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1. Botrytis cinerea strains infecting grapevine and tomato display contrasted repertoires of accessory chromosomes, transposons and small RNAs

Author

Simon, Adeline, Mercier, Alex, Gladieux, Pierre, Poinssot, Benoît, Walker, Anne-Sophie, and Viaud, Muriel

Subjects
Archaeology, CC1-960, Science
Abstract

The fungus Botrytis cinerea is a polyphagous pathogen that encompasses multiple host-specialized lineages. While several secreted proteins, secondary metabolites and retrotransposons-derived small RNAs have been characterized as virulence factors, their roles in host specialization remain unknown. The aim of this study was to identify the genomic correlates of host-specialization in populations of B. cinerea associated with grapevine and tomato. Using PacBio sequencing, we produced complete assemblies of the genomes of strains Sl3 and Vv3 that represent the French populations T and G1 of B. cinerea, specialized on tomato and grapevine, respectively. Both assemblies revealed 16 core chromosomes that were highly syntenic with chromosomes of the reference strain B05.10. The main sources of variation in gene content were the subtelomeric regions and the accessory chromosomes, especially the chromosome BCIN19 of Vv3 that was absent in Sl3 and B05.10. The repertoires and density of transposable elements were clearly different between the genomes of Sl3 and Vv3 with a larger number of subfamilies (26) and a greater genome coverage in Vv3 (7.7%) than in Sl3 (14 subfamilies, 4.5% coverage). An Helitron-like element was found in almost all subtelomeric regions of the Vv3 genome, in particular in the flanking regions of a highly duplicated gene encoding a Telomere-Linked Helicase, while both features were absent from the Sl3 and B05.10 genomes. Different retrotransposons in the Sl3 and the Vv3 strains resulted in the synthesis of distinct sets of small RNAs. Finally, extending the study to additional strains indicated that the accessory chromosome BCIN19 and the small RNAs producing retrotransposons Copia_4 and Gypsy_7 are common features of the G1 population that are scarcely if ever found in strains isolated from other populations. This research reveals that accessory chromosomes, repertoires of transposons and their derived small RNAs differ between populations of B. cinerea specialized on different hosts. The genomic data characterized in our study pave the way for further studies aiming at investigating the molecular mechanisms underpinning host specialization in a polyphagous pathogen.

Published
2022
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4. Building integrated plant health surveillance: A proactive research agenda for anticipating and mitigating disease and pest emergence

Author

Soubeyrand, Samuel, Estoup, Arnaud, Cruaud, Astrid, Malembic-Maher, S., Meynard, Charles, Ravigne, Virginie, Barbier, M., Barrès, Benoit, Berthier, Karine, Boitard, S., Dallot, Sylvie, Gaba, Sabrina, Grosdidier, Marie, Hannachi, Mourad, Jacques, Marie Agnès, Leclerc, M., Lucas, P., Martinetti, D., Mougel, Christophe, Robert, Corinne, Roques, Alain, Rossi, Jean-Pierre, Suffert, Frédéric, Abad, Pierre, Auger-Rozenberg, M.A., Ay, Jean-Sauveur, Bardin, Marc, Bernard, H., Bohan, David A., Candresse, Thierry, Castagnone-Sereno, Philippe, Danchin, Etienne G. J., Delmas, Chloé E. L., Ezanno, Pauline, Fabre, Frédéric, Facon, Benoît, Gabriel, E., Gaudin, Jacqueline, Gauffre, Bertrand, Gautier, Mathieu, Guinat, Claire, Lavigne, Claire, Lemaire, Olivier, Martinez, C., Michel, L., Moury, Benoit, Nam, Kiwoong, Nédellec, Claire, Ogliastro, Mylène, Papaïx, Julien, Parisey, N., Poggi, Sylvain, Radici, A., Rasplus, Jean-Yves, Reboud, Xavier, Robin, C., Roche, Mathieu, Rusch, Adrien, Sauvion, Nicolas, Streito, Jean-Claude, Verdin, Eric, Walker, Anne Sophie, Xuereb, Anne, Thébaud, Gaël, Morris, Cindy E., Soubeyrand, Samuel, Estoup, Arnaud, Cruaud, Astrid, Malembic-Maher, S., Meynard, Charles, Ravigne, Virginie, Barbier, M., Barrès, Benoit, Berthier, Karine, Boitard, S., Dallot, Sylvie, Gaba, Sabrina, Grosdidier, Marie, Hannachi, Mourad, Jacques, Marie Agnès, Leclerc, M., Lucas, P., Martinetti, D., Mougel, Christophe, Robert, Corinne, Roques, Alain, Rossi, Jean-Pierre, Suffert, Frédéric, Abad, Pierre, Auger-Rozenberg, M.A., Ay, Jean-Sauveur, Bardin, Marc, Bernard, H., Bohan, David A., Candresse, Thierry, Castagnone-Sereno, Philippe, Danchin, Etienne G. J., Delmas, Chloé E. L., Ezanno, Pauline, Fabre, Frédéric, Facon, Benoît, Gabriel, E., Gaudin, Jacqueline, Gauffre, Bertrand, Gautier, Mathieu, Guinat, Claire, Lavigne, Claire, Lemaire, Olivier, Martinez, C., Michel, L., Moury, Benoit, Nam, Kiwoong, Nédellec, Claire, Ogliastro, Mylène, Papaïx, Julien, Parisey, N., Poggi, Sylvain, Radici, A., Rasplus, Jean-Yves, Reboud, Xavier, Robin, C., Roche, Mathieu, Rusch, Adrien, Sauvion, Nicolas, Streito, Jean-Claude, Verdin, Eric, Walker, Anne Sophie, Xuereb, Anne, Thébaud, Gaël, and Morris, Cindy E.

Abstract

In an era marked by rapid global changes, the reinforcement and modernization of plant health surveillance systems have become imperative. Sixty-five scientists present here a research agenda for an enhanced and modernized plant health surveillance to anticipate and mitigate disease and pest emergence. Our approach integrates a wide range of scientific fields (from life, social, physical and engineering sciences) and identifies the key knowledge gaps, focusing on anticipation, risk assessment, early detection, and multi-actor collaboration. The research directions we propose are organized around four complementary thematic axes. The first axis is the anticipation of pest emergence, encompassing innovative forecasting, adaptive potential, and the effects of climatic and cropping system changes. The second axis addresses the use of versatile broad-spectrum surveillance tools, including molecular or imaging diagnostics supported by artificial intelligence, and monitoring generic matrices such as air and water. The third axis focuses on surveillance of known pests from new perspectives, i.e., using novel approaches to detect known species but also anticipating and detecting, within a species, the populations or genotypes that pose a higher risk. The fourth axis advocates the management of plant health as a commons through the establishment of multi-actor and cooperative surveillance systems for long-term data-driven alert systems and information dissemination. We stress the importance of integrating data and information from multiple sources through open science databases and metadata, alongside developing methods for interpolating and extrapolating incomplete data. Finally, we advocate an Integrated Health Surveillance approach in the One Health context, favoring tailored and versatile solutions to plant health problems and recognizing the interconnected risks to the health of plants, humans, animals and the environment, including food insecurity, pesticide residues, e

Published
2024

5. Plan Ecophyto : tout comprendre aux annonces du gouvernement

Author

Barbu, Corentin, Aulagnier, Alexis, Walker, Anne Sophie, Labeyrie, Baptiste, Maugin, Emilie, Le Bellec, Fabrice, Omnes, François, Richard, Freddie-Jeanne, Ozier-Lafontaine, Harry, Aubertot, Jean-Noël, Gallien, Marc, Garnault, Maxime, Gouy Boussada, Véronique, Humbert, Laura, Barbu, Corentin, Aulagnier, Alexis, Walker, Anne Sophie, Labeyrie, Baptiste, Maugin, Emilie, Le Bellec, Fabrice, Omnes, François, Richard, Freddie-Jeanne, Ozier-Lafontaine, Harry, Aubertot, Jean-Noël, Gallien, Marc, Garnault, Maxime, Gouy Boussada, Véronique, and Humbert, Laura

Published
2024

6. Evaluation of two indicators according to the objectives of the Sustainable Use of pesticides Directive (SUD). A French case study

Author

Garnault, Maxime, Barbu, Corentin, Aulagnier, Alexis, Bockstaller, Christian, Gouy-Boussada, Véronique, Kudsk, Per, Labeyrie, Baptiste, Le Bellec, Fabrice, Dachbrodt-­Saaydeh, Silke, Richard, Freddie-Jeanne, Gallien, Marc, Grimonprez, Benoît, Klinghammer, Alfred, Landrieu, Tanguy, Maugin, Emilie, Ozier-Lafontaine, Harry, Strassemeyer, Jörn, Walker, Anne Sophie, Humbert, Laura, Omnes, François, Aubertot, Jean-Noël, Garnault, Maxime, Barbu, Corentin, Aulagnier, Alexis, Bockstaller, Christian, Gouy-Boussada, Véronique, Kudsk, Per, Labeyrie, Baptiste, Le Bellec, Fabrice, Dachbrodt-­Saaydeh, Silke, Richard, Freddie-Jeanne, Gallien, Marc, Grimonprez, Benoît, Klinghammer, Alfred, Landrieu, Tanguy, Maugin, Emilie, Ozier-Lafontaine, Harry, Strassemeyer, Jörn, Walker, Anne Sophie, Humbert, Laura, Omnes, François, and Aubertot, Jean-Noël

Abstract

The European agricultural protests of 2023/2024 have prompted a reassessment of public policies at the EU level with the SUR put on a stand still. In France, in early 2024, the government replaced the historical monitoring indicator "NoDU'' with the European Harmonized Risk Indicator HRI1 to monitor the progress in the use of Plant Protection Products (PPP) in its National Action Plan (NAP). This study aimed to assess the relevance of these two indicators regarding the objectives outlined in the Sustainable Use of pesticides Directive (“SUD”) that defines the framework within which they operate. To this effect, we analyzed the PPPs they consider, the official calculation formulas, but also their past evolution and possible future evolutions through putative scenarios of changes in PPP use and regulation: ban or not; substitution or not; for the top 5 synthetic insecticides; all synthetic insecticides; glyphosate; mancozeb; and the top five active ingredients from HRI1 risk group 3 (candidates for substitution). French PPP sales data from 2011 to 2021 were used for past evolutions and we used the last available figures in France, 2021, for simulations. Designed to monitor the use of PPPs by farmers, the NoDU mostly monitors achievement with regards to one aim of the SUD: to "reduce dependency on the use of pesticides" and promote "the use of Integrated Pest Management". Its value does not change with the mere substitution of a product by another, even if the second is deemed less toxic. This limits its ability to assess the "risks and impacts of pesticide use on human health and the environment", the first aim of the directive. The HRI1 indicator is not supposed to strictly quantify the use of PPP and was found to inadequately reflect significant changes in PPP use, but also in the induced risk: 1) changes of use without a ban on a substance are limited and as such, past correlation of HRI1 with the QAI of the fourth group (banned PPPs) is very high (0.90); 2) the im

Published
2024

7. Preventing multiple resistance above all: New insights for managing fungal adaptation.

Author

Ballu, Agathe, Ugazio, Claire, Duplaix, Clémentine, Noly, Alicia, Wullschleger, Juerg, Torriani, Stefano F. F., Dérédec, Anne, Carpentier, Florence, and Walker, Anne‐Sophie

Subjects
PLANT protection, SPATIAL variation, FOOD security, PHYSIOLOGICAL adaptation
Abstract

Sustainable crop protection is vital for food security, yet it is under threat due to the adaptation of a diverse and evolving pathogen population. Resistance can be managed by maximising the diversity of selection pressure through dose variation and the spatial and temporal combination of active ingredients. This study explores the interplay between operational drivers for maximising the sustainability of management strategies in relation to the resistance status of fungal populations. We applied an experimental evolution approach to three artificial populations of Zymoseptoria tritici, an economically significant wheat pathogen, each differing in initial resistance status. Our findings reveal that diversified selection pressure curtails the selection of resistance in naïve populations and those with low frequencies of single resistance. Increasing the number of modes of action most effectively delays resistance development, surpassing the increase in the number of fungicides, fungicide choice based on resistance risk, and temporal variation in fungicide exposure. However, this approach favours generalism in the evolved populations. The prior presence of multiple resistant isolates and their subsequent selection in populations override the effects of diversity in management strategies, thereby invalidating any universal ranking. Therefore, the initial resistance composition must be specifically considered in sustainable resistance management to address real‐world field situations. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Metagenomic Next-Generation Sequencing (mNGS) Data Reveal the Phyllosphere Microbiome of Wheat Plants Infected by the Fungal Pathogen Zymoseptoria tritici

Author

Barroso-Bergadà, Didac, primary, Massot, Marie, additional, Vignolles, Noémie, additional, Faivre d'Arcier, Julie, additional, Chancerel, Emilie, additional, Guichoux, Erwan, additional, Walker, Anne-Sophie, additional, Vacher, Corinne, additional, Bohan, David A., additional, Laval, Valérie, additional, and Suffert, Frédéric, additional

Published
2022
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15. Monitoring systems for resistance to plant protection products across the world: Between redundancy and complementarity

Author

network, R4P, Barrès, Benoit, Corio-Costet, Marie-France, Debieu, Daniele, Délye, Christophe, Fillinger, Sabine, Gauffre, Bertrand, Le Goff, Gaëlle, Grosman, Jacques, Hannachi, Mourad, DE JERPHANION, Pauline, Jorgensen, Lise Nistrup, Plantamp, Christophe, Siegwart, Myriam, Walker, Anne-Sophie, CAractérisation et Suivi des Phénomènes d'Evolution de Résistance aux pesticides (CASPER), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Direction Régionale de l'Alimentation, de l'Agriculture et de la Forêt Rhône-Alpes (DRAAF Rhône Alpes), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Aarhus University [Aarhus], French Agency for Food, Environmental and Occupational Health & Safety (ANSES) via the tax on sales of plant protection products, and Plant Health division of INRAE

Subjects
0106 biological sciences, 01 natural sciences, 03 medical and health sciences, herbicide, fungicide, Redundancy (engineering), institutional analysis and development, Human Development Index, health care economics and organizations, 030304 developmental biology, 0303 health sciences, Resistance (ecology), insecticide, Monitoring system, General Medicine, Environmental economics, pesticide resistance monitoring, Resistance monitoring, Reliability engineering, 010602 entomology, Insect Science, Complementarity (molecular biology), [SDE]Environmental Sciences, surveillance, Business, Agronomy and Crop Science
Abstract

BACKGROUNDMonitoring resistance to Plant Protection Products (PPPs) is crucial for understanding the evolution of resistances in bioagressors, thereby allowing scientists to design sound bioagressor management strategies. Globally, resistance monitoring is implemented by a wide range of actors that fall into three distinct categories: academic, governmental, and private. The purpose of this study was to investigate worldwide diversity in PPP resistance monitoring systems, and to shed light on their different facets.RESULTSA large survey involving 162 experts from 48 countries made it possible to identify and analyze 250 resistance monitoring systems. Through an in-depth analysis, the features of the different monitoring systems were identified. The main factor differentiating monitoring systems was essentially the capabilities (funding, manpower, technology, etc.) of the actors involved in each system. In most countries, and especially in those with a high Human Development Index, academic, governmental, and private monitoring systems coexist. Overall, systems focus far more on monitoring established resistances than on the detection of emerging resistances. Governmental and private resistance monitoring systems generally have considerable capacities to generate data, whereas academic resistance monitoring systems are more specialized. Governmental actors federate and enroll a wider variety of stakeholders.CONCLUSIONThe results show functional complementarities between the coexisting actors in countries where they coexist. We suggest PPP resistance monitoring might be enhanced if the different actors focus more on detecting emerging resistances (and associated benefits) and increase collaborative and collective efforts and transparency.

Published
2021
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18. Report on the Annual Meeting of the Working Croup 'Host-Parasite Interactions'

Author

Conrath, Uwe, Hoefle, Caroline, Schultheiss, Holger, Eichmann, Ruth, Frank, Markus, Hueckelhoven, Ralph, Pretsch, Klara, Kemen, Ariane, Kemen, Eric, Geiger, Matthias, Mendgen, Kurt, Voegele, Ralf T., Himmelbach, Axel, Liu, Luo, Schweizer, Patrick, Dirks, Mareike E., Richter, Carolin, Moerschbacher, Bruno M., Djulic, Alma, Doehlemann, Gunther, Reißmann, Stefanie, Fleckenstein, Martin, Kahmann, Regine, Friehe, Sven, Schlaich, Nikolaus L., Gay, Alexandra, Zimmermann, Grit, Goellner, Katharina, Langenbach, Caspar, Schaffrath, Ulrich, Kretschmer, Matthias, Leroch, Michaela, Wiwiorra, Melanie, Schoonbeek, Henk-Jan, Walker, Anne-Sophie, Leroux, Pierre, Fillinger, Sabine, de Waard, Maarten, Hahn, Matthias, Moldenhauer, Jennifer, van der Westhuizen, Amie J., Prins, Renée, Pretorius, Zacharias A., Schäfer, Patrick, Pfiffi, Stefanie, Sonnewald, Sophia, Waller, Frank, Pons-Kühnemann, Jörn, Sonnewald, Uwe, Kogel, Karl-Heinz, Paulert, Roberta, Stadnik, Marciel, Schmitz, Gudrun, Spees, Nicole, Behr, Michael, Deising, Holger B., and Wirsel, Stefan G.R.

Published
2008

20. NGS data reveals the phyllosphere microbiome of wheat plants infected by the fungal pathogen Zymoseptoria tritici

Author

Barroso-Bergada, Didac, primary, Massot, Marie, additional, Vignolles, Noémie, additional, d’Arcier, Julie Faivre, additional, Chancerel, Emilie, additional, Guichoux, Erwan, additional, Walker, Anne-Sophie, additional, Vacher, Corinne, additional, Bohan, David A., additional, Laval, Valérie, additional, and Suffert, Frédéric, additional

Published
2022
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30. USE OF 4-PHENYLBUTYRIC ACID AND/OR 3-PHENYLBUTYRIC ACID AND/OR 2-PHENYLBUTYRIC ACID IN PREVENTING AND TREATING CRYPTOGAMIC DISEASES

Author

Cacas, Jean‐luc, Vasselon, Damien, Lamotte, Olivier, Poinssot, Benoit, Walker, Anne-Sophie, and MILLOT, Dominique

Subjects
[SDV] Life Sciences [q-bio]
Abstract

The present invention relates to the use of 2-phenylbutyric acid or 3-phenylbutyric acid or 4-phenylbutyric acid, or a salt thereof, or a combination thereof, to combat cryptogamic diseases which are caused by fungi or oomycetes. The present invention also relates to the use of these compounds and these combinations as fungicidal or fungistatic agents in preventing or curing cryptogamic diseases., La présente invention concerne l'utilisation de l'acide 2-phénylbutyrique, ou de l'acide 3-phénylbutyrique, ou de l'acide 4-phénylbutyrique, ou de l'un de leurs sels, ou de l'une de leurs combinaisons, pour lutter contre les maladies cryptogamiques causées par les champignons et les oomycètes. La présente invention porte également sur l'utilisation de ces composés et de ces combinaisons comme agents fongicides ou fongistatiques pour la prévention ou le traitement curatif de maladies cryptogamiques.

Published
2021

31. Large‐scale study validates that regional fungicide applications are major determinants of resistance evolution in the wheat pathogen Zymoseptoria tritici in France

Author

Garnault, Maxime, Duplaix, Clémentine, Leroux, Pierre, Couleaud, Gilles, David, Olivier, Walker, Anne-Sophie, Carpentier, Florence, Garnault, Maxime, Duplaix, Clémentine, Leroux, Pierre, Couleaud, Gilles, David, Olivier, Walker, Anne-Sophie, and Carpentier, Florence

Abstract

In modern cropping systems, the near-universal use of plant protection products selects for resistance in pest populations. The emergence and evolution of this adaptive trait threaten treatment efficacy. We identified determinants of fungicide resistance evolution and quantified their effects at a large spatiotemporal scale. We focused on Zymoseptoria tritici, which causes leaf blotch in wheat. Phenotypes of qualitative or quantitative resistance to various fungicides were monitored annually, from 2004 to 2017, at about 70 sites throughout 22 regions of France (territorial units of 25000km2 on average). We modelled changes in resistance frequency with regional anti-Septoria fungicide use, yield losses due to the disease and the regional area under organic wheat. The major driver of resistance dynamics was fungicide use at the regional scale. We estimated its effect on the increase in resistance and relative apparent fitness of each resistance phenotype. The predictions of the model replicated the spatiotemporal patterns of resistance observed in field populations (R2 from 0.56 to 0.82). The evolution of fungicide resistance is mainly determined at the regional scale. This study therefore showed that collective management at the regional scale could effectively complete local actions.This article is protected by copyright. All rights reserved.

Published
2021

33. Prévenir et gérer les résistances aux produits phyto: Pour limiter la diffusion de bioagresseurs résistants aux pratiques de contrôle, deux principes sont à retenir : diversité et efficacité des principes

Author

R4P (Réseau de Réflexion et de Recherches sur les Résistances aux Pesticides), ., Barrès, Benoît, Corio-Costet, Marie-France, Debieu, Danièle, Délye, Christophe, Fillinger, Sabine, Gauffre, Bertrand, Hannachi, Mourad, Grosman, Jacques, Le Goff, Gaëlle, Plantamp, Christophe, Siegwart, Myriam, Walker, Anne-Sophie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Direction Générale de l'Alimentation (DGAL), Ministère de l'agriculture, de l'agroalimentaire et de la forêt, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA)

Subjects
Résistance aux produits de protection des plantes, [SDE]Environmental Sciences, Produit phytosanitaire, Mode d'action, Bioagresseur
Published
2020

34. Les 'mots' de la résistance

Author

Network, R4p, Barrès, Benoît, Corio-Costet, Marie-France, Debieu, Daniele, Délye, Christophe, Fillinger, Sabine, Gauffre, Bertrand, Hannachi, Mourad, Le Goff, Gaëlle, Plantamp, Christophe, Siegwart, Myriam, Walker, Anne-Sophie, and DESAILLY, Marion

Subjects
[SDE] Environmental Sciences, Pathologie végétale, Produit phytopharmaceutique, Protection des plantes
Abstract

Avant d'entamer le dossier, voici un petit glossaire à l'usage des gestionnaires de la résistance aux produits phytopharmaceutiques.La résistance aux PPP est un phénomène souvent complexe, faisant appel à des notions de biochimie, génétique, sciences de l’évolution. De ce fait, pour apprécier au mieux les articles de ce dossier, il apparaît utile d’avoir sous la main un mémento donnant une définition scientifique des termes les plus courants.

Published
2020

36. The genetic basis of resistance to anticoagulants in rodents

Author

Pelz, Hans-Joachim, Rost, Simone, Hunerberg, Mirja, Fregin, Andreas, Heiberg, Ann-Charlotte, Baert, Kristof, MacNicoll, Alan D., Prescott, Colin V., Walker, Anne-Sophie, Oldenburg, Johannes, and Muller, Clemens R.

Subjects
Rodenticides -- Research, Genetics -- Research, Anticoagulants (Medicine) -- Research, Anticoagulants (Medicine) -- Usage, Anticoagulants (Medicine) -- Genetic aspects, Genetic research, Biological sciences
Abstract

Anticoagulant compounds, i.e., derivatives of either 4-hydroxycoumarin (e.g., warfarin, bromadiolone) or indane-l,3-dione (e.g., diphacinone, chlorophacinone), have been in worldwide use as rodenticides for >50 years. These compounds inhibit blood coagulation by repression of the vitamin K reductase reaction (VKOR). Anticoagulant-resistant rodent populations have been reported from many countries and pose a considerable problem for pest control. Resistance is transmitted as an autosomal dominant trait although, until recently, the basic genetic mutation was unknown. Here, we report on the identification of eight different mutations in the VKORC1 gene in resistant laboratory strains of brown rats and house mice and in wild-caught brown rats from various locations in Europe with five of these mutations affecting only two amino acids (Tyr139Cys, Tyr139Ser, Tyr139Phe and Leu128Gln, Leu128Ser). By recombinant expression of VKORC1 constructs in HEK293 cells we demonstrate that mutations at Tyr139 confer resistance to warfarin at variable degrees while the other mutations, in addition, dramatically reduce VKOR activity. Our data strongly argue for at least seven independent mutation events in brown rats and two in mice. They suggest that mutations in VKORC1 are the genetic basis of anticoagulant resistance in wild populations of rodents, although the mutations alone do not explain all aspects of resistance that have been reported. We hypothesize that these mutations, apart from generating structural changes in the VKORC1 protein, may induce compensatory mechanisms to maintain blood clotting. Our findings provide the basis for a DNA-based field monitoring of anticoagulant resistance in rodents.

Published
2005

39. Directed evolution predicts cytochrome b G37V target site modification as probable adaptive mechanism towards the QiI fungicide fenpicoxamid in Zymoseptoria tritici.

Author

Fouché, Guillaume, Michel, Thomas, Lalève, Anaïs, Wang, Nick X., Young, David H., Meunier, Brigitte, Debieu, Danièle, Fillinger, Sabine, and Walker, Anne‐Sophie

Subjects
CYTOCHROME b, FUNGICIDES, STROBILURINS, PATHOGENIC fungi, PROOF of concept, QUINONE
Abstract

Summary: Acquired resistance is a threat to antifungal efficacy in medicine and agriculture. The diversity of possible resistance mechanisms and highly adaptive traits of pathogens make it difficult to predict evolutionary outcomes of treatments. We used directed evolution as an approach to assess the resistance risk to the new fungicide fenpicoxamid in the wheat pathogenic fungus Zymoseptoria tritici. Fenpicoxamid inhibits complex III of the respiratory chain at the ubiquinone reduction site (Qi site) of the mitochondrially encoded cytochrome b, a different site than the widely used strobilurins which inhibit the same complex at the ubiquinol oxidation site (Qo site). We identified the G37V change within the cytochrome b Qi site as the most likely resistance mechanism to be selected in Z. tritici. This change triggered high fenpicoxamid resistance and halved the enzymatic activity of cytochrome b, despite no significant penalty for in vitro growth. We identified negative cross‐resistance between isolates harbouring G37V or G143A, a Qo site change previously selected by strobilurins. Double mutants were less resistant to both QiIs and quinone outside inhibitors compared to single mutants. This work is a proof of concept that experimental evolution can be used to predict adaptation to fungicides and provides new perspectives for the management of QiIs. [ABSTRACT FROM AUTHOR]

Published
2022
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40. Assessing the risk of resistance towards SDHI fungicides in France

Author

Walker, Anne-Sophie, Gazeau, Gwilherm, Couleaud, Gilles, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COMUE), ARVALIS - Institut du végétal [Paris], and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
resistance, Botrytis cinerea, SDHI, [SDV]Life Sciences [q-bio], food and beverages, mutation
Abstract

Succinate dehydrogenase inhibitor (SDHI) fungicides have been registered since 2006 on a large number of crops in France and resistance has been detected in nine fungal species, including Botrytis cinerea, Ustilago nuda, Helminthosporium teres, Zymoseptoria tritici and Sclerotinia sclerotiorum. In most cases, resistance is associated with a wide variety of mutations in SDHI subunits B, C, or D. Depending on the mutation and the mutation location, contrasting levels of resistance and cross-resistance spectra are observed for SDHIs. Moreover, contrasted resistance costs (e. g. in B. cinerea) were also measured, depending on the mutation.In Z. tritici, the pathogen responsible for septoria leaf blotch on wheat, resistance is associated with two distinct mechanisms, not yet combined in populations. Increased efflux (leading to multidrug resistance or MDR) generates low levels of resistance to several modes of action, while target site-based resistance is associated with low to high resistance factors. Crosses between isolates carrying the two distinct mechanisms revealed semi-isogenic progeny that we used to characterize resistance. Progeny with both mechanisms of resistance had increased resistance factors and limited fitness penalty with regard to sexual and asexual traits. Population studies showed that resistance based on mutations in SDHI subunits is emerging in French populations and that MDR also evolves rapidly. This ultimately increases the risk of natural recombination by sexual reproduction between isolates carrying the two distinct mechanisms. Field trials identified treatment strategies most favorable for the selection of each mechanism and thus allowed for the design of specific resistance management strategies with regard to SDHI use.

Published
2019

41. Assessing the risk of resistance selection towards Qil fungicides in Zymoseptoria tritici

Author

FOUCHE, Guillaume, Walker, Anne-Sophie, Fillinger, Sabine, Meunier , Brigitte, Young, David, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Centre National de la Recherche Scientifique (CNRS), and Dow AgroSciences

Subjects
cytochrome b, Zymoseptoria tritici, fungicide resistance, Qil, antiresistance strategy, experimental evolution, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2018

42. Contrasted spatiotemporal dynamics of resistance and its drivers in the pathogenic fungus Zymoseptoria tritici in France revealed by statistical analysis

Author

GARNAULT, Maxime, Couleaud, Leroux, Pierre, Duplaix, Clémentine, David, Olivier, Carpentier, Florence, Walker, Anne-Sophie, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), and ARVALIS - Institut du végétal [Paris]

Subjects
modelling, [SDV]Life Sciences [q-bio], Zymoseptoria tritici, [SDE]Environmental Sciences, [INFO]Computer Science [cs], [MATH]Mathematics [math], spatio-temporal dynamics, fungicide resistance, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2018

43. Comment prévenir et gérer la résistance aux fongicides? La résistance de certaines maladies aux fongicides exige une utilisation raisonnée des traitements avec la mise en oeuvre de stratégies adaptées

Author

Walker, Anne-Sophie, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Université Paris Saclay (COmUE)

Subjects
alternance, mélange, fongicide, méthodes alternatives, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, résistance, stratégies anti-résistance, mosaïque, modulation de la dose, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2018

44. Population structure and host specialization in Botrytis cinerea

Author

Mercier, Alex, Simon, Adeline, Duplaix, Clémentine, Cuel, Marguerite, Pradier, Jean-Marc, Viaud, Muriel, Gladieux, Pierre, Walker, Anne-Sophie, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), 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'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
genome sequencing, Botrytis cinerea, [SDV]Life Sciences [q-bio], cross-inoculation test, [SDE]Environmental Sciences, population structure, adaptation, host specialization, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2018

45. Auteurs du site web Réseau de Réflexion et de Recherche sur la Résistance aux Pesticides (R4P) www.r4p-inra.fr

Author

Barrès, Benoit, Corio-Costet, M.-F., Debieu, Daniele, Délye, Christophe, Fillinger, Sabine, Grosman, Jacques, Le Goff, Gaëlle, Plantamp, Christophe, Siegwart, Myriam, Walker, Anne Sophie, and EL Mjiyad, Noureddine

Subjects
prévention, [SDE] Environmental Sciences, R4P, résistance, pesticide
Abstract

Réseau de Réflexion et de Recherche sur la Résistance aux Pesticides (R4P) : www.r4p-inra.frCe site met à disposition des outils et des informations sur la résistance aux produits de protection des plantes. Ces informations peuvent intéresser les professionnels impliqués dans la prévention et la gestion des résistances, des enseignants ou étudiants, et quiconque intéressé par cette thématique.Ring for Research and Reflection on Resistance to Pesticides (R4P) :www.r4p-inra.frThis site provides tools and information on resistance to plant protection products. This information may be of interest to professionals involved in the prevention and management of resistance, teachers or students, and anyone interested in this topic.

Published
2018

46. Strain effect on extracellular laccase activities from Botrytis cinerea

Author

Quijada Morin, Natalia, Garcia, François, Lambert, Karen, Walker, Anne-Sophie, Tiers, Laurent, Viaud, Muriel, Sauvage, Francois Xavier, Hirtz, Christophe, Saucier, Cédric, Sciences Pour l'Oenologie (SPO), 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)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Biolaffort Company, Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-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)

Subjects
moissisure de la grappe, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Laccase-3-BcLCC7, enzyme, Laccase-2-BcLCC2, spectrométrie de masse, mass spectrum analysis, botrytis cinerea, peptide, séquençage de gènes, laccase
Abstract

Background and Aims: Laccase enzymes produced by Botrytis cinerea are involved in the oxidation of phenolic substances during the development of grey mould, which causes significant economic losses. The aim of this work was to study the structural and activity characteristics of the laccase enzymes secreted by three B. cinerea strains that are involved in the development of grey mould. Methods and Results: Laccase enzymes obtained from three B. cinerea strains [one reference strain (B05.10) and two strains obtained from two French vineyards (VA612 and RM344)] were characterised. Analysis by LC-QTOF-MS revealed that the three strains contained a mixture of Laccase-2-BcLCC2 and Laccase-3-BcLCC7. The structural characteristics of the laccases from the three strains, such as molecular weight and glycosylation degree, were identical. Nevertheless, their catalytic activities were significantly different. Conclusions: Differences in catalytic activities could be due either to possible differences in the relative amount of Laccase-2- BcLCC2 and Laccase-3-BcLCC7 produced by each strain or to differences in the glycosidic fraction of the enzymes. Significance of the Study: The severity of the infection caused by B. cinerea may be not only related to the infection level but also to the strain involved.

Published
2018
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50. Population structure and host specialization in Botrytis cinerea

Author

Walker, Anne-Sophie, Mercier, Alex, Cuel, Marguerite, Pradier, Jean-Marc, Simon, Adeline, Viaud, Muriel, Gladieux, Pierre, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-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 de la Recherche Agronomique (INRA)-AgroParisTech, 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), Universidad de Chile. CHL., Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), and Institut 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
botritis cinerea, botrytis cinerea, adaptation, population structure, host specialization, genome, sequencing, cross-inoculation test, inoculations croisées, crossed inoculations, Mycology, champignon pathogène, host's specialization, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, fungal pathogen, génomique des populations, pathologie végétale, ComputingMilieux_MISCELLANEOUS, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, genomics of the populations, Vegetal Biology, Microbiology and Parasitology, food and beverages, Microbiologie et Parasitologie, Mycologie, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, spécialisation d'hôte, protection des cultures, Biologie végétale
Abstract

BGPI :équipe 5; The Botrytis genus encompasses more than 30 species, most of them being able to infect a restricted range of host plants. Nevertheless, B. cinerea is considered a generalist pathogen, recently found to infect 586 plant genera. This makes B. cinerea an interesting candidate to study ecological specialization. This was first approached while describing population structure in France, from strains collected on greenhouse tomato, grapevine, blackberry, strawberry and hydrangea. Understanding the causes of population subdivision is of fundamental importance, as studying barriers to gene flow between populations may reveal key aspects of the process of adaptive divergence and, for pathogens, may help forecasting disease emergence and implementing sound management strategies. Population genetics analyses revealed a weak association between population structure and geography, but a clear differentiation according to the host plant of origin, and especially for greenhouse tomato and grapevine. Host specialization was validated by cross-inoculation experiments, carried out in vitro on detached leaves. Genomes from strains contrasting for their specialization on tomato, grapevine, blackberry and hydrangea were Illumina-sequenced and genomic phylogeny analysis confirmed the similarities between genomes from strains collected on the same host. Population genomics analysis used to compare variation between and within lines of strains provided promising sets of genes that may induce host specialization. In addition to coding sequences, analysis of small RNAs from strains collected either on tomato or grapevine was initiated. Preliminary sequencing data suggest that these two populations have contrasted repertories of small RNAs. Further analysis and additional genomes and small RNA sequencing are required to definitely identify the determinants of host specialization. Our findings open up new perspectives for disease control by managing Botrytis hosts in agricultural landscapes, and reinforcing prophylactic measures.

Published
2017

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