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201 results on '"Station de Pathologie Végétale (AVI-PATHO)"'

101. Joint estimation of effective population size and selection coefficient without neutrel markers: method validation and application to experimental evolution of viruses

Author: Rousseau, Elsa, Moury, B., Mailleret, Ludovic, Senoussi, R., Palloix, A., Simon, V., Grognard, Frédéric, Valiere, S., Fabre, F., 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), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Biostatistique et Processus Spatiaux (BIOSP), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), 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), GeT PlaGe, Genotoul, 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), Unité de Pathologie Végétale (PV), 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), Biostatistique et Processus Spatiaux (BioSP), Génétique et Amélioration des Fruits et Légumes (GAFL), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Département de Génétique Animale [Toulouse], 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), 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 Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SPI]Engineering Sciences [physics], [SDV]Life Sciences [q-bio], [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Experimental evolution studies deserve considerable attention to the estimation of basic evolutionary forces such as selection and genetic drift. With the advent of high-throughput sequencing techniques, these studies gained a renewed attention. However the joint estimation of selection and genetic drift still remain challenging when no neutral markers are available, a common situation with many microbes, such as viruses, due to their small tightly packed genomes.
Published: 2016

102. Genetic drift as a tool to increase the durability of plant qualitative resistance to viruses

Author: Rousseau, Elsa, Bonneault, Mélanie, Fabre, Frédéric, Moury, Benoît, Mailleret, Ludovic, Grognard, Frédéric, 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), Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), 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), 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), 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), 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), 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), 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), and Station de Pathologie Végétale (AVI-PATHO)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SPI]Engineering Sciences [physics], [SDV]Life Sciences [q-bio], [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, fungi, food and beverages, [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Plant qualitative (i.e. total) resistance to viruses is an efficient way of protecting crops, but it is often broken down by the emergence of adapted virus variants, able to infect those resistant plants. This evolutionary phenomenon can occur particularly quickly in monocultures deployed in vast areas. Different strategies have been studied, aiming at increasing the durability of resistant crops, such as the use of multiline cultivars or cultivar mixtures in space and time. Here we study a complementary strategy that can yield interesting results in terms of yield increase and resistance durability. It exploits the evolutionary principles governing virus populations for the management of plant resistance, particularly regarding the effect of genetic drift on the evolution of plant viruses.
Published: 2016

103. Stochastic epidemiological model for the analysis of plant resistance break- down to pathogens subjected to genetic drift

Author: Rousseau, Elsa, Bonneault, Mélanie, Fabre, Frédéric, Moury, Benoît, Mailleret, Ludovic, Grognard, Frédéric, 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), Station de Pathologie Végétale (AVI-PATHO), 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), Santé Végétale (SV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB), 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), Unité de Pathologie Végétale (PV), 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), 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)-Inria Sophia Antipolis - Méditerranée (CRISAM), and ProdInra, Archive Ouverte
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, [STAT.AP]Statistics [stat]/Applications [stat.AP], [STAT.AP] Statistics [stat]/Applications [stat.AP], [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, fungi, food and beverages, [INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering
Abstract: Conférence donnée dans le cadre du mini symposium de ETAMM2016 : Mathematical Modelling, Analysis and Simulations in BiologyConférence donnée dans le cadre du mini symposium de ETAMM2016 : Mathematical Modelling, Analysis and Simulations in Biology; International audience; The deployment of pathogen-resistant crops often leads to the emergence of resistance-breaking pathogens that suppress the yield bene t provided by the resistance. In this work, we analyze if and how a modulation of the genetic drift experienced by the pathogens can slow this emergence down. For that purpose, we consider a crop patch in which a given proportion of the plants carry the qualitative resistance and suppose that genetic drift, which is genetically based, can either be added to the initial infection phases of the resistant or of the susceptible plants in the crop. We develop a stochastic SI model of the crop patch, in which only the number of susceptible and resistant infected plants need to be represented. In that model, the infection events follow a Poisson process and undergo bottleneck induced drift, limiting the probability of infection of a plant by a pathogen.Through intensive simulations of this model with the Gillespie algorithm, we show which model parameters most influence the effciency of the genetic drift for improving crop yield. Also, we analyze which combination of genetic drift level and proportion of resistant plants in the crop most improves crop yield.
Published: 2016

104. Effet de la dérive génétique et de la sélection sur la durabilité de la résistance des plantes aux virus

Author: Rousseau, Elsa, 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), Université Nice Sophia Antipolis, Jean-Luc Gouzé, Benoit Moury, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 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), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Laboratoire d'océanographie de Villefranche (LOV), 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 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), Jean-Luc Gouzé, STAR, ABES, 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), and Unité de Pathologie Végétale (PV)
Subjects: Évolution expérimentale, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SPI.OTHER]Engineering Sciences [physics]/Other, Epidemiology, contournement de la résistance, Durabilité des résistances, Dérive génétique, modèle stochastique, sélection, évolution des populations, these, épidémiologie végétale, pathologie végétale, Selection, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, virus phytopathogène, [SPI.OTHER] Engineering Sciences [physics]/Other, Agricultural sciences, Épidémiologie, Experimental evolution, méthode de lutte, Genetic drift, Resistance durability, sélection variétale, Sciences agricoles, dérive génétique, durabilité des résistances, évolution expérimentale, épidémiologie
Abstract: Une plante peut être totalement protégée d'un agent pathogène grâce à un gène majeur de résistance, mais ce dernier peut être rapidement contourné suite à l'apparition et à la propagation de variants pathogènes adaptés. Cette thèse s'intéresse aux mécanismes évolutifs permettant le ralentissement de ce contournement chez les virus de plantes en agissant sur deux forces évolutives majeures, la dérive génétique et la sélection, depuis le niveau de l'hôte jusqu'à celui de la parcelle. D'abord, un modèle épidémiologique stochastique de type SI au niveau d'une parcelle agricole a montré que la dérive génétique pouvait être particulièrement bénéfique au rendement agricole lorsque l'adaptation du virus au gène majeur induit un coût de fitness intermédiaire dans les plantes sensibles. Ensuite, la conception et la validation d'un modèle basé sur des équations déterministes de Lotka-Volterra et des processus stochastiques Dirichlet-multinomiaux a permis de distinguer les effets de la dérive génétique et ceux de la sélection sur des données temporelles de compétition intra-plante entre variants viraux, et de mettre en évidence le contrôle génétique de ces effets par les plantes. Enfin, une analyse de la corrélation entre ces estimations des intensités de dérive génétique et de sélection et une estimation expérimentale de la durabilité d'un gène majeur a montré qu'une forte dérive génétique lors des stades précoces de l'infection augmentait la durabilité du gène majeur. Ces résultats ouvrent des perspectives pour une gestion plus durable de la résistance des plantes, par la sélection de variétés de plantes induisant une forte dérive génétique sur les populations d'agents pathogènes., Plants can be fully protected from their pathogens when they carry major resistance genes, but the efficiency of these genes is limited by the emergence and spread of adapted, resistance-breaking pathogen variants. This thesis studies how evolutionary forces imposed by the plants on pathogen populations may increase the durability of major resistance genes. Using plant viruses as a biological model, this thesis investigates the effect of genetic drift and selection, from the within-host to the host population level. Firstly, a stochastic epidemiological SI model at the field level showed that genetic drift could be particularly beneficial for crop yield when the fitness cost associated with virus adaptation to resistance was intermediate in susceptible plants. Then, the design and validation of a mechanistic-statistical model based on deterministic Lotka-Volterra equations and stochastic Dirichlet-multinomial processes allowed to disentangle the effects of genetic drift from those of selection on temporal data of within-host competition between virus variants. The intensities of genetic drift and selection acting on virus populations were shown to be controlled genetically by the hosts. Finally, a correlation analysis between these estimations of genetic drift and selection intensities and an experimental estimation of the durability of a major resistance gene showed that strong genetic drift during the early stages of plant infection led to an increase in resistance durability. These results open new perspectives for more durable management of plant resistance, by breeding plant varieties inducing strong genetic drift on pathogen populations.
Published: 2016

105. Tomato response traits to pathogenic Pseudomonas species: Does nitrogen limitation matter?

Author: Christophe Robin, Philippe C. Nicot, Stéphane Adamowicz, Romain Larbat, Jacques Le Bot, Mathilde Royer, Laboratoire Agronomie et Environnement (LAE), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Station de Pathologie Végétale (AVI-PATHO), Unité de Pathologie Végétale (PV), Regional Council of Lorraine (grant 609-2010 'projet emergent'), and Ph.D grant of Mathilde Royer co-funded by INRA (Départe-ment Environnement et Agronomie) and the Regional Council of Lorraine (grant 692-2009)
Subjects: 0106 biological sciences, 0301 basic medicine, Nitrogen, Carbohydrates, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Plant Science, Biology, medicine.disease_cause, 01 natural sciences, 03 medical and health sciences, N limitation, Solanum lycopersicum, Pseudomonas, Botany, Genetics, Pseudomonas syringae, medicine, Pathogen, 2. Zero hunger, Phenylpropanoid, Inoculation, fungi, food and beverages, Pathogenic bacteria, Elicitation, General Medicine, interactions, biology.organism_classification, Tomato-Pseudomonas pathogenic, Pseudomonas corrugata, 030104 developmental biology, PEST analysis, Phenolics, Agronomy and Crop Science, Systemic response, 010606 plant biology & botany
Abstract: International audience; Induced chemical defence is a cost-efficient protective strategy, whereby plants induce the biosynthesis of defence-related compounds only in the case of pest attack. Plant responses that are pathogen specific lower the cost of defence, compared to constitutive defence. As nitrogen availability (N) in the root zone is one of the levers mediating the concentration of defence-related compounds in plants, we investigated its influence on response traits of tomato to two pathogenic bacteria, growing plants hydroponically at low or high N supply. Using two sets of plants for each level of N supply, we inoculated one leaf of one set of plants with Pseudomonas syringae, and inoculated the stem of other set of plants with Pseudomonas corrugata. Tomato response traits (growth, metabolites) were investigated one and twelve days after inoculation. In infected areas, P. syringae decreased carbohydrate concentrations whereas they were increased by P. corrugata. P. syringae mediated a redistribution of carbon within the phenylpropanoid pathway, regardless of N supply: phenolamides, especially caffeoylputrescine, were stimulated, impairing defence-related compounds such as chlorogenic acid. Inoculation of P. syringae produced strong and sustainable systemic responses. By contrast, inoculation of P. corrugata induced local and transient responses. The effects of pathogens on plant growth and leaf gas exchanges appeared to be independant of N supply. This work shows that the same genus of plant pathogens with different infection strategies can mediate contrasted plant responses.
Published: 2016
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106. Ground covers in orchards: reservoirs and potential sources of inoculum of Pseudomonas syringae

Author: Borschinger, Benoit, Parisi, Luciana, Lacroix, Christelle, Chandeysson, Charlotte, Guilbaud, Caroline, Bourgeay, Jean-François, Berge, Odile, Buisson, Elise, Morris, Cindy E., Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Ouest]), Aix Marseille Université (AMU), Unité de Pathologie Végétale (PV), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS). FRA.
Subjects: bactérie phytopathogène, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, structure génétique des populations, écologie microbienne, pseudomonas syringae, sud est france, phytopathogenic bacteria, apricot tree, microbial ecology, verger, orchard, abricotier, réservoir de pathogènes, stone fruit, fruit à noyau, épidémiologie végétale, kiwi, pathologie végétale, source d'inoculum
Abstract: National audience; Blights and cankers of fruit trees caused by Pseudomonas syringae generate significant economic losses worldwide. Given the epiphytic lifestyle of P. syringae orchard ground covers represent a potential source of inoculum of P. syringae for fruit trees. They also represent a reservoir of bacterial diversity that could be beneficial for plant health via natural antagonistic and competitive interactions within the microbial flora. This microbial reservoir could be exploited for the development of ecological engineering practices, specifically the management of ground covers to reduce their negative impact on plant health and in particular as a source of pathogenic strains of P. syringae. Within the species P. syringae there is a very high genetic variability, and strains are distributed into 13 phylogroups (Berge et al., 2014) with very marked differences in pathogenicity among some of these phylogroups. Until now the only method for phylogenetic identification was the sequencing of specific and conserved genes. We have now replaced this with a PCR-based method allowing fast and accurate identification of 9 of the 13 current phylogroups (Borschinger et al., submitted). Here we will present the results of an exploratory study of P. syringae populations hosted by different compartments from 4 kiwifruit and 3 apricot orchards located in the southwest of France. The analysis of the phylogenetic structure of the P. syringae populations isolated from samples of ground cover, buds, leaves, twigs, irrigation water and soil, indicates a very large inter- and intra-orchard variability. Populations are largely constituted by an assembly of strains belonging to different phylogroups. Similarities between the phylogenetic structures of populations, and genetic similarities between strains, from different samples suggests a connection between these different compartments.
Published: 2016

107. Articulating microbiology with disease and community ecology to further understanding of pathogen emergence

Author: Lacroix, Christelle, Borschinger, Benoit, Berge, Odile, Parisi, Luciana, Morris, Cindy E., Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Ouest]), Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS). FRA., Station de Pathologie Végétale (AVI-PATHO), and Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, cycle de l'eau, Biodiversité et Ecologie, phytopathogenic bacteria, microbial ecology, Biodiversity and Ecology, processus atmosphérique, ice nucleating bacteria, emergence de maladies, emergence, pathogenicity, épidémiologie végétale, pathologie végétale, bactérie phytopathogène, écologie microbienne, agronomy, pseudomonas syringae, fungi, microbiology, food and beverages, Agricultural sciences, ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, bactérie glacogène, Sciences agricoles
Abstract: National audience; Anticipating emerging plant infectious diseases (PIDs) and mitigating their impacts on host health are major socio-economic challenges. Accumulating evidence is demonstrating that PID emergence is mediated by multiple processes, including changes specific to micro-organisms, their biotic and abiotic environment and their dissemination both within and outside of agricultural systems. Management of emerging PIDs could benefit from the One Health concept that has greatly facilitated the understanding and management of emerging diseases of humans and animals due to its comprehensive integration of the ecology and biology of pathogens, and land-use considerations. The complex ecology of the bacterial plant pathogen Pseudomonas syringae provides a unique opportunity for developing such an approach for PIDs. This bacteria resides in a wide range of crop and non-crop plants, aquatic environments and in soil organic matter; and its dissemination is linked to the water cycle. P. syringae currently represents a complex of 13 genetic lineages of strains for which molecular tools of detection are available, allowing the analysis of P. syringae population structure. Phenotypic traits are highly variable and are involved in different stages of P. syringae life cycle as an epiphyte, saprophyte, pathogen and biological ice nucleator, an important property that underlies P. synringae role in rain and snow precipitation. For such a ubiquitous micro-organism as P. syringae, strategies of complete eradication are unrealistic. We will present a framework to assess how P. syringae abundance and communities can be regulated in crops in order to limit the emergence and dissemination of pathogenic strains while preserving the beneficial role of this bacteria in atmospheric processes. Specifically, we will test hypotheses on the role of i) trade-offs between phenotypic traits to explain the evolution of aggressiveness, and of ii) biotic (e.g. abundance and diversity of plant communities reservoirs of microbial diversification such as plant ground covers in fruit tree orchards) and abiotic environmental factors in pathogen emergence.
Published: 2016

108. Agrifood systems and the microbial safety of fresh produce: Trade-offs in the wake of increased sustainability

Author: Odile Berge, Pierre Renault, Véronique Broussolle, Annette Bérard, Marc Tchamitchian, Christophe Nguyen-The, Cindy E. Morris, Frédéric Carlin, Julien Brillard, Marc Bardin, Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Avignon Université (AU)-Institut National de la Recherche Agronomique (INRA), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Unité de recherche d'Écodéveloppement (ECODEVELOPPEMENT), Unité de Pathologie Végétale (PV), Nguyen The, Christophe, Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), and Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Food Safety, Natural resource economics, système agroalimentaire, Ingénierie des aliments, Wildlife, human health, Ecosystem services, agriculture biologique, Environmental protection, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Information system, Climate change, Sustainability organizations, Waste Management and Disposal, Risk management, 2. Zero hunger, changement climatique, Agriculture, 04 agricultural and veterinary sciences, santé humaine, Pollution, 6. Clean water, sécurité alimentaire, Organic farming, protection de la biodiversite, Waste water, risque de contamination, Conservation of Natural Resources, Environmental Engineering, Livestock, 030106 microbiology, Food Contamination, évaluation agro environnementale, 12. Responsible consumption, 03 medical and health sciences, fresh product, organic farming, Food engineering, Environmental Chemistry, Ecosystem, global change, business.industry, 15. Life on land, Food safety, stockage post récolte, Foodborne pathogens, Food, 13. Climate action, impact sur l' écosystème, Sustainability, produit frais, Food Microbiology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Business
Abstract: Fresh produce has been a growing cause of food borne outbreaks world-wide prompting the need for safer production practices. Yet fresh produce agrifood systems are diverse and under constraints for more sustainability. We analyze how measures taken to guarantee safety interact with other objectives for sustainability, in light of the diversity of fresh produce agrifood systems. The review is based on the publications at the interface between fresh produce safety and sustainability, with sustainability defined by low environmental impacts, food and nutrition security and healthy life. The paths for more sustainable fresh produce are diverse. They include an increased use of ecosystem services to e.g. favor predators of pests, or to reduce impact of floods, to reduce soil erosion, or to purify run-off waters. In contrast, they also include production systems isolated from the environment. From a socio-economical view, sustainability may imply maintaining small tenures with a higher risk of pathogen contamination. We analyzed the consequences for produce safety by focusing on risks of contamination by water, soil, environment and live stocks. Climate change may increase the constraints and recent knowledge on interactions between produce and human pathogens may bring new solutions. Existing technologies may suffice to resolve some conflicts between ensuring safety of fresh produce and moving towards more sustainability. However, socio-economic constraints of some agri-food systems may prevent their implementation. In addition, current strategies to preserve produce safety are not adapted to systems relying on ecological principles and knowledge is lacking to develop the new risk management approaches that would be needed.
Published: 2016
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109. Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens

Author: Caroline L. Monteil, Leonardos Mageiros, Koji Yahara, Boris A. Vinatzer, Samuel K. Sheppard, Guillaume Méric, Cindy E. Morris, Bryan Swingle, David J. Studholme, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Microbiologie Environnementale et Moléculaire (MEM), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Swansea University, Virginia Tech [Blacksburg], Institute of Life Science, College of Medicine, Swansea University (Dept. of Sports Science), National Institute of Infectious Diseases [Tokyo], Biosciences, The Milner Centre for Evolution, Department of Biology and Biotechnology, University of Bath [Bath], School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University [New York], Department of Plant Pathology, Physiology, and Weed Science [Blacksburg] (PPPWS), Department of Zoology [Oxford], University of Oxford [Oxford], National Science Foundation of the USA, Hatch Program of the National Institute of Food and Agriculture, U.S. Department of Agriculture, Medical Research Council (MRC) grant MR/L015080/1, and the Wellcome Trust grant 088786/C/09/Z, NISCHR Health Research Fellowship, INRA, European Project: 221922, Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), School of Integrative Plant Science [CALS], College of Agriculture and Life Sciences [Cornell University] (CALS), Cornell University [New York]-Cornell University [New York], University of Oxford, Station de Pathologie Végétale (AVI-PATHO), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), National Institute of Infectious Diseases of Tokyo, Cornell University, Vinatzer, Boris A., and Sheppard, Samuel K.
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Phytopathology and phytopharmacy, cycle de l'eau, Biodiversité et Ecologie, Population, Virulence, Pseudomonas syringae, Disease emergence, pathoadaptation, crop diseases, type III secreted effectors, Locus (genetics), Biology, phytopathogenic bacteria, microbial ecology, analyse phylogénétique, 01 natural sciences, Microbiology, habitat non agricole, Biodiversity and Ecology, 03 medical and health sciences, Microbial ecology, genetique des populations, épidémiologie végétale, education, Pathogen, pathologie végétale, 2. Zero hunger, Genetics, bactérie phytopathogène, education.field_of_study, écologie microbienne, Effector, fungi, Outbreak, food and beverages, General Medicine, Phytopathologie et phytopharmacie, Agricultural sciences, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 030104 developmental biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, source d'inoculum, Sciences agricoles, 010606 plant biology & botany
Abstract: Many bacterial pathogens are well characterized but, in some cases, little is known about the populations from which they emerged. This limits understanding of the molecular mechanisms underlying disease. The crop pathogen Pseudomonas syringae sensu lato has been widely isolated from the environment, including wild plants and components of the water cycle, and causes disease in several economically important crops. Here, we compared genome sequences of 45 P. syringae crop pathogen outbreak strains with 69 closely related environmental isolates. Phylogenetic reconstruction revealed that crop pathogens emerged many times independently from environmental populations. Unexpectedly, differences in gene content between environmental populations and outbreak strains were minimal with most virulence genes present in both. However, a genome-wide association study identified a small number of genes, including the type III effector genes hopQ1 and hopD1, to be associated with crop pathogens, but not with environmental populations, suggesting that this small group of genes may play an important role in crop disease emergence. Intriguingly, genome-wide analysis of homologous recombination revealed that the locus Psyr 0346, predicted to encode a protein that confers antibiotic resistance, has been frequently exchanged among lineages and thus may contribute to pathogen fitness. Finally, we found that isolates from diseased crops and from components of the water cycle, collected during the same crop disease epidemic, form a single population. This provides the strongest evidence yet that precipitation and irrigation water are an overlooked inoculum source for disease epidemics caused by P. syringae.
Published: 2016
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110. Mapping averaged pairwise information (MAPI): a new exploratory tool to uncover spatial structure

Author: Julien Papaïx, Bertrand Gauffre, Sylvain Piry, Astrid Cruaud, Karine Berthier, Marie Pierre Chapuis, Piry, Sylvain, Centre de Biologie pour la Gestion des Populations (UMR CBGP), 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)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Pathologie Végétale (PV), COPACABANA project (INRA Metaprogram 'Sustainable Management of Crop Health'), 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), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, cartographie spatiale, ge ne ﬂow, Similarity (geometry), Biodiversité et Ecologie, logiciel, isolation by distance, flux de gènes, computer.software_genre, pairwise information, 010603 evolutionary biology, 01 natural sciences, F30 - Génétique et amélioration des plantes, Biodiversity and Ecology, 03 medical and health sciences, exploratory method, Spatial network, genetique des populations, data base, geovisualisation, Ecology, Evolution, Behavior and Systematics, Mathematics, base de données, spat ial genetics, Ecological Modeling, distribution spatiale, landscape genetics, spatial genetics, isolation-by-distance, barrier, gene flow, GIS, database, 15. Life on land, Grid, Agricultural sciences, 030104 developmental biology, [SDE]Environmental Sciences, Metric (mathematics), visualisation de données, MAPI, Pairwise comparison, Geovisualization, Data mining, U30 - Méthodes de recherche, computer, Sciences agricoles, Geogr aphical Information System, Test data
Abstract: 1.Visualisation of spatial networks based on pairwise metrics such as (dis)similarity coefficients provides direct information on spatial organization of biological systems. However, for large networks, graphical representations are often unreadable as nodes (samples), and edges (links between samples) strongly overlap. We present a new method, MAPI (Mapping Averaged Pairwise Information), allowing translation from spatial networks to variation surfaces.[br/] 2.MAPI relies on i) a spatial network in which samples are linked by ellipses and, ii) a grid of hexagonal cells encompassing the study area. Pairwise metric values are attributed to ellipses and averaged within the cells they intersect. The resulting surface of variation can be displayed as a colour map in Geographical Information System (GIS), along with other relevant layers, such as land cover. The method also allows the identification of significant discontinuity in grid cell values through a nonparametric randomisation procedure.[br/] 3.The interest of MAPI is here demonstrated in the field of spatial and landscape genetics. Using simulated test datasets, as well as observed data from three biological models, we show that MAPI is i) relatively insensitive to confounding effects resulting from isolation-by-distance (i.e. over-structuring), ii) efficient in detecting barriers when they are not too permeable to gene flow and, iii) useful to explore relationships between spatial genetic patterns and landscape features.[br/] 4.MAPI is freely provided as a PostgreSQL/PostGIS database extension allowing easy interaction with GIS or the R software and other programming languages. Although developed for spatial and landscape genetics, the method can also be useful to visualise spatial organisation from other kinds of data from which pairwise metrics can be computed.
Published: 2016
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111. Brown rot strikes Prunus fruit: an ancient fight almost always lost

Author: Isabelle Bornard, Bénédicte Quilot-Turion, Daniele Bassi, Leandro Oliveira Lino, Igor Pacheco, Franco Faoro, Vincent Mercier, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Fundação) = CAPES Foundation [Brasilia] (CAPES), INTA, Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Udine - University of Udine [Italie], Unité Expérimentale Recherches Intégrées - Gotheron (UERI), Unité de Pathologie Végétale (PV), CONICYT, Chile (Post-Doctoral Fellowship 74130043 and Academy Insertion Grant 79140020), European Project: 265582, Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Unité de Recherches Intégrées - Gotheron (GOTH RI UERI), Station de Pathologie Végétale (AVI-PATHO), and Pacheco, Igor
Subjects: 0106 biological sciences, 0301 basic medicine, Germplasm, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Phytopathology and phytopharmacy, monilinia spp, brown rot, prunus, qtl, 01 natural sciences, 03 medical and health sciences, Prunus, Ascomycota, résistance aux agents pathogènes, Botany, monilia, Plant Diseases, 2. Zero hunger, Resistance (ecology), biology, food and beverages, Plant models, General Chemistry, Monilinia, 15. Life on land, biology.organism_classification, Phytopathologie et phytopharmacie, Disease control, Agricultural sciences, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, mécanisme biochimique, Horticulture, 030104 developmental biology, Fruit, Postharvest, Orchard, General Agricultural and Biological Sciences, Sciences agricoles, 010606 plant biology & botany
Abstract: Brown rot (BR) caused by Monilinia spp., has been an economic problem for the stone fruit market due to the dramatic losses, with the biggest losses mainly during the postharvest period. There is much literature about basic aspects of Monilinia spp. infection, which indicates that environment significantly influences its occurrence in the orchard. However, progress is needed to sustainably limit this disease: the pathogen is able to develop resistance to pesticides and most of BR resistance research programs in plant models perish. Solving this problem becomes important due to the need to decrease chemical treatments and reduce residues on fruit. Thus, research has recently increased, exploring a wide range of disease control strategies (e.g. genetic, chemical, physical). Summarizing this information is difficult, as studies evaluate different Monilinia and Prunus model species, with diverse strategies and protocols. Thus, the purpose of this review is to present the diversity and distribution of agents causing BR, focusing on the biochemical mechanisms of Monilinia spp. infection both of the fungi and of the fruit, and report on the resistance sources in Prunus germplasm. In this review, we comprehensively compile the information currently available to better understand mechanisms related to BR resistance.
Published: 2016
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112. Dossier Melon - Préserver le gène Vat

Author: Véronique Bargain, Alexandra Schoeny, Nathalie Boissot, Réussir Fruits et légumes, Partenaires INRAE, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Génétique et Amélioration des Fruits et Légumes (GAFL), Groupe réussir, Station de Pathologie Végétale (AVI-PATHO), and Unité de recherche Génétique et amélioration des fruits et légumes (GALF)
Subjects: résistance variétale, virus phytopathogène, durabilité des résistances, puceron du melon, phytopathogenic virus, méthode de lutte, [SDV]Life Sciences [q-bio], weed control methods, pathologie végétale, gène vat, lutte prophylactique, vecteur de virus, source de résistance
Abstract: Dossier Melon - Préserver le gène Vat
Published: 2016

113. Black rat invasion of inland Sahel: insights from interviews and population genetics in south-western Niger

Author: Raphaël Leblois, Sama Gagaré, Ambroise Dalecky, Anne Loiseau, Sylvain Piry, Philippe Gauthier, Gauthier Dobigny, Karine Berthier, Madougou Garba, Carine Brouat, Miguel Navascués, Caroline Tatard, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Université Abdou Moumouni [Niamey], Direction Générale de la Protection des Végétaux, Ministère de l'Agriculture du Niger, Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), 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)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre Régional AGRHYMET (CRA), Laboratoire Population-Environnement-Développement (LPED), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), partnership agreement (number 301027/00) between IRD and the Republic of Niger, SRC-IRD research bursary for international mobility (2011–2012), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), 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), and Station de Pathologie Végétale (AVI-PATHO)
Subjects: 0106 biological sciences, 0301 basic medicine, Current distribution, [SDE.MCG]Environmental Sciences/Global Changes, Population, Population genetics, 010603 evolutionary biology, 01 natural sciences, Rattus rattus, Interview data, 03 medical and health sciences, trade-mediated invasion, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, biology, Ecology, Propagule pressure, Genetic data, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, 030104 developmental biology, Black rat, Africa, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, urban habitat
Abstract: International audience; Human population migrations, as well as long-distance trade activities, have been responsible for the spread of many invasive organisms. The black rat, Rattus rattus, has colonized most of the world following ship-mediated trade. Owing to its tight association with human infrastructures, this species has been able to survive in unfavourable environments, such as Sahelian Africa. In this work, we combined interview-based and population genetic surveys to investigate the processes underlying the ongoing invasion of southwestern Niger by black rats, with special emphasis on the capital city, Niamey. Our trapping and interview data are quite congruent, and all together point towards a patchy, but rather widespread, current distribution of R. rattus. Genetic data strongly suggest that road network development for truck-based commercial flow from/to international harbours located in neighbouring countries (Benin, Togo, and Nigeria) facilitates the passive dispersal of black rats over a long distance through unfavourable landscapes. Another potentially, more ancient, invasion route may be associated with boat transport along the Niger River. Human-mediated dispersal thus probably allows the foundation of persisting populations within highly anthropized areas while population dynamics may be more unstable in remote areas and mostly depends on propagule pressure.
Published: 2016
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114. Current status of some cucurbit viruses in Cukurova region (Adana and Mersin provinces) of Turkey and molecular characterization of zucchini yellow mosaic virus isolates

Author: Kamberoglu, Muharrem Arap, Caliskan, Asime Filiz, Desbiez, Cecile, Faculty of Agriculture, Department of Plant Protection, Ankara University, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), and Unité de Pathologie Végétale (PV)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Cucurbits, virus phytopathogène, viruses, RT-PCR, ZYMV, culture légumière de plein champ, Molecular characterization, turquie, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, genetique des populations, phytopathogenic virus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, ELISA, épidémiologie végétale, pathologie végétale, détection de virus
Abstract: Surveys were conducted from 2008 to 2010 to identify the viruses infecting cucurbit fields in Adana and Mersin provinces of Cukurova region in Turkey. All cucurbit samples collected from 18 districts were tested for Cucumber mosaic virus (CMV), Cucurbit aphid-borne yellow virus (CABYV), Papaya ringspot virus (PRSV), Squash mosaic virus (SqMV), Zucchini yellow mosaic virus (ZYMV) and Watermelon mosaic virus (WMV) by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) using polyclonal antisera. Overall, 449 out of 485 samples were found positive for the tested viruses; 327 out of 350 samples in Adana and 122 out of 135 in Mersin were infected at least with one virus. During the entire surveys, 258 of 281 squash samples, 33 of 33 cucumber samples, 84 of 88 melon samples and 74 of 83 watermelon samples were found to have a single or mix virus infection. All six viruses were detected on cucurbits in Adana while all samples from Mersin province were found to be negative for CABY. Sequence analyses indicated that the Turkish ZYMV isolates (ZYMV-TR3, ZYMV-TR15 and ZYMV-TR17) belong to the most common molecular cluster of ZYMV worldwide, including isolates from Europe, Africa, the Middle East, the Indian subcontinent and South America.
Published: 2016

115. Characterization and occurrence of squash chlorotic leaf spot virus, a tentative new torradovirus infecting cucurbits in Sudan

Author: Eric Verdin, Mark Tepfer, Catherine Wipf-Scheibel, Hervé Lecoq, G. Dafalla, Pauline Millot, Cécile Desbiez, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Plant Pathology Center, University of Gezira, and Unité de Pathologie Végétale (PV)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Melon, soudan, cucurbitacees, Picornaviridae, Disease Vectors, 01 natural sciences, Sudan, torradovirus, Squash chlorotic leaf spot virus, melon, pathologie végétale, Phylogeny, vecteur de virus, Spots, espèce nouvelle, food and beverages, General Medicine, RNA, Plant, Torradovirus, aleurode, food.ingredient, RT-PCR, Whitefly, Biology, squash, Virus, Hemiptera, 03 medical and health sciences, food, caractérisation biologique, Cucurbita, phytopathogenic virus, Virology, Plant virus, whitefly, Animals, Plant Diseases, new species, virus phytopathogène, SCLSV, biology.organism_classification, Plant Leaves, 030104 developmental biology, next-generation sequencing, 010606 plant biology & botany, Squash
Abstract: During a survey conducted in Sudan in 2012, a virus with spherical particles was isolated from a squash plant showing chlorotic leaf spots. The virus was transmitted mechanically and by two whitefly species, but not by aphids. RT-PCR with generic torradovirus primers yielded a band of expected size from total RNA of a symptomatic plant. Next-generation sequencing confirmed that this is tentatively a new torradovirus, for which we propose the name 'squash chlorotic leaf spot virus'. Using specific RT-PCR primers, the virus was detected in cucurbit samples collected since 1992 at different locations in Sudan.
Published: 2016
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116. Comparison of the development in planta of a pyrrolnitrin-resistant mutant of Botrytis cinerea and its sensitive wild-type parent isolate

Author: Marc Bardin, Mohamed El Maâtaoui, Philippe C. Nicot, Sakhr Ajouz, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Pathologie Végétale, EA 4279 Laboratoire Physiologie des Fruits et Légumes, Avignon Université (AU), Unité de Pathologie Végétale (PV), INRA (SPE project), ANR-05-PADD-0009,EcoSerre,Viabilité des systèmes de cultures protégées dans un contexte d'agriculture durable(2005), and Bardin, Marc
Subjects: 0106 biological sciences, microscopie, [SDV]Life Sciences [q-bio], Mutant, résistance aux antibiotiques, champignon phytopathogène, lutte biologique, Plant Science, Horticulture, Biology, 01 natural sciences, Petiole (botany), Microbiology, Conidium, tomate, 03 medical and health sciences, chemistry.chemical_compound, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, cytologie, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Mycelium, 030304 developmental biology, Botrytis cinerea, évolution biologique, 0303 health sciences, Vegetal Biology, Inoculation, fungi, Wild type, durabilité, food and beverages, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, botrytis, Pyrrolnitrin, chemistry, plante légumière, lycopersicon esculentum, Agronomy and Crop Science, Biologie végétale, 010606 plant biology & botany
Abstract: International audience; Botrytis cinerea is able to build-up resistance to pyrrolnitrin, an antibiotic produced by diverse biocontrol agents, possibly compromising the durability of this method of disease control. The development of two near-isogenic lines of B. cinerea differing in their level of resistance to pyrrolnitrin was compared in tomato plants and on PDA medium. In tomato plants, significant differences in the percentage of infected petioles 1 day after inoculation and in symptom progression on petioles and stems were observed between the resistant mutant and the sensitive wild-type parent, suggesting a difference in their level of aggressiveness. Cytohistological investigations revealed that conidia of both near-isogenic lines germinated 6 h after inoculation and mycelium developed within petiole tissues 12 h after inoculation. However, while the wild-type parent isolate spread throughout the petiole and rapidly invaded the stem tissues via the leaf-abscission zone 72 h after inoculation, the pyrrolnitrin-resistant mutant failed to extend beyond petiole tissues to invade the stem. Moreover, 72 h after inoculation, the mycelial development of the pyrrolnitrin-resistant mutant was accompanied by abnormal glycogen accumulation and chlamydospore-like cell formation. In contrast, wild-type parent mycelium was normally structured with intensive colonization of stem tissues. Additionally, on PDA medium the mycelium of the pyrrolnitrin-resistant mutant was less vigorous than the wild-type isolate. These results suggest that the acquisition of pyrrolnitrin-resistance in B. cinerea is accompanied by changes in mycelial structure and reduction in mycelial growth, leading to a noticeable loss of aggressiveness on tomato plants.
Published: 2010
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117. Joint estimation of the strength of genetic drift and selection from next generation sequencing time-sampled data : a case study on the adaptation of virus populations to host plant resistance

Author: Rousseau, Elsa, Fabre, Frédéric, Coville, Jérôme, Mailleret, Ludovic, Palloix, Alain, Senoussi, Rachid, Moury, Benoît, Grognard, Frédéric, 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), 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), Biostatistique et Processus Spatiaux (BIOSP), Institut National de la Recherche Agronomique (INRA), 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), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Station de Pathologie Végétale (AVI-PATHO), 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), Unité de Pathologie Végétale (PV), 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), 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), Biostatistique et Processus Spatiaux (BioSP), Génétique et Amélioration des Fruits et Légumes (GAFL), Society for molecular biology and evolution (SMBE). Lawrence, USA., 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), 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), and Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, résistance variétale, virus phytopathogène, dérive génétique, [SDV]Life Sciences [q-bio], poivron, culture legumiere, modèle d'évolution, maladie des plantes, virus y de la pomme de terre, Agricultural sciences, durabilité des résistances, [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, évolution génétique des populations, population virale, lutte génétique, pathologie végétale, ComputingMilieux_MISCELLANEOUS, Sciences agricoles
Abstract: National audience
Published: 2015

118. Relationship between Aphis gossypii population dynamics and Cucurbit aphid-borne yellows virus (CABYV) epidemics in melon crops

Author: Alexandra Schoeny, Patrick Gognalons, Catherine Wipf-Scheibel, Pauline Millot, Karine Nozeran, Hervé Lecoq, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Unité de Pathologie Végétale (PV), Réseau Biologie Adaptative des Pucerons et des Organismes Associés (BAPOA). FRA., Aphids Special Interest Group of the Royal Entomological Society. GBR., and ProdInra, Archive Ouverte
Subjects: [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, virus phytopathogène, aphide vecteur, virus de la jaunisse des cucurbitacees, food and beverages, weed control methods, aphis gossypii, culture légumière de plein champ, lutte prophylactique, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, phytopathogenic virus, méthode de lutte, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, melon, épidémiologie végétale, pathologie végétale, [SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, vecteur de virus
Abstract: International audience; The temporal dynamics of alate aphids and viruses were established in eight field trials conducted between 2010 and 2014. Alate aphids visiting melon crops were sampled daily using succion traps and frequently encountered aphid species (Aphis craccivora, Aphis fabae, Aphis gossypii, Myzus persicae) were identified. Persistant Cucurbit aphid-borne yellows virus (CABYV) and non-persistent Cucumber mosaic virus (CMV), Watermelon mosaic virus (WMV) and Zucchini yellow mosaic virus (ZYMV) were monitored weekly by DAS-ELISA. Gompertz model was fitted to each incidence data set by nonlinear regression and AUDPCs (Area Under the Disease Progress Curve) were calculated. A statistical analysis was performed to explore the relationships existing between several “aphid” variables (cumulative abundances over different periods of time, per species or globally) and several “virus” variables (cumulative numbers of infected plants over different periods of time, newly infected plants per week, AUDPCs, disease onset day, Gompertz model parameter estimates). No relationship was highlighted between aphids and non-persistent viruses. More interestingly a predictive relationship was established between Aphis gossypii population dynamics and CABYV epidemics. Indeed, the number of Aphis gossypii trapped between the 14 first days of the crop explained more than 50% of the variability of the CABYV total AUDPC. This result suggests that controlling precociously the population of Aphis gossypii could impact favourably the epidemic onset and progress of this virus in melon crops.
Published: 2015

119. Amino acids as orobanchicides: an innovative approach for biocontrol broomrape weeds

Author: Fernandez-Aparicio, Monica, Gibot-Leclerc, Stéphanie, Moreau, Delphine, Steinberg, Christian, Bohan, David A., Chauvel, Bruno, Bernard, Alexandre, Marget, Pascal, Falchetto, Laurent, Farcy, Pascal, Ratchinskiy, Coralie, Gerbaud, Bastien, Boari, A., Vurro, Maurizio, Sands, David, Morris, Cindy E., Buttin, P., Arhancet, G.B., Reboud, Xavier, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Domaine expérimental d'Époisses (DIJ EPOISSES), Institut National de la Recherche Agronomique (INRA), Italian National Research Council, National Research Council [Italy] (CNR), Montana State University (MSU), Station de Pathologie Végétale (AVI-PATHO), Novus International, AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Domaine expérimental d'Époisses - UE0115 U2E (DIJ EPOISSES), Consiglio Nazionale delle Ricerche (CNR), Unité de Pathologie Végétale (PV), Santé des Plantes et Environnement division, European Weed Research Society (EWRS). GBR., Syngenta France. FRA., Monsanto SAS. FRA., Dow Agrosciences. ROU., Association Française de Protection des Plantes (AFPP). FRA., BASF AG. DEU., and Région Languedoc-Roussillon. FRA.
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2015

120. Caractérisation de l'inoculum aérien de[i] Botrytis cinerea[/i] pour la prévision des épidémies de pourriture grise

Author: Leyronas, Christel, Nicot, Philippe, Halkett, Fabien, Martin, Olivier, Soubeyrand, Samuel, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Biostatistique et Processus Spatiaux (BIOSP), Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Biostatistique et Processus Spatiaux (BioSP), and Societe Francaise de Phytopathologie (SFP). FRA.
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences
Abstract: absent
Published: 2015

121. Estimation of genetic drift and selection from next generation sequencing time-sampled data

Author: Rousseau, Elsa, Fabre, Frédéric, Coville, Jérôme, Mailleret, Ludovic, Palloix, Alain, Senoussi, Rachid, Grognard, Frédéric, Moury, Benoît, 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), Biostatistique et Processus Spatiaux (BioSP), 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), Génétique et Amélioration des Fruits et Légumes (GAFL), Unité de Pathologie Végétale (PV), 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), 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), 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), University of Leicester. GBR., 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 Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), Biostatistique et Processus Spatiaux (BIOSP), 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), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Station de Pathologie Végétale (AVI-PATHO), 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: [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], [MATH.MATH-RT]Mathematics [math]/Representation Theory [math.RT], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 2015

122. Joint estimation of effective population sizes and selection coefficients from time-sampled data: a case study on virus populations exposed to plant resistance

Author: Rousseau, Elsa, Fabre, Frédéric, Coville, Jérôme, Mailleret, Ludovic, Palloix, Alain, Senoussi, Rachid, Grognard, Frédéric, Moury, Benoît, 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), Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), 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), 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), Biostatistique et Processus Spatiaux (BioSP), Génétique et Amélioration des Fruits et Légumes (GAFL), 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), 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), 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 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), Biostatistique et Processus Spatiaux (BIOSP), 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), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Station de Pathologie Végétale (AVI-PATHO), 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), and Unité de recherche Génétique et amélioration des fruits et légumes (GAFL)
Subjects: [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], [MATH.MATH-RT]Mathematics [math]/Representation Theory [math.RT], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, [SDV]Life Sciences [q-bio], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract: National audience; no abstract
Published: 2015

123. A critical evaluation of whether recombination in virus-resistant transgenic plants will lead to the emergence of novel viral diseases

Author: Mireille Jacquemond, Fernando García-Arenal, Mark Tepfer, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Centro de Biotecnologıa y genomica de plantas UPM-INIA and ETSI agronomos, Universidad Politécnica de Madrid (UPM), and Station de Pathologie Végétale (AVI-PATHO)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Genes, Viral, Physiology, Transgene, Plant Science, Genetically modified crops, Biology, 01 natural sciences, Cucumovirus, Virus, Cucumber mosaic virus, 03 medical and health sciences, genetically modified organism, Pathogen, 030304 developmental biology, Plant Diseases, 2. Zero hunger, Recombination, Genetic, 0303 health sciences, virus emergence, biosafety, risk assessment, virus-resistant transgenic plants, Plants, Genetically Modified, Virology, Adaptation, Physiological, recombination, Genetically modified organism, Potential harm, Host-Pathogen Interactions, Recombination, 010606 plant biology & botany
Abstract: In the evaluation of the potential impacts of first-generation genetically modified (GM) crops, one of the most complex issues has been whether the expression of viral sequences would lead to the emergence of novel viruses, which could occur through recombination between transgene mRNA and that of an infecting non-target virus. Here, we examine this issue, focusing on Cucumber mosaic virus (CMV), which is a particularly pertinent choice, as it is both a major plant pathogen and also the virus with which this question has been studied in the most detail. Using recent results on recombination in CMV, we employ a novel framework giving particular prominence to the formulation of the risk hypothesis and to hypothesis testing via examination of the potential pathway to harm. This allows us to conclude with greater certainty that the likelihood of this potential harm, the emergence of novel viruses, is low.
Published: 2015
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124. Genetic variability of Potato virus Y (PVY) and Tobacco etch virus (TEV) from naturally infected pepper fields in the Hatay region of Turkey

Author: Benoît Moury, Nihal Buzkan, M. Zencirkıran, Bekir Bülent Arpaci, G. Görsoy, University of Sütçü Imam, Partenaires INRAE, University of Kilis, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), TUBITAK-FRANCE PIA BOSPHORUS Project [grant number 109 O 447], Kahramanmaras Sütçü İman university (Agriculture Faculty, Plant Protection Department), Agriculture Faculty, Horticulture Department, Kilis Yedi Aralik University, and Station de Pathologie Végétale (AVI-PATHO)
Subjects: Capsicum annuum, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, virus de la gravure du tabac, tobacco etch virus, culture légumière de plein champ, PVY, resistance gene, phytopathogenic virus, potato virus y, Pepper, Genetic variation, Genetic variability, Allele, pathologie végétale, virus phytopathogène, structure génétique des populations, biology, Tobacco etch virus, durabilité des méthodes de lutte, Potyvirus, biology.organism_classification, gène de résistance, Virology, virus y de la pomme de terre, turquie, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Potato virus Y, Genetic structure, genetic variation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, TEV, Agronomy and Crop Science
Abstract: The genetic structure of Potato virus Y (PVY) and Tobacco etch virus (TEV) (Potyvirus) populations was investigated in pepper fields in two regions in Turkey. The diversity of PVY and TEV populations according to coat protein (CP) and VPg coding regions showed some similarity. All the isolates built a monophyletic group due to a single introduction event or multiple introductions of genetically similar isolates. All the isolates of both viruses showed evidence to the diversification for a long time. Based on VPg and CP sequences, all PVY isolates corresponded to clade C1. Turkish potyvirus isolates were only able to break the pvr21 resistance allele and therefore belonged to pathotype (0, 1). The Pvr4 dominant gene was found to be efficient and durable against PVY but not at all efficient against TEV. Consequently, the pvr22 resistance allele, efficient resistance against PVY and TEV pathotype (0, 1) isolates, would be the most suitable strategy to control potyviruses.
Published: 2015
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125. First report of Pepper vein yellows virus in field-grown pepper in Ivory Coast

Author: Bolou Bi, Bolou Antoine, Moury, Benoît, Abo, K., Kakou, D. Jr., Girardot, Gregory, Kouassi, N’dri P., Kouadio, E.J.N., Kouakou, B.S.M., Koné, Daouda, Laboratoire de Physiologie Végétale, UFR Biosciences, Université Félix Houphouët-Boigny (UFHB), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Ecole Supérieure d’Agronomie, Institut National Polytechnique Félix Houphouët-Boigny, and Unité de Pathologie Végétale (PV)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, virus phytopathogène, fungi, food and beverages, virus de la marbrure du piment, pepper mottle virus, culture légumière de plein champ, capsicum annuum, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, phytopathogenic virus, émergence d'isolat, séquençage, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, capsicum chinense, pathologie végétale, côte d'ivoire
Abstract: In 2014 and 2015, leaf samples from field-grown pepper (Capsicum annuum L. and C. chinense Jacq.) plants showing different kinds of viral symptoms were collected in Ivory Coast. Samples were dehydrated onto calcium chloride before RNA extraction (Tri Reagent, Molecular Research Center, USA). Two-step RT-PCRs were performed as de- scribed by Knierim et al. (2010) with polyvalent primers for poleroviruses targeting part of the RNA-dependent RNA polymerase, coat protein and movement protein genes. Am- plicons of the expected size (ca. 1,100 bp) were obtained from four of 20 analyzed C. chinense samples originating from Arrah and Bongouanou (South-East Ivory Coast). The source plants exhibited leaf yellowing and rolling as well as stunting. PCR products were sequenced directly (GenBank accession Nos KT825996 to KT825999). Sequence analysis with the BLASTN software showed 97 to 98% nucleotide identity with Pepper vein yellows virus (PeVYV) isolates from Mali as closest sequences (Knierim et al., 2013). These se- quences were aligned with additional ones available in Gen- Bank using ClustalW, leading to a 964-nucleotide alignment. Phylogenetic trees obtained with MEGA6 were consistent between neighbor-joining, maximum-likelihood and maxi- mum parsimony methods and showed that the sequences from Ivory Coast isolates clustered with two pepper isolates collected in 2009 in Mali (accession Nos JX427535 and JX427536) in a separate clade (92% bootstrap value). Pepper veinal mottle virus (genus Potyvirus) and Cucumber mosaic virus (genus Cucumovirus) are the two most widespread pep- per viruses in Ivory Coast but PeVYV is an additional threat to pepper production in this area.
Published: 2015
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126. Joint estimation of effective population sizes and selection coefficients from time-sampled data: a case study on virus populations submitted to plant resistance

Author: Rousseau, Elsa, Fabre, Frédéric, Coville, Jérôme, Mailleret, Ludovic, Palloix, Alain, Senoussi, Rachid, Grognard, Frédéric, Moury, Benoît, 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), 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), Biostatistique et Processus Spatiaux (BIOSP), Institut National de la Recherche Agronomique (INRA), 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), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Station de Pathologie Végétale (AVI-PATHO), 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), Unité de Pathologie Végétale (PV), 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), 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), Biostatistique et Processus Spatiaux (BioSP), Génétique et Amélioration des Fruits et Légumes (GAFL), Societe Francaise de Phytopathologie (SFP). FRA., 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), 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), Unité de recherche Génétique et amélioration des fruits et légumes (GAFL), 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: [STAT]Statistics [stat], [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], [MATH.MATH-RT]Mathematics [math]/Representation Theory [math.RT], [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract: National audience; no abstract
Published: 2015

127. The Water Cycle, a Potential Source of the Bacterial Pathogen Bacillus cereus

Author: Marina Gillon, Claire Dargaignaratz, Claude Doussan, Christian Dupont, Julien Brillard, Véronique Broussolle, Odile Berge, Annette Bérard, Thierry Clavel, Stéphanie Oriol-Gagnier, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Infection et inflammation (2I), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), funded by the INRA and by a grant from the Université d’Avignon, Brillard, Julien, Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), Physiopathologie et diagnostic des infections microbiennes (EPIM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Station de Pathologie Végétale (AVI-PATHO), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA))
Subjects: Article Subject, cycle de l'eau, Biodiversité et Ecologie, Bacillus cereus, lcsh:Medicine, Biology, Environment, General Biochemistry, Genetics and Molecular Biology, Foodborne Diseases, Biodiversity and Ecology, transfert bactérien, 03 medical and health sciences, Water Cycle, Botany, medicine, réservoir de pathogènes, Food microbiology, Animals, Soil Microbiology, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Food poisoning, écologie microbienne, General Immunology and Microbiology, contamination alimentaire, 030306 microbiology, Ecology, lcsh:R, bacillus cereus, fungi, General Medicine, santé humaine, 15. Life on land, spore bactérienne, biology.organism_classification, medicine.disease, Spore, écosystème aquatique, Cereus, Soil water, [SDE]Environmental Sciences, Food Microbiology, bacteria, Water Microbiology, bactérie pathogène, Soil microbiology, Groundwater, Research Article
Abstract: The behaviour of the sporulating soil-dwellingBacillus cereus sensu lato(B. cereus sl) which includes foodborne pathogenic strains has been extensively studied in relation to its various animal hosts. The aim of this environmental study was to investigate the water compartments (rain and soil water, as well as groundwater) closely linked to the primaryB. cereus slreservoir, for which available data are limited.B. cereus slwas present, primarily as spores, in all of the tested compartments of an agricultural site, including water from rain to groundwater through soil. During rain events, leachates collected after transfer through the soil eventually reached the groundwater and were loaded withB. cereus sl. In groundwater samples, newly introduced spores of aB. cereusmodel strain were able to germinate, and vegetative cells arising from this event were detected for up to 50 days. This firstB. cereus slinvestigation in the various types of interrelated environments suggests that the consideration of the aquatic compartment linked to soil and to climatic events should provide a better understanding ofB. cereus slecology and thus be relevant for a more accurate risk assessment of food poisoning caused byB. cereus slpathogenic strains.
Published: 2015
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128. Relationship between the genetic characteristics of[i] Botrytis[/i] sp. airborne inoculum and meteorological parameters, seasons and the origin of air masses

Author: Christel Leyronas, Fabien Halkett, Philippe C. Nicot, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), INRA department of Plant Health and Environment, Unité de Pathologie Végétale (PV), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Veterinary medicine, food.ingredient, spores, Immunology, Plant Science, Biology, 01 natural sciences, diversity, 03 medical and health sciences, food, Abundance (ecology), genetic clusters, Botany, Immunology and Allergy, Botrytis sp, 030304 developmental biology, Botrytis cinerea, Botrytis, 2. Zero hunger, 0303 health sciences, fungi, food and beverages, grey mould, biology.organism_classification, Spore, botrytis, 13. Climate action, Genetic structure, Microsatellite, 010606 plant biology & botany
Abstract: Grey mould is a worldwide disease on many economically important crops. It is caused by two fungal species, [i]Botrytis cinerea[/i] and[i] B. pseudocinerea[/i], which are mainly airborne dispersed. Although several studies have considered the abundance of airborne inoculum of [i]B. cinerea[/i] in models forecasting the risk of grey mould epidemics, the genetic characteristics of this inoculum are poorly known. In the present study, airborne inoculum of [i]B. cinerea[/i] and [i]B. pseudocinerea[/i] was collected on 29 dates over a 2.5-year period on a site in south-eastern France. The 683 sampled isolates were genotyped with nine microsatellites markers, and 616 were identified as [i]B. cinerea[/i]. The genetic structure of[i] B. cinerea[/i] airborne inoculum was inferred with Bayesian assignment tests. Eight genetic clusters were identified. Cluster abundance showed temporal variation and was statistically linked to the season (P = 0.0009) and the origin of air masses (P < 0.0001). The proportion of isolates belonging to the species[i] B. pseudocinerea[/i] was equal to 9.8 % on average, but it showed temporal variation; it tended to be higher in winter. This study is the first to provide information about the genetic characteristics of airborne inoculum of[i] B. cinerea[/i] and [i]B. pseudocinerea[/i] and to bring evidence of relationship with seasons, meteorological parameters and with the origin of air masses.
Published: 2015
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129. Protection of the durability of major resistance genes to plant viruses with quantitative resistance, a modeling approach

Author: Rousseau, Elsa, Coville, Jerome, Palloix, Alain, Fabre, Frédéric, Mailleret, Ludovic, Moury, Benoît, Grognard, Frédéric, Station de Pathologie Végétale (AVI-PATHO), 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), Biostatistique et Processus Spatiaux (BIOSP), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), 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), 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), 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), Unité de recherche Génétique et amélioration des fruits et légumes (GAFL), 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), 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), and 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)
Subjects: [SPI]Engineering Sciences [physics], quantitative resistance, selection advantage, [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], durable resistance, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, [SDV]Life Sciences [q-bio], fungi, food and beverages, genetic drift, viral population dynamics
Abstract: International audience; The deployment of virus-resistant crops often leads to the emergence of resistance-breaking (RB) pathogens that suppress the yield benefit provided by the resistance. Although breakdowns are well known for plant genes conferring total, i.e. qualitative, resistance to the virus, they are still poorly understood for plant genetic factors conferring partial, i.e. quantitative resistance. Furthermore, it has been proved for several pathosystems that combining qualitative and quantitative resistances can increase the durability of the qualitative resistance. Two mechanisms can explain this result : either (i) an increase of genetic drift in the virus population, or (ii) a decrease of the selection advantage of the RB mutant. Here, we aim at disentangling the role of these two mechanisms on the durability of plant qualitative resistances to viruses. To investigate this, we follow by high-throughput sequencing the within-host demo-genetic dynamics of five Potato virus Y (PVY) variants in sixteen contrasted pepper plant genotypes, carrying a qualitative resistance and different combinations of quantitative resistances. PVY variants carry distinct mutations, each mutation conferring weak to strong adaptation to the qualitative resistance. We measure the within-host virus variants frequencies and the relative virus population size at different time points. We estimate the fitness of each virus variant by fitting a Lotka-Volterra model of competition between variants to these data. We assess the strength of genetic drift by analysing and modeling between-host variances of the variants frequencies at each time point. With this modeling approach, we can determine how quantitative resistance can increase the durability of qualitative resistance, and provide criteria to screen host genotypes with sustainable pathogen resistance.
Published: 2014

130. Short-term variations in gene flow related to cyclic density fluctuations in the common vole

Author: Vincent Bretagnolle, Yannick Chaval, Pablo Inchausti, Karine Berthier, Jean-François Cosson, Bertrand Gauffre, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Etudes Biologiques de Chizé [France] (USC 1339 INRA), Institut National de la Recherche Agronomique (INRA), Unité de Pathologie Végétale (PV), Centro Universtario Regional de Este, Universidad de República, Centre de Biologie pour la Gestion des Populations (UMR CBGP), 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)-Université de Montpellier (UM)-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), INRA (ECOGER national program, grant from ACI ECCO, Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), INRA CEBC, INRA-CEBC, and Station de Pathologie Végétale (AVI-PATHO)
Subjects: Male, Genotype, Rodent, Population Dynamics, migration, Microtus arvalis, Gene flow, biology.animal, Genetics, Animals, Microtus, Ecology, Evolution, Behavior and Systematics, Population Density, Genetic diversity, cyclic rodent populations, biology, Arvicolinae, Ecology, Genetic Variation, genetic diversity, biology.organism_classification, Genetics, Population, Evolutionary biology, Genetic structure, [SDE]Environmental Sciences, Microsatellite, Biological dispersal, Female, Vole, France, Animal Distribution, Microsatellite Repeats, spatial genetic structure
Abstract: International audience; : In highly fluctuating populations with complex social systems genetic patterns are likely to vary in space and time due to demographic and behavioural processes. Cyclic rodents are extreme examples of demographically instable populations that often exhibit strong social organisation. In such populations, kin structure and spacing behaviour may vary with density fluctuations and impact both the composition and spatial structure of genetic diversity. In this study, we analysed the multiannual genetic structure of a cyclic rodent, Microtus arvalis, using a sample of 875 individuals trapped over three complete cycles (from 1999 to 2007) and genotyped at 10 microsatellite loci. We tested the predictions that genetic diversity and gene flow intensity vary with density fluctuations. We found evidences for both spatial scale-dependant variations in genetic diversity and higher gene flow during high density. Moreover, investigation of sex-specific relatedness patterns revealed that, although dispersal is biased toward males in this species, distances moved by both sexes were lengthened during high density. Altogether, these results suggest that an increase of migration with density allows to restore the local loss of genetic diversity occurring during low density. We then postulate that this change in migration results from local competition, which enhances female colonisation of empty spaces and male dispersal among colonies. This article is protected by copyright. All rights reserved.
Published: 2014
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131. Draft Genome Sequences of a Phylogenetically Diverse Suite of Pseudomonas syringae Strains from Multiple Source Populations

Author: Caroline Guilbaud, David Sands, Scott Yourstone, David A. Baltrus, Corbin D. Jones, Jeffrey L. Dangl, Cindy E. Morris, Abigail L. Lind, Baltrus, David A, School of Plant Sciences, University of Arizona, Department of Biology, Northern Arizona University [Flagstaff], Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Department Plant Sciences and Plant Pathology [Bozeman], Montana State University (MSU), Carolina Center for Genome Sciences, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), Howard Hughes Medical Institute, University of California, Unité de Pathologie Végétale (PV), and Howard Hughes Medical Institute (HHMI)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, bactérie phytopathogène, Genetics, Biodiversité et Ecologie, pseudomonas syringae, séquençage du génome complet, Outbreak, Biology, phytopathogenic bacteria, Crop species, Multiple source, Genome, Agricultural sciences, Biodiversity and Ecology, bactérie saprophyte, Botany, Pseudomonas syringae, Prokaryotes, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Molecular Biology, Sciences agricoles, relation habitat population
Abstract: Here, we report the draft genome sequences for 7 phylogenetically diverse isolates of Pseudomonas syringae , obtained from numerous environmental sources and geographically proximate crop species. Overall, these sequences provide a wealth of information about the differences (or lack thereof) between isolates from disease outbreaks and those from other sources.
Published: 2014
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132. Evolutionary pathways to break down the resistance of allelic versions of the PVY resistance gene va

Author: Christelle Lacroix, Emmanuel Jacquot, J.L. Verrier, Michel Tribodet, Bérenger Janzac, Benoît Moury, 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, 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), 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)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), SEITA, Institut du Tabac, Imperial Tobacco Group, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), the Association for Research on Nicotianae (ARN), 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), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, AGROCAMPUS OUEST-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 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)
Subjects: Genetics, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, biology, Virulence, Plant Science, biology.organism_classification, Virology, Virulence factor, Virus, Potato virus Y, Genotype, Allele, Adaptation, Agronomy and Crop Science, Gene
Abstract: Emergence of viral genotypes can make control strategies based on resistance genes ineffective. A few years after the deployment of tobacco genotypes carrying alleles of the Potato virus Y (PVY) recessive resistance gene va, virulent PVY isolates have been reported, suggesting the low durability of va. To have a broader view of the evolutionary processes involved in PVY adaptation to va, we studied mutational pathways leading to the emergence of PVY resistance-breaking populations. The viral genome-linked protein (VPg) has been described to be potentially involved in va adaptation. Analyses of the VPg sequence of PVY isolates sampled from susceptible and resistant tobacco allowed us to identify mutations in the central part of the VPg. Analysis of the virulence of wild-type isolates with known VPg sequences and of mutated versions of PVY infectious clones allowed us to (i) validate VPg as the PVY virulence factor corresponding to va, (ii) highlight the fact that virulence gain in PVY occurs rapidly and preferentially by substitution at position AA105 in the VPg, and (iii) show that the 101G substitution in the VPg of a PVYC isolate is responsible for cross-virulence toward two resistance sources. Moreover, it appears that the evolutionary pathway of PVY adaptation to va depends on both virus and host genetic backgrounds.
Published: 2014
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133. Prospects for Using Environmental Levers in Greenhouses to Stimulate Plant Defences and the Quality of Fruits and Vegetables

Author: Laurent Urban, Jawad Aarrouf, Philippe C. Nicot, EA 4279 Laboratoire Physiologie des Fruits et Légumes, Avignon Université (AU), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Unité de Pathologie Végétale (PV), Urban, Laurent, and Déposants HAL-Avignon, bibliothèque Universitaire
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, qualité des produits végétaux, phytonutriment, Phytopathology and phytopharmacy, [SDV]Life Sciences [q-bio], Greenhouse, Mycology, Large range, Horticulture, Biology, Vegetable crops, 01 natural sciences, stress, agriculture biologique, stress photooxydant, Mild stress, organic farming, culture sous serre, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Secondary metabolism, défense de la plante, Beneficial effects, 2. Zero hunger, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, secondary metabolism, light, business.industry, fungi, food and beverages, 04 agricultural and veterinary sciences, Phytopathologie et phytopharmacie, couverture de serre, maladie des plantes, Agricultural sciences, Biotechnology, Mycologie, fertilisation azotée, méthode de lutte, 13. Climate action, Fruits and vegetables, 040103 agronomy & agriculture, Organic farming, 0401 agriculture, forestry, and fisheries, business, Sciences agricoles, 010606 plant biology & botany
Abstract: Communication orale non invitée à la conférence : 2. International Symposium on Organic Greenhouse Horticulture, Avignon, France, 28-31/10/2013; International audience; The environment of greenhouses is commonly modified to reduce the pressure of pests and diseases, but it can also be exploited to stimulate natural defences of plants. In addition to genetic influences, several agronomic factors can be used as levers to increase the concentrations of secondary metabolites involved in the defence of fruit and vegetable crops. Many secondary metabolites involved in plant defences are also phytonutrients, i.e. compounds that have beneficial effects on human health, including protection against cardiovascular diseases, cancers, and metabolic or neurodegenerative diseases. Nitrogen deprivation, photooxidative stress and exposure to specific wavelengths such as those supplied by UV radiations are well known for stimulating the production of secondary metabolites in a large range of plants. We propose here a review of factors meeting the specifications of organic farming, which are both effective and applicable in greenhouse conditions. Among all these factors, mild stress and innovative covering materials emerge as especially promising.
Published: 2014
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134. Protecting the durability of major resistance genes to plant viruses with quantitative resistance

Author: Rousseau, Elsa, Fabre, Frédéric, Mailleret, Ludovic, Palloix, Alain, Simon, Vincent, Valière, Sophie, Moury, Benoît, Grognard, Frédéric, Gouzé, Jean-Luc, 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 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), 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), Génétique et Amélioration des Fruits et Légumes (GAFL), Département de Génétique Animale [Toulouse], 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), Station de Pathologie Végétale (AVI-PATHO), 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), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), 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), 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), 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), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Département Génétique Animale (DEPT GA), Centre National de la Recherche Scientifique (CNRS). FRA., 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), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), 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), 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)-Inria Sophia Antipolis - Méditerranée (CRISAM)
Subjects: quantitative resistance, [MATH.MATH-RT]Mathematics [math]/Representation Theory [math.RT], durable resistance, [SPI] Engineering Sciences [physics], [SDV]Life Sciences [q-bio], food and beverages, [MATH] Mathematics [math], [SDV] Life Sciences [q-bio], [SPI]Engineering Sciences [physics], viral evolution, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, landscape epidemiology, [INFO]Computer Science [cs], genetic drift, [MATH]Mathematics [math], [INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The deployment of virus-resistant crops often leads to the emergence of resistance-breaking (RB) pathogens that suppress the yield benefit provided by the resistance (Fabre et al,2012). Although breakdowns are well known for qualitative resistances conferring total resistance to the virus, they are still poorly understood for quantitative resistances conferring partial resistance. Furthermore, it has been proved for several pathosystems that combining qualitative and quantitative resistances can increase the durability of the qualitative resistance (Palloix et al, 2009, Quenouille et al, 2013). Two mechanisms can explain this result : either (i) an increase of genetic drift in the virus population, or (ii) a decrease of the selection advantage of the RB mutant. The purpose of the ongoing work presented here is to disentangle the role of these two mechanisms on the durability of plant qualitative resistances to viruses.To investigate this, we concentrated on a pepper Potato virus Y (PVY) pathosystem on which we report consistent variability in bottlenecks undergone by viral populations at inoculation and in viral accumulation, both determined by the host genotype. We follow by high-throughput sequencing the within-host demo-genetic dynamics of several virus variants in contrasted plant genotypes, carrying a qualitative resistance and different combinations of quantitative resistances. The respective effects of genetic drift and selection are evaluated by fitting models to these data (Fabre, 2012). We further aim at predicting the potential of combining qualitative and quantitative plant resistances to achieve sustainable plant resistance management at the epidemic scale.
Published: 2014

135. Special Issue for the Plant Resistance Sustainability International Conference, La Colle sur Loup, France, 16-19 October 2012

Author: Alain Palloix, Marie-Hélène Jeuffroy, Benoît Moury, Francois-Christophe Coleno, Carole Caranta, Christian Lannou, Charles-Eric Durel, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut de Recherche en Horticulture et Semences (IRHS), 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 d'Angers (UA), Agronomie, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Département Santé des Plantes et Environnement (DPT SPE), Unité de Pathologie Végétale (PV), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Station de Pathologie Végétale (AVI-PATHO), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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: Microbiology (medical), [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0303 health sciences, Resistance (ecology), 030306 microbiology, Library science, Biology, Microbiology, 03 medical and health sciences, Infectious Diseases, Environmental protection, Sustainability, Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: absent
Published: 2014
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136. Adapting apple ideotypes to low-input fruit production agro-ecosystems

Author: Pierre-Eric Lauri, Laurent Jamar, Luciana Parisi, Marc Lateur, François Laurens, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Department of Life Sciences, Unit Breeding & Biodiversity, Centre Wallon de Recherches Agronomiques (CRA-W), Institut de Recherche en Horticulture et Semences (IRHS), 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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), 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 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), Station de Pathologie Végétale (AVI-PATHO), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), (Eds.), S. Bellon and S. Penvern, and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Engineering, Cultural practices, Sustainable orchard, Agricultural engineering, 01 natural sciences, 03 medical and health sciences, Malus x domestica, Production (economics), [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ecosystem, Integrated fruit production (IFP), Apple breeding, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, business.industry, Low input, Ideotype, Pest and disease control, 15. Life on land, Low-input systems, Agronomy, Organic fruit production (OFP), Orchard, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 010606 plant biology & botany
Abstract: UMR 1334 AGAP : Equipe AFEF ‘Architecture et fonctionnement des espèces fruitières’ ; Team AFFS ‘Architecture and Functioning of Fruit Species’; Current commercial apple growing is highly dependent on off-farm inputs and it is urgent to develop new strategies to remedy this situation. The challenge for the future is to achieve lower-input apple orchards, whether under Integrated Fruit Production (IFP) or Organic Fruit Production (OFP) systems. This paper analyses the different agronomic factors that play key roles both in the current and future ‘More Sustainable Orchard’, with particular attention on plant protection. Firstly, the concept of ‘ideotype’ is developed, emphasizing the most important characteristics of optimal ideotypes for apple. Secondly, current knowledge on the relationships between genotype, cultural practices and the environment is presented and discussed. This paper deals with properties that need to be combined at plant material and orchard levels to optimise the IFP and OFP low-input systems. The focus is on: (a) the main characteristics of apple ideotypes; (b) breeding strategies; and (c) adapted cultural practices and control measures in the orchards.
Published: 2014
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137. Origine de l'inoculum aérien de [i]Botrytis cinerea[/i] : sources locales vs introduction à partir de sources éloignées ?

Author: Leyronas, Christel, Soubeyrand, Samuel, Martin, Olivier, Halkett, Fabien, Nicot, Philippe, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Biostatistique et Processus Spatiaux (BIOSP), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), AAP SPE, Unité de Pathologie Végétale (PV), Biostatistique et Processus Spatiaux (BioSP), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, dispersion, aérobiologie, rétro-trajectoires
Abstract: absent
Published: 2013

138. Evolution of plant eukaryotic initiation factor 4E (eIF4E) and potyvirus genome-linked protein (VPg): a game of mirrors impacting resistance spectrum and durability

Author: Alain Palloix, Benoît Moury, Jean-Luc Gallois, Vincent Simon, Bérenger Janzac, Carine Charron, Carole Caranta, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), 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), Génétique et Amélioration des Fruits et Légumes (GAFL), Station de Pathologie Végétale (AVI-PATHO), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Unité de recherche Génétique et amélioration des fruits et légumes (GALF)
Subjects: Nonsynonymous substitution, Polymorphisme génétique, Eukaryotic Initiation Factor-4E, Potyvirus, Évolution, Genome, host resistance, Cluster Analysis, Disease Resistance, Plant Proteins, Genetics, biology, EIF4E, food and beverages, Plants, Infectious Diseases, Potato virus Y, host-parasite coevolution, Host-Pathogen Interactions, Microbiology (medical), Molecular Sequence Data, Microbiology, Virus, capsicum annuum, Evolution, Molecular, Open Reading Frames, Viral Proteins, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection, Genetic, Codon, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, H20 - Maladies des plantes, Plant Diseases, VPg, Génome, fungi, Résistance aux maladies, biology.organism_classification, Haplotypes, eIF4E, Mutation
Abstract: Polymorphism in the plant eukaryotic translation initiation factor 4E (eIF4E) and potyvirus genome-linked protein (VPg) determine, in many cases, the outcome of the confrontation between these two organisms: compatibility (i.e. infection of the plant by the virus) or incompatibility (i.e. resistance of the plant to the virus). The two interacting proteins eIF4E and VPg show strikingly similar evolution patterns. Most codon positions in their coding sequences are highly constrained for nonsynonymous substitutions but a small number shows evidence for positive selection. Several of these latter positions were shown to be functionally important, conferring resistance to the host or pathogenicity to the virus. Determining the mutational pathways involved in pepper eIF4E diversification revealed a link between an increase of the pepper resistance spectrum towards a panel of potyvirus species and an increase of durability of the resistance towards Potato virus Y. This relationship questions the interest of using more generally the spectrum of action of a plant resistance gene as a predictor of its durability potential.
Published: 2013
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139. 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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140. Twitter dans un contexte académique

Author: Aventurier, Pascal, Decognet, Veronique, Services déconcentrés d'appui à la recherche - PACA (SDAR PACA), Institut National de la Recherche Agronomique (INRA), Station de Pathologie Végétale (AVI-PATHO), Services déconcentrés d'appui à la recherche Provence-Alpes-Côte d'Azur (SDAR Paca), Unité de Pathologie Végétale (PV), Institut National de Recherche Agronomique (INRA). UAR Direction de la Valorisation / Information Scientifique et Technique (1266)., and ProdInra, Archive Ouverte
Subjects: ComputingMilieux_GENERAL, évolution des pratiques, réseau social, information scientifique et technique, Contexte académique, [SHS.INFO]Humanities and Social Sciences/Library and information sciences, Twitter, Library and information sciences, InformationSystems_MISCELLANEOUS, Sciences de l'information et de la communication, [SHS.INFO] Humanities and Social Sciences/Library and information sciences
Abstract: Twitter dans un contexte académique
Published: 2013

141. Potato virus Y infecting tobacco crops adapts rapidly to the recessive resistance gene va: evolutionary pathways to breakdown the resistance

Author: Janzac, Bérenger, Tribodet, Michel, Lacroix, Christelle, Moury, Benoît, Verrier, J.L., Jacquot, Emmanuel, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), 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), 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), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, University of Minnesota System, Unité de Pathologie Végétale (PV), 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 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: [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract: Bgpi : équipe 6Bgpi : équipe 6; absent
Published: 2013

142. Host-directed selection of Cucumber mosaic virus (CMV) reassortants in plants co-infected with different isolates of CMV subgroups lA and lB

Author: Ben Tamarzizt, Hana, Girardot, Gregory, Fakhfakh, Hatem, Tepfer, Mark, Jacquemond, Mireille, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Pathologie Végétale (PV), Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), and Université de Tunis El Manar (UTM)-Université de Tunis El Manar (UTM)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, food and beverages
Abstract: Reassortment is thought to constitute an advantage for multipartite viroses, facilitating their adaptation to varying environmental conditions through exchange of genomic segments in plants co-infected by different isolates. However, for CMV, natural reassortants were rarely found in the open field until recently, when an in-depth survey of CMV in Tunisian pepper (Capsicum annuum) crops revealed that most of the isolates were reassortants between subgroups lA and IB (Ben Tamarzizt et al., submitted). These isolates were composed of an RNAI from subgroup IB, an RNA2 from subgroup lA and an RNA3 from either subgroup. In order to evaluate the role of pepper in the selection of reassortants, we analysed the progeny virus during seriai passages in greenhouse-grown pepper plants co-infected by isolates ofboth subgroups. The results showed a strong and rapid (frrst or second passage) selection of subgroup IB RNAs 1 and 3. In contrast, the RNA2 of both subgroups was present even after four passages, after which subgroup IB RNA2 progressively supplanted its lA counterpart. Genetically diverse subgroup IB strains collected on different hosts were then tested. Similar results were obtained, with strong and rapid selection of RNAsl and 3 and a slower selection ofRNA2, except that, for RNAl , which RNA was selected differed according to the IB strain. When infections of melon and tobacco were tested, results indicated a similar tendency: quicker selection of RNAs 1 and 3 than RNA2, but which RNAs were selected differed also according to the host species. In all cases, the progeny identified in the systemic leaves of plants infected with a subgroup lA and a subgroup IB strain corresponded to either the IB strain or reassortants between the two strains; the complete lA strain was not recovered. These results showed that CMV is prone to reassortment under experimental conditions, and are coherent with the prevalence of reassortants in the field in Tunisia, although the reassortants we observed under experimental condition.s were not strictly the same as those in the Tunisian pepper fields. Perhaps the strong bottleneck exerted on virus populations during natural transmission by aphids could account for a selective dissemination of reassortant populations. However, these results also illustrate a rather complicated situation, since the subgrouping of each genomic segment of the progeny virus depended not only on the strain but also on the host species. These results also raise the question of the low prevalence of reassortants in the open field elsewhere than in Tunisia. That reassortants did not emerge in the two other countries where in-depth surveys were carried out will be discussed. Finally, it would be interesting to analyse carefully the genetic features of CMV populations in countries where all subgroups are abundant, as is the case in Asia.
Published: 2013

143. High-throughput sequencing for the diagnosis of viral diseases: example of ornamental plants

Author: Verdin, Eric, Girardot, Gregory, Gognalons, Patrick, Jacquemond, Mireille, Tepfer, Mark, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Unité de Pathologie Végétale (PV)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, fungi, food and beverages
Abstract: The production of omamental plants (eut flowers, plants in pots or for gardens) concems a far greater number of plant species than those used in agriculture, and the value of omamental plants imported into France is six times that the value of the corresponding experts. Omamentals can harbor viruses that can infect and be disseminated in more valuable species, in particular vegetable and fruit crops, and thus present a potential source of damaging new viral diseases. The currently used serological and molecular tests are effective for screening for known viruses, but considering the ever increasing number of omamental species and the scope of their tracte worldwide, it is critical to develop means to also detect plant viruses that are not current targets of sanitary surveillance in a manner as exhaustive as possible. Further, viruses und er quarantine restriction are of particular concem. Two techniques of high-throughput sequencing that can detect unknown viruses have been used to characterize viroses of cultivated plants and also of plants growing in natural environments. One strategy is based on 454 pyrosequencing of cDNAs synthesized from viral double-stranded RNAs (dsRNAs), and the other is based on Illumina HiSeq sequencing of small RNAs (siRNAs) of 21-24 nt. In the first phase of a project of high-throughput sequencing of viroses in omamental plants of unknown sanitary condition, we have used both sequencing strategies in a model study of petunia plants infected either singly or in rnixed infection by Cucumber mosaic virus (CMV), Potato virus Y (PVY) and Tobacco mosaic virus (TMV). We present here the results of this pilot study, in which these two sequencing strategies have been compared according to severa!criteria: 1) number, size and identity of contigs, 2) quality of the sequences obtained compared to the reference sequences of the viruses inoculated, 3) completeness of coverage of the viral genomes, 4) sensitivity of detection of minor viral components, and 5) the presence of contaminating sequences. Globally, the sequences generated by Illumina sequencing of siRNAs were of better quality; in fact they were nearly always exactly identical to the reference sequences. Both techniques allowed detection of viral genomes that were not detectable by RT-PCR but Illumina sequencing of siRNAs was even more sensitive than pyrosequencing. Further, siRNA sequencing detected the presence of a viral genome integrated in the petunia genome. However, the sensitivity of both techniques revealed contaminating viral sequences that probably arose by contamination between samples. Neither strategy allowed assembly of complete viral genomes, and in particular the 5 '- and 3'-terminal sequences were not present in the contigs, except in sorne cases when a full-length reference sequence was provided. In spite of its high cost, Illumina sequencing of siRNAs seems to be superior to pyrosequencing of dsRNAs according to severa!criteria. We are currently collecting samples of omamental plants from producers in order to determine by siRNA sequencing to what extent known and unknown viruses are present. This type of study should contribute to our understanding of the potential importance of omamental plants as sources of emerging viruses in Europe, and more globally of the respective contributions of crops, wild plants and ornamentals to plant virus epiderniology.
Published: 2013

144. Deep Sequencing of Recombinant Virus Populations in Transgenic and Nontransgenic Plants Infected with Cucumber mosaic virus

Author: Mireille Jacquemond, M. Morroni, Mark Tepfer, Biosafety Outstn, Plant Virol Grp, ICGEB Biosafety Outstation, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AIP Bio-Resources, Institut National de la Recherche Agronomique (INRA), Fondazione Cassamarca, and Unité de Pathologie Végétale (PV)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Physiology, Transgene, Molecular Sequence Data, TOMATO ASPERMY CUCUMOVIRUS, Genome, Viral, Biology, Recombinant virus, Cucumovirus, Virus, Deep sequencing, law.invention, Cucumber mosaic virus, 03 medical and health sciences, symbols.namesake, law, Tobacco, Gene, 3' Untranslated Regions, 030304 developmental biology, Sanger sequencing, Genetics, 0303 health sciences, Base Sequence, RELATIVE FITNESS, 030306 microbiology, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, RNA, Genetic Variation, High-Throughput Nucleotide Sequencing, food and beverages, General Medicine, Plants, Genetically Modified, Virology, RISKS, GENOMIC RNAS, symbols, Recombinant DNA, RNA, RNA, Viral, Capsid Proteins, Agronomy and Crop Science, Sequence Alignment, RESISTANCE
Abstract: Recombination is a major source of virus variability, and the question of whether novel recombinant viruses would emerge in transgenic plants expressing viral sequences has been a biosafety issue. We describe the results of pyrosequencing the recombinant viral RNAs appearing in transgenic plants expressing the coat protein (CP) gene and 3′ noncoding region of Cucumber mosaic virus RNA3, as well as in nontransgenic controls. The populations of recombinants in both transgenic and nontransgenic plants were similar to those previously described from Sanger sequencing but many more recombinant types were observed, including a novel class of large deletions removing all or nearly the entire CP gene. These results show that populations of recombinant viral genomes arising de novo can be characterized in detail by pyrosequencing, and confirm that the transgenic plants did not harbor novel recombinants of biosafety concern.
Published: 2013
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145. Cucumber mosaic virus populations in Tunisian pepper crops are mainly composed of virus reassortants with resistance-breaking properties

Author: Hatem Fakhfakh, M. Tepfer, Mireille Jacquemond, H. Ben Tamarzizt, Gregory Girardot, Josselin Montarry, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), 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 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, 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 Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Station de Pathologie Végétale (AVI-PATHO), Faculté des Sciences de Tunis, AGROCAMPUS OUEST-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: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Reassortment, Plant Science, Horticulture, Biology, 01 natural sciences, Virus, Cucumber mosaic virus, 03 medical and health sciences, pepper, resistance-breaking capacity, Pepper, Genetics, Nomenclature, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, Resistance (ecology), Haplotype, Virology, recombination, reassortment, epidemiology, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Cucumber mosaic virus is one of the most prevalent viruses in Tunisian pepper crops, where it has been detected in 68% of plants developing mosaic symptoms, making it essential to characterize the molecular and biological properties of local CMV populations. Two hundred and seventy-eight isolates collected in the late 1990s, 2006 and 2008–2010 were characterized genetically. Isolates belonging to the three phylogenetic subgroups of CMV (IA, IB and II) were detected, but surprisingly, 90% of the isolates were reassortants between subgroups IA and IB, with two predominant haplotypes, IB-IA-IA and IB-IA-IB (nomenclature according to the subgrouping of the three genomic RNAs). The IB-IA-IA haplotype was present in all regions surveyed, while IB-IA-IB was observed only in northern Tunisia. This situation was unexpected, because CMV reassortants were previously thought to be counterselected in nature, and this raises the questions of the origin of IB strains in Tunisia and of the widespread distribution of these two reassortant types. Phylogenetic studies revealed low diversity within haplotypes, whatever the locality or the year of sampling. However, analysis of haplotype frequencies revealed a high genetic differentiation between CMV populations, which was better explained by the localities of sampling than by years. Geographic distances affected the differentiation of CMV populations, mainly between north and central Tunisia. When tested against a polygenic resistance to CMV movement in pepper, 55 of 57 isolates tested were able to break the resistance, indicating that this resistance would not be useful for controlling CMV in Tunisian pepper fields.
Published: 2013
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146. Farther, slower, stronger: how the plant genetic background protects a major resistance gene from breakdown

Author: Quenouille, Julie, Montarry, Josselin, Palloix, Alain, Moury, Benoît, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), 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, the Comité Technique Permanent de la Sélection (CTPS, French Ministry of Agriculture and Fisheries), the Agence Nationale de la Recherche (ANR), the Pôle Européen d'Innovation Fruits et Légumes (PEIFL), the Région Provence Alpes Côte d'Azur (PACA), Gautier Semences, Clause Vegetable Seeds, Vilmorin SA, Rijk Zwaan, Sakata Vegetables Europe, AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Unité de Pathologie Végétale (PV), Génétique et Amélioration des Fruits et Légumes (GAFL), 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), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Multifactorial Inheritance, Ribonucleoproteins, Mutation, Potyvirus, Genome, Viral, Original Articles, Viral Nonstructural Proteins, Capsicum, Genes, Plant, Models, Biological, Disease Resistance, Plant Diseases
Abstract: International audience; Genetic resistance provides efficient control of crop diseases, but is limited by pathogen evolution capacities which often result in resistance breakdown. It has been demonstrated recently, in three different pathosystems, that polygenic resistances combining a major-effect gene and quantitative resistance controlled by the genetic background are more durable than monogenic resistances (with the same major gene in a susceptible genetic background), but the underlying mechanisms are unknown. Using the pepper–Potato virus Y system, we examined three mechanisms that could account for the greater durability of the polygenic resistances: (i) the additional quantitative resistance conferred by the genetic background; (ii) the increase in the number of mutations required for resistance breakdown; and (iii) the slower selection of adapted resistance-breaking mutants within the viral population. The three mechanisms were experimentally validated. The first explained a large part of the variation in resistance breakdown frequency and is therefore expected to be a major determinant of resistance durability. Quantitative resistance factors also had an influence on the second mechanism by modifying the virus mutational pathways towards resistance breakdown and could also have an influence on the third mechanism by increasing genetic drift effects on the viral population. The relevance of these results for other plant–pathogen systems and their importance in plant breeding are discussed.
Published: 2013
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147. Effet des rayonnements UV-C sur la résistance de la laitue Romaine contre Botrytis cinerea

Author: Ouhibi, Chayma, Attia, Houneida, Nicot, Philippe C., Urban, Laurent, Lachaâl, Mokhtar, Aarrouf, Jawad, Déposants HAL-Avignon, bibliothèque Universitaire, EA 4279 Laboratoire Physiologie des Fruits et Légumes, Avignon Université (AU), Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Physiologie et Biochimie de la Tolérance au Sel des Plantes, Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM)-Université de Tunis El Manar (UTM), Station de Pathologie Végétale (AVI-PATHO), and Faculté des Sciences de Tunis
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2013

148. Putting problem formulation at the forefront of GMO risk analysis

Author: Mark Tepfer, Wendy Craig, Monica Racovita, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Biosafety unit, ICGEB, Biosafet unit, Bill and Melinda gates fundation, Unité de Pathologie Végétale (PV), and Craig, Wendy
Subjects: Risk analysis, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, problem formulation, training, Organisms, Genetically Modified, Process (engineering), GMO, risk analysis, Stakeholder, risk assessment, ogm, Risk analysis (engineering), Research Design, Order (exchange), Business, Risk assessment, Agronomy and Crop Science, GMO, problem formulation,risk analysis, risk assessment, training, analyse de risque, Food Science, Biotechnology
Abstract: When applying risk assessment and the broader process of risk analysis to decisions regarding the dissemination of genetically modified organisms (GMOs), the process has a tendency to become remarkably complex. Further, as greater numbers of countries consider authorising the large-scale dissemination of GMOs, and as GMOs with more complex traits reach late stages of development, there has been increasing concern about the burden posed by the complexity of risk analysis. We present here an improved approach for GMO risk analysis that gives a central role to problem formulation. Further, the risk analysis strategy has been clarified and simplified in order to make rigorously scientific risk assessment and risk analysis more broadly accessible to diverse stakeholder groups.
Published: 2013
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149. Évolution des populations aériennes de [i]Botrytis cinerea[/i] : un exemple d’aéromicrobiologie

Author: Leyronas, Christel, Halkett, Fabien, DUFFAUD, Magali, Nicot, Philippe, Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Unité de Pathologie Végétale (PV), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: agent phytopathogène, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, caractérisation, aérobiologie, quantification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: absent
Published: 2012

150. Exploiting naturals factors in greenhouses to stimulate plants’ defences and the concentrations in bioactive compounds of fruits and vegetables

Author: Urban, Laurent, Aarrouf, Jawad, Nicot, Philippe, EA 4279 Laboratoire Physiologie des Fruits et Légumes, Avignon Université (AU), Station de Pathologie Végétale (AVI-PATHO), and Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, plastic film cover, secondary metabolites, [SDV]Life Sciences [q-bio], food and beverages, fruit
Abstract: International audience; Many secondary metabolites, such as carotenoids, flavonoids, glucosinolates, contribute to the health benefits of fruits and vegetables. It has been repeatedly observed that environmental factors can be used as a powerful lever, besides genetic factors, to increase the concentrations in bioactive compounds of fruits and vegetables. More specifically, it has been observed in a large range of vegetables, including lettuce, pepper, tomato, and strawberry, that high light intensity, red and UV light, high electrical conductivity of the nutrient solution, elevated CO2, may substantially enhance concentrations in phenolic compounds (much more than 100 % in several cases). Ecological, deterministic theories, such as the Growth Differenciation Balance Hypothesis, as well as the physiological insight we have gained in the role played by stress and nitrogen deprivation on flux-determining enzymes of the synthetic pathway of phenolic compounds, such as phenylammonium lyase and chalcone synthase, provide the scientific basis for the observed effects. Interestingly, numerous secondary metabolites, many of them phenolic compounds, which contribute to the health benefits of fruits and vegetables, are also involved in plants’ defences. Stressing conditions and nitrogen deprivation represent the two most important factors that can be easily and currently exploited by growers in greenhouses and soilless systems to stimulate synthesis and accumulation of phenolic compounds
Published: 2012

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