1006111
Published: 2017
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13. Mosaics often outperform pyramids: insights from a model comparing strategies for the deployment of plant resistance genes against viruses in agricultural landscapes

Author: Frédéric Fabre, Ramsès Djidjou-Demasse, Benoît Moury, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), CIVB project ‘Recherche, expérimentation, études et outils’, European Project: 609398, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), and Station de Pathologie Végétale (AVI-PATHO)
Subjects: 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Physiology, échelle du paysage, Plant Science, Plant Viruses, landscape epidemiology, pyramids of plant resistance, regional deployment strategy, stratégie de lutte, épidémiologie végétale, pathologie végétale, Disease Resistance, 2. Zero hunger, Ecology, durabilité des méthodes de lutte, food and beverages, Agriculture, gène de résistance, agricultural landscape, Host-Pathogen Interactions, Regression Analysis, Seasons, résistance génétique, Agricultural landscapes, Landscape epidemiology, Plant disease resistance, Biology, Genes, Plant, modelling, 03 medical and health sciences, phytopathogenic virus, resistance gene, Plant virus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Computer Simulation, Gene, Plant Diseases, modélisation, paysage agricole, virus phytopathogène, Resistance (ecology), Models, Theoretical, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, major resistance gene, 030104 developmental biology, Evolutionary biology, Software deployment, durable disease resistance, évolution génétique des populations, mosaic of plant resistance, Landscape connectivity
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.
Published: 2017
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14. Temporal niche differentiation of parasites sharing the same plant host: oak powdery mildew as a case study

Author: Marie-Laure Desprez-Loustau, Ludovic Mailleret, Frédéric Fabre, Frédéric Hamelin, Anne Bisson, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Institut des Sciences de la Vigne et du Vin (ISVV)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut National de la Recherche Agronomique (INRA), Biological control of artificial ecosystems (BIOCORE), Institut National de la Recherche Agronomique (INRA)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), ANR‐13‐BSV7‐0011, Agence Nationale de la Recherche, Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), ANR-13-BSV7-0011,FunFit,Une approche basée sur les traits d'histoire de vie des champignons phytopathogènes pour faire le lien entre fitness individuelle et stratégies écologiques.(2013), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), and Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, media_common.quotation_subject, Population, Niche, 010603 evolutionary biology, 01 natural sciences, Competition (biology), Erysiphe alphitoides, Competitive exclusion principle, lcsh:QH540-549.5, semidiscrete model, coexistence, semi-discrete model, pathogen, epidemiology, trade-off, seasonality, trade‐off, education, Ecology, Evolution, Behavior and Systematics, media_common, education.field_of_study, Ecology, biology, Host (biology), Niche differentiation, périodicité, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, épidémiologie, lcsh:Ecology, Powdery mildew, 010606 plant biology & botany, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Plant diseases are often caused by complexes of closely related parasite species. The coexistence of species sharing the same niche challenges the competitive exclusion principle. Here we performed the mathematical analysis of a generic model of sibling parasite species coexistence based on seasonality. We showed that coexistence through temporal niche partitioning is biologically plausible as it occurred in a significant part of the parameter space of the model. Moreover, the reversal of species relative frequencies (i.e. the most frequent species at the beginning of the season becoming the last frequent at the end) can occur without compromising the long%term coexistence of the two species. We provided data showing that this reversal pattern does repeat over years in the case of two sibling species responsible for oak powdery mildew (Erysiphe alphitoides and Erysiphe quercicola) in Europe. Last, the model was fitted to the data and satisfactorily described the population dynamics of oak powdery mildew species. The seasonal succession of these two plant pathogen species provides one of the few examples of coexistence by temporal niche partitioning at the scale of the season caused by exploitative competition. We discuss whether evolutionary branching may have led to temporal niche differentiation in this system.
Published: 2016
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15. Hierarchical Bayesian Modelling of plant colonisation by winged aphids: Inferring dispersal processes by linking aerial and field count data

Author: Charles-Antoine Dedryver, Frédéric Fabre, Etienne Rivot, Maurice Hullé, Manuel Plantegenest, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, Integrated pest management, sitobion-avenae f, Field mortality, Population, state-space models, 010603 evolutionary biology, 01 natural sciences, Rhopalosiphum padi, rothamsted insect survey, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, animal, cherry-oat aphid, education, rhopalosiphum-padi l, Suction trap, Rhopalosiphum, education.field_of_study, Aphid, biology, Ecology, Ecological Modeling, population-dynamics, Aphididae, Dispersal, biology.organism_classification, risk-a, 010602 entomology, Biological dispersal, padi, movement
Abstract: Understanding and modelling insect pest dispersal is an important prerequisite for designing integrated pest management programs. Nevertheless, studies investigating the dispersal of small insects in natural conditions remain scarce mainly because of the difficulty of tracking the movements of these organisms. Here we propose to use Hierarchical Bayesian Modelling (HBM) framework to gain knowledge on hidden processes that cannot be observed directly in natura, such as insect landing and insect mortality, through the definition of latent variables. An HBM describing crop colonization by winged aphids was fitted to a large dataset of field observations issued from a long term survey at a wide scale of both aerial and field densities of the bird cherry-oat aphid Rhopalosiphum padi. This study provides the first evidence that suction trap data are reliable proxies of aphid colonizing rates in cereal fields in autumn and can be a nice alternative to the very time-consuming crop sampling. The proportion of winged aphids landing in cereal fields is shown to vary between regions according to the degree of investment of local R. padi population in sexual reproduction. Results also indicate that under autumnal field conditions, less than 5% of winged aphids survive more than 10 days after landing. This HBM provides the basis of a predictive model for aphid crop colonization that fully accounts for all sources of uncertainty. It should be of great value to improve the trust of users in any decision making systems.
Published: 2010
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16. Molecular, biological and serological variability ofZucchini yellow mosaic virusin Tunisia

Author: S. Yakoubi, Mohamed Marrakchi, Cécile Desbiez, Catherine Wipf-Scheibel, Hervé Lecoq, Hatem Fakhfakh, Frédéric Fabre, Michel Pitrat, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM)-Université de Tunis El Manar (UTM), Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), and Génétique et Amélioration des Fruits et Légumes (GAFL)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, Serotype, PHYLOGENY, Plant Science, Horticulture, ZYMV, 01 natural sciences, Virus, 03 medical and health sciences, Phylogenetics, CITROUILLE, Genetics, MULTIPLE COMPONENT ANALYSIS, ZUCCHINI YELLOW MOSAIC VIRUS, CUCURBITS, RELATION HOTE-PARASITE, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Zucchini yellow mosaic virus, biology, Potyviridae, Potyvirus, RNA virus, biology.organism_classification, Virology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, PATHOTYPE, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, SYMPTOMATOLOGY, SEROTYPE, Agronomy and Crop Science, 010606 plant biology & botany, Squash
Abstract: International audience; A study was conducted to better understand the population structure of Zucchini yellow mosaic virus (ZYMV), a severe virus affecting cucurbit crops worldwide, in Tunisia and to estimate whether the use of resistant cultivars may provide durable control. Analysis of the polymerase and coat protein (NIb-CP) partial sequences of 83 isolates collected in the three main cucurbit-growing areas in Tunisia showed that ZYMV grouped into two distinct clusters within ZYMV molecular group A. An important variability was observed in the MREK motif of the P3 protein, a motif associated with tolerance breaking in ZYMV-tolerant zucchini squash cultivars. Interestingly, significant differences were found in the distribution of the MREK variants in the two clusters defined by the partial NIb-CP sequences, MREK and MKEK sequences being more common in cluster 1 and cluster 2, respectively. When combining NIb-CP and P3 sequence information, ZYMV molecular variability was shown to be significantly higher in the Cap Bon region than in the Bizerte area. An important biological variability was observed in a subset of 23 isolates regarding symptomatology in susceptible or resistant cucurbits. Some isolates overcame ZYMV tolerance or resistance in zucchini squash and melon, but not in cucumber. Three serotypes were differentiated using a set of 13 monoclonal antibodies (MAbs). Seven parameters characterizing the 23 isolates, including molecular, serological and biological properties, were used for a multiple component analysis (MCA). This analysis revealed that symptom intensity of a given isolate was similar in different susceptible cucurbit hosts, suggesting similar degrees of aggressiveness in different hosts.
Published: 2008
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17. Adaptation of a plant pathogen to partial host resistance: selection for greater aggressiveness in grapevine downy mildew

Author: Frédéric Fabre, François Delmotte, Isabelle D. Mazet, Jérôme Jolivet, Laurent Delière, Chloé E. L. Delmas, Sylvie Richart Cervera, Santé et agroécologie du vignoble (UMR SAVE), and Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)
Subjects: 0301 basic medicine, quantitative resistance, caractère phénotypique, [SDV]Life Sciences [q-bio], fitness cost, Quantitative trait locus, différenciation génétique, evolvability, plante résistante, 03 medical and health sciences, Botany, Genetics, mildiou de la vigne, inoculation, host specificity, erosion, obligate plant pathogen, virulence, Vitis vinifera, Pathogen, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, biology, Directional selection, Host (biology), Phenotypic trait, Original Articles, gestion durable, biology.organism_classification, 030104 developmental biology, extraction d'adn, Plasmopara viticola, Downy mildew, Original Article, Adaptation, General Agricultural and Biological Sciences, agent pathogène
Abstract: International audience; An understanding of the evolution of pathogen quantitative traits in response to host selective pressures is essential for the development of durable management strategies for resistant crops. However, we still lack experimental data on the effects of partial host resistance on multiple phenotypic traits (aggressiveness) and evolutionary strategies in pathogens. We performed a cross-inoculation experiment with four grapevine hosts and 103 isolates of grapevine downy mildew (Plasmopara viticola) sampled from susceptible and partially resistant grapevine varieties. We analysed the neutral and adaptive genetic differentiation of five quantitative traits relating to pathogen transmission. Isolates from resistant hosts were more aggressive than isolates from susceptible hosts, as they had a shorter latency period and higher levels of spore production. This pattern of adaptation contrasted with the lack of neutral genetic differentiation, providing evidence for directional selection. No specificity for a particular host variety was detected. Adapted isolates had traits that were advantageous on all resistant varieties. There was no fitness cost associated with this genetic adaptation, but several trade-offs between pathogen traits were observed. These results should improve the accuracy of prediction of fitness trajectories for this biotrophic pathogen, an essential element for the modelling of durable deployment strategies for resistant varieties.
Published: 2015
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18. Effects of climate and land use on the occurrence of viruliferous aphids and the epidemiology of barley yellow dwarf disease

Author: Frédéric Fabre, Lucie Mieuzet, Emmanuel Jacquot, Charles Antoine Dedryver, Manuel Plantegenest, Jean-Luc Leterrier, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Bayer SAS, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Homoptera, virus, 01 natural sciences, Crop, 03 medical and health sciences, céréale, rhopalosiphum padi, Disease management (agriculture), Rhopalosiphum padi, jaunisse nanisanté de l'orge, épidémiologie végétale, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 2. Zero hunger, virus phytopathogène, 0303 health sciences, Aphid, climat, Ecology, biology, protection intégrée, food and beverages, Aphididae, 15. Life on land, biology.organism_classification, Agronomy, puceron, Barley yellow dwarf, Animal Science and Zoology, Hordeum vulgare, BYD-PAV, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Barley yellow dwarf (BYD) disease is one of the most severe viral diseases in autumn sown cereals. In Western Europe, crop losses are mainly due to the PAV species of BYD viruses transmitted by Rhopalosiphum padi, the most abundant aphid in autumn. The proportion of migrant winged aphids that carry viruses in autumn is considered a major epidemiological factor for determining the disease incidence. In the main French cereal areas, during a 6-week period in autumn 1999-2002, the proportion of viruliferous R. padi assessed using a TAS-ELISA technique was on average of 4.98% (range 2.01-9.91%). Variations according to trap location were correlated with land use at the regional scale, annual variations being correlated with the climate of the year. Implementations of these results to improve BYD disease management program are discussed.
Published: 2005
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19. Aphid Abundance on Cereals in Autumn Predicts Yield Losses Caused by Barley yellow dwarf virus

Author: Manuel Plantegenest, Frédéric Fabre, Charles-Antoine Dedryver, J L Leterrier, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Bayer SAS, and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: BARLEY YELLOW DWARF VIRUS, 0106 biological sciences, Integrated pest management, hordeum vulgare, BYDV, Phytopathology and phytopharmacy, plante céréaliere, Homoptera, Population, virus, Plant Science, orge, HEMIPTERA, 01 natural sciences, APHIDIDAE, Rhopalosiphum padi, education, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, virus phytopathogène, Aphid, education.field_of_study, INTEGRATED PEST MANAGEMENT, biology, aide à la décision, prévision des risques, protection intégrée, Aphididae, RHOPALOSIPHUM PADI, biology.organism_classification, Phytopathologie et phytopharmacie, VIRUS EPIDEMIOLOGY, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, dynamique des populations, 010602 entomology, Agronomy, Barley yellow dwarf, probabilité, Hordeum vulgare, Agronomy and Crop Science, analyse de risque, 010606 plant biology & botany
Abstract: Barley yellow dwarf virus (BYDV) damage to winter cereals and population dynamics of the aphid Rhopalosiphum padi during fall were monitored in fields during 10 years at various locations in the northern half of France. Logistic regression was used to examine whether a simple risk probability algorithm based only on the autumnal population dynamics of R. padi can accurately predict yield losses caused by BYDV and, therefore, the need for insecticide treatment. Results showed that the area under the curve of the percentage of plants infested by R. padi during autumn was highly significantly related to BYDV yield losses. Then, a cost/benefit analysis was performed to estimate the optimal decision threshold resulting in the lowest annual average costs of BYDV damage and control. A “model use” strategy allowed a reduction in the annual average costs of BYDV disease and control of up to 36% when compared with a “prophylactic spraying” strategy. The optimal decision threshold was highly sensitive to variation in disease prevalence. This property was used to propose an easy way to adapt the model to any production situation through the determination of the most accurate decision threshold.
Published: 2003
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20. Improvement of Barley yellow dwarf virus-PAV detection in single aphids using a fluorescent real time RT-PCR

Author: Aude Vialatte, Lucie Mieuzet, Frédéric Fabre, Christine Kervarrec, Emmanuel Jacquot, Gérard Riault, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: BARLEY YELLOW DWARF VIRUS, 0106 biological sciences, plante céréaliere, Virologie, 01 natural sciences, BYDV-PAV, VIRULIFEROUS APHIDS, Plant Viruses, TAQMAN PROBE, Taq Polymerase, REAL-TIME PCR, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Aphid, biology, Reverse Transcriptase Polymerase Chain Reaction, food and beverages, 3. Good health, Reverse transcription polymerase chain reaction, méthode de détection, Real-time polymerase chain reaction, Barley yellow dwarf, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Viral, insecte vecteur, acide nucléique, hordeum vulgare, Molecular Sequence Data, RT-PCR, Enzyme-Linked Immunosorbent Assay, virus, Luteoviridae, orge, Sensitivity and Specificity, Virus, 03 medical and health sciences, VIRUS QUANTITATION, Virology, Luteovirus, TaqMan, Animals, Fluorescent Dyes, Plant Diseases, 030304 developmental biology, virus phytopathogène, Base Sequence, Hordeum, biology.organism_classification, Molecular biology, Aphids, Nucleic acid, 010606 plant biology & botany
Abstract: One of the major factors determining the incidence of Barley yellow dwarf virus (BYDV) on autumn-sown cereals is the viruliferous state of immigrant winged aphids. This variable is assessed routinely using the enzyme-linked immunosorbant assay (ELISA). However, the threshold for virus detection by ELISA can lead to false negative results for aphids carrying less than 10(6) particles. Although molecular detection techniques enabling the detection of lower virus quantities in samples are available, the relatively laborious sample preparation and data analysis have restricted their use in routine applications. A gel-free real-time one-step reverse transcription polymerase chain reaction (RT-PCR) protocol is described for specific detection and quantitation of BYDV-PAV, the most widespread BYDV species in Western Europe. This new assay, based on TaqMan technology, detects and quantifies from 10(2) to 10(8) BYDV-PAV RNA copies. This test is 10 and 10(3) times more sensitive than the standard RT-PCR and ELISA assays published previously for BYDV-PAV detection and significantly improves virus detection in single aphids. Extraction of nucleic acids from aphids using either phenol/chloroform or chelatin resin-based protocols allow the use of pooled samples or of a small part (up to 1/1600th) of a single aphid extract for efficient BYDV-PAV detection.
Published: 2003
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21. Interaction pattern between Potato virus Y and eIF4E-mediated recessive resistance in the Solanaceae

Author: Alain Palloix, Mekki Ben Khalifa, Bérenger Janzac, Youna Ruellan, Frédéric Fabre, Benoît Moury, Vincent Simon, Hatem Fakhfakh, Moury, Benoit, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Génétique et Amélioration des Fruits et Légumes (GAFL), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM)-Université de Tunis El Manar (UTM), Institut Supérieur de Biotechnologie, SYSTERRA program of the Agence Nationale de la Recherche, French-Tunisian PHC Utique bilateral project (10G0905), and Maladies Infectieuses Emergentes interdisciplinary program of the Centre National de la Recherche Scientifique.
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, méthode du matching, Potyvirus, Immunology, distribution spatio temporelle, Adaptation, Biological, solanaceae, medicine.disease_cause, Microbiology, Host Specificity, Virus, Virology, Genotype, medicine, Allele, pathologie végétale, Infectivity, résistance variétale, Mutation, pouvoir pathogène, virus phytopathogène, biology, mélange de variétés, Host (biology), durabilité des méthodes de lutte, biology.organism_classification, gène de résistance, maladie des plantes, virus y de la pomme de terre, rotation culturale, Agricultural sciences, Eukaryotic Initiation Factor-4E, Genetic Diversity and Evolution, Potato virus Y, Protein Biosynthesis, Insect Science, Host-Pathogen Interactions, interaction gène pour gène, Sciences agricoles, mutation virale
Abstract: The structural pattern of infectivity matrices, which contains infection data resulting from inoculations of a set of hosts by a set of parasites, is a key parameter for our understanding of biological interactions and their evolution. This pattern determines the evolution of parasite pathogenicity and host resistance, the spatiotemporal distribution of host and parasite genotypes, and the efficiency of disease control strategies. Two major patterns have been proposed for plant-virus genotype infectivity matrices. In the gene-for-gene model, infectivity matrices show a nested pattern, where the host ranges of specialist virus genotypes are subsets of the host ranges of less specialized viruses. In contrast, in the matching-allele (MA) model, each virus genotype is specialized to infect one (or a small set of) host genotype(s). The corresponding infectivity matrix shows a modular pattern where infection is frequent for plants and viruses belonging to the same module but rare for those belonging to different modules. We analyzed the structure of infectivity matrices between Potato virus Y (PVY) and plant genotypes in the family Solanaceae carrying different eukaryotic initiation factor 4E (eIF4E)-coding alleles conferring recessive resistance. Whereas this system corresponds mechanistically to an MA model, the expected modular pattern was rejected based on our experimental data. This was mostly because PVY mutations involved in adaptation to a particular plant genotype displayed frequent pleiotropic effects, conferring simultaneously an adaptation to additional plant genotypes with different eIF4E alleles. Such effects should be taken into account for the design of strategies of sustainable control of PVY through plant varietal mixtures or rotations. IMPORTANCE The interaction pattern between host and virus genotypes has important consequences on their respective evolution and on issues regarding the application of disease control strategies. We found that the structure of the interaction between Potato virus Y (PVY) variants and host plants in the family Solanaceae departs significantly from the current model of interaction considered for these organisms because of frequent pleiotropic effects of virus mutations. These mutational effects allow the virus to expand rapidly its range of host plant genotypes, make it very difficult to predict the effects of mutations in PVY infectivity factors, and raise concerns about strategies of sustainable management of plant genetic resistance to viruses.
Published: 2014
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22. Narrow Bottlenecks Affect Pea Seedborne Mosaic Virus Populations during Vertical Seed Transmission but not during Leaf Colonization

Author: Vincent Simon, Frédéric Fabre, Benoît Moury, Mireille Jacquemond, Elisabeth Johansen, Rachid Senoussi, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), University of Copenhagen = Københavns Universitet (KU), Biostatistique et Processus Spatiaux (BioSP), INRA (Institut National de la Recherche Agronomique), Fabre, Frédéric, and Moury, Benoit
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Potyvirus, modèle stochastique, plante fourragère legumineuse, Transmission of plant viruses, bottlenecks, Biology (General), pisum sativum, 2. Zero hunger, 0303 health sciences, dérive génétique, food and beverages, Agricultural sciences, fitness, transmission par la graine, Viral evolution, Seeds, Horizontal transmission, Research Article, particule virale, transmission verticale, QH301-705.5, Immunology, taille de la population, Biology, Microbiology, Virus, 03 medical and health sciences, Genetic drift, transmission de virus, Virology, Plant virus, Botany, Genetics, colonisation foliaire, Molecular Biology, Plant Diseases, 030304 developmental biology, virus phytopathogène, Mosaic virus, 030306 microbiology, Peas, RC581-607, biology.organism_classification, maladie des plantes, virulence, Plant Leaves, Agronomy, évolution génétique des populations, Parasitology, Immunologic diseases. Allergy, Sciences agricoles
Abstract: The effective size of populations (Ne) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Populations having high Ne adapt faster, as selection acts more intensely, than populations having low Ne, where random effects of genetic drift dominate. Estimating Ne for various steps of plant virus life cycle has been the focus of several studies in the last decade, but no estimates are available for the vertical transmission of plant viruses, although virus seed transmission is economically significant in at least 18% of plant viruses in at least one plant species. Here we study the co-dynamics of two variants of Pea seedborne mosaic virus (PSbMV) colonizing leaves of pea plants (Pisum sativum L.) during the whole flowering period, and their subsequent transmission to plant progeny through seeds. Whereas classical estimators of Ne could be used for leaf infection at the systemic level, as virus variants were equally competitive, dedicated stochastic models were needed to estimate Ne during vertical transmission. Very little genetic drift was observed during the infection of apical leaves, with Ne values ranging from 59 to 216. In contrast, a very drastic genetic drift was observed during vertical transmission, with an average number of infectious virus particles contributing to the infection of a seedling from an infected mother plant close to one. A simple model of vertical transmission, assuming a cumulative action of virus infectious particles and a virus density threshold required for vertical transmission to occur fitted the experimental data very satisfactorily. This study reveals that vertically-transmitted viruses endure bottlenecks as narrow as those imposed by horizontal transmission. These bottlenecks are likely to slow down virus adaptation and could decrease virus fitness and virulence., Author Summary Short generation times and high mutation rates are the hallmarks of virus. They favor their fast adaptation as illustrated by their ability to overcome natural as well as man-made barriers such as host resistance or drug treatments. However, such a fast adaptation could be slowed down when genetic drift, which introduces random sampling effects in the evolution of virus populations, is important. Whether genetic drift or selection dominates depends on the effective size of populations (Ne). Ne has been estimated for several steps of plant virus infectious cycle, such as horizontal transmission by insects and the colonization of plant cells and tissues. However, although economically important, no estimate of Ne during vertical transmission of viruses, i.e. the infection of plant progenies from parental plants, is available. Here, we report that Pea seedborne mosaic virus (PSbMV), a seed transmitted virus infecting pea crops, undergoes very drastic genetic drift during vertical transmission, with an average number of infectious virus particles contributing to the infection of a seedling from an infected mother plant close to one. Such bottlenecks, as narrow as those imposed by horizontal transmission, could slow down virus adaptation and should be taken into account to improve plant protection strategies.
Published: 2014
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23. High throughput quantitative phenotyping of plant resistance using chlorophyll fluorescence image analysis

Author: Charles Manceau, Céline Rousseau, Marie-Agnès Jacques, Etienne Belin, Jacky Guillaumes, Romain Berruyer, Frédéric Fabre, Tristan Boureau, David Rousseau, Edouard Bove, Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratoire d'Ingéniérie des Systèmes Automatisés (LISA), Université d'Angers (UA), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Laboratoire de la santé des végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), This work was supported by Angers Loire Métropole, Conseil Général Département de Maine-et-Loire and Région Pays de la Loire (Phenotic) and by Institut National de la Recherche Agronomique and Région Pays de la Loire., Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de Pathologie Végétale (PV), Boureau, Tristan, BMC, Ed., Laboratoire de santé des végétaux (LSV Angers), Laboratoire de la santé des végétaux (LSV), and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, détection de la maladie, fluorescence chlorophyllienne, Plant Science, Bioinformatics, 01 natural sciences, pixel, résistance des plantes aux agents pathogènes, Contrast (vision), Segmentation, logiciel r, Throughput (business), Chlorophyll fluorescence, media_common, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 0303 health sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], résistance quantitative, mise au point de technique, Thresholding, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Agricultural sciences, automatisation, Biotechnology, notation des maladies, media_common.quotation_subject, Biology, analyse d'image, Image (mathematics), 03 medical and health sciences, Genetics, Cluster analysis, imagerie quantitative, 030304 developmental biology, modélisation, bactérie phytopathogène, Pixel, business.industry, imagerie in vivo, méthode de quantification, Methodology, Pattern recognition, phaseolus vulgaris, maladie des plantes, Artificial intelligence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, xanthomonas fuscans, Sciences agricoles, 010606 plant biology & botany
Abstract: Background: In order to select for quantitative plant resistance to pathogens, high throughput approaches that can precisely quantify disease severity are needed. Automation and use of calibrated image analysis should provide more accurate, objective and faster analyses than visual assessments. In contrast to conventional visible imaging, chlorophyll fluorescence imaging is not sensitive to environmental light variations and provides single-channel images prone to a segmentation analysis by simple thresholding approaches. Among the various parameters used in chlorophyll fluorescence imaging, the maximum quantum yield of photosystem II photochemistry (Fv/Fm) is well adapted to phenotyping disease severity. Fv/Fm is an indicator of plant stress that displays a robust contrast between infected and healthy tissues. In the present paper, we aimed at the segmentation of Fv/Fm images to quantify disease severity., Results: Based on the Fv/Fm values of each pixel of the image, a thresholding approach was developed to delimit diseased areas. A first step consisted in setting up thresholds to reproduce visual observations by trained raters of symptoms caused by Xanthomonas fuscans subsp. fuscans (Xff) CFBP4834-R on Phaseolus vulgaris cv. Flavert. In order to develop a thresholding approach valuable on any cultivars or species, a second step was based on modeling pixel-wise Fv/Fm-distributions as mixtures of Gaussian distributions. Such a modeling may discriminate various stages of the symptom development but over-weights artifacts that can occur on mock-inoculated samples. Therefore, we developed a thresholding approach based on the probability of misclassification of a healthy pixel. Then, a clustering step is performed on the diseased areas to discriminate between various stages of alteration of plant tissues. Notably, the use of chlorophyll fluorescence imaging could detect pre-symptomatic area. The interest of this image analysis procedure for assessing the levels of quantitative resistance is illustrated with the quantitation of disease severity on five commercial varieties of bean inoculated with Xff CFBP4834-R., Conclusions: In this paper, we describe an image analysis procedure for quantifying the leaf area impacted by the pathogen. In a perspective of high throughput phenotyping, the procedure was automated with the software R downloadable at http://www.r-project.org/. The R script is available at http://lisa.univ-angers.fr/PHENOTIC/telechargements.html.
Published: 2013
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24. Modelling the evolutionary dynamics of viruses within their hosts: a case study using high-throughput sequencing

Author: Benoît Moury, Frédéric Fabre, Rachid Senoussi, Josselin Montarry, Jérôme Coville, Vincent Simon, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), UR0407, Pathologie Végétale, Santé des plantes et environnement, Centre de Recherche PACA, Biostatistique et Processus Spatiaux (BIOSP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Biostatistique et Processus Spatiaux (BioSP), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, SELECTION, [SDV]Life Sciences [q-bio], POTATO VIRUS Y, PVY, GENETIC DRIFT, CLONE, PEPPER, INTRA-HOST VIRUS DYNAMIC, RELATION HOTE-PARASITE, Potyvirus, Population Modeling, Population genetics, 01 natural sciences, piment, Natural Selection, épidémiologie végétale, lcsh:QH301-705.5, Genetics, évolution biologique, 0303 health sciences, education.field_of_study, Natural selection, Statistics, Agriculture, dynamique des populations, Viral evolution, capsicum, Research Article, lcsh:Immunologic diseases. Allergy, Evolutionary Processes, séquence nucleique, Immunology, Population, virus, Biostatistics, Biology, Models, Biological, Microbiology, Evolution, Molecular, 03 medical and health sciences, Integrated Control, Genetic drift, Effective Population Size, Virology, Tobacco, Evolutionary Modeling, Evolutionary dynamics, education, Molecular Biology, Selection (genetic algorithm), Plant Diseases, 030304 developmental biology, modélisation, Evolutionary Biology, virus phytopathogène, Computational Biology, Sustainable Agriculture, lcsh:Biology (General), Nonlinear Dynamics, Epistasis, Parasitology, Pest Control, mutation, lcsh:RC581-607, Infectious Disease Modeling, Population Genetics, Mathematics, 010606 plant biology & botany
Abstract: Uncovering how natural selection and genetic drift shape the evolutionary dynamics of virus populations within their hosts can pave the way to a better understanding of virus emergence. Mathematical models already play a leading role in these studies and are intended to predict future emergences. Here, using high-throughput sequencing, we analyzed the within-host population dynamics of four Potato virus Y (PVY) variants differing at most by two substitutions involved in pathogenicity properties. Model selection procedures were used to compare experimental results to six hypotheses regarding competitiveness and intensity of genetic drift experienced by viruses during host plant colonization. Results indicated that the frequencies of variants were well described using Lotka-Volterra models where the competition coefficients βij exerted by variant j on variant i are equal to their fitness ratio, rj/ri. Statistical inference allowed the estimation of the effect of each mutation on fitness, revealing slight (s = −0.45%) and high (s = −13.2%) fitness costs and a negative epistasis between them. Results also indicated that only 1 to 4 infectious units initiated the population of one apical leaf. The between-host variances of the variant frequencies were described using Dirichlet-multinomial distributions whose scale parameters, closely related to the fixation index F ST, were shown to vary with time. The genetic differentiation of virus populations among plants increased from 0 to 10 days post-inoculation and then decreased until 35 days. Overall, this study showed that mathematical models can accurately describe both selection and genetic drift processes shaping the evolutionary dynamics of viruses within their hosts., Author Summary Natural selection and genetic drift drive the evolution of virus populations within their hosts and therefore influence strongly virus emergences. To help predict future virus emergences, we developed a model that estimates simultaneously genetic drift and selection intensities using high-throughput sequence data representing the within-host population dynamics of Potato virus Y variants differing at most by two substitutions involved in pathogenicity properties. The competitiveness costs induced by these mutations as well as the mathematical expressions of the competition coefficients of virus variants were derived from Lotka–Volterra equations. High genetic differentiation of virus populations between hosts was evidenced as well as its hump-shaped behaviour with time. The modelling framework proposed here was intended to help design control strategies aiming to prevent virus emergences.
Published: 2012
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25. Durable strategies to deploy plant resistance in agricultural landscapes

Author: Ludovic Mailleret, Elsa Rousseau, Benoît Moury, Frédéric Fabre, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Unité Recherches Intégrées en Horticulture (URIH), Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Biological control of artificial ecosystems (BIOCORE), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Societe Francaise de Phytopathologie (SFP). Paris, FRA., Station de Pathologie Végétale (AVI-PATHO), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM)
Subjects: 0106 biological sciences, EVOLUTIONARY EPIDEMIOLOGY, Physiology, Virologie, Biodiversité et Ecologie, [SDV]Life Sciences [q-bio], Plant Science, 01 natural sciences, Plant Viruses, [SPI]Engineering Sciences [physics], durabilité des résistances, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, réservoir de pathogènes, ComputingMilieux_COMPUTERSANDEDUCATION, Cultivar, DURABLE RESISTANCE, épidémiologie végétale, Disease Resistance, 2. Zero hunger, 0303 health sciences, Agroforestry, aménagement du territoire, food and beverages, Agriculture, Viral Load, gène de résistance, dynamique des populations, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, DEPLOYMENT STRATEGY, GENE FOR GENE MODEL, LANDSCAPE EPIDEMIOLOGY, aménagement paysager, résistance durable, Landscape planning, résistance aux maladies, Crops, Agricultural, Landscape epidemiology, Phytopathology and phytopharmacy, GeneralLiterature_INTRODUCTORYANDSURVEY, Context (language use), virus, Biology, ressource génétique, Models, Biological, Biodiversity and Ecology, 03 medical and health sciences, modèle mathématique, InformationSystems_MODELSANDPRINCIPLES, [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], Disease management (agriculture), Virology, Plant virus, pratique culturale, 030304 developmental biology, modélisation, virus phytopathogène, Resistance (ecology), ComputingMilieux_THECOMPUTINGPROFESSION, business.industry, 15. Life on land, Phytopathologie et phytopharmacie, Biotechnology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, stomatognathic diseases, gestion du paysage, mutation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 010606 plant biology & botany, Landscape connectivity
Abstract: International audience; The deployment of resistant crops often leads to the emergence of resistance-breaking pathogens that suppress the yield benefit provided by the resistance. Here, we theoretically explored how farmers' main leverages (resistant cultivar choice, resistance deployment strategy, landscape planning and cultural practices) can be best combined to achieve resistance durability while minimizing yield losses as a result of plant viruses. Assuming a gene-for-gene type of interaction, virus epidemics are modelled in a landscape composed of a mosaic of resistant and susceptible fields, subjected to seasonality, and a reservoir hosting viruses year-round. The model links the genetic and the epidemiological processes, shaping at nested scales the demogenetic dynamics of viruses. The choice of the resistance gene (characterized by the equilibrium frequency of the resistance-breaking virus at mutation-selection balance in a susceptible plant) is the most influential leverage of action. Our results showed that optimal strategies of resistance deployment range from 'mixture' (where susceptible and resistant cultivars coexist) to 'pure' strategies (with only resistant cultivar) depending on the resistance characteristics and the epidemiological context (epidemic incidence and landscape connectivity). We demonstrate and discuss gaps concerning virus epidemiology across the agro-ecological interface that must be filled to achieve sustainable disease management.
Published: 2012
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26. Variability of Botrytis cinerea sensitivity to pyrrolnitrin, an antibiotic produced by biological control agents

Author: Marc Bardin, Pierre Leroux, Sakhr Ajouz, Anne-Sophie Walker, Frédéric Fabre, Philippe C. Nicot, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Pathologie Végétale (PV), French National Research Agency (ANR-ADD ECOSERRE), Syrian government, and Bardin, Marc
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, DURABILITY, résistance aux antibiotiques, champignon phytopathogène, lutte biologique, BASELINE, 01 natural sciences, Microbiology, tomate, chemistry.chemical_compound, AGRESSIVENESS, Botany, résistance aux pesticides, Spore germination, EC50, Botrytis cinerea, biology, fongicide, fungi, durabilité, biology.organism_classification, Pseudomonas chlororaphis, MULTIPLE-DRUG RESISTANCE, 3. Good health, botrytis, Multiple drug resistance, 010602 entomology, Pyrrolnitrin, chemistry, Animal ecology, plante légumière, Insect Science, lycopersicon esculentum, PSEUDOMONAS CHLORORAPHIS, Agronomy and Crop Science, Bacteria, 010606 plant biology & botany, BIOLOGICAL CONTROL
Abstract: To establish a baseline sensitivity of Botrytis cinerea to pyrrolnitrin, an antibiotic produced by several biological control agents, 204 isolates were tested for sensitivity to pyrrolnitrin using a spore germination assay. The results showed that the isolates exhibited a wide range of sensitivity to pyrrolnitrin, with an 8.4-fold difference in EC50 (effective concentration to reduce spore germination by 50% comparing to the control) values between the least and the most sensitive isolates. The model-based clustering analysis indicates that the distribution of the EC50 values best fit a normal mixture model with three components and unequal variance. The less sensitive isolates were also multidrug resistant isolates. The efficacy of the pyrrolnitrin-producing Pseudomonas chlororaphis ChPhzS24 strain was tested in vitro and on tomato plants with isolates of B. cinerea having different EC50 values. Whatever the EC50 value of the isolates tested, no significant differences in sensitivity were observed towards this bacterium indicating an absence of resistance to this biological control agent within B. cinerea isolates and suggesting also that additional mechanisms of action are probably operated by this biological control agent.
Published: 2011
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27. Search for factors involved in the rapid shift in watermelon mosaic virus (WMV) populations in south-eastern France

Author: B. Joannon, Alexandra Schoeny, Hervé Lecoq, Cécile Desbiez, Catherine Wipf-Scheibel, Charlotte Chandeysson, Frédéric Fabre, Lecoq, Herve, Unité de Pathologie Végétale (PV), and Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, displacement, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Cancer Research, Virologie, spread, Disease Vectors, 01 natural sciences, émergence, potyvirus, déplacement, propagation, aphid transmission, melon, souche, immunologie, épidémiologie végétale, courgette, évolution biologique, 0303 health sciences, Aphid, biologie des populations, mixed infection, host range, cross protection, emergence, complex plant pathogen, leaf curl virus, transmission, strains, variability, competition, biology, sérum, Potyvirus, Agricultural sciences, Phylogeography, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, France, food.ingredient, séquence nucleique, Phytopathology and phytopharmacy, Ranunculus sardous, virus, cucumis melo, provence alpes côte d'azur, Virus, Host Specificity, 03 medical and health sciences, food, Cucurbita, vecteur de maladies, Virology, Genetic variation, Animals, Watermelon mosaic virus, 030304 developmental biology, Plant Diseases, cucurbita pepo, virus phytopathogène, interaction plante pathogène, Potyviridae, Genetic Variation, biology.organism_classification, Phytopathologie et phytopharmacie, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Aphids, plante légumière, compétition, Sciences agricoles, 010606 plant biology & botany
Abstract: International audience; Watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) was reported for the first time in France in 1974, and it is now the most prevalent virus in cucurbit crops. In 2000, new strains referred as ‘emerging’ (EM) strains were detected in South-eastern France. EM strains are generally more severe and phylogenetically distinct from those previously reported in this country and referred as ‘classic’ (CL) strains. Since 2000, EM strains have been progressively replacing CL strains in several areas where they co-exist. In order to explain this rapid shift in virus populations, the biological properties of a set of 17 CL and EM WMV isolates were compared. No major differences were observed when comparing a limited host range including 48 different plant species or cultivars. Only two species were differential; Chenopodium quinoa was systemically infected by CL and not by EM isolates whereas Ranunculus sardous was systemically infected by EM and not by CL isolates. A considerable variability was observed in aphid transmission efficiencies but this could not be correlated to the CL or EM types. Two subsets of five isolates of each group were used to compare aphid transmission efficiencies from single and double (CL–EM) infections using six different cucurbit and non-cucurbit hosts. EM isolates were generally better transmitted from mixed CL–EM infections than CL isolates and CL transmission rates were significantly lower from double than from single infections. Cross-protection was only partial between CL and EM strains leading to frequent double infections, and only a slight asymmetry was observed in cross-protection efficiencies. Since double infections occur very commonly in fields, the preferential transmission of EM from mixed CL–EM infections could be one of the factors leading to the displacement of CL isolates by EM isolates.
Published: 2011
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28. The conflicting relationships between aphids and men: a review of aphid damage and control strategies

Author: Charles-Antoine Dedryver, Frédéric Fabre, Anne Le Ralec, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, Integrated pest management, Insecticides, PRELEVEMENT DE SEVE, Biological pest control, 01 natural sciences, PLANT REACTION, BYDD, MESH: Plant Diseases, MESH: Insect Control, MESH: Pest Control, Biological, MESH: Animals, Economic impact analysis, PLANT RESISTANCE, 2. Zero hunger, Aphid, JAUNISSE NANISANTE DE L'ORGE, Ecology, biology, MESH: Plant Physiological Phenomena, food and beverages, Agriculture, Aphididae, General Medicine, INSECTICIDE, General Agricultural and Biological Sciences, MESH: Aphids, MESH: Agriculture, BIOLOGICAL CONTROL, Crops, Agricultural, MESH: Ecology, PLANTE RESISTANCE, REACTIONS DE LA PLANTE, Insect Control, General Biochemistry, Genetics and Molecular Biology, Animals, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Agricultural productivity, Pest Control, Biological, Plant Physiological Phenomena, Plant Diseases, SIEVE DRAIN, MESH: Humans, General Immunology and Microbiology, business.industry, Pest control, biology.organism_classification, MESH: Crops, Agricultural, Biotechnology, MESH: Insecticides, 010602 entomology, Agronomy, Aphids, IPM, business, 010606 plant biology & botany
Abstract: In this review, after giving some figures on the economic impact of aphids on agricultural production, we describe the different mechanisms leading to yield losses (direct damage due to sieve drain and plant reaction, indirect damage, often the most important, due to virus transmission). Then, after a history of chemical control and of its limits, the main control strategies (chemical control with decision rules, plant resistance, biological control, farming practices) are reviewed in the light of an integrated pest management approach. Several topics tackled in this article are exemplified for cereal aphids, which are among the most important in Europe as direct feeders and virus vectors.
Published: 2010
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29. Asymmetrical over-infection as a process of plant virus emergence

Author: Joël Chadœuf, Frédéric Fabre, Hervé Lecoq, Caroline Costa, Cécile Desbiez, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), and Biostatistique et Processus Spatiaux (BioSP)
Subjects: 0106 biological sciences, Statistics and Probability, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, food.ingredient, Epidemiology, Secondary infection, Potyvirus, Biology, 01 natural sciences, Models, Biological, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, food, Cucurbita, Species Specificity, Plant virus, Computer Simulation, Landscape, Watermelon mosaic virus, 030304 developmental biology, Plant Diseases, 0303 health sciences, General Immunology and Microbiology, Strain (chemistry), Ecology, Applied Mathematics, State-space model, General Medicine, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Evolutionary biology, Modeling and Simulation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, France, General Agricultural and Biological Sciences, Biological invasion, 010606 plant biology & botany
Abstract: International audience; Disentangling the role of epidemiological factors in plant pathogen emergences is a prerequisite to identify the most likely future invaders. An example of emergence was recently observed in France: in 10 years, "classic" (CL) strains of virus (WMV) were displaced at a regional scale by newly introduced "emerging" (EM) strains. Here we analyse a 3 years dataset describing the co-dynamics of CL and EM strains at field scale using state-space models estimating jointly (i) probabilities of primary and secondary infection and (ii) probabilities of over-infecting with a CL [EM] strain a plant already infected with an EM [CL] strain. Results especially indicate that it is more than 3 times less probable for a CL strain to over-infect an EM infected plant than for an EM strain to over-infect a CL infected plant. To investigate if these asymmetric interactions can explain the CL/EM shift observed at regional scale, an exploratory model describing WMV epidemiology over several years in a landscape composed of a reservoir and a cultivated compartment is introduced. In most simulations a shift is observed and both strains do coexist in the landscape, reaching an equilibrium that depends on the probabilities of over-infection.
Published: 2010
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30. Molecular epidemiology of Zucchini yellow mosaic virus in France: an historical overview

Author: Frédéric Fabre, Cécile Desbiez, A. Lê Van, Charlotte Chandeysson, Hervé Lecoq, Catherine Wipf-Scheibel, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), and Unité de recherche Pathologie végétale et phytobactériologie
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Cancer Research, Molecular Sequence Data, Potyvirus, 01 natural sciences, Genome, ZYMV, Virus, 03 medical and health sciences, Cucurbita, Phylogenetics, MOLECULAR EPIDEMIOLOGY, Virology, Plant virus, ZUCCHINI YELLOW MOSAIC VIRUS, Overwintering, Phylogeny, 030304 developmental biology, Plant Diseases, Genetics, 0303 health sciences, Zucchini yellow mosaic virus, biology, Molecular epidemiology, Haplotype, biology.organism_classification, 3. Good health, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, France, HAPLOTYPES, 010606 plant biology & botany
Abstract: International audience; Cucurbit viruses are involved in complex and changing pathosystems in France, with new virus strains or species regularly reported. Zucchini yellow mosaic virus (ZYMV) is an archetypal emerging virus that was reported in France in 1979. It has since caused sporadic but occasionally very severe economic losses and its epidemiology still remains poorly understood. Partial sequencing of the viral genome has been used to characterize ZYMV isolates that occurred over a 29-year period in experimental plots at Montfavet, France (n = 227), or that were received through a national survey for cucurbit viruses conducted in France from 2004 to 2007 (n = 198). A total of 34 haplotypes were differentiated belonging to five molecular groups, three including isolates already described in France and two corresponding to isolates that emerged in France within the last 5 years. Comparison of haplotypes found at one location during successive years revealed contrasting situations. When they were either the same or closely related haplotypes, this suggested the availability of overwintering hosts, whereas when they belonged to different molecular groups this indicated shifts in viral populations with possible new introductions. The contribution of molecular epidemiology in tracing the origin of ZYMV in the French West Indies is also reviewed
Published: 2009
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31. Comparative whitefly transmission of tomato chlorosis virus and tomato infectious chlorosis virus from single or mixed infections

Author: Laurent Guilbaud, Frédéric Fabre, Hervé Lecoq, Anne Dalmon, Mireille Jacquemond, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Abeilles et Environnement (AE), and Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU)
Subjects: 0106 biological sciences, ALEYRODIDAE, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Homoptera, TICV, BEMISIA TABACI, Trialeurodes, Plant Science, Whitefly, Horticulture, 01 natural sciences, HEMIPTERA, Virus, TOCV, 03 medical and health sciences, Crinivirus, Plant virus, Genetics, GENERALIZED LINEAR MIXED MODEL, TRIALEURODES ABUTILONEA, Closteroviridae, 030304 developmental biology, 0303 health sciences, biology, food and beverages, RNA virus, RELATION VIRUS-VECTEUR, biology.organism_classification, Virology, TRIALEURODES VAPORARIORUM, TRANSMISSION PROBABILITIES, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, CLOSTEROVIRIDAE, TOMATO INFECTIOUS CHLOROSIS VIRUS, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, TOMATO, CRINIVIRUS, Agronomy and Crop Science, TOMATO CHLOROSIS VIRUS, 010606 plant biology & botany
Abstract: International audience; Tomato chlorosis virus (ToCV) and Tomato infectious chlorosis virus (TICV) are two criniviruses that are emerging worldwide, and induce similar yellowing diseases in tomato crops. While TICV is transmitted only by Trialeurodes vaporariorum, ToCV is transmitted by three whitefly species in two genera Trialeurodes vaporariorum, T. abutilonea and Bemisia tabaci. The efficiency of transmission by T. vaporariorum from plants infected by one virus or by both was compared, and the probability of virus transmission by a single whitefly was derived from group testing experiments. The estimated transmission probabilities ranged from 0·01 to 0·13, and were not significantly different between ToCV and TICV, or between single and mixed infections. Experiments using B. tabaci as a vector and source plants infected by TICV and ToCV did not reveal any functional trans-complementation for transmission of TICV by ToCV, suggesting that if this phenomenon occurs in nature, it is at a very low frequency. Possible reasons why TICV did not establish in southern France while ToCV is now endemic are discussed
Published: 2009
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32. Constraints on evolution of virus avirulence factors predict the durability of corresponding plant resistances

Author: Alain Palloix, Benoît Moury, Bérenger Janzac, Frédéric Fabre, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), and Unité de Pathologie Végétale (PV)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV]Life Sciences [q-bio], Plant Science, 01 natural sciences, Plant Viruses, Long period, Databases, Genetic, DISEASE RESISTANCE, DURABLE RESISTANCE, AVIRULENCE FACTORS, ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, Vegetal Biology, food and beverages, Agricultural sciences, résistance durable, AVIRULENCE FACTOR, résistance aux maladies, Phytopathology and phytopharmacy, Virulence Factors, Soil Science, virus, Plant disease resistance, Biology, Genes, Plant, Virus, PLANT VIRUS INTERACTIONS, Evolution, Molecular, 03 medical and health sciences, Plant virus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, Gene, 030304 developmental biology, Plant Diseases, RELATION HOTE-PARASITE, virus phytopathogène, Resistance (ecology), business.industry, Original Articles, Durability, Phytopathologie et phytopharmacie, Immunity, Innate, Biotechnology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, plante légumière, business, Agronomy and Crop Science, Function (biology), Biologie végétale, Sciences agricoles, 010606 plant biology & botany
Abstract: International audience; Understanding the factors driving pathogen emergence and re-emergence is a major challenge, particularly in agriculture, where the use of resistant plant cultivars imposes strong selective pressures on plant pathogen populations and leads frequently to 'resistance breakdown'. Presently, durable resistances are only identified after a long period of large-scale cultivation of resistant cultivars. We propose a new predictor of the durability of plant resistance. Because resistance breakdown involves modifications in the avirulence factors of pathogens, we tested for correlations between the evolutionary constraints acting on avirulence factors or their diversity and the durability of the corresponding resistance genes in the case of plant–virus interactions. An analysis performed on 20 virus species–resistance gene combinations revealed that the selective constraints applied on amino acid substitutions in virus avirulence factors correlate with the observed durability of the corresponding resistance genes. On the basis of this result, a model predicting the potential durability of resistance genes as a function of the selective constraints applied on the corresponding avirulence factors is proposed to help breeders to select the most durable resistance genes
Published: 2008
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33. Estimation of the number of virus particles transmitted by an insect vector

Author: Benoît Moury, Rachid Senoussi, Frédéric Fabre, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), and Biostatistique et Processus Spatiaux (BioSP)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, viruses, Virologie, Potyvirus, APHID, 01 natural sciences, law.invention, modèle stochastique, law, épidémiologie végétale, 0303 health sciences, education.field_of_study, Multidisciplinary, biology, Virulence, food and beverages, Biological Sciences, compétition virale, Agricultural sciences, dynamique des populations, Transmission (mechanics), Potato virus Y, Virus Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses, Horizontal transmission, Phytopathology and phytopharmacy, Population, virus, Virus, NONPERSISTENT VIRUS, 03 medical and health sciences, vecteur de maladies, Plant virus, Virology, dérivé génétique, Animals, population virale, education, 030304 developmental biology, Plant Diseases, Solanum tuberosum, virus phytopathogène, Host (biology), GENETIC DRIFT, POPULATION BOTTLENECK, POTYVIRUS, transmission virale, biology.organism_classification, Phytopathologie et phytopharmacie, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Insect Vectors, Aphids, Sciences agricoles, 010606 plant biology & botany
Abstract: Plant viruses are submitted to narrow population bottlenecks both during infection of their hosts and during horizontal transmission between host individuals. The size of bottlenecks exerted on virus populations during plant invasion has been estimated in a few pathosystems but is not addressed yet for horizontal transmission. Using competition for aphid transmission between two Potato virus Y variants, one of them being noninfectious but equally transmissible, we obtained estimates of the size of bottlenecks exerted on an insect-borne virus during its horizontal transmission. We found that an aphid transmitted on average 0.5–3.2 virus particles, which is extremely low compared with the census viral population into a plant. Such narrow bottlenecks emphasize the strength of stochastic events acting on virus populations, and we illustrate, in modeling virus emergence, why estimating this parameter is important.
Published: 2007
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34. Biological properties and relative fitness of inter-subgroup cucumber mosaic virus RNA 3 recombinants produced in vitro

Author: Laurent Guilbaud, Mireille Jacquemond, Mark Tepfer, Olivier Pierrugues, Frédéric Fabre, Isabelle Fernandez-Delmond, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Laboratoire de biologie cellulaire et moléculaire, and International Centre for Genetic Engineering and Biotechnology (ICGEB)
Subjects: DNA, Complementary, RT-PCR, Virus, CUCUMBER MOSAIC VIRUS, Plant Viruses, Cucumber mosaic virus, 03 medical and health sciences, Virology, Tobacco, Movement protein, Cloning, Molecular, Gene, 030304 developmental biology, Plant Diseases, Genetics, Recombination, Genetic, 0303 health sciences, biology, CUCUMOVIRUS, 030306 microbiology, RECOMBINAISON GENETIQUE, CMV, RNA, Cucumovirus, Genetic Variation, biology.organism_classification, 3. Good health, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Plant Leaves, Capsid, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Viral, GENETIC DIVERSITY, Bromoviridae, Plasmids
Abstract: In vitro reverse transcription of a mixture of total RNA from plants infected with the I17F or R strains of cucumber mosaic virus (CMV), representative of subgroups IA and II, respectively, results in viral cDNA populations including rare recombinant RNA 3 molecules, some of which also have point mutations. The biological properties of 17 recombinants in the capsid gene or the 3′ non-coding region of RNA 3 were evaluated when associated with I17F RNAs 1 and 2. Six viruses displayed deficiencies (non-viability, deficiencies for movement and/or replication, delayed infection, loss of aphid transmissibility). Nine induced symptoms close to those of I17F-CMV on tobacco and pepper plants. All recombinants bearing the movement protein (MP) of R-CMV and part or most of the capsid protein (CP) of I17F-CMV, as well as the recombinant created in vitro by exchanging the corresponding open reading frames, also induced filiformism on tobacco, but induced only faint symptoms on melon. Two recombinants induced atypically severe symptoms on both tobacco and pepper. Most of the recombinants generally accumulated to lower levels than the wild-type I17F strain in tobacco. Three recombinants, however, including one responsible for severe symptoms, accumulated to generally higher levels than I17F-CMV. When two of these were tested in co-infection experiments with I17F RNA 3, they proved to be poorly competitive, suggesting that they would be unlikely to emerge in the field.
Published: 2007
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35. Financial benefit of using crop protection decision rules over systematic spraying strategies

Author: Jonathan Yuen, Manuel Plantegenest, Frédéric Fabre, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences (SLU), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: 0106 biological sciences, AGENT PHYTOPATHOGENE, Phytopathology and phytopharmacy, LUTTE INTEGREE, CONTROL STRATEGIES, ROC CURVE, INTEGRATED CROP PROTECTION, DECISION SUPPORT SYSTEM, ANALYSE COUT BENEFICE, ECONOMIC ADVANTAGE, COURBE ROC, CONTROLE, Decision tree, Plant Science, Biology, 01 natural sciences, prévision de rendement, 03 medical and health sciences, économie de la production, Business decision mapping, Average cost, modélisation, 030304 developmental biology, Finance, stratégie, 0303 health sciences, business.industry, aide à la décision, prévision des risques, Evidential reasoning approach, Decision rule, Phytopathologie et phytopharmacie, innovation, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Quantitative analysis (finance), indicateur, business, Agronomy and Crop Science, 010606 plant biology & botany, Optimal decision, Decision analysis
Abstract: Fabre, F., Plantegenest, M., and Yuen, J. 2007. Financial benefit of using crop protection decision rules over systematic spraying strategies. Phytopathology 97:1484-1490. Decision rule models are considered to be one of the main cornerstones of the implementation of integrated pest management (IPM) programs. Even if the need for such programs to offer cost advantages over conventional strategies is a major incentive for IPM adoption, few studies focus on this financial dimension. In this article, a modeling approach of the response of a pathosystem to a disease control method and of the predictive performance of decision rules is used to explore how some basic factors act on the likelihood of adoption of decision rule models strategies (such as using an IPM system) over systematic strategies (such as systematic-spraying and never-spraying strategies). Even if the average cost of using the decision rule strategies is always lower than the average cost of systematic strategies in several different scenarios, the models developed here showed strong effects of different pathosystems and decision rules on financial benefits. The number of production situations where decision rules are of interest is highly correlated with their accuracy. However, because of the inescapable trade-offs between decision rule accuracy and limiting factors such as its user-friendly characteristics, the use of decision rules is unlikely to reduce costs to
Published: 2007
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36. Landscape epidemiology of plant diseases

Author: Christophe Le May, Frédéric Fabre, Manuel Plantegenest, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Landscape epidemiology, Biomedical Engineering, Biophysics, Bioengineering, Review, Biology, 010603 evolutionary biology, 01 natural sciences, Biochemistry, Plant Viruses, Biomaterials, Pesticides, Demography, Plant Diseases, 2. Zero hunger, Bacteria, Ecology, Landscape structure, Technological change, Agriculture, 15. Life on land, Biological Evolution, Spatial heterogeneity, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Spatial ecology, Biological dispersal, Landscape ecology, Agricultural landscapes, 010606 plant biology & botany, Biotechnology
Abstract: International audience; Many agricultural landscapes are characterized by a high degree of heterogeneity and fragmentation. Landscape ecology focuses on the influence of habitat heterogeneity in space and time on ecological processes. Landscape epidemiology aims at applying concepts and approaches originating from landscape ecology to the study of pathogen dynamics at the landscape scale. However, despite the strong influence that the landscape properties may have on the spread of plant diseases, landscape epidemiology has still received little attention from plant pathologists. Some recent methodological and technological progress provides new and powerful tools to describe and analyse the spatial patterns of host–pathogen interactions. Here, we review some important topics in plant pathology that may benefit from a landscape perspective. These include the influence of: landscape composition on the global inoculum pressure; landscape heterogeneity on pathogen dynamics; landscape structure on pathogen dispersal; and landscape properties on the emergence of pathogens and on their evolution.
Published: 2007
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37. Tracing individual movements of aphids reveals preferential routes of population transfers in agroecosystems

Author: Manuel Plantegenest, Charles-Antoine Dedryver, Aude Vialatte, Jean-Christophe Simon, Frédéric Fabre, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Integrated pest management, Crops, Agricultural, Sitobion avenae, stable-isotope ratios, [SDV]Life Sciences [q-bio], Population, Population biology, Biology, Zea mays, Crop, aphid movement, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Animals, education, Ecosystem, RELATION HOTE-PARASITE, 2. Zero hunger, education.field_of_study, insect migration, landscape ecology, Ecology, Host (biology), [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, INSECTE, pest management, Habitat, Agronomy, Aphids, Insect migration, host specialization, land-use changes
Abstract: International audience; Agricultural pests are not restricted to crops, but often simultaneously or successively use different cultivated and uncultivated hosts. Nevertheless, the source-sink role of cultivated and uncultivated habitats in the life cycle of crop pests remains poorly understood. This is largely due to the difficulty of tracking displacements of small organisms in agricultural landscapes. We used stable-isotope ratios in order to infer the natal host plant of individuals of the English grain aphid Sitobion avenae colonizing wheat fields in autumn. We showed that among the numerous plant sources of S. avenae, maize, which has been intensively grown in western France since the 1960s, provided most aphids that attack wheat fields early in autumn. This study illustrates how insect pests respond to land-use changes within a relatively short period of time, rapidly acquiring a new host that in turn affected their population biology considerably by playing a pivotal role on their annual life cycle
Published: 2006

38. Barley yellow dwarf disease risk assessment based on Bayesian modelling of aphid population dynamics

Author: Frédéric Fabre, Charles-Antoine Dedryver, Jean-Sébastien Pierre, Manuel Plantegenest, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Bayer SAS, Ethologie animale et humaine (EthoS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)
Subjects: bioagresseur, 0106 biological sciences, Integrated pest management, Biodiversité et Ecologie, Population, 010603 evolutionary biology, 01 natural sciences, Biodiversity and Ecology, rhopalosiphum padi, Rhopalosiphum padi, RELATION PLANTE-INSECTE, Statistical inference, education, 2. Zero hunger, virus phytopathogène, Aphid, education.field_of_study, biology, Ecology, lutte intégrée, Ecological Modeling, Aphididae, biology.organism_classification, dynamique des populations, bydv, Agronomy, puceron, Barley yellow dwarf, Hordeum vulgare, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: International audience; A stochastic population dynamics model is proposed to improve integrated pest management strategies against the aphid Rhopalosiphum padi, the main Barley yellow dwarf virus (BYDV) vector in winter cereals during autumn in Europe. The model is based on a temperature-dependent simulation of R. padi population dynamics. The model requires a single early assessment of the proportion of plants infested by aphids. To account for sampling errors and for uncertainty caused by the numerous factors acting on aphid population dynamics under field conditions, Bayesian statistical inference was used. The model allows assessment of the probability distribution of the area under the curve of the percentage of plants infested by R. padi during autumn, a predictor of the need for insecticide sprays against BYDV vectors. The accuracy of model predictions was tested on an independent data set collected from 1995 to 1998 in the main French small grain production areas. The use of this model as ! a basis for a user-friendly decision support system improving BYDV management is discussed
Published: 2006
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39. Determinants of host species range in plant viruses

Author: Eugénie Hébrard, Benoît Moury, Rémy Froissart, Frédéric Fabre, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Du gène à l'écosystème (MIVEGEC-GeneSys), Pathogènes, Environnement, Santé Humaine (EPATH), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), MIE (Maladies Infectieuses Emergentes) interdisciplinary programme of CNRS (Centre National de la Recherche Scientifique), Santé et agroécologie du vignoble (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Station de Pathologie Végétale (AVI-PATHO), Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Institut des Sciences de la Vigne et du Vin (ISVV)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut National de la Recherche Agronomique (INRA), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Moury, Benoit, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche pour le Développement (IRD [Réunion]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Subjects: mode de transmission, 0106 biological sciences, 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, bipartite network, genome segmentation, Virologie, viruses, [SDV]Life Sciences [q-bio], Generalist and specialist species, 01 natural sciences, Genome, Plant Viruses, pathologie végétale, Pathogen, vecteur de virus, ComputingMilieux_MISCELLANEOUS, base de données, 2. Zero hunger, Genetics, Infectivity, gamme d'hôtes, espèce nouvelle, Plants, Agricultural sciences, Phenotype, modèle statistique, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, génome viral, taxonomie, vertical transmission, host range, vector, plant virus, Genome, Viral, Biology, 010603 evolutionary biology, Host Specificity, Virus, 03 medical and health sciences, transmission de virus, Virology, Plant virus, emergence de maladies, Plant Diseases, phénotype viral, virus phytopathogène, Host (biology), maladie des plantes, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 030104 developmental biology, Vector (epidemiology), Sciences agricoles
Abstract: International audience; Prediction of pathogen emergence is an important field of research, both in human health and in agronomy. Most studies of pathogen emergence have focused on the ecological or anthropic factors involved rather than on the role of intrinsic pathogen properties. The capacity of pathogens to infect a large set of host species, i.e. to possess a large host range breadth (HRB), is tightly linked to their emergence propensity. Using an extensive plant virus database, we found that four traits related to virus genome or transmission properties were strongly and robustly linked to virus HRB. Broader host ranges were observed for viruses with single-stranded genomes, those with three genome segments and nematode-transmitted viruses. Also, two contrasted groups of seed-transmitted viruses were evidenced. Those with a single-stranded genome had larger HRB than non-seed-transmitted viruses, whereas those with a double-stranded genome (almost exclusively RNA) had an extremely small HRB. From the plant side, the family taxonomic rank appeared as a critical threshold for virus host range, with a highly significant increase in barriers to infection between plant families. Accordingly, the plant–virus infectivity matrix shows a dual structure pattern: a modular pattern mainly due to viruses specialized to infect plants of a given family and a nested pattern due to generalist viruses. These results contribute to a better prediction of virus host jumps and emergence risks.
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