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1. CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes

Author: Oliveira, Leonor, Chevrollier, Nicolas, Dallery, Jean-Felix, O’connell, Richard, Lebrun, Marc-Henri, Viaud, Muriel, Lespinet, Olivier, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Herbifun project 16-CE20-0023-01 ANR, ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Multidisciplinary, [SDV]Life Sciences [q-bio], Annotation, polyketide synthase, [SDE]Environmental Sciences, Software
Abstract: We report here a new application, CustomProteinSearch (CusProSe), whose purpose is to help users to search for proteins of interest based on their domain composition. The application is customizable. It consists of two independent tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows the iterative construction of Hidden Markov Model (HMM) profiles for conserved domains of selected protein sequences, while ProSeCDA scans a proteome of interest against an HMM profile database, and annotates identified proteins using user-defined rules. CusProSe was successfully used to identify, in fungal genomes, genes encoding key enzyme families involved in secondary metabolism, such as polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), hybrid PKS-NRPS and dimethylallyl tryptophan synthases (DMATS), as well as to characterize distinct terpene synthases (TS) sub-families. The highly configurable characteristics of this application makes it a generic tool, which allows the user to refine the function of predicted proteins, to extend detection to new enzymes families, and may also be applied to biological systems other than fungi and to other proteins than those involved in secondary metabolism.
Published: 2023

2. Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae

Author: João Leodato Nunes Maciel, Pierre Gladieux, Timothy Stitt, Paulo Cezar Ceresini, Nicholas J. Talbot, Nicola M. Cook, Dipali Rani Gupta, Moin U. Salam, Sébastien Ravel, Pallab Bhattacharjee, Daniel Croll, M. Golam Mahboob, Vanina Lilián Castroagudín, Tofazzal Islam, Daniel Swan, Md. Mahbubur Rahman, Juliana Teodora de Assis Reges, Md. Shaid Hossain, Antonio NhaniJúnior, Ronny Kellner, Musrat Zahan Surovy, Bruce A. McDonald, Darren M. Soanes, Antoine Persoons, Vanessa Bueno Sancho, Joe Win, Elisabeth Fournier, Sophien Kamoun, Marc-Henri Lebrun, Didier Tharreau, Diane G. O. Saunders, Islam, M. Tofazzal, Bangladesh Agricultural University, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), 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), University of Exeter, BBSRC Earlham Institute, Partenaires INRAE, Bandaglesh Agricultura Research Institute, Government of Western Australia, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Norwich Research Park, Max Planck Institute for Plant Breeding Research (MPIPZ), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, BBSRC John Innes Centre, World Bank under HEQEP : CP 2071, BBSRC fellowship in computational biology award, Brazilian National Council for Scientific and Technological Development - CNPq : Pq-2, 307295/2015-0, Sao Paulo Research Foundation - FAPESP : 2014/25904-2, 2013/10655-4, 2014/25904-2, Gatsby Charitable Foundation, BBSRC, NBI Computing infrastructure for Science (CiS) group, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Plant Pathology, UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI, College of Life and Environmental Sciences, Earlham Institute, Argo-Environmental Remote Sensing and Modeling Lab, Directorate of Grains Industry, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Universidade Estadual Paulista (Unesp), The Sainsbury Laboratory, Max Planck Institute for Plant Breeding Research, UMR 1290 Biologie et Gestion des Risques en agriculture BIOGER, John Innes Centre, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), M. TOFAZZAL ISLAM, BANGABANDHU SHEIKH MUJIBUR RAHMAN AGRICULTURAL UNIVERSITY, BANGLADESH, DANIEL CROLL, PIERRE GLADIEUX, DARREN M. SOANES, ANTOINE PERSOONS, PALLAB BHATTACHARJEE, SHAID HOSSAIN, DIPALI RANI GUPTA, MAHBUBUR RAHMAN, GOLAM MAHBOOB, NICOLA COOK, MOIN U. SALAM, MUSRAT ZAHAN SUROVY, VANESSA BUENO SANCHO, JOAO LEODATO NUNES MACIEL, CNPT, ANTONIO NHANI JUNIOR, CNPT, VANINA LILIÁN CASTROAGUDÍN, JULIANA T. DE ASSIS REGES, PAULO CEZAR CERESINI, SEBASTIEN RAVEL, RONNY KELLNER, ELISABETH FOURNIER, DIDIER THARREAU, MARC-HENRI LEBRUN, BRUCE A. MCDONALD, TIMOTHY STITT, DANIEL SWAN, NICHOLAS J. TALBOT, DIANE G. O. SAUNDERS, JOE WIN, and SOPHIEN KAMOUN.
Subjects: 0106 biological sciences, Veterinary medicine, Magnaporthe, 0211 other engineering and technologies, Plant Science, 02 engineering and technology, 01 natural sciences, magnaporthe oryzae, Population genomics, education.field_of_study, Vegetal Biology, wheat blast, Doença fúngica, food and beverages, 3. Good health, Épidémiologie, Fungal disease, phylogenomic analysis, Arroz, South american, General Agricultural and Biological Sciences, Lineage (genetic), Oryza sativa, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Wheat blast, Surveillance épidémiologique, education, Ecology, Evolution, Behavior and Systematics, Plant Diseases, H20 - Maladies des plantes, Oryza Sativa, Outbreak, Phytopathologie et phytopharmacie, Biotechnology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, field pathogenomics, Eleusine indica, 030104 developmental biology, Biologie végétale, Developmental Biology, 0301 basic medicine, Phylogénie, Physiology, [SDV]Life Sciences [q-bio], 010501 environmental sciences, Rice, maladie fongique, Génétique des populations, Structural Biology, Gene Expression Regulation, Plant, Triticum, 2. Zero hunger, Agricultural and Biological Sciences(all), 021107 urban & regional planning, Plant disease, Provenance, bangladesh, protection des cultures, Capim Pé de Galinha, Research Article, Distribution géographique, Phytopathology and phytopharmacy, Population, Fungus, Biology, Fungal diseases of plants, génomique, Surveillance des cultures, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 0105 earth and related environmental sciences, business.industry, Biochemistry, Genetics and Molecular Biology(all), Transcription génique, Field pathogenomics, Cell Biology, biology.organism_classification, Phylogenomic analysis, Magnaporthe oryzae, Brusone, Enquête pathologique, business, 010606 plant biology & botany
Abstract: Made available in DSpace on 2018-12-11T17:06:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-10-03 Background: In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16% of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100%. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields. Results: Reinoculation of seedlings with strains isolated from infected wheat grains showed wheat blast symptoms on leaves of wheat but not rice. Our phylogenomic and population genomic analyses revealed that the wheat blast outbreak in Bangladesh was most likely caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae. Conclusion: Our findings suggest that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent. Bangabandhu Sheikh Mujibur Rahman Agricultural University Department of Biotechnology Institute of Integrative Biology ETH Zurich Plant Pathology INRA UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI University of Exeter College of Life and Environmental Sciences Norwich Research Park Earlham Institute Bangladesh Agricultural Research Institute Argo-Environmental Remote Sensing and Modeling Lab, Joydebpur 1701 Directorate of Grains Industry Department of Agriculture and Food Western Australia (DAFWA), 3 Baron-Hay Court Brazilian Agricultural Research Enterprise - EMBRAPA Wheat/Trigo University of São Paulo State - UNESP Department of Crop Protection Rural Engineering and Soil Science, IlhaSolteira Campus CIRAD UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI Norwich Research Park The Sainsbury Laboratory Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10 INRA UMR 1290 Biologie et Gestion des Risques en agriculture BIOGER Norwich Research Park John Innes Centre University of São Paulo State - UNESP Department of Crop Protection Rural Engineering and Soil Science, IlhaSolteira Campus
Published: 2016

3. Improving sustainable crop protection using population genetics concepts

Author: Méline Saubin, Clémentine Louet, Lydia Bousset, Frédéric Fabre, Pascal Frey, Isabelle Fudal, Frédéric Grognard, Frédéric Hamelin, Ludovic Mailleret, Solenn Stoeckel, Suzanne Touzeau, Benjamin Petre, Fabien Halkett, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), 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), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), ANR-18-CE32-0001,Clonix2D,Les conséquences génétiques de reproduction partiellement clonale dans les populations colonisant de nouveaux territoires(2018), Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers
Subjects: Plant immunity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], Transient dynamics, Host-pathogen coevolution, [SDV]Life Sciences [q-bio], Genetics, Citation network, Genetic drift, Resistance durability, Ecology, Evolution, Behavior and Systematics, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: accepted; International audience; Growing genetically resistant plants allows pathogen populations to be controlled and reduces the use of pesticides. However, pathogens can quickly overcome such resistance. In this context, how can we achieve sustainable crop protection? This crucial question has remained largely unanswered despite decades of intense debate and research effort. In this study, we used a bibliographic analysis to show that the research field of resistance durability has evolved into three subfields: (i) ‘plant breeding’ (generating new genetic material), (ii) ‘molecular interactions’ (exploring the molecular dialogue governing plant–pathogen interactions) and (iii) ‘epidemiology and evolution’ (explaining and forecasting of pathogen population dynamics resulting from selection pressure(s) exerted by resistant plants). We argue that this triple split of the field impedes integrated research progress and ultimately compromises the sustainable management of genetic resistance. After identifying a gap among the three subfields, we argue that the theoretical framework of population genetics could bridge this gap. Indeed, population genetics formally explains the evolution of all heritable traits, and allows genetic changes to be tracked along with variation in population dynamics. This provides an integrated view of pathogen adaptation, in particular via evolutionary–epidemiological feedbacks. In this Opinion Note, we detail examples illustrating how such a framework can better inform best practices for developing and managing genetically resistant cultivars.
Published: 2023

4. Exploitation of the Leptosphaeria maculans late effector repertoire for diversification of resistances to blackleg in Brassica napus

Author: JIQUEL, Audren, Gervais, Julie, Geistodt-Kiener, Aude, Delourme, Régine, Mas, Justine, George, Pierre, Wagner, Armand, Fior, Adrien, Faure, Sébastien, Balesdent, Marie-Hélène, Rouxel, Thierry, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), innolea, Susanne Zeilinger-Migsich, and Hubertus Haas
Subjects: resistance, Phenotype, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, gene-for-gene, interaction
Abstract: International audience; Leptosphaeria maculans is a phytopathogenic fungus being responsible for a damaging disease of oilseed rape (Brassica napus): stem canker. The disease is mainly controlled by plant genetic resistance: single-gene specific resistance or quantitative, adult-stage resistance. During its particularly complex and long infectious cycle, L. maculans colonizes asymptomatically the stems of oilseed rape, producing late effectors specific to this colonization stage. In the context of a strong need to identify new sources of disease resistance, we exploited the repertoire of ‘late’ effectors to identify genes in the plant that could contribute to quantitative disease resistance. Our hypothesis was that quantitative resistance partly rely on gene-for-gene interactions, with fungal effectors produced during stem infection being recognized by resistance proteins. Using an innovative strategy of early expression of late effector genes, we validated that the interaction between the late effector LmSTEE98 and the resistance RlmSTEE98 obeys a typical gene-for-gene interaction, occurring during the colonization of oilseed rape stems by L. maculans, that contributes partly to quantitative resistance, in controlled conditions. We then used the same strategy to search for new sources of resistance after having established criteria to select the most relevant late effectors, and chosen ten of these for screening. Our screening approach of 130 diversified genotypes representative of the available diversity of B. napus, allowed us to identify new sources of resistance, displaying diversified interaction phenotypes. The next steps of this project now are further validation of the efficacy of the new sources of resistance in the field and of the validity of the quantitative resistance markers. However, as it stands, our results demonstrate the existence of unsuspected sources of resistance that are potentially more durable than the classic major genes expressed early after penetration in plant tissues.
Published: 2023

5. Protéger les cultures en augmentant la diversité végétale des espaces agricoles.: Rapport scientifique de l’Expertise scientifique collective

Author: Vialatte, A., Martinet, Vincent, Tibi, Anaïs, Alignier, Audrey, Angeon, Valérie, Bedoussac, Laurent, Bohan, David, Bougherara, Douadia, Carpentier, A., Castagneyrol, Bastien, Cordeau, Stéphane, Courtois, Pierre, Deguine, Jean-Philippe, Doelher, Marianne, Enjalbert, Jérôme, Fabre, Frédéric, Femenia, Fabienne, Fréville, Hélène, Goulet, Frederic, Grateau, Regis, Grimonprez, Benoît, Gross, Nicolas, Hannachi, Mourad, Jeanneret, Philippe, Labarthe, Pierre, Launay, Marie, Lelievre, Virginie, Lemarié, Stéphane, Martel, Gilles, Masson, Abel, Navarrete, Mireille, Plantegenest, Manuel, Ravigné, Virginie, Rusch, Adrien, Suffert, Frédéric, Tapsoba, Abdoulaye, Thoyer, Sophie, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Paris-Saclay Applied Economics (UMR PSAE), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction de l'Expertise scientifique collective, de la Prospective et des Etudes, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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 recherche d'Écodéveloppement (ECODEVELOPPEMENT), AGroécologie, Innovations, teRritoires (AGIR), École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Centre d'Economie de l'Environnement - Montpellier (CEE-M), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Structures et Marché Agricoles, Ressources et Territoires (SMART), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Centre d’études et de coopération juridique interdisciplinaire (CECOJI), Université de Poitiers, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Agroscope, Agroclim (AGROCLIM), Département agronomie et sciences de l'environnement pour les agroécosystèmes (AgroEcoSystem), Laboratoire d'Economie Appliquée de Grenoble (GAEL), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Office Français de la Biodiversité (Plan Ecophyto II+), and INRAE
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SHS]Humanities and Social Sciences
Published: 2023

6. A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown

Author: Axelle Andrieux, Pascal Frey, Clémentine Louet, Fabien Halkett, Mathilde Gorse, Bénédicte Fabre, Sébastien Duplessis, Jérémy Pétrowski, Antoine Persoons, Stéphane De Mita, Méline Saubin, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), ANR-17-CE32-0010,WABSARF,Adaptation intraspécifique et interspécifique des champignons responsables des rouilles(2017), ANR-18-CE32-0001,Clonix2D,Les conséquences génétiques de reproduction partiellement clonale dans les populations colonisant de nouveaux territoires(2018), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, biology, molecular evolution, food and beverages, Population genetics, Locus (genetics), Melampsora, gene-for-gene interaction, biology.organism_classification, 01 natural sciences, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 03 medical and health sciences, effector, Molecular evolution, Genetic variation, Genotype, fungal pathogen, Allele, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; The deployment of plant varieties carrying resistance genes (R) exerts strong selection pressure on pathogen populations. Rapidly evolving avirulence genes (Avr) allow pathogens to escape R-mediated plant immunity through a variety of mechanisms, leading to virulence. The poplar rust fungus Melampsora larici-populina is a damaging pathogen of poplars in Europe. It underwent a major adaptive event in 1994, with the breakdown of the poplar RMlp7 resistance gene. Population genomics studies identified a locus in the genome of M. larici-populina that probably corresponds to the candidate avirulence gene AvrMlp7. Here, to further characterize this effector, we used a population genetics approach on a comprehensive set of 281 individuals recovered throughout a 28-year period encompassing the resistance breakdown event. Using two dedicated molecular tools, genotyping at the candidate locus highlighted two different alterations of a predominant allele found mainly before the resistance breakdown: a nonsynonymous mutation and a complete deletion of this locus. This results in six diploid genotypes: three genotypes related to the avirulent phenotype and three related to the virulent phenotype. The temporal survey of the candidate locus revealed that both alterations were found in association during the resistance breakdown event. They pre-existed before the breakdown in a heterozygous state with the predominant allele cited above. Altogether, these results suggest that the association of both alterations at the candidate locus AvrMlp7 drove the poplar rust adaptation to RMlp7-mediated immunity. This study demonstrates for the first time a case of adaptation from standing genetic variation in rust fungi during a qualitative resistance breakdown.
Published: 2021

7. Tandem metalloenzymes gate plant cell entry by pathogenic fungi

Author: Bastien Bissaro, Sayo Kodama, Takumi Nishiuchi, Anna Maria Díaz-Rovira, Hayat Hage, David Ribeaucourt, Mireille Haon, Sacha Grisel, A. Jalila Simaan, Fred Beisson, Stephanie M. Forget, Harry Brumer, Marie-Noëlle Rosso, Victor Guallar, Richard O’Connell, Mickaël Lafond, Yasuyuki Kubo, Jean-Guy Berrin, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Faculté d’agriculture, Université Setsunan, 573-0101 Osaka, Japon., Division de génomique fonctionnelle, Centre de recherche scientifique avancée, Université de Kanazawa, 920-0934 Kanazawa, Japon., Barcelona Supercomputing, Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), 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), Michael Smith Laboratories, Université de la Colombie-Britannique, ICREA, Passeig Lluís Companys, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Faculté d’agriculture, Université Setsunan, and Barcelona Supercomputing Center
Subjects: Fungal Proteins, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], Genòmica, Multidisciplinary, Fungal plant diseases, Crop protection, Virulence, Plant Cells, Metalloproteins, Fungi, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Enzims, Fungal phytopathogens
Abstract: Global food security is endangered by fungal phytopathogens causing devastating crop production losses. Many of these pathogens use specialized appressoria cells to puncture plant cuticles. Here, we unveil a pair of alcohol oxidase–peroxidase enzymes to be essential for pathogenicity. Using Colletotrichum orbiculare, we show that the enzyme pair is cosecreted by the fungus early during plant penetration and that single and double mutants have impaired penetration ability. Molecular modeling, biochemical, and biophysical approaches revealed a fine-tuned interplay between these metalloenzymes, which oxidize plant cuticular long-chain alcohols into aldehydes. We show that the enzyme pair is involved in transcriptional regulation of genes necessary for host penetration. The identification of these infection-specific metalloenzymes opens new avenues on the role of wax-derived compounds and the design of oxidase-specific inhibitors for crop protection. Fungal phytopathogens secrete tandem metalloenzymes that catalyze cuticle oxidation and drive plant cell entry This study was supported by the “Agence Nationale de la Recherche” and by the Natural Sciences and Engineering Research Council of Canada through the ANR-NSERC project “FUNTASTIC” (ANR-17-CE07-0047, STPGP 493781-16). We are grateful to MANE & Fils and the “Association Nationale Recherche Technologie” (ANRT) for funding the Ph.D. fellowship of D.R. (grant no. 2017/1169). Work in Japan was supported by the Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research—KAKENHI, grant numbers 15H05780 and 20H02989 to Y.K., and 20K15529 to S.K. Peer Reviewed "Article signat per 18 autors/es: Bastien Bissaro and Sayo Kodama and Takumi Nishiuchi and Anna Maria Díaz-Rovira and Hayat Hage and David Ribeaucourt and Mireille Haon and Sacha Grisel and A. Jalila Simaan and Fred Beisson and Stephanie M. Forget and Harry Brumer and Marie-Noëlle Rosso and Victor Guallar and Richard O’Connell and Mickaël Lafond and Yasuyuki Kubo and Jean-Guy Berrin "
Published: 2022

8. Annual dynamics of Zymoseptoria tritici populations in wheat cultivar mixtures: A compromise between the efficacy and durability of a recently broken‐down resistance gene?

Author: Tiphaine Vidal, Frédéric Suffert, Sandrine Gélisse, Sébastien Saint-Jean, Anne-Lise Boixel, Carolina Orellana-Torrejon, 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), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
Subjects: 0106 biological sciences, 2. Zero hunger, Genetics, 0303 health sciences, Resistance (ecology), [SDV]Life Sciences [q-bio], food and beverages, Virulence, Plant Science, Horticulture, Biology, 01 natural sciences, Durability, 03 medical and health sciences, cultivar mixtureresistance breakdownStb16qvirulencewheat disease epidemicsZymoseptoria tritici, [SDE]Environmental Sciences, Cultivar, Agronomy and Crop Science, Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Cultivar mixtures slow polycyclic epidemics but may also affect the evolution of pathogen populations by diversifying the selection pressures exerted by their plant hosts at field scale. We compared the dynamics of natural populations of the fungal pathogen Zymoseptoria tritici in pure stands and in three binary mixtures of wheat cultivars (one susceptible cultivar and one cultivar carrying the recently broken-down Stb16q gene) over two annual field epidemics. We combined analyses of population "size" based on disease severity, and of population "composition" based on changes in the frequency of virulence against Stb16q in seedling assays with more than 3000 strains. Disease reductions were observed in mixtures late in the epidemic, at the whole-canopy scale and on both cultivars, suggesting the existence of a reciprocal protective effect. The three cultivar proportions in the mixtures (0.25, 0.5, and 0.75) modulated the decrease in (a) the size of the pathogen population relative to the two pure stands, (b) the size of the virulent subpopulation, and (c) the frequency of virulence relative to the pure stand of the cultivar carrying Stb16q. Our findings suggest that optimal proportions may differ slightly between the three indicators considered. We argue potential trade-offs that should be taken into account when deploying a resistance gene in cultivar mixtures: between the dual objectives "efficacy" and "durability," and between the "size" and "frequency" of the virulent subpopulation. Based on current knowledge, it remains unclear whether virulent subpopulation size or frequency has the largest influence on interepidemic virulence transmission.
Published: 2021

9. The Colletotrichum higginsianum secreted effector protein ChEC91 induces plant cell death

Author: Jochen Kleemann, Kenji Ogura, Natsuki Omura, Shota Nakajima, Hiroyuki Takahara, Sho Yamaguchi, Satomi Tanaka, Richard J. O'Connell, Kasumi Otoku, ISHIKAWA PREFECTURAL UNIVERSITY JPN, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Max Planck Inst Plant Breeding Res, Dept Plant Breeding & Genet, Cologne, Germany, Partenaires 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), Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of ScienceGrants-in-Aid for Scientific Research (KAKENHI)JP25850029, and Mitani Foundation for Research and Development
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Protein domain, Mutant, Nicotiana benthamiana, Plant Science, Biology, 01 natural sciences, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Cell death-inducing proteinColletotrichum higginsianumEffectorRecombinant proteinTransient expression, Arabidopsis thaliana, Gene, Colletotrichum higginsianum, 030304 developmental biology, 0303 health sciences, Effector, fungi, Callose, food and beverages, biology.organism_classification, chemistry, [SDE]Environmental Sciences, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; ChEC91, a novel cell death-inducing effector protein from the fungal pathogen Colletotrichum higginsianum, causal agent of crucifer anthracnose disease, is described. Both transient expression of ChEC91 and infiltration of purified recombinant protein induced necrotic lesions in Nicotiana benthamiana leaves. The recombinant protein also induced electrolyte leakage and callose deposition in Arabidopsis thaliana leaf tissue and the expression of defence marker genes. Moreover, fungal mutants constitutively over-expressing ChEC91 in C. higginsianum were impaired in appressorial penetration on Brassica rapa cotyledons. These results suggest that inappropriate expression of ChEC91 might negatively affect the early stage of C. higginsianum infection by inducing plant defence responses. Protein domain deletion analysis showed that the C-terminal region of ChEC91 was necessary, but not sufficient, for activity in N. benthamiana. Homologous effector proteins cloned from C. gloeosporioides, Fusarium graminearum, and Pyricularia oryzae differed in their cell death-inducing activity, which appeared related to sequence variations in the C-terminal region of these proteins. Moreover, this region contained amino acid residues that were well conserved within Colletotrichum species. These results suggest that the amino acid residues in the C-terminal region may be important for inducing cell death in plants.
Published: 2021

10. Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean

Author: Juan C. Alvarez-Diaz, Richard Laugé, Etienne Delannoy, Stéphanie Huguet, Christine Paysant-Le Roux, Ariane Gratias, Valérie Geffroy, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-17-CE20-0025,HIPATH,Induction des réponses pathogenesis-related par le fort CO2 chez les plantes: signalisation, voies métaboliques, et impact agronomique(2017), and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
Subjects: NL, Ecology, Phaseolus vulgaris, Colletotrichum lindemuthianum, RNA-seq, transcriptome, Co-resistance genes, resistance response, PR10, Bet vI, NLR, [SDV]Life Sciences [q-bio], Plant Science, [SDE]Environmental Sciences, RPR10, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Bean anthracnose caused by the hemibiotrophic fungus Colletotrichum lindemuthianum is one of the most important diseases of common bean (Phaseolus vulgaris) in the world. In the present study, the whole transcriptome of common bean infected with C. lindemuthianum during compatible and incompatible interactions was characterized at 48 and 72 hpi, corresponding to the biotrophy phase of the infection cycle. Our results highlight the prominent role of pathogenesis-related (PR) genes from the PR10/Bet vI family as well as a complex interplay of different plant hormone pathways including Ethylene, Salicylic acid (SA) and Jasmonic acid pathways. Gene Ontology enrichment analysis reveals that infected common bean seedlings responded by down-regulation of photosynthesis, ubiquitination-mediated proteolysis and cell wall modifications. In infected common bean, SA biosynthesis seems to be based on the PAL pathway instead of the ICS pathway, contrarily to what is described in Arabidopsis. Interestingly, ~30 NLR were up-regulated in both contexts. Overall, our results suggest that the difference between the compatible and incompatible reaction is more a question of timing and strength, than a massive difference in differentially expressed genes between these two contexts. Finally, we used RT-qPCR to validate the expression patterns of several genes, and the results showed an excellent agreement with deep sequencing.
Published: 2022

11. A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat

Author: Reda Amezrou, Colette Audéon, Jérôme Compain, Sandrine Gélisse, Aurélie Ducasse, Cyrille Saintenac, Nicolas Lapalu, Clémentine Louet, Simon Orford, Daniel Croll, Joëlle Amselem, Sabine Fillinger, Thierry C. Marcel, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), Université de Neuchâtel (UNINE), FSOV 2008 H, ANR-12-ADAP-0009,GANDALF,Génomique et adaptation des traits de vie des champignons impliqués dans les interactions plante-pathogène(2012), and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
Subjects: Filamentous fungi, Ascomycota, [SDV]Life Sciences [q-bio], Virology, [SDE]Environmental Sciences, Immunology, Genetics, Pathotyping, Parasitology, gene, Molecular Biology, Microbiology
Abstract: Zymoseptoria tritici is the fungal pathogen responsible for Septoria tritici blotch on wheat. Disease outcome in this pathosystem is partly determined by isolate-specific resistance, where wheat resistance genes recognize specific fungal factors triggering an immune response. Despite the large number of known wheat resistance genes, fungal molecular determinants involved in such cultivar-specific resistance remain largely unknown. We identified the avirulence factor AvrStb9 using association mapping and functional validation approaches. Pathotyping AvrStb9 transgenic strains on Stb9 cultivars, near isogenic lines and wheat mapping populations, showed that AvrStb9 interacts with Stb9 resistance gene, triggering an immune response. AvrStb9 encodes an unusually large avirulence gene with a predicted secretion signal and a protease domain. It belongs to a S41 protease family conserved across different filamentous fungi in the Ascomycota class and may constitute a core effector. AvrStb9 is also conserved among a global Z. tritici population and carries multiple amino acid substitutions caused by strong positive diversifying selection. These results demonstrate the contribution of an ‘atypical’ conserved effector protein to fungal avirulence and the role of sequence diversification in the escape of host recognition, adding to our understanding of host-pathogen interactions and the evolutionary processes underlying pathogen adaptation.
Published: 2023

12. Blocked at the Stomatal Gate, a Key Step of Wheat Stb16q-Mediated Resistance to Zymoseptoria tritici

Author: Battache, Mélissa, Lebrun, Marc-Henri, Sakai, Kaori, Soudière, Olivier, Cambon, Florence, Langin, Thierry, Saintenac, Cyrille, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-16-IDEX-0001,CAP 20-25,CAP 20-25(2016)
Subjects: resistance, leaf penetration, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV]Life Sciences [q-bio], Septoria tritici blotch, stomata, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Plant Science, Stb16q, avirulence
Abstract: Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is among the most threatening wheat diseases in Europe. Genetic resistance remains one of the main environmentally sustainable strategies to efficiently control STB. However, the molecular and physiological mechanisms underlying resistance are still unknown, limiting the implementation of knowledge-driven management strategies. Among the 22 known major resistance genes (Stb), the recently cloned Stb16q gene encodes a cysteine-rich receptor-like kinase conferring a full broad-spectrum resistance against Z. tritici. Here, we showed that an avirulent Z. tritici inoculated on Stb16q quasi near isogenic lines (NILs) either by infiltration into leaf tissues or by brush inoculation of wounded tissues partially bypasses Stb16q-mediated resistance. To understand this bypass, we monitored the infection of GFP-labeled avirulent and virulent isolates on Stb16q NILs, from germination to pycnidia formation. This quantitative cytological analysis revealed that 95% of the penetration attempts were unsuccessful in the Stb16q incompatible interaction, while almost all succeeded in compatible interactions. Infectious hyphae resulting from the few successful penetration events in the Stb16q incompatible interaction were arrested in the sub-stomatal cavity of the primary-infected stomata. These results indicate that Stb16q-mediated resistance mainly blocks the avirulent isolate during its stomatal penetration into wheat tissue. Analyses of stomatal aperture of the Stb16q NILs during infection revealed that Stb16q triggers a temporary stomatal closure in response to an avirulent isolate. Finally, we showed that infiltrating avirulent isolates into leaves of the Stb6 and Stb9 NILs also partially bypasses resistances, suggesting that arrest during stomatal penetration might be a common major mechanism for Stb-mediated resistances.
Published: 2022

13. 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

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

Author: Gilles Couleaud, Anne-Sophie Walker, Clémentine Duplaix, Maxime Garnault, Olivier David, Florence Carpentier, Pierre Leroux, 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), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ARVALIS - Institut du Végétal [Boigneville], ARVALIS - Institut du végétal [Paris], AgroParisTech, INRAE SMaCH projet FONDU, Bayer Crop Science CIFRE n ° 2016‐0695, and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Plant Science, Large-scale evolution, Biology, 01 natural sciences, 03 medical and health sciences, Septoria leaf blotch, Ascomycota, Resistance determinants, Plant Diseases, 2. Zero hunger, Adaptive traits, Mathematical modelling, Resistance (ecology), food and beverages, 15. Life on land, biology.organism_classification, Treatment efficacy, Fungicides, Industrial, Fungicide, 030104 developmental biology, Agronomy, Mycosphaerella graminicola, Zymoseptoria tritici, [SDE]Environmental Sciences, Regional fungicide use, France, PEST analysis, Resistance dynamics, Scale (map), Cropping, 010606 plant biology & botany
Abstract: International audience; 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

15. Is virulence phenotype evolution driven exclusively by Lr gene deployment in French Puccinia triticina populations?

Author: Fontyn, Cécilia, Zippert, Anne‐Catherine, Delestre, Ghislain, Marcel, Thierry C., Suffert, Frédéric, Goyeau, Henriette, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), and European Project: 773311-2,RUSTWATCH
Subjects: virulence, Lr gene, pathotype distribution, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, Genetics, varietal landscape, Puccinia triticina, Plant Science, Horticulture, aggressiveness, Agronomy and Crop Science
Abstract: Puccinia triticina is a highly damaging wheat pathogen. The efficacy of leaf rust control by genetic resistance is mitigated by the adaptive capacity of the pathogen, expressed as changes in its virulence combinations (pathotypes). An extensive P. triticina population survey has been carried out in France over the last 30 years, describing the evolution dynamics of this pathogen in response to cultivar deployment. We analyzed the dataset for the 2006-2016 period to determine the relationship between the Lr genes in the cultivars and virulence in the pathotypes. Rust populations were dominated by a small number of pathotypes, with variations in most of the virulence frequencies related to the corresponding Lr gene frequencies in the cultivated landscape. Furthermore, the emergence and spread of a new virulence matched the introduction and use of the corresponding Lr gene (Lr28), confirming that the deployment of qualitative resistance genes is an essential driver of evolution in P. triticina populations. However, PCA revealed that certain pathotype-cultivar associations cannot be explained solely by the distribution of Lr genes in the landscape. This conclusion is supported by the predominance of a few pathotypes on some cultivars, with the persistence of several other compatible pathotypes at low frequencies. Specific interactions are not, therefore, sufficient to explain the distribution of virulence in rust populations. Our findings suggest that aggressiveness is a driver of changes in pathotype frequencies. Accordingly, the hypothesis of “dual selection”, based on both qualitative and quantitative interactions between P. triticina populations and bread wheat cultivars, is favored.
Published: 2022

16. Promoting crop pest control by plant diversification in agricultural landscapes: A conceptual framework for analysing feedback loops between agro-ecological and socio-economic effects

Author: Aude Vialatte, Anaïs Tibi, Audrey Alignier, Valérie Angeon, Laurent Bedoussac, David A. Bohan, Douadia Bougherara, Alain Carpentier, Bastien Castagneyrol, Stéphane Cordeau, Pierre Courtois, Jean-Philippe Deguine, Jérôme Enjalbert, Frédéric Fabre, Fabienne Féménia, Hélène Fréville, Frédéric Goulet, Régis Grateau, Benoît Grimonprez, Nicolas Gross, Mourad Hannachi, Philippe Jeanneret, Laure Kuhfuss, Pierre Labarthe, Marie Launay, Marianne Lefebvre, Virginie Lelièvre, Stéphane Lemarié, Gilles Martel, Abel Masson, Mireille Navarrete, Manuel Plantegenest, Virginie Ravigné, Adrien Rusch, Frédéric Suffert, Abdoulaye Tapsoba, Olivier Therond, Sophie Thoyer, Vincent Martinet, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction de l'Expertise scientifique collective, de la Prospective et des Etudes, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche d'Écodéveloppement (ECODEVELOPPEMENT), AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA), 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), Centre d'Economie de l'Environnement - Montpellier - UMR 5211 (CEE-M), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Structures et Marché Agricoles, Ressources et Territoires (SMART-LERECO), AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), 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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), Département Environnements et Sociétés (Cirad-ES), Economie Publique (ECO-PUB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Etudes et de Coopération Juridique Interdisciplinaire (CECOJI), Université de Poitiers, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Agroscope, University of St Andrews [Scotland], Agroclim (AGROCLIM), Institut National de la Recherche Agronomique (INRA), Groupe de Recherche Angevin en Economie et Management (GRANEM), Institut National de l'Horticulture et du Paysage-AGROCAMPUS OUEST-Université d'Angers (UA), Département agronomie et sciences de l'environnement pour les agroécosystèmes (AgroEcoSystem), Laboratoire d'Economie Appliquée de Grenoble (GAEL), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), AGROCAMPUS OUEST-Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Agronomie et Environnement - Antenne Colmar (LAE-Colmar ), Laboratoire Agronomie et Environnement (LAE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Economie de l'Environnement - Montpellier (CEE-M), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Centre d’études et de coopération juridique interdisciplinaire - Université de Poitiers (CECOJI-UP), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de l'Horticulture et du Paysage, Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, French Office for Biodiversity (OFB) through the national ECOPHYTO plan, David A. Bohan, Alex J. Dumbrell, Adam J. Vanbergen, Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AGROCAMPUS OUEST, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de l'Horticulture et du Paysage-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université d'Angers (UA), 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)-Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Gestion des ressources renouvelables et environnement (UPR GREEN), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Angers (UA)-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)-Institut National de l'Horticulture et du Paysage
Subjects: 2. Zero hunger, 0106 biological sciences, 13. Climate action, 11. Sustainability, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, 04 agricultural and veterinary sciences, 15. Life on land, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, 01 natural sciences, 010606 plant biology & botany, [SHS]Humanities and Social Sciences
Abstract: International audience; Given the negative environmental effects of conventional agricultural techniques, the need for biodiversity-friendly agriculture systems that rely more on ecosystem services and less on chemical inputs is becoming increasingly urgent. In this paper, we focus on crop protection strategies that are alternatives to the use of pesticides. Diversification of the plant component of agricultural areas at different space and time scales has been presented as a powerful socio-economic and agro-ecological mechanism for the sustainable control of pests. Our interdisciplinary group of scientific experts examined the literature on the ecological effects of plant diversification on pests and their natural enemies, as well as the social science literature on the conditions for farmers to adopt the corresponding practices, to assess the potential offered by plant diversification.We developed a conceptual framework that connects the agro-ecological and socio-economic components of an agricultural landscape in a dynamic loop accounting for interactions among elements at different spatial and temporal scales and their feedback effects. This article presents this framework and illustrates its application to the case of wheat production and protection. By explicitly connecting each level of agro-ecological organization with the potential socio-economic drivers and limitations underpinning the adoption and implementation of plant diversification in landscapes, this framework makes it possible to ana yse the synergies and antagonisms between different modes of diversification and the conditions of their deployment. Exploring this framework is a prerequisite to the identification of opportunities and key feed-back loops for designing diversification strategies that unlock the agro-ecological potential of f uture production systems. We conclude that there is a need for interdisciplinary research in experimental landscapes involving farmers and other local stakeholders to design sustainable future agricultural landscapes that deliver high levels of biological control services..
Published: 2022

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

Author: Adeline Simon, Alex Mercier, Pierre Gladieux, Benoît Poinssot, Anne-Sophie Walker, Muriel Viaud, EL Mjiyad, Noureddine, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, 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), grant from the Doctoral School « Sciences du Végétal », Université Paris-Saclay, INRAE department SPE, ANR-20-PCPA-0010,VITAE,Cultivating the grapevine without pesticides : towards agroecological wine-producing socio-ecosystems(2020), ANR-11-LABX-0034,BASC,Biodiversité, Agroécosystèmes, Société, Climat(2011), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was supported by a grant overseen by the French National Research Agency (ANR) as part ofthe 'Investissements d’Avenir' (LabEx BASC, ANR-11-LABX-0034) and 'Priority Research' programs (PPRVITAE, and ANR-20-PCPA-0010) and by the INRAE department SPE. The BIOGER unit also benefits from thesupport of 'Saclay Plant Science-SPS' (ANR-17-EUR-0007). AM was supported by a grant from the Doctoral School « Sciences du Végétal », Université Paris-Saclay.
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, plant pathology, phytopagenic fungus, [SDV]Life Sciences [q-bio], tomato, Chromosome, grapevine, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, botrytis, [SDV] Life Sciences [q-bio], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Botrytis cinerea stands out for having a wide host range and is qualified as generalist.Nevertheless, recent studies suggest that it actually corresponds to co-existing populationsthat show a certain level of host specialization, as described for the French populations T andG1, specialized on tomato and grapevine, respectively (Mercier et al., 2019, Env. Microbiol.21, 4808–21; Mercier et al., 2021 Phytopathology, 111,2355-66).What are the molecular determinants responsible for such host-specialization? PreviousIllumina sequencing data revealed genes under positive selection encoding cellulases,pectinases and enzymes involved in the oxidative stress response suggesting that theseactivities may contribute to the specialization on tomato. Here, using PacBio sequencing, weproduced complete assemblies and annotation of the genomes of strains Sl3 and Vv3 thatrepresent the T and G1 populations in order to identify all possible genomic correlates of hostspecialization. Both assemblies revealed 16 core chromosomes that were highly syntenic withthose of the reference strain B05.10. The main sources of variation in gene content were thesubtelomeric regions and the accessory chromosomes (ACs), especially the AC BCIN19 of Vv3that was absent in Sl3 and B05.10. The repertoires and density of transposable elements (TEs)were clearly different between the genomes of Sl3 and Vv3 with a larger number ofsubfamilies (26) and a greater genome coverage in Vv3 (7.7%) than in Sl3 (14 subfamilies, 4.5%coverage). An Helitron-like TE 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-LinkedHelicase, while both features were absent from the Sl3 and B05.10 genomes. Differentretrotransposons in the Sl3 and the Vv3 strains resulted in the synthesis of distinct sets ofsmall RNAs. Finally, extending the study to additional strains indicated that the AC BCIN19 andthe small RNAs producing TE Copia_4 and Gypsy_7 are common features of the G1 populationthat are scarcely if ever found in strains isolated from other populations. This research revealsthat ACs, TEs and their derived small RNAs differ between populations of B. cinerea specializedon different hosts and paves the way for further studies aiming at investigating the molecularmechanisms underpinning host specialization in a polyphagous pathogen (Simon et al.,BioRxiv, https://doi.org/10.1101/2022.03.07.483234).
Published: 2022

18. Protéger les cultures en augmentant la diversité végétale des espaces agricoles. Synthèse de l’expertise scientifique collective

Author: Tibi, Anaïs, Martinet, Vincent, Vialatte, A., Alignier, Audrey, Angeon, Valérie, Bohan, David, Bougherara, Douadia, Cordeau, Stéphane, Courtois, Pierre, Deguine, Jean-Philippe, Enjalbert, Jérôme, Fabre, Frédéric, Fréville, Hélène, Grateau, Regis, Grimonprez, Benoît, Gross, Nicolas, Hannachi, Mourad, Launay, Marie, Lelievre, Virginie, Lemarié, Stéphane, Martel, Gilles, Navarrete, Mireille, Plantegenest, Manuel, Ravigné, Virginie, Rusch, Adrien, Suffert, Frédéric, Thoyer, Sophie, Direction de l'Expertise scientifique collective, de la Prospective et des Etudes, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Paris-Saclay Applied Economics (UMR PSAE), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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 recherche d'Écodéveloppement (ECODEVELOPPEMENT), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Centre d'Economie de l'Environnement - Montpellier (CEE-M), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Centre d’études et de coopération juridique interdisciplinaire (CECOJI), Université de Poitiers, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Agroclim (AGROCLIM), Département agronomie et sciences de l'environnement pour les agroécosystèmes (AgroEcoSystem), Laboratoire d'Economie Appliquée de Grenoble (GAEL), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and INRAE
Subjects: [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Published: 2022

19. Genetic diversity and structure of Bipolaris oryzae and Exserohilum rostratum populations causing brown spot of rice in Burkina Faso based on genotyping-by-sequencing

Author: Kabore, Kouka Hilaire, Kassankogno, Abalo Itolou, Adreit, Henri, Milazzo, Joëlle, Guillou, Sonia, Blondin, Laurence, Chopin, Laurie, Ravel, Sébastien, Charriat, Florian, Barro, Mariam, Tollenaere, Charlotte, Lebrun, Marc-Henri, Tharreau, Didier, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Institut de l'Environnement et Recherches Agricoles [Ouagadougou] (INERA), Centre national de la recherche scientifique et technologique [Ouagadougou] (CNRST), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RICE CRP and the Islamic Development Bank, and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: Oryza, Maladie fongique, recombination, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Recombinaison, reproduction, rice disease, fungal pathogen, mating type, linkage disequilibrium, H20 - Maladies des plantes
Abstract: International audience; In recent years, Brown spot disease of rice (BSR) has been observed on leaves and seeds of rice in all rice-growing areas of Burkina Faso. Bipolaris oryzae and Exserohilum rostratum are the main fungal species isolated from BSR infected tissues and they are frequently observed in the same field. However, we are lacking information on the genetic diversity and population structure of these fungi in Burkina Faso. The mode of reproduction is also unknown. The genetic diversity of isolates of B. oryzae (n=61) and E. rostratum (n=151), collected from major ricegrowing areas of Burkina Faso, was estimated using genotyping-by-sequencing (GBS). The mean values for nucleotide diversity (p) were 1.9 x10-4 for B. oryzae and 4.8 x10-4 for E. rostratum. There is no genetic differentiation between the geographical populations of each species. The analysis of molecular variance revealed that 89% and 94% of the genetic variances were within the populations of B. oryzae and E. rostratum, respectively. For each species, four genetic clusters were identified by two clustering methods (DAPC and sNMF). The distribution of these genetic groups was independent of the geographical origin of the isolates. Evidence of recombination was detected in the populations of B. oryzae and E. rostratum. For B. oryzae balanced mating type ratios were supporting sexual reproduction. For E. rostratum overrepresentation of MAT1-2 isolates (79%) suggested a predominant asexual reproduction. This study provides important information on the biology and genetics of the two major fungi causing brown spot disease of rice in Burkina Faso.
Published: 2022

20. Protéger les cultures en augmentant la diversité végétale des espaces agricoles. Rapport de l’expertise scientifique collective

Author: Vialatte, A., Martinet, Vincent, Tibi, Anaïs, Alignier, Audrey, Angeon, Valérie, Bedoussac, Laurent, Bohan, David, Bougherara, Douadia, Carpentier, A., Castagneyrol, Bastien, Cordeau, Stéphane, Courtois, Pierre, Deguine, Jean-Philippe, Doelher, Marianne, Enjalbert, Jérôme, Fabre, Frédéric, Femenia, Fabienne, Fréville, Hélène, Goulet, Frederic, Grateau, Regis, Grimonprez, Benoît, Gross, Nicolas, Hannachi, Mourad, Jeanneret, Philippe, Labarthe, Pierre, Launay, Marie, Lelievre, Virginie, Lemarié, Stéphane, Martel, Gilles, Masson, Abel, Navarrete, Mireille, Plantegenest, Manuel, Ravigné, Virginie, Rusch, Adrien, Suffert, Frédéric, Tapsoba, Abdoulaye, Thoyer, Sophie, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Paris-Saclay Applied Economics (UMR PSAE), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction de l'Expertise scientifique collective, de la Prospective et des Etudes, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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 recherche d'Écodéveloppement (ECODEVELOPPEMENT), AGroécologie, Innovations, teRritoires (AGIR), École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Centre d'Economie de l'Environnement - Montpellier (CEE-M), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Structures et Marché Agricoles, Ressources et Territoires (SMART), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Centre d’études et de coopération juridique interdisciplinaire (CECOJI), Université de Poitiers, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Agroscope, Agroclim (AGROCLIM), Département agronomie et sciences de l'environnement pour les agroécosystèmes (AgroEcoSystem), Laboratoire d'Economie Appliquée de Grenoble (GAEL), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Office Français de la Biodiversité (Plan Ecophyto II+), and INRAE
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SHS]Humanities and Social Sciences
Published: 2022
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21. Success and failure of invasive races of plant pathogens: The case of Puccinia striiformis f. sp. tritici in France

Author: Tiphaine Vidal, Anne‐Lise Boixel, Essia Maghrebi, Rémi Perronne, Philippe du Cheyron, Jérôme Enjalbert, Marc Leconte, Claude de Vallavieille‐Pope, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Univ Carthage,Natl Agron Inst Tunisia INAT, Lab Pests & Integrated Protect Agr LR BPIA, Tunis, Tunisia (INAT), Université de Rennes (UR), ARVALIS - Institut du végétal [Paris], Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RUSTFIGHT, Innovation Fund Denmark, Ministry of Science and Higher Education, Poland, FSOV, European Project: Programme 7 265865, PURE, European Project: Programme 6 513959,BIOEXPLOIT, and European Project: 031499,Eurowheat ENDURE
Subjects: virulence, competitiveness, sp, [SDE]Environmental Sciences, Genetics, food and beverages, yellow (stripe) rust, Plant Science, Horticulture, triticithermal performance curves, Agronomy and Crop Science, Puccinia striiformis f, invasive races
Abstract: Early Access MAY 2022; International audience; Invasions of new races can have contrasting consequences on populations of Puccinia striiformis f. sp. tritici, causing yellow rust of wheat. For example, the emergence of PstS7 (Warrior race) had major impacts in Europe and in France. By contrast, PstS2 had no impact in France, while it significantly affected other parts of the world. The objective of this study was to better understand factors that govern the success of an invasive race, taking the contrasting history of PstS7 and PstS2 in France as a case study. We compared these two races for three key factors driving invasive potential: (a) virulence against local cultivars, (b) aggressiveness in local environmental conditions, and (c) competitiveness against local races. During the period when PstS2 was detected, 70% of the grown wheat area was protected against this race by at least one known Yr resistance gene. By contrast, we found that only 15% of the wheat area had a low risk of infection by PstS7. In planta competition experiments suggested a higher competitiveness of PstS7 against local isolates compared to PstS2 in optimal thermal conditions. In silico experiments, based on thermal performance curves, suggested a high competitiveness of PstS7 considering infection efficiency. PstS2 was extremely competitive against local races in all considered environments (20 French sites x 15 years) due to its short latency period. Our findings highlight the importance of considering adaptation to environmental conditions, particularly temperature, in addition to virulence spectrum, in order to understand the evolutionary trajectories of emerging strains in pathogen populations.
Published: 2022

22. Which potential of service plants for ‘multi-pest’ regulation in agroecosystems? An integrative conceptual framework highlighting complementarities in mechanisms and traits

Author: Moreau, Delphine, Ballini, Elsa, Djian‐caporalino, Caroline, Chave, Marie, Cordeau, Stéphane, Lavoir, Anne Violette, Suffert, Frédéric, Cortesero, Anne, EL Mjiyad, Noureddine, Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, 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), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Institut Sophia Agrobiotech (ISA), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Agrosystèmes tropicaux (ASTRO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), and Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: International audience; Alternatives to synthetic pesticide use are required to increase the sustainability of crop protection strategies. Identifying technical options based on the biological regulation of pests (pathogens, animal pests and weeds) is a promising and complex challenge. Among the options to be developed are ‘service plants’, also called ‘cover plants’, ‘companion plants’ or ‘biocontrol plants’. The principle is to sow these plants, either in association or in rotation with cash crops, to provide different ecosystem services, among which pest regulation. Past studies demonstrated the usefulness of service plants for regulating one category of pest, i.e. either pathogens, animal pests or weeds. However, few of them considered the role of these plants for multi-pest regulation. Yet, meeting the challenge of agroecological transition definitely requires an integrated view of the mechanisms leading to a pest regulation. To what extent can service plants provide a relevant option to promote multi-pest regulation, while limiting potential disservices of these plants, is still an open question? Given the diversity of the academic disciplines concerned and the scarcity of the scientific references, developing a conceptual framework appeared as a prerequisite to address this question. Such a framework allowed to synthesize the mechanisms and traits of the service plants potentially involved in the regulation of each category of pest. Both direct (i.e. directly targeting the pest) and indirect (i.e. targeting the pest through the mediation of natural enemies) mechanisms were considered, involving traits of service plants related to growth, morphology, phenology, biochemistry and immunity. Mechanisms and traits by which service plants can trigger unintended effects (e.g. by competing with cash crops for resources, promoting non-targeted pests, etc.) were also synthetized. This framework allowed to identify optimal ranges of trait values promoting the regulation of each category of pest and limiting negative impacts of service plants. It also highlighted different synergies and antagonisms between the different categories of pests, leading to a comprehensive view of the potential for multi-pest regulation. For most of the traits, we identified synergies. For example, tall service plants with a rapid growth rate can promote weed regulation (by competition for light) as well as aerial pathogens and phytophagous insects (by providing a physical barrier or increasing emission of volatile organic compounds affecting these pests). However, synergies and antagonisms need to be studied in more details for traits related to emission of chemical compounds. Indeed, a given molecule may promote the regulation of different types of pests but also may repel beneficial organisms such as natural enemies.323 As a last step, synergies and antagonisms between overall pest regulation and disservices provided by the service plants were also considered. This framework lays the foundations of a plant-trait-based approach that will be useful to prioritize research actions to identify efficient service plants and their way of use in agroecological contexts. Such framework, in combination with the development of databases, will be crucial to help farmers choose the most efficient and resilient service plant Species/varieties to combine in order to enhance multi-pest regulation. Funding: Métaprogramme SuMCrop of INRAE.
Published: 2022

23. First report of rice brown spot caused by Exserohilum rostratum in Mali

Author: Kaboré, Kouka Hilaire, Diagne, Diariatou, Milazzo, Joelle, Adreit, Henri, Lebrun, Marc-Henri, Tharreau, Didier, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Bamako [Mali], Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RICE CRP (grant to CIRAD), the Centre de Coopération Internationale en Recherche Agronomique pour le Développement, and The Islamic Bank of Development
Subjects: Subject Areas, Field crops, cereals and grains, [SDV]Life Sciences [q-bio], Fungi, food and beverages, Pathogen detection, Pathologie végétale, Maladie fongique, Causal Agent, Champignon pathogène, Maladie des plantes, [SDE]Environmental Sciences, Crop Type, H20 - Maladies des plantes
Abstract: International audience; Rice brown spot is an emerging disease of concern in many rice-growing countries. Different fungal species of the genera Bipolaris and Exserohilum were reported as the causal agents of this disease. These fungal pathogens cause similar necrotic lesions on leaves and infect grains with a significant effect on seed germination. In 2018, samples of rice seed and leaves with typical brown spot symptoms were collected from irrigated (Manikoura and Niono) and lowlands (M’pegnesso and Loulouni) rice fields in Mali and incubated for 5 to 7 days on wet filter paper at 25°C with 12 h photoperiod. Conidia observed under microscope were straight or slightly curved and light-brown or dark. They were also rostrate or obclavate and measured 31.4 to 275.6 x 7.3 to 18 µm (n=40). These morphological characteristics are identical to those of Exserohilum rostratum (Hernández-Restrepo et al. 2018). DNA from eight single-spored isolates was extracted by a CTAB-based protocol (Doyle and Doyle, 1987). Internal transcribed spacer (ITS) rDNA region, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and translation elongation factor 1 alpha (TEF1-α) genes were amplified by PCR with the primers ITS5/ITS4 (White et al. 1990), GPD1/GPD2 (Berbee et al. 1999) and EF1 983/EF1 2218 (Rehner et al. 2005), respectively. The amplicons were sequenced and deposited in NCBI GenBank. Sequence similarity between Malian strain was 100% for ITS and GAPDH, and 99.8-100% for TEF1. Sequence similarity between Malian strains and reference E. rostratum sequences BRIP 11417 (GenBank acc. no. LT837836, LT882553 and LT896656) and CBS 128061 (GenBank acc. no. KT265240, LT715900 and LT896658) were 99.6-100%. The maximum-likelihood phylogenetic tree generated with ITS, GAPDH and TEF1-α concatenated sequences, using MEGA-X 10.1.7 grouped all eight strains from Mali in the E. rostratum clade with a bootstrap value of 100%. For pathogenicity test, four strains from leaves and seed were grown on rabbit food agar (50 g/liter steeped filtrate of rabbit food pellets, Kaytee Products, Inc. Chilton, WI, USA, and 15 g agar) for 14 days at 25°C with a 12 h photoperiod (Hau and Rush 1980). Spores were collected and the concentration of spore suspension adjusted to 1.5 x 105 conidia/ml with 0.5% gelatin. The rice varieties ADNY 11, ARICA 9 and Shwetasoké were grown in pots with peat soil and NPK 13-5-18 at 3.5 g/liter of soil for 21 days. Four pots of each variety (5 seedlings/pot) were placed in a tray (60 plants per tray) and the leaves were sprayed with 30 ml of the conidial suspension or water at 0.5% gelatin (negative control). Plants were kept at maximum humidity (100%) at 21°C for one night and then transferred to a phytotron at 27°C. Seven days after inoculation, circular or oval foliar lesions of less than 5 mm long, either brown or dark, sometimes whitish in their centers were observed . These lesions were identical to those observed in the field. E. rostratum was reisolated from these lesions. E. rostratum affects a wide range of plant species, particularly grasses and has been observed on rice in many countries (Cardona and Gonzàlez 2007; Majeed et al. 2016; Silva et al. 2016; Toher et al. 2016). However, to our knowledge, this is the first report of E. rostratum causing brown spot in rice in Mali.
Published: 2022

24. Auxin biosynthesis in the phytopathogenic fungus Leptosphaeria maculans is associated with enhanced transcription of indole-3-pyruvate decarboxylase LmIPDC2 and tryptophan aminotransferase LmTAM1

Author: Vladimír Šašek, Lenka Burketová, Marie-Hélène Balesdent, Hana Leontovyčová, Petre I. Dobrev, Lucie Trdá, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Faculty of Sciences, Charles University in Prague, 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), and funding n° GAUK 992416, SVV260427/2019, Czech Grant Agency, Czech Republic (Grantová agentura České Republiky)-funding n° 13-26798S
Subjects: Tryptamine, Transcription, Genetic, Carboxy-Lyases, Metabolite, Microbiology, Nitrilase, 03 medical and health sciences, chemistry.chemical_compound, Plant Growth Regulators, Leptosphaeria maculans, Aminohydrolases, Tryptophan Transaminase, Auxin, Gene Expression Regulation, Fungal, Gene expression, heterocyclic compounds, Molecular Biology, Gene, Phylogeny, 030304 developmental biology, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, Indoleacetic Acids, biology, 030306 microbiology, Brassica napus, fungi, Fungi, Tryptophan, food and beverages, General Medicine, biology.organism_classification, Hormone, Tryptamines, Biosynthetic Pathways, Up-Regulation, Tryptophan aminotransferase, chemistry, Biochemistry, Dothideomycetes, [SDE]Environmental Sciences, Indole-3-pyruvate decarboxylase, Leptosphaeria
Abstract: International audience; Auxins are hormones that regulate growth and development in plants. Besides plants, various microorganisms also produce auxins. Here we investigate whether and how the phytopathogenic fungus Leptosphaeria maculans biosynthesizes auxins. We characterized the auxin profile of invitro grown L.maculans. The culture was further supplied with the auxin biosynthetic-precursors tryptophan and tryptamine and gene expression and phytohormone content was analyzed. L.maculans invitro produced IAA (indole-3-acetic acid) as the predominant auxin metabolite. IAA production could be further stimulated by supplying precursors. Expression of indole-3-pyruvate decarboxylase LmIPDC2, tryptophan aminotransferase LmTAM1 and nitrilase LmNIT1 genes was mainly upregulated after adding tryptophan and correlated with IAA production, suggesting that these genes are the key components of auxin biosynthesis in L.maculans. Tryptamine acted as a potent inducer of IAA production, though a pathway independent of LmIPDC2/LmTAM1 may be involved. Despite L.maculans being a rich source of bioactive IAA, the auxin metabolic profile of host plant Brassica napus was not altered upon infection. Exogenous IAA inhibited the growth of L.maculans invitro when supplied in high concentration. Altogether, we showed that L.maculans is capable of IAA production and we have identified biosynthetic genes that were responsive to tryptophan treatment.
Published: 2020

25. Cultivar mixture effects on disease and yield remain despite diversity in wheat height and earliness

Author: Pauline Lusley, Anne-Lise Boixel, M. Leconte, Tiphaine Vidal, Safa Ben Krima, Sébastien Saint-Jean, Claude de Vallavieille-Pope, 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), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), and ANR-13-AGRO-0008,WHEATAMIX,Augmenter la diversité génétique au sein des parcelles de blé pour renforcer la multifonctionnalité et la durabilité de la production dans le Bassin Parisien(2013)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Field experiment, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Puccinia striiformis f. sp. tritici, Plant Science, Horticulture, Biology, Plant disease resistance, 01 natural sciences, wheat diseases, intrafield diversity, 03 medical and health sciences, Disease severity, Yield (wine), Genetics, Cultivar, 2. Zero hunger, Wheat diseases, fungi, cultivar mixture, food and beverages, yield, component number, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 030104 developmental biology, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Cultivar mixtures can stabilize yield and reduce pathogen spread in plant populations. A field experiment was performed to determine (a) whether a large difference between the cultivars in the mixture (e.g., plant height or earliness) would have an impact on mixture performance, and (b) whether such differences would modify the classical rules for mixture design. Mixtures were constituted from wheat cultivars with diversity for many traits, including plant height, flowering date, disease resistance, and yield potential. The field experiment was conducted over 3 years, testing each year 72–90 mixtures of two, four, or eight cultivars, and their corresponding pure stands. Disease severity and yield of cultivar mixtures were strongly related to the mean values of the component cultivars in pure stands. Despite the considerable diversity of the mixtures tested, the classic rules (e.g., proportion of susceptible cultivars) already tested in mixtures with similar height and earliness were effective for decreasing disease severity. Agronomic heterogeneity for traits such as plant height, yield potential, or earliness of the cultivars in mixtures did not have a negative impact on disease severity and yield relative to pure stands. Increasing the number of cultivars in the mixture from two to eight had no impact on the mean disease severity and yield of the mixtures, but reduced the variability of disease severity and yield in the mixture relative to pure stands. These results suggest that it may be possible to increase within‐field wheat diversity by combining more contrasting cultivars in mixtures than was previously thought.
Published: 2020

26. Pathotype diversification in the invasive PstS2 clonal lineage of Puccinia striiformis f. sp. tritici causing yellow rust on durum and bread wheat in Lebanon and Syria in 2010–2011

Author: Claude de Vallavieille-Pope, Bochra A. Bahri, M. Leconte, Rola El Amil, Sajid Ali, K. Nazari, 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), Lebanese Agricultural Research Institute (LARI), Bekaa, Lebanon, Institute of Biotechnology & Genetic Engineering, the University of Agriculture, University of Georgia [USA], Université de Carthage - University of Carthage, International Center for Agricultural Research in the Dry Areas [Turquie] (ICARDA), International Center for Agricultural Research in the Dry Areas (ICARDA), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Borlaug Global Rust Initiative and Egide France, Innovation Fund Denmark, Ministry of Higher Education and Science, and RUSTFIGHT, Grant/Award Number: 11-116241
Subjects: 0106 biological sciences, 0301 basic medicine, Veterinary medicine, Lineage (genetic), CLONAGE POPULATIONS, INVASION, Population, Virulence, Plant Science, Horticulture, Biology, 01 natural sciences, Rust, 03 medical and health sciences, Genotype, Genetics, education, 2. Zero hunger, education.field_of_study, WHEAT YELLOW (STRIPE) RUST, Host (biology), SSR, PATHOTYPE, 030104 developmental biology, [SDE]Environmental Sciences, VIRULENCE, Microsatellite, Puccinia striiformis, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Yellow rust is the major wheat disease in central West Asia and North Africa. Recently, severe epidemics have occurred, with major yield losses in 2010–2011 in Lebanon and Syria. We conducted an extensive field survey, with a collection of 273 samples of Puccinia striiformis f. sp. tritici , to explore the origin of these epidemics. All samples were genotyped with 20 microsatellite markers, and 54 isolates were pathotyped. The population was dominated by the PstS2 lineage, which has spread worldwide since 2000 and displays considerable pathotype diversity (10 pathotypes). The 22 multilocus genotypes (MLGs) detected corresponded to variants of the clonal lineage PstS2, but they differed from the common PstS2 genotype found in the worldwide study conducted between 1981 and 2010. No strong differentiation was observed between Lebanon and Syria. The dominant MLG in Syria was common to both countries. Nine MLGs were found exclusively in the Syrian population and four were restricted to the Lebanese population, including the dominant MLG in Lebanon. The predominant MLG‐11 was found in nine pathotypes, at high frequency. The dominant pathotype in Syria was virulent against widely deployed resistance genes (Yr2 , Yr6 , Yr7 , Yr9 , Yr25 , and Yr27 ); virulence against Yr3 , Yr8 , Yr17 , and YrSP occurred at various frequencies, but Yr1 , Yr4 , Yr5 , Yr10 , Yr15 , and Yr32 were effective against all isolates. No host effect was detected. The presence of diverse host populations consisting of landraces and elite varieties, and diverse climatic conditions may account for the unexpectedly high diversity of this clonal population.
Published: 2020

27. The polyphagous plant pathogenic fungusBotrytis cinereaencompasses host‐specialized and generalist populations

Author: Annie Auger, Clémentine Duplaix, Pierre Gladieux, Alex Mercier, Jean-Marc Pradier, Anne Sophie Walker, Florence Carpentier, Muriel Viaud, Université Paris Sud Orsay, 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), AgroParisTech, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Institut National de la Recherche Agronomique (INRA), and Doctoral School 'Sciences du Vegetal', Universite Paris-Saclay
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Population, Zoology, Hydrangea, Generalist and specialist species, 01 natural sciences, Fragaria, molecular epidemiology, Microbiology, Host Specificity, Gene flow, 03 medical and health sciences, Solanum lycopersicum, Botany, Specialization (functional), Vitis, education, Ecology, Evolution, Behavior and Systematics, Plant Diseases, 030304 developmental biology, Botrytis cinerea, 2. Zero hunger, 0303 health sciences, education.field_of_study, biology, 030306 microbiology, Host (biology), fungi, food and beverages, Host specialization, population structure, grey mould, Pathogenic fungus, biology.organism_classification, crosspathogenicity, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Host-Pathogen Interactions, Botrytis, Solanum, gene flow, 010606 plant biology & botany
Abstract: The host plant is often the main variable explaining population structure in fungal plant pathogens, because specialization contributes to reduce gene flow between populations associated with different hosts. Previous population genetic analysis revealed that French populations of the grey mould pathogen Botrytis cinerea were structured by hosts tomato and grapevine, suggesting host specialization in this highly polyphagous pathogen. However, these findings raised questions about the magnitude of this specialization and the possibility of specialization to other hosts. Here we report specialization of B. cinerea populations to tomato and grapevine hosts but not to other tested plants. Population genetic analysis revealed two pathogen clusters associated with tomato and grapevine, while the other clusters co-occurred on hydrangea, strawberry and bramble. Measurements of quantitative pathogenicity were consistent with host specialization of populations found on tomato, and to a lesser extent, populations found on grapevine. Pathogen populations from hydrangea and strawberry appeared to be generalist, while populations from bramble may be weakly specialized. Our results suggest that the polyphagous B. cinerea is more accurately described as a collection of generalist and specialist individuals in populations. This work opens new perspectives for grey mold management, while suggesting spatial optimization of crop organization within agricultural landscapes.
Published: 2019

28. Une structure emboîtée universelle pour les interactions quantitatives entre les plantes et leurs parasites ?

Author: Moury, Benoît, Audergon, Jean-Marc, Baudracco-Arnas, Sylvie, Ben Krima, Safa, Bertrand, François, Boissot, Nathalie, Buisson, Mireille, Caffier, Valérie, Cantet, Melissa, Chanéac, Sylvia, Constant, Carole, Delmotte, Francois, Dogimont, Catherine, Doumayrou, Juliette, Fabre, Frédéric, Fournet, Sylvain, Grimault, Valérie, Jaunet, Thierry, Justafré, Isabelle, Lefebvre, Véronique, Losdat, Denis, Marcel, Thierry C., Montarry, Josselin, Morris, Cindy E., Omrani, Mariem, Paineau, Manon, Perrot, Sophie, Pilet-Nayel, Marie-Laure, Ruellan, Youna, Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Amélioration des Fruits et Légumes (GAFL), Laboratoires ASL, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Bayer seeds SAS, Gautier semences, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Takii France SAS, Sakata Vegetables Europe, Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Unité expérimentale du GEVES, Institut National de la Recherche Agronomique (INRA), HM. CLAUSE [France], Vilmorin, Rijk Zwaan, and Partenaires INRAE
Subjects: [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, ComputingMilieux_MISCELLANEOUS, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: National audience
Published: 2021

29. Resistance of the Wheat Cultivar ‘Renan’ to Septoria Leaf Blotch Explained by a Combination of Strain Specific and Strain Non-Specific QTL Mapped on an Ultra-Dense Genetic Map

Author: Camilla Langlands-Perry, Murielle Cuenin, Christophe Bergez, Safa Ben Krima, Sandrine Gélisse, Pierre Sourdille, Romain Valade, Thierry C. Marcel, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ARVALIS - Institut du Végétal [Boigneville], ARVALIS - Institut du végétal [Paris], Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), CIFRE 2019/0608, WHEALBI FP7-613556, FSOV 2016 W MABRUNE, ANR-10-BTBR-0003,BREEDWHEAT,Développer de nouvelles variétés de blé pour une agriculture durable(2010), and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
Subjects: [SDV]Life Sciences [q-bio], bread wheat, Quantitative Trait Loci, QH426-470, Polymorphism, Single Nucleotide, Article, Chromosomes, Plant, Stb20q, Ascomycota, Species Specificity, Gene Expression Regulation, Plant, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genetics (clinical), Triticum, Septoria tritici blotch, quantitative trait loci, strain specificity, resistance durability, Disease Resistance, Plant Diseases, Plant Proteins, [SDV.GEN]Life Sciences [q-bio]/Genetics, food and beverages, Chromosome Mapping, Plant Leaves, Plant Breeding, Transcriptome
Abstract: Quantitative resistance is considered more durable than qualitative resistance as it does not involve major resistance genes that can be easily overcome by pathogen populations, but rather a combination of genes with a lower individual effect. This durability means that quantitative resistance could be an interesting tool for breeding crops that would not systematically require phytosanitary products. Quantitative resistance has yet to reveal all of its intricacies. Here, we delve into the case of the wheat/Septoria tritici blotch (STB) pathosystem. Using a population resulting from a cross between French cultivar Renan, generally resistant to STB, and Chinese Spring, a cultivar susceptible to the disease, we built an ultra-dense genetic map that carries 148,820 single nucleotide polymorphism (SNP) markers. Phenotyping the interaction was done with two different Zymoseptoria tritici strains with contrasted pathogenicities on Renan. A linkage analysis led to the detection of three quantitative trait loci (QTL) related to resistance in Renan. These QTL, on chromosomes 7B, 1D, and 5D, present with an interesting diversity as that on 7B was detected with both fungal strains, while those on 1D and 5D were strain-specific. The resistance on 7B was located in the region of Stb8 and the resistance on 1D colocalized with Stb19. However, the resistance on 5D was new, so further designated Stb20q. Several wall-associated kinases (WAK), nucleotide-binding and leucine-rich repeats (NB-LRR) type, and kinase domain carrying genes were present in the QTL regions, and some of them were expressed during the infection. These results advocate for a role of Stb genes in quantitative resistance and for resistance in the wheat/STB pathosystem being as a whole quantitative and polygenic.
Published: 2021

30. Identification of Copper-Containing Oxidoreductases in the Secretomes of Three Colletotrichum Species with a Focus on Copper Radical Oxidases for the Biocatalytic Production of Fatty Aldehydes

Author: Safwan Saker, Jean-Guy Berrin, David Ribeaucourt, Richard J. O'Connell, Fanny Lambert, Mickael Lafond, Lydie Oliveira Correia, Sacha Grisel, David Navarro, Bastien Bissaro, Nicolas Lapalu, Mireille Haon, Elodie Drula, Bernard Henrissat, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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), V MANE Fils, ANR-17-CE07-0047,FUNTASTIC,Nouvelles oxydases à radical cuivre fongiques utilisées comme biocatalyseurs pour la valorisation de la biomasse végétale et d'alcools(2017), ANR-17-CAPS-0401,CAPS,ANR-17-CAPS-0004-01, Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département des sciences biologiques, Université du Roi Abdulaziz, CIFFRE n°2017/1169, ANR-17-CAPS-0004,Exosomes,Rôle des vésicules extra cellulaires dans les interactions plantes microbes(2017), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France, INRAE, USC1408, AFMB, Marseille, France., CNRS, Aix Marseille Univ, UMR7257, AFMB, Marseille, France., Centre de résonance magnétique biologique et médicale (CRMBM), and Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], viruses, alcohol oxydase, Context (language use), Applied Microbiology and Biotechnology, flavors and fragrances, Pichia pastoris, Fungal Proteins, 03 medical and health sciences, phytopathogen, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], scopper-containing enzymes, Colletotrichum, secretomics, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 030304 developmental biology, alcohol oxidase, Secretome, Laccase, 0303 health sciences, Oxidase test, copper radical oxidase, Aldehydes, Ecology, biology, 030306 microbiology, Chemistry, filamentous fungi, Fatty Acids, food and beverages, Secretomics, biology.organism_classification, Alcohol oxidase, Biochemistry, CAZyme, Alcohols, Heterologous expression, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Oxidoreductases, Copper-containing enzymes, CAZymes, Copper, Food Science, Biotechnology
Abstract: Copper radical alcohol oxidases (CRO-AlcOx), which have been recently discovered among fungal phytopathogens, are attractive for the production of fragrant fatty aldehydes. With the initial objective to investigate the secretion of CRO-AlcOx by natural fungal strains, we undertook time course analyses of the secretomes of three Colletotrichum species (C. graminicola, C. tabacum, and C. destructivum) using proteomics. The addition of a copper-manganese-ethanol mixture in the absence of any plant-biomass mimicking compounds to Colletotrichum cultures unexpectedly induced the secretion of up to 400 proteins, 29 to 52% of which were carbohydrate-active enzymes (CAZymes), including a wide diversity of copper-containing oxidoreductases from the auxiliary activities (AA) class (AA1, AA3, AA5, AA7, AA9, AA11, AA12, AA13, and AA16). Under these specific conditions, while a CRO-glyoxal oxidase from the AA5_1 subfamily was among the most abundantly secreted proteins, the targeted AA5_2 CRO-AlcOx were secreted at lower levels, suggesting heterologous expression as a more promising strategy for CRO-AlcOx production and utilization. C. tabacum and C. destructivum CRO-AlcOx were thus expressed in Pichia pastoris, and their preference toward both aromatic and aliphatic primary alcohols was assessed. The CRO-AlcOx from C. destructivum was further investigated in applied settings, revealing a full conversion of C(6) and C(8) alcohols into their corresponding fragrant aldehydes. IMPORTANCE In the context of the industrial shift toward greener processes, the biocatalytic production of aldehydes is of utmost interest owing to their importance for their use as flavor and fragrance ingredients. Copper radical alcohol oxidases (CRO-AlcOx) have the potential to become platform enzymes for the oxidation of alcohols to aldehydes. However, the secretion of CRO-AlcOx by natural fungal strains has never been explored, while the use of crude fungal secretomes is an appealing approach for industrial applications to alleviate various costs pertaining to biocatalyst production. While investigating this primary objective, the secretomics studies revealed unexpected results showing that under the oxidative stress conditions we probed, Colletotrichum species can secrete a broad diversity of copper-containing enzymes (laccases, sugar oxidoreductases, and lytic polysaccharide monooxygenases [LPMOs]) usually assigned to “plant cell wall degradation,” despite the absence of any plant-biomass mimicking compound. However, in these conditions, only small amounts of CRO-AlcOx were secreted, pointing out recombinant expression as the most promising path for their biocatalytic application.
Published: 2021

31. A single amino acid polymorphism in a conserved effector of the multihost blast fungus pathogen expands host-target binding spectrum

Author: Yohann Petit-Houdenot, Izumi Chuma, Mark J. Banfield, Joe Win, Adam R. Bentham, Sophien Kamoun, Thorsten Langner, Ryohei Terauchi, John Innes Ctr, Dept Biol Chem, University of East Anglia [Norwich] (UEA), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Obihiro Univ Agr & Vet Med, Kyoto University [Kyoto], Iwate Biotechnology Research Center (IBRC), UK Research & Innovation (UKRI)Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574, UK Research & Innovation (UKRI)Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9797BBS/E/J/000PR9798, European Project: 743165,ERC, AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Kyoto University
Subjects: 0106 biological sciences, Conservation Biology, Rice Blast Fungus, [SDV]Life Sciences [q-bio], Plant Science, 01 natural sciences, Physical Chemistry, Fungal Evolution, Biology (General), Pathogen, Phylogeny, Conservation Science, Data Management, Plant Proteins, Genetics, 0303 health sciences, Phylogenetic tree, Virulence, Effector, Plant Fungal Pathogens, Eukaryota, food and beverages, Phylogenetic Analysis, Genomics, Phylogenetics, Chemistry, Magnaporthe, Physical Sciences, Host-Pathogen Interactions, [SDE]Environmental Sciences, Conservation Genetics, Research Article, Ancestral reconstruction, Computer and Information Sciences, QH301-705.5, Immunology, Plant Pathogens, Mycology, Biology, Microbiology, Evolution, Molecular, 03 medical and health sciences, Molecular evolution, Virology, Evolutionary Systematics, Molecular Biology, Gene, 030304 developmental biology, Taxonomy, Plant Diseases, Evolutionary Biology, Polymorphism, Genetic, Chemical Bonding, Ecology and Environmental Sciences, Organisms, Fungi, Biology and Life Sciences, Hydrogen Bonding, Oryza, RC581-607, Plant Pathology, Amino Acid Substitution, Genetic Loci, Parasitology, Immunologic diseases. Allergy, 010606 plant biology & botany
Abstract: Accelerated gene evolution is a hallmark of pathogen adaptation and specialization following host-jumps. However, the molecular processes associated with adaptive evolution between host-specific lineages of a multihost plant pathogen remain poorly understood. In the blast fungus Magnaporthe oryzae (Syn. Pyricularia oryzae), host specialization on different grass hosts is generally associated with dynamic patterns of gain and loss of virulence effector genes that tend to define the distinct genetic lineages of this pathogen. Here, we unravelled the biochemical and structural basis of adaptive evolution of APikL2, an exceptionally conserved paralog of the well-studied rice-lineage specific effector AVR-Pik. Whereas AVR-Pik and other members of the six-gene AVR-Pik family show specific patterns of presence/absence polymorphisms between grass-specific lineages of M. oryzae, APikL2 stands out by being ubiquitously present in all blast fungus lineages from 13 different host species. Using biochemical, biophysical and structural biology methods, we show that a single aspartate to asparagine polymorphism expands the binding spectrum of APikL2 to host proteins of the heavy-metal associated (HMA) domain family. This mutation maps to one of the APikL2-HMA binding interfaces and contributes to an altered hydrogen-bonding network. By combining phylogenetic ancestral reconstruction with an analysis of the structural consequences of allelic diversification, we revealed a common mechanism of effector specialization in the AVR-Pik/APikL2 family that involves two major HMA-binding interfaces. Together, our findings provide a detailed molecular evolution and structural biology framework for diversification and adaptation of a fungal pathogen effector family following host-jumps., Author summary Plant pathogens secrete effector proteins inside the host where they interact with host target proteins to alter cellular processes and enable infection and disease progression. These effector proteins evolve rapidly to adapt to changing host targets and to avoid recognition by the plant immune system, especially in multihost pathogens that frequently undergo host jumps or host-range expansions. The blast fungus Magnaporthe oryzae is one of the most destructive disease of cereals. Host specialization of M. oryzae lineages is generally associated with gains and losses of effector genes and selection of adaptive mutations. However, the molecular mechanisms of how effector proteins adapt to host targets is poorly understood. Here, we unravelled the biochemical and structural basis underlying adaptive evolution of the effector APikL2. APikL2 belongs to a six gene family of sequence related effectors including the well-studied effector AVR-Pik. APikL2 is exceptionally conserved across host-specific lineages but displays host-specific polymorphisms. We combine biochemical, structural and evolutionary biology methods to provide a molecular evolutionary framework how this effector family adapts to changing host targets. In APikL2, a single amino acid change expands binding to a host-target of the heavy-metal associated domain containing protein family. By reconstructing the evolutionary history of the effector family, we show that this amino acid polymorphism is a derived trait. We combine the knowledge gained from our evolutionary and structural biology analyses to unravel a common mechanism of adaptation in the APikL effector family that involves diversification of two major target-binding interfaces. Together, our findings expand our knowledge about how pathogen effectors adapt to changing host targets following host jumps.
Published: 2021

32. Are Efficient-Dose Mixtures a Solution to Reduce Fungicide Load and Delay Evolution of Resistance? An Experimental Evolutionary Approach

Author: Agathe Ballu, Anne Deredec, Anne-Sophie Walker, Florence Carpentier, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, and French Ministry of Higher Education Research and Innovation and Syngenta France viaCIFRE program n 2017/1363 (PhD scholarship of A.B.).
Subjects: selection drivers, dose variation, QH301-705.5, [SDV]Life Sciences [q-bio], selection heterogeneity, Zymoseptoria tritici, Article, fungicide resistance, ecological specialization, mixture, environmental variation, generalism, [SDE]Environmental Sciences, selection drivers selection heterogeneity, experimental evolution, Biology (General)
Abstract: International audience; Pesticide resistance poses a critical threat to agriculture, human health and biodiversity. Mixtures of fungicides are recommended and widely used in resistance management strategies. However, the components of the efficiency of such mixtures remain unclear. We performed an experimental evolutionary study on the fungal pathogen Z. tritici to determine how mixtures managed resistance. We compared the effect of the continuous use of single active ingredients to that of mixtures, at the minimal dose providing full control of the disease, which we refer to as the “efficient” dose. We found that the performance of efficient-dose mixtures against an initially susceptible population depended strongly on the components of the mixture. Such mixtures were either as durable as the best mixture component used alone, or worse than all components used alone. Moreover, efficient dose mixture regimes probably select for generalist resistance profiles as a result of the combination of selection pressures exerted by the various components and their lower doses. Our results indicate that mixtures should not be considered a universal strategy. Experimental evaluations of specificities for the pathogens targeted, their interactions with fungicides and the interactions between fungicides are crucial for the design of sustainable resistance management strategies.
Published: 2021
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33. Promoting crop pest control by plant diversification in agricultural landscapes: A conceptual framework for analysing feedback loops between agro-ecological and socio-economic effects

Author: Vialatte, A., Tibi, Anaïs, Alignier, Audrey, Angeon, Valérie, Bedoussac, Laurent, Bohan, David, Bougherara, Douadia, Carpentier, A., Castagneyrol, Bastien, Cordeau, Stephane, Courtois, Pierre, Deguine, Jean-Philippe, Enjalbert, Jerome, Fabre, Frédéric, Femenia, Fabienne, Fréville, Hélène, Goulet, Frederic, Grateau, Regis, GRIMONPREZ, Benoît, Gross, Nicolas, Hannachi, Mourad, Jeanneret, Philippe, Kühfuss, Laure, Labarthe, Pierre, Launay, Marie, Lefebvre, Marianne, Lelievre, Virginie, Lemarié, Stephane, Martel, Guillaume, Masson, A., Navarrete, Mireille, Plantegenest, Manuel, Ravigné, Virginie, Rusch, Adrien, Suffert, Frederic, Tapsoba , A., Therond, Olivier, Thoyer, Sophie, Martinet, Vincent, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction de l'Expertise scientifique collective, de la Prospective et des Etudes, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), 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)-Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche d'Écodéveloppement (ECODEVELOPPEMENT), AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA), 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), Centre d'Economie de l'Environnement - Montpellier - UMR 5211 (CEE-M), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Structures et Marché Agricoles, Ressources et Territoires (SMART-LERECO), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), 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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), Economie Publique (ECO-PUB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Etudes et de Coopération Juridique Interdisciplinaire (CECOJI), Université de Poitiers, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Agroscope, University of St Andrews [Scotland], Agroclim (AGROCLIM), Groupe de Recherche Angevin en Economie et Management (GRANEM), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de l'Horticulture et du Paysage, Département agronomie et sciences de l'environnement pour les agroécosystèmes (AgroEcoSystem), Laboratoire d'Economie Appliquée de Grenoble (GAEL), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), 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 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 GEstion des Risques en agriculture (BIOGER), Laboratoire Agronomie et Environnement (LAE), and Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Crop protection, Intercropping, Spatio-temporal heterogeneity, Biological control, Value chains, Varietal mixture, Natural enemies, Wheat, Semi-natural habitats, Institutions, Crop mosaic
Abstract: International audience; Given the negative environmental effects of conventional agricultural techniques, the need for biodiversity-friendly agriculture systems that rely more on ecosystem services and less on chemical inputs is becoming increasingly urgent. In this paper, we focus on crop protection strategies that are alternatives to the use of pesticides. Diversification of the plant component of agricultural areas at different space and time scales has been presented as a powerful socio-economic and agro-ecological mechanism for the sustainable control of pests. Our interdisciplinary group of scientific experts examined the literature on the ecological effects of plant diversification on pests and their natural enemies, as well as the social science literature on the conditions for farmers to adopt the corresponding practices, to assess the potential offered by plant diversification. We developed a conceptual framework that connects the agro-ecological and socio-economic components of an agricultural landscape in a dynamic loop accounting for interactions among elements at different spatial and temporal scales and their feedback effects. This article presents this framework and illustrates its application to the case of wheat production and protection. By explicitly connecting each level of agro-ecological organization with the potential socio-economic drivers and limitations underpinning the adoption and implementation of plant diversification in landscapes, this framework makes it possible to analyse the synergies and antagonisms between different modes of diversification and the conditions of their deployment. Exploring this framework is a prerequisite to the identification of opportunities and key feed-back loops for designing diversification strategies that unlock the agro-ecological potential of future production systems. We conclude that there is a need for interdisciplinary research in experimental landscapes involving farmers and other local stakeholders to design sustainable future agricultural landscapes that deliver high levels of biological control services.
Published: 2021

34. Spatiotemporal Changes in Varietal Resistance to Wheat Yellow Rust in France Reveal an Increase in Field Resistance Level During the Period 1985-2018

Author: M. Leconte, Jérôme Enjalbert, Rémi Perronne, Philippe du Cheyron, Florence Dubs, Claude de Vallavieille-Pope, Tiphaine Vidal, Valérie Cadot, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), ARVALIS, GEVES, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ARVALIS - Institut du végétal [Paris], 773311, European Union’s Horizon 2020 Research and Innovation Programme, 513959, European Framework Programme 6, 031499, European Framework Programme 6 Rex, 265865, European Framework Programme 7, 11-116241, Ministry of Higher Education and Science, ANR-11-LABX-0034, Agence Nationale de la Recherche, European Project: 773311,European Union, European Project: 513959,EFP6, European Project: 031499,EFP6Rex, and European Project: 265865,EFP7
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Plant Science, Biology, Plant disease resistance, all-stage race-specific resistance, 01 natural sciences, Rust, epidemic, resistance, 03 medical and health sciences, stripe (yellow) rust, disease control and pest management, genetics and resistance, pathogene, weighted average age of varieties, Triticum, 030304 developmental biology, Disease Resistance, Plant Diseases, 2. Zero hunger, 0303 health sciences, adult plant non-race-specific resistance, Resistance (ecology), Basidiomycota, food and beverages, Agronomy, agricultural, [SDE]Environmental Sciences, fungal pathogens, France, field adult plant resistance level, genetic, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: Online; International audience; Monitoring spatiotemporal changes in varietal resistance and understanding its drivers seem essential to managing plant diseases but require having access to the genetic basis of disease resistance and to its deployment. In this study, we focused on yellow rust (Puccinia striiformis f. sp. tritici ) for three decades in France, by using field adult plant resistance levels, Yr race-specific resistance genes of varieties, presence of Puccinia striiformis f. sp. tritici pathotypes and their virulence profiles, and systematic surveys of the acreages of bread wheat varieties available at a yearly survey time and at a district level. Based on these data, we studied spatiotemporal changes in varietal resistance over the period from 1985 to 2018 in 54 French administrative districts (hereafter “departments”) by using a set of relevant indicators weighted by the relative acreage proportion of the varieties sown at the department level. Our analyses revealed an increase in varietal resistance over decades that would be due to the accumulation of both quantitative resistance and different race-specific resistance genes. We suggest that, beyond breeders, several actors, including examination offices, agricultural advisory services, and farmers, may have had a substantial influence on these spatiotemporal changes, promoting more resistant varieties and the rapid replacement of newly susceptible varieties by still resistant ones at the beginning of each epidemic.
Published: 2021

35. Improving the design of sustainable crop protection strategies thanks to population genetics concepts

Author: Saubin, Méline, Louet, Clémentine, Bousset, Lydia, Fabre, Frédéric, Fudal, Isabelle, Grognard, Frédéric, Mailleret, Ludovic, Stoeckel, Solenn, Touzeau, Suzanne, Petre, Benjamin, Halkett, Fabien, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA)
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [MATH.MATH-GM]Mathematics [math]/General Mathematics [math.GM], food and beverages, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Cropping genetically resistant plants allows to control pathogen populations while substantially reducing chemical inputs. However, resistances are often quickly defeated by pathogens. In this context, how can sustainable crop protection be achieved? This question has shaped the debate about the durability of genetic resistances in agriculture for decades, and, despite active research efforts, has not been satisfactorily answered yet. Here we demonstrate from a bibliography analysis that the research field of resistance durability evolved into two non-overlapping directions: (i) the subfield of 'epidemiology and evolution', which aims to forecast and explain pathogen population dynamics; (ii) the subfield of 'molecular interactions', which studies the molecular processes involved in the overcoming of resistance and in the dialogue between plants and pathogens. After reviewing briefly these two subfields and the gap between the corresponding research communities, we propose strategies to merge these approaches into one by using the concepts of population genetics. Ultimately, such new eco-evolutionary studies could be used to determine the best strategy for the deployment of genetically resistant cultivars by integrating, from gene to landscape, all relevant and contextual biological knowledge into sound theoretical models.
Published: 2021

36. Evaluating fungicide resistance management strategies by means of experimental evolution : the case of Zymoseptoria tritici, the causal agent of Septoria leaf blotch

Author: Ballu, Agathe, 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), Syngenta France SAS, Syngenta France, Université Paris-Saclay, Anne-Sophie Walker, Anne Dérédec, Florence Carpentier, and Stefano Torriani
Subjects: Environmental variation, Variation environnementale, Déterminants de la sélection, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Generalism, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Fungal adaptation, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Spécialisation écologique, Ecological specialization, Evolution artificielle, Artificial evolution, Adaptation fongique, Généralisme, Selection drivers
Abstract: The evolution of resistance to pesticides is a major economic and environmental burden in agriculture. Resistance management involves maximizing selection pressure heterogeneity, particularly by combining active ingredients (AIs) with different modes of action. Yet, there is still no consensus on the best strategy to delay the emergence and selection of resistance in pathogen populations. Here, we aimed at contributing to this debate while addressing two questions: (i) How can we enhance the performance of anti-resistance strategies and what are the drivers of their optimization? (ii) How the initial status of resistance in populations modulates the performance of strategies? We used Zymoseptoria tritici, the causal agent of the major wheat disease, which is resistant in Europe to most fungicides to varying degrees, to exemplify this debate. We applied an innovative approach for fungi, experimental evolution, to mimic and accelerate, in laboratory-controlled conditions, fungicide resistance usually occurring in the field. In particular, we disentangled the relative impact in reducing resistance selection of multiple drivers of alternation, mixture and dose modulation strategies by submitting a susceptible strain to heterogeneous selection regimes as compared to the single use of the same AIs. In a first experiment, alternation was found a beneficial or neutral strategy to decrease the rate of evolution of resistance, relative to continuous fungicide use, but resulted in higher levels of generalism. We demonstrated that the relative intrinsic resistance risk of AI probably underpinned such trade-off, more than the number of fungicides used or alternation frequency. In a second experiment, we dissected how an efficient-dose mixture, i.e. a mixture with reduced doses of its components but still allowing a disease control similar to that provided by these components used alone, may delay resistance evolution of a naïve population. We concluded that the durability of such mixtures was detrimental to beneficial, strongly depending on its components. Such mixtures possibly favoured generalist or multiple resistance patterns, depending on the combined AIs. Dose reduction in sequence strategies didn’t prevent the selection of highly resistant specialist strains, nor of generalist resistance in some lines. A final experiment was designed to validate the previous findings, while submitting a susceptible isolate and two artificial populations containing low frequencies of single vs. multiple field resistances to selection regimes displaying patterns differing for four possible sources of heterogeneity. Preliminary results concluded that increasing the number of AIs and varying their modes of actions were efficient to delay resistance build-up, either in mixture or alternation regimes, although it facilitated the selection of some generalism in addition to the initially introduced specialist resistances. However, none of these sources of heterogeneity were found efficient at mitigating resistance evolution when multiple resistance was introduced in populations, suggesting that recombination, occurring during sexual reproduction in field populations, should be considered for fungicide sustainability management. At last, fitness cost associated to some resistance alleles shortly delayed resistance evolution and may reshaped population structure in some situations. Experimental evolution has proven to be a powerful tool to enrich the debate on anti-resistance strategies whilst dissecting the interplay between their drivers in realistic biological conditions. These findings open up new possibilities for tailoring resistance management and suggest that the prevention of resistance emergence would be more sustainable than the mitigation of selection.; La résistance aux pesticides impacte économiquement la production agricole et la biodiversité. Sa gestion implique de maximiser l'hétérogénéité des pressions de sélection, notamment en combinant des substances actives (SA) de modes d'action différents. Or, le débat concernant l’efficacité des différentes stratégies pour retarder l'émergence et la sélection de la résistance dans les populations pathogènes reste ouvert. Cette thèse aborde deux questions : (i) Comment améliorer la performance des stratégies anti-résistance et quels sont les facteurs permettant leur optimisation ? (ii) Comment le statut initial de la résistance dans les populations module-t-il la performance des stratégies ? Pour illustrer ce débat, nous avons utilisé Zymoseptoria tritici, agent causal de la principale maladie du blé, résistant à la plupart des fongicides en Europe. Nous avons appliqué une approche innovante pour les champignons, l'évolution expérimentale, qui permet d’imiter et d’accélérer, en conditions contrôlées de laboratoire, la résistance aux fongicides habituellement sélectionnée au champ. En particulier, en soumettant un isolat sensible à des régimes de sélection hétérogènes par comparaison avec l'utilisation en séquence des mêmes SA, nous avons dissocié l'impact relatif de plusieurs facteurs sur la réduction de la sélection au sein de stratégies d'alternance, de mélange et de modulation de dose. Dans une première expérimentation, l'alternance s'est avérée être une stratégie bénéfique ou neutre pour diminuer le taux d'évolution de la résistance par rapport à une utilisation continue, mais a favorisé du généralisme. Nous avons démontré que ce compromis résidait probablement dans le risque de résistance intrinsèque des SA, plutôt que dans le nombre de fongicides utilisés ou le rythme de l'alternance. Dans une deuxième expérimentation, nous avons exploré comment un mélange à dose efficace, c'est-à-dire un mélange avec des doses réduites de ses composants permettant un contrôle de la maladie similaire à celui fourni par ses composants utilisés seuls, peut retarder l'évolution de la résistance d'une population sensible. Nous avons conclu qu’un tel mélange pouvait être, selon ses composants, préjudiciable à bénéfique pour la durabilité. Des résistances généralistes ou multiples ont plus ou moins été favorisées en fonction des combinaisons de SA. La réduction de la dose dans des séquences n'a pas empêché la sélection de souches spécifiques fortement résistantes, ni la résistance généraliste dans certaines lignées. Une dernière expérimentation a été conçue pour valider les résultats précédents en soumettant un isolat sensible et deux populations artificielles, contenant de faibles fréquences de résistances simples ou multiples, à des régimes de sélection contrastés par quatre sources d'hétérogénéité. Les résultats ont conclu que l'augmentation du nombre de SA et la variation des modes d'action étaient efficaces pour retarder la sélection de la résistance, que ce soit en mélange ou alternance. Toutefois cela faciliterait un certain généralisme des isolats sélectionnés, en plus des résistances spécifiques initialement introduites. Aussi, aucune de ces sources d'hétérogénéité ne s'est avérée efficace pour atténuer l'évolution de la résistance lorsque la résistance multiple était présente dans les populations. Cela suggère que la recombinaison, pouvant survenir lors de la reproduction sexuée au champ, est un facteur majeur à considérer. Enfin, la réduction de la valeur sélective associée à certains allèles résistants retarde légèrement leur sélection et peut moduler la structure des populations. L'évolution expérimentale s'avère être un outil puissant pour enrichir le débat sur les stratégies de lutte en analysant les interactions entre ses déterminants. Ces résultats ouvrent de nouvelles perspectives pour optimiser la gestion des résistances et suggèrent que la prévention de l'émergence serait plus durable que de limiter la sélection.
Published: 2021

37. Many different recipes but one flavor: A universal nested structure of quantitative interactions between plant genotypes and their parasites, including viruses

Author: Moury, Benoît, Audergon, Jean-Marc, Baudracco-Arnas, Sylvie, Ben Krima, Safa, Bertrand, François, Boissot, Nathalie, Buisson, Mireille, Caffier, Valérie, Cantet, Melissa, Chanéac, Sylvia, Constant, Carole, Delmotte, François, Dogimont, Catherine, Doumayrou, Juliette, Fabre, Frédéric, Fournet, Sylvain, Grimault, Valérie, Jaunet, Thierry, Justafré, Isabelle, Lefebvre, Véronique, Losdat, Denis, Marcel, Thierry C., Montarry, Josselin, Morris, Cindy E., Omrani, Mariem, Paineau, Manon, Perrot, Sophie, Pilet-Nayel, Marie-Laure, Ruellan, Youna, Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Amélioration des Fruits et Légumes (GAFL), Laboratoires ASL, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), bayer seeds, Gautier semences, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Takii France SAS, Sakata Vegetables Europe, Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Unité expérimentale du GEVES, Institut National de la Recherche Agronomique (INRA), HM. CLAUSE [France], Vilmorin, Rijk Zwaan, Partenaires INRAE, INRAE, and CIRAD
Subjects: [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: National audience
Published: 2021

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

Author: Anaïs Laleve, Nick X. Wang, Sabine Fillinger, Anne Sophie Walker, Danièle Debieu, Brigitte Meunier, David Young, Guillaume Fouché, Thomas Michel, Corteva Agriscience, Corteva agriscience, Indianapolis, USA, Université Paris-Saclay, 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), and French National Research Agency (ANR) French National Association for Research and Technology (ANRT) through the CIFRE fellowship2017/1255
Subjects: 0106 biological sciences, Pyridines, [SDV]Life Sciences [q-bio], Mutant, Respiratory chain, Biology, 01 natural sciences, mycosphaerella graminicola, resistance, 03 medical and health sciences, Lactones, Botrytis cinerea, Ascomycota, Drug Resistance, Fungal, multydrug-resistance, 030304 developmental biology, Plant Diseases, Genetics, 0303 health sciences, Experimental evolution, Cytochrome b, Pathogenic fungus, Cytochromes b, Directed evolution, Strobilurins, 3. Good health, Fungicides, Industrial, Fungicide, [SDE]Environmental Sciences, 010606 plant biology & botany
Abstract: Acquired resistance is a threat for antifungal efficacy in medicine and agriculture. The diversity of possible resistance mechanisms, as well as the highly adaptive traits of pathogens make it difficult to predict evolutionary outcomes of treatments. We used directed evolution as an approach to assess the risk of resistance to the new fungicide fenpicoxamid in the wheat pathogenic fungus Zymoseptoria tritici. Fenpicoxamid inhibits complexIII 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 the respiratory complex by binding to 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. In addition, we identified a negative cross-resistance between isolates harboring G37V or G143A, a Qo site change previously selected by strobilurins. Moreover, double mutants were less resistant to both QiIs and QoIs 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.Originality-Significance StatementThe highly adaptive traits of pathogens render evolutionary outcomes of antifungal treatments difficult to predict.We used directed evolution to assess the risk of resistance to the new fungicide fenpicoxamid in the wheat pathogenic fungus Zymoseptoria tritici.We identified a target modification as the most likely resistance mechanism to be selected.This change triggered high fenpicoxamid resistance and halved the activity of the target enzyme despite no significant penalty for in vitro growth.This work supports the use of experimental evolution as a method to predict adaptation to fungicides and provides important information for the management of QiIs.
Published: 2021

39. A new avirulence gene of Leptosphaeria maculans , AvrLm14 , identifies a resistance source in American broccoli ( Brassica oleracea ) genotypes

Author: Degrave, Alexandre, Wagner, Marine, George, Pierre, Coudard, Laurent, Pinochet, Xavier, Ermel, Magali, Gay, Elise, Fudal, Isabelle, Moreno‐Rico, Onesimo, Rouxel, Thierry, Balesdent, Marie‐Hélène, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), innolea, Terres Inovia, Universidad Autónoma de Aguascalientes, ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ANR GPLA07‐024C, Agence Nationale de la Recherche
Subjects: Genotype, [SDV]Life Sciences [q-bio], Brassica napus, food and beverages, gene‐for‐gene, Original Articles, Brassica, stem canker, resistance introgression, Ascomycota, [SDE]Environmental Sciences, gene-for-gene, Original Article, Leptosphaeria, Plant Diseases
Abstract: In many cultivated crops, sources of resistance to diseases are sparse and rely on introgression from wild relatives. Agricultural crops often are allopolyploids resulting from interspecific crosses between related species, which are sources of diversity for resistance genes. This is the case for Brassica napus (oilseed rape, canola), an interspecific hybrid between Brassica rapa (turnip) and Brassica oleracea (cabbage). B. napus has a narrow genetic basis and few effective resistance genes against stem canker (blackleg) disease, caused by the fungus Leptosphaeria maculans, are currently available. B. rapa diversity has proven to be a valuable source of resistance (Rlm, LepR) genes, while B. oleracea genotypes were mostly considered susceptible. Here we identified a new resistance source in B. oleracea genotypes from America, potentially effective against French L. maculans isolates under both controlled and field conditions. Genetic analysis of fungal avirulence and subsequent cloning and validation identified a new avirulence gene termed AvrLm14 and suggested a typical gene‐for‐gene interaction between AvrLm14 and the postulated Rlm14 gene. AvrLm14 shares all the usual characteristics of L. maculans avirulence genes: it is hosted in a genomic region enriched in transposable elements and heterochromatin marks H3K9me3, its expression is repressed during vegetative growth but shows a strong overexpression 5–9 days following cotyledon infection, and it encodes a small secreted protein enriched in cysteine residues with few matches in databases. Similar to the previously cloned AvrLm10‐A, AvrLm14 contributes to reduce lesion size on susceptible cotyledons, pointing to a complex interplay between effectors promoting or reducing lesion development., Cloning of avirulence gene AvrLm14 in Leptosphaeria maculans allowed us to identify the first resistance gene to the fungus in Brassica oleracea; therefore B. oleracea diversity may be exploited to find novel resistance to the disease.
Published: 2021

40. Models of plant resistance deployment

Author: Frédéric Fabre, Julien Papaïx, Luke G. Barrett, Benoît Moury, Loup Rimbaud, Christian Lannou, Peter H. Thrall, Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CSIRO Agriculture and Food (CSIRO), Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biostatistique et Processus Spatiaux (BioSP), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), GRDC grant CSP00192, AFB Ecophyto II-Leviers Territoriaux Project Médée (2020–2022), INRA-CSIRO linkage program, and ANR-18-CE32-0004,ArchiV,Architecture génétique des caractères quantitatifs dans les interactions plante-virus: conséquences pour la gestion des variétés résistantes et/ou tolérantes à l'échelle du paysage.(2018)
Subjects: Crops, Agricultural, 0106 biological sciences, Plant Science, Computational biology, adaptation, Biology, 01 natural sciences, host–microbe interaction, 03 medical and health sciences, evolution, Disease Resistance, Plant Diseases, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Resistance (ecology), 15. Life on land, simulation, immunity, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Software deployment, durability, Adaptation, 010606 plant biology & botany
Abstract: International audience; Owing to their evolutionary potential, plant pathogens are able to rapidly adapt to genetically controlled plant resistance, often resulting in resistance breakdown and major epidemics in agricultural crops. Various deployment strategies have been proposed to improve resistance management. Globally, these rely on careful selection of resistance sources and their combination at various spatiotemporal scales (e.g., via gene pyramiding, crop rotations and mixtures, landscape mosaics). However, testing and optimizing these strategies using controlled experiments at large spatiotemporal scales are logistically challenging. Mathematical models provide an alternative investigative tool, and many have been developed to explore resistance deployment strategies under various contexts. This review analyzes 69 modeling studies in light of specific model structures (e.g., demographic or demogenetic, spatial or not), underlying assumptions (e.g., whether preadapted pathogens are present before resistance deployment), and evaluation criteria (e.g., resistance durability, disease control, cost-effectiveness). It highlights major research findings and discusses challenges for future modeling efforts.
Published: 2021

41. Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures

Author: Colin Clairet, Muriel Viaud, Bérengère Dalmais, Nicolas Lapalu, Zehraoui E, Ponts N, Isabelle Fudal, Adeline Simon, Jessica L. Soyer, 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), Unité de recherche Mycologie et Sécurité des Aliments (MycSA), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 2. Zero hunger, Transposable element, Whole genome sequencing, 0303 health sciences, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Computational biology, Biology, Pathogenicity, 01 natural sciences, Genome, Housekeeping gene, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene expression, Nucleosome, Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract: Fungal pathogens represent a serious threat towards agriculture, health, and environment. Control of fungal diseases on crops necessitates a global understanding of fungal pathogenicity determinants and their expression during infection. Genomes of phytopathogenic fungi are often compartmentalized: the core genome contains housekeeping genes whereas the fast-evolving genome mainly contains transposable elements and species-specific genes. In this study, we analysed nucleosome landscapes of four phytopathogenic fungi with contrasted genome organizations to describe and compare nucleosome repartition patterns in relation with genome structure and gene expression level. We combined MNase-seq and RNA-seq analyses to concomitantly map nucleosome-rich and transcriptionally active regions during fungal growth in axenic culture; we developed the MNase-seq Tool Suite (MSTS) to analyse and visualise data obtained from MNase-seq experiments in combination with other genomic data and notably RNA-seq expression data. We observed different characteristics of nucleosome profiles between species, as well as between genomic regions within the same species. We further linked nucleosome repartition and gene expression. Our findings support that nucleosome positioning and occupancies are subjected to evolution, in relation with underlying genome sequence modifications. Understanding genomic organization and its role in expression regulation is the next gear to understand complex cellular mechanisms and their evolution.
Published: 2021

42. Spatio-temporal distribution of DMI and SDHI fungicide resistance of Zymoseptoria tritici throughout Europe based on frequencies of key target-site alterations

Author: Hellin, Pierre, Duvivier, Maxime, Heick, Thies, Fraaije, Bart, Bataille, Charlotte, Clinckemaillie, Aurélie, Legrève, Anne, Jørgensen, Lise, Andersson, Björn, Samils, Berit, Rodemann, Bernd, Berg, Gunilla, Hutton, Fiona, Garnault, Maxime, El Jarroudi, Moussa, Couleaud, Gilles, Kildea, Steven, Walloon Agr Res Ctr, Plant & Forest Hlth Unit, Aarhus University [Aarhus], National Institute of Agricultural Botany (NIAB), Université Catholique de Louvain = Catholic University of Louvain (UCL), Swedish University of Agricultural Sciences (SLU), Julius Kühn-Institut (JKI), Swedish Board of Agriculture, Partenaires INRAE, Teagasc - The Agriculture and Food Development Authority (Teagasc), 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), Univ Liege, Dept Environm Sci & Management, Arlon Campus Environm, ARVALIS - Institut du Végétal [Boigneville], ARVALIS - Institut du végétal [Paris], Belgium (Moerman research fund, RESIST project at CRA-W), Denmark (Aarhus University, Department of Agroecology), Germany (JKI), Ireland (Teagasc), and Swedish Research Council Formas
Subjects: disease control, septoria tritici blotch, [SDV]Life Sciences [q-bio], Succinic Acid, food and beverages, Triazoles, Fungicides, Industrial, Europe, Succinate Dehydrogenase, triazole, Ascomycota, wheat, ensitivity, [SDE]Environmental Sciences, Mycosphaerella graminicolas, Plant Diseases
Abstract: International audience; BACKGROUND Over the past decade, demethylation inhibitor (DMI) and succinate dehydrogenase inhibitor (SDHI) fungicides have been extensively used to control to septoria tritici blotch, caused by Zymoseptoria tritici on wheat. This has led to the development and selection of alterations in the target-site enzymes (CYP51 and SDH, respectively). RESULTS Taking advantage of newly and previously developed qPCR assays, the frequency of key alterations associated with DMI (CYP51-S524T) and SDHI (SDHC-T79N/I, C-N86S and C-H152R) resistance was assessed in Z. tritici-infected wheat leaf samples collected from commercial crops (n = 140) across 14 European countries prior to fungicide application in the spring of 2019. This revealed the presence of a West to East gradient in the frequencies of the most common key alterations conferring azole (S524T) and SDHI resistance (T79N and N86S), with the highest frequencies measured in Ireland and Great Britain. These observations were corroborated by sequencing (CYP51 and SDH subunits) and sensitivity phenotyping (prothioconazole-desthio and fluxapyroxad) of Z. tritici isolates collected from a selection of field samples. Additional sampling made at the end of the 2019 season confirmed the continued increase in frequency of the targeted alterations. Investigations on historical leaf DNA samples originating from different European countries revealed that the frequency of all key alterations (except C-T79I) has been gradually increasing over the past decade. CONCLUSION Whilst these alterations are quickly becoming dominant in Ireland and Great Britain, scope still exists to delay their selection throughout the wider European population, emphasizing the need for the implementation of fungicide antiresistance measures.
Published: 2021

43. Assessing the Cultivability of Bacteria and Fungi from Arable Crop Residues Using Metabarcoding Data as a Reference

Author: Coralie Marais, Marie-Hélène Balesdent, Lydie Kerdraon, Matthieu Barret, Marion Fischer-Le Saux, Anne-Lise Liabot, Frédéric Suffert, Valérie Laval, Benjamin Boudier, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
Subjects: microbial, Crop residue, oilseed rape, QH301-705.5, media_common.quotation_subject, Microorganism, [SDV]Life Sciences [q-bio], microbiome, Biology, Competition (biology), 03 medical and health sciences, wheat, Botany, Microbiome, Biology (General), bacteria, 030304 developmental biology, Nature and Landscape Conservation, media_common, 2. Zero hunger, 0303 health sciences, Ecology, 030306 microbiology, Ecological Modeling, 15. Life on land, biology.organism_classification, Isolation (microbiology), Agricultural and Biological Sciences (miscellaneous), Taxon, Microbial population biology, crop residue, [SDE]Environmental Sciences, metabarcoding, community, fungi, microbial community, isolation, Bacteria
Abstract: International audience; This study combined culture-dependent (strain isolation plus molecular identification) and culture-independent (metabarcoding) approaches to characterize the diversity of microbiota on wheat and oilseed rape residues. The goal was to develop a methodology to culture microorganisms with the aim of being able to establish synthetic crop residue microbial communities for further study, i.e., testing potential interactions within these communities and characterizing groups of beneficial taxa that could be used as biological control agents against plant pathogens. We generated community-based culture collections. We adapted the isolation strategy to the potential differences in the spatial and temporal distribution of diversity between bacteria and fungi. We performed (i) a high-throughput isolation from few samples with no a priori for bacteria and (ii) a low-throughput isolation from several samples with a priori—i.e., morphotype selection—for fungi. Although isolation using a single medium did not allow us to characterize the microbiome as precisely as metabarcoding, the bacterial diversity (158 ASVs, 36 genera) was relatively higher than the fungal diversity (131 ASVs, 17 genera) known to be limited by competition for growth on non-selective solid media. Isolation and metabarcoding provided consistent and complementary information: they revealed several common but also specific ASVs, leading to close microbial community profiles of the most abundant fungal and bacterial taxa in residues. Finally, by empirically comparing the different profiles, we assessed the cultivability of the most abundant fungal and bacterial taxa obtained in metabarcoding.
Published: 2021

44. Annual dynamics of Zymoseptoria tritici populations in wheat cultivar mixtures: a compromise between the efficiency and durability of a recently broken-down resistance gene?

Author: Sébastien Saint-Jean, Carolina Orellana-Torrejon, Sandrine Gélisse, Suffert Frédéric, Anne-Lise Boixel, Tiphaine Vidal, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and BIOlogie et GEstion des Risques en agriculture (BIOGER)
Subjects: 0106 biological sciences, Canopy, [SDE.MCG]Environmental Sciences/Global Changes, Population, Virulence, Biology, [SDU.STU.ME]Sciences of the Universe [physics]/Earth Sciences/Meteorology, 01 natural sciences, 03 medical and health sciences, Cultivar, education, Gene, Pathogen, 030304 developmental biology, 2. Zero hunger, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, education.field_of_study, Resistance (ecology), [SDE.IE]Environmental Sciences/Environmental Engineering, food and beverages, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Agronomy, Seedling, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: Cultivar mixtures slow polycyclic epidemics but may also affect the evolution of pathogen populations by diversifying the selection pressures exerted by their plant hosts at field scale. We compared the dynamics of natural populations of the fungal pathogen Zymoseptoria tritici in pure stands and in three binary mixtures of wheat cultivars (one susceptible cultivar and one cultivar carrying the recently broken-down Stb16q gene) over two annual field epidemics. We combined analyses of population ‘size’ based on disease severity, and of population ‘composition’ based on changes in the frequency of virulence against Stb16q in seedling assays with more than 3000 strains. Disease reductions were observed in mixtures late in the epidemic, at the whole canopy scale and on both cultivars, suggesting the existence of a reciprocal ‘protective’ effect. The three cultivar proportions in the mixtures (0.25, 0.5 and 0.75) modulated the decrease in (i) the size of the pathogen population relative to the two pure stands, (ii) the size of the virulent subpopulation, and (iii) the frequency of virulence relative to the pure stand of the cultivar carrying Stb16q. Our findings suggest that optimal proportions may differ slightly between the three indicators considered. We argued potential trade-offs that should be taken into account when deploying a resistance gene in cultivar mixtures: between the dual objectives ‘efficacy’ and ‘durability’, and between the ‘size’ and ‘frequency’ of the virulent subpopulation. Based on current knowledge, it remains unclear whether virulent subpopulation size or frequency has the largest influence on interepidemic virulence transmission.
Published: 2021

45. 'Phytopathological strolls' in the dual context of COVID‐19 lockdown and IYPH2020: Transforming constraints into an opportunity for public education about plant pathogens

Author: Frédéric Suffert, Muriel Suffert, 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), and European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes (EPPO)
Subjects: 0106 biological sciences, media_common.quotation_subject, Internet privacy, Context (language use), Plant Science, Horticulture, Biology, 010603 evolutionary biology, 01 natural sciences, 030308 mycology & parasitology, lockdown, 03 medical and health sciences, Genetics, fungal pathogen, 030304 developmental biology, media_common, 0303 health sciences, education, business.industry, Original Articles, rust, DUAL (cognitive architecture), Geography, Mobile phone, Beauty, [SDE]Environmental Sciences, Original Article, Identification (biology), The Internet, business, Agronomy and Crop Science, Amateur, Diversity (politics)
Abstract: The experience presented here relates to 2020, a particularly timely year for plant disease‐related communication (International Year of Plant Health, IYPH2020), but also a unique year because of the COVID‐19 pandemic. Our goal was to illustrate the diversity and beauty of fungal plant pathogens through a naturalist approach that could be followed by any amateur. We achieved this end through “phytopathological strolls”, in which we observed and determined the origin of symptoms on diseased plants found in our garden, in the local streets, and in nearby open spaces, and shared this matter with a broad public. The lockdown imposed in France created an additional motivation to take up the challenge, and to involve our children, even under strong constraints such as movement restrictions. We observed and described fungal pathogens through hundreds of photographs, shared our findings with a large audience on Twitter, and received feedback. The material used was deliberately simple and transportable: a digital reflex camera, an old microscope, a mobile phone, some books, and an internet connection. Between 17 March 2020 and 20 June 2021 we found 196 plant pathogens, including 97 rusts, 27 powdery mildews, and 28 septoria‐like diseases. We discuss here the importance of promoting searches for plant pathogens, their description and conservation, through a combination of classical approaches and digital tools in tune with the times, such as Twitter, by treating pathogen identification like a detective game and, more surprisingly, by making use of the addictive nature of collection approaches, drawing a parallel with Pokémon GO., In the dual context of COVID‐19 lockdown and of the International Year of Plant Health, we used "phytopathological strolls" and communication on the microblogging platform Twitter to promote public education about plant pathogens.
Published: 2021

46. The quasi-universality of nestedness in the structure of quantitative plant-parasite interactions

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

47. Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization

Author: Jessica L. Soyer, Colin Clairet, Elise J. Gay, Nicolas Lapalu, Thierry Rouxel, Eva H. Stukenbrock, Isabelle Fudal, 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), Max Planck Institute for Evolutionary Biology, Christian-Albrechts University of Kiel, Max Planck Society (GERMANY), Contrat Jeune Scientifique' grant from INRA, Max Planck Society, ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), and ANR-19-CE20-0022,CHOPIN,Deciphering in planta CHrOmatin dynamics of a Phytopathogenic fungus during INfection(2019)
Subjects: 0106 biological sciences, Euchromatin, Heterochromatin, [SDV]Life Sciences [q-bio], [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, host-pathogen interaction, 01 natural sciences, Genome, 03 medical and health sciences, Leptosphaeria maculans, Ascomycota, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Gene, 030304 developmental biology, Genomic organization, 0303 health sciences, biology, Effector, Brassica napus, heterochromatin, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Genomics, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Histone Code, ChIP-seq, [SDE]Environmental Sciences, Original Article, comparative epigenomics, Chromatin immunoprecipitation, 010606 plant biology & botany, Leptosphaeria, effectors
Abstract: Leptosphaeria maculans ‘brassicae’ (Lmb) and Leptosphaeria maculans ‘lepidii’ (Lml) are closely related phytopathogenic species that exhibit a large macrosynteny but contrasting genome structure. Lmb has more than 30% of repeats clustered in large repeat-rich regions, while the Lml genome has only a small amount of evenly distributed repeats. Repeat-rich regions of Lmb are enriched in effector genes, expressed during plant infection. The distinct genome structures of Lmb and Lml provide an excellent model for comparing the organization of pathogenicity genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation (ChIP) during axenic culture, targeting histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyze the influence of chromatin organization on gene expression. In both species, we found that facultative heterochromatin is enriched with genes lacking functional annotation, including numerous effector and species-specific genes. Notably, orthologous genes located in H3K27me3 domains are enriched with effector genes. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3 domains associated with repeat-rich regions that contain numerous species-specific effector genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection and the selective advantage to the fungus to host effector genes in H3K9me3 or H3K27me3 domains. Supplementary Information The online version contains supplementary material available at 10.1007/s10577-021-09658-1.
Published: 2021

48. Impacts of Sodium Arsenite on Wood Microbiota of Esca-Diseased Grapevines

Author: Bruez, Emilie, Larignon, Philippe, Bertsch, Christophe, Robert-Siegwald, Guillaume, Lebrun, Marc Henri, Rey, Patrice, FLORENCE, FONTAINE, Unité de Recherche Oenologie [Villenave d'Ornon], Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Français de la Vigne et du Vin (IFV), Laboratoire Vigne Biotechnologie et Environnement (LVBE), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), 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), 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), Résistance Induite et Bioprotection des Plantes - EA 4707 (RIBP), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), and Ministère de l'Agriculture et Comité Interprofessionnel de la Vigne en France (CNIV). (Projet CASDAR V1301)
Subjects: QH301-705.5, [SDV]Life Sciences [q-bio], metabarcoding, Fomitiporia mediterranea, fungicide, trunk disease, white rot, Biology (General), Article
Abstract: International audience; Although sodium arsenite was widely used in Europe until its ban in 2003, its effects on microorganisms is not clearly understood. To improve our understanding of sodium arsenite curative effect on GTDs, grapevines displaying esca-foliar symptoms from different French regions (Alsace, Champagne, Languedoc) were treated or not with sodium arsenite, and analyzed for their wood microbiota. Using metabarcoding, we identified the fungal and bacterial taxa composition of microbiota colonizing woody trunk tissues. Large differences in fungal microbiota composition between treated and untreated grapevines were observed while no major impacts were observed on bacteria microbiota. The main fungal species detected in untreated necrotic woody tissues was Fomitiporia mediterranea (63-94%), a fungal pathogen associated with esca. The relative abundance of this fungal species significantly decreased after sodium arsenite treatment in the three vineyards, in particular in white-rot necrotic tissues and their borders (-90%). F. mediterranea was the most sensitive to sodium arsenite among fungi from grapevine woody tissues. These results strongly suggest that the effect of sodium arsenite on GTDs is due to its ability to efficiently and almost specifically eliminate F. mediterranea from white-rot necrotic tissues, allowing saprobic fungi to colonize the tissues previously occupied by this pathogenic fungus.
Published: 2021

49. New specific quantitative real‐time PCR assays shed light on the epidemiology of two species of the Leptosphaeria maculans – Leptosphaeria biglobosa species complex

Author: Valerie Laval, Marie-Hélène Balesdent, Thierry Rouxel, Noémie Jacques, 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), and Institut National de la Recherche Agronomique
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, Species complex, biology, Leptosphaeria maculans &#8216, real&#8208, Leptosphaeria biglobosa, food and beverages, Plant Science, Leptosphaeria biglobosa &#8216, Horticulture, biology.organism_classification, 01 natural sciences, 03 medical and health sciences, Quantitative Real Time PCR, Leptosphaeria maculans, [SDE]Environmental Sciences, epidemiology, time PCR assays, Agronomy and Crop Science, brassicae&#8217, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Phoma stem canker, a highly damaging disease of oilseed rape (Brassica napus), is caused by fungi of the Leptosphaeria maculans/Leptosphaeria biglobosa species complex. On B. napus, at least in Europe, L. maculans ‘brassicae’ (LMB) and L. biglobosa ‘brassicae’ (LBB) are often found together, in the same fields. The biology and epidemiology of LMB have been intensively studied, but few studies have investigated the infection and colonization processes of LBB, and unanswered questions remain concerning the relative contributions of these two species to phoma stem canker disease. We addressed this question by developing two species-specific robust quantitative PCR (qPCR) assays, one for each species, for detecting and quantifying these species in field samples of oilseed rape. The assays were highly specific, reproducible, and sensitive. We used them to obtain an overview of stem canker epidemiology in a two-year field study of a B. napus genotype susceptible to LMB, and a near-isogenic line harbouring Rlm11, a gene conferring effective resistance to LMB. Inoculum pressure differed considerably between the two years of the experiment, and we found that LMB leaf spotting intensity at limited observation time points was insufficient for predicting final disease severity. We also found that LBB was more prevalent than previously thought, with epidemiological and colonization biology characteristics very similar to those of LMB, but a necrotrophic lifestyle. The general presence of these two species together on leaves and in the stem tissues of the same individual plant raises questions about their relative incidence and biological interactions within plant tissues.
Published: 2021

50. Nonproteinaceous effectors: the terra incognita of plant–fungal interactions

Author: Marc-Henri Lebrun, Jérôme Collemare, Richard J. O'Connell, Westerdijk Fungal Biodiversity Insitute [Utrecht] (WI), Royal Netherlands Academy of Arts and Sciences (KNAW), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), ANR-17-CAPS-0004-01, Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Fungal Natural Products
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, [SDV]Life Sciences [q-bio], Secondary Metabolism, Plant Science, functional analyses, Biology, 01 natural sciences, Extracellular vesicles, Transcriptome, 03 medical and health sciences, Gene Expression Regulation, Fungal, Plant Cells, Functional methods, CRISPR, Functional studies, noncoding small RNAs, secondary metabolites, Effector, Fungi, plant defences, heterologous expression, Plants, Cell biology, Interaction studies, 030104 developmental biology, Host-Pathogen Interactions, [SDE]Environmental Sciences, extracellular vesicles, transcriptome, Terra incognita, 010606 plant biology & botany
Abstract: International audience; Molecular plant-fungal interaction studies have mainly focused on small secreted protein effectors. However, accumulating evidence shows that numerous fungal secondary metabolites are produced at all stages of plant colonization, especially during early asymptomatic/biotrophic phases. The discovery of fungal small RNAs targeting plant transcripts has expanded the fungal repertoire of nonproteinaceous effectors even further. The challenge now is to develop specific functional methods to fully understand the biological roles of these effectors. Studies on fungal extracellular vesicles are also needed because they could be the universal carriers of all kinds of fungal effectors. With this review, we aim to stimulate the nonproteinaceous effector research field to move from descriptive to functional studies, which should bring a paradigm shift in plant-fungal interactions.
Published: 2019

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