Author: "Julius Kühn-Institut (JKI)" - Searchworks@Jio Institute Digital Library Search Results

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1. = Institute for Plant Protection in Fruit Crops and Viticulture

Author: Julius Kühn-Institut (JKI), Institut Für Pflanzenschutz In Obst- Und Weinbau
Abstract: Broschüren aus dem JKI, p. 1
Published: 2022
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2. ENTAM - Prüfbericht, D - 2228 : gezogenes Raumsprühgerät Lochmann RPS 10/80 UQ 2A

Author: Julius Kühn-Institut (JKI), Bundesforschungsinstitut für Kulturpflanzen, Institut für Anwendungstechnik im Pflanzenschutz
Published: 2020
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3. ENTAM - Test Report D - 2228, Trailed air assisted sprayer Lochmann RPS 10/80 UQ 2A

Author: Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Application Techniques in Plant Protection
Published: 2020
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4. ENTAM - Prüfbericht, D - 2227 : gezogenes Raumsprühgerät Lochmann RPS 10/90 UQH 2A

Author: Julius Kühn-Institut (JKI), Bundesforschungsinstitut für Kulturpflanzen, Institut für Anwendungstechnik im Pflanzenschutz, Braunschweig, Deutschland
Published: 2020
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5. ENTAM - Prüfbericht, D - 2197 : gezogenes Feldspritzgerät LEMKEN Orion 12

Author: Julius Kühn-Institut (JKI), Bundesforschungsinstitut für Kulturpflanzen, Institut für Anwendungstechnik im Pflanzenschutz
Published: 2020
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6. ENTAM - Test Report D - 2197, Trailed field crop sprayer LEMKEN Orion 12

Author: Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Application Techniques in Plant Protection
Published: 2020
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7. C-MIP: An international model inter-comparison simulating organic carbon dynamics in bare fallow soils

Author: Farina, Roberta, Ehrhardt, Fiona, Bellocchi, Gianni, Chenu, Claire, Soussana, Jean-François, Abdalla, Mohamed, Álvaro-Fuentes, Jorge, Blauer, Mira, Brilli, Lorenzo, Chakrabarti, Bidisha, CLIVOT, Hugues, De Antoni, Max, di bene, claudia, Dorich, Cristopher, Ferchaud, Fabien, Nuala, Fitton, Francaviglia, Rosa, Franko, Uwe, Grant, Brian B, Guenet, Bertrand, Harrison, Matthew T., Kirschbaum, Miko U.F., Kuka, Katrin, Lehtonen, Aleksi, Martin, Raphaël, Meier, Elizabeth Anne, Menichetti, Lorenzo, Mula, Laura, Nendel, Claas, Rolinski, Susanne, Sharp, Joanna, Shepherd, Anita, Smith, Ward, Snow, Val, Taghizadeh-Toosi, Arezoo, Tsutskikh, Elena, Zhang, Qing, Recous, Sylvie, Research Centre for the Soil-Plant System, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), Collège de Direction, Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institute of Biological and Environmental Sciences, (SFIRC), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Consejo Superior de Investigaciones Científicas, Istituto di Biometeorologia [Firenze] (IBIMET), Consiglio Nazionale delle Ricerche (CNR), Indian Agricultural Research Institute (IARI), UR 1158 AgroImpact Agroressources et Impacts environnementaux, Queensland University of Technology, Colorado State University [Fort Collins] (CSU), Helmholtz Centre for Environmental Research (UFZ), Agriculture Canada, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Tasmanian Institute of Agriculture, Landcare Research, Julius Kühn-Institut (JKI), Natural Resources Institute Finland, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Swedish University of Agricultural Sciences (SLU), Dipartimento di Agraria e Nucleo Ricerca Desertificazione, Università degli Studi di Sassari, Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Potsdam Institute for Climate Impact Research (PIK), The New Zealand Institute for Plant and Food Research, Rothamsted Research, Agriculture and Agri-Food [Ottawa] (AAFC), AgResearch Ltd, Aarhus University, Institute of Atmospheric Physics [Beijing] (IAP), Chinese Academy of Sciences [Beijing] (CAS), Fractionnement des AgroRessources et Environnement - UMR-A 614 (FARE), Université de Reims Champagne-Ardenne (URCA)-Institut National de la Recherche Agronomique (INRA)-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), Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria ( CREA ), Institut National de la Recherche Agronomique ( INRA ), Unité de Recherche sur l'Ecosystème Prairial, ( SFIRC ), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes ( ECOSYS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Istituto di Biometeorologia [Firenze] ( IBIMET ), Consiglio Nazionale delle Ricerche ( CNR ), Indian Agricultural Research Institute ( IARI ), Colorado State University, Helmholtz Centre for Environmental Research ( UFZ ), LSCE, Centre National de la Recherche Scientifique ( CNRS ), Julius Kühn-Institut ( JKI ), Commonwealth Scientific and Industrial Research Organisation, Swedish University of Agricultural Sciences ( SLU ), Leibniz Centre for Agricultural Landscape Research, Potsdam Institute for Climate Impact Research ( PIK ), Agriculture and Agri-Food Canada ( AAFC ), Institute of Atmospheric Physics [Beijing] ( IAP ), Chinese Academy of Sciences [Beijing] ( CAS ), Fractionnement des AgroRessources et Environnement - UMR-A 614 ( FARE ), Université de Reims Champagne-Ardenne ( URCA ) -Institut National de la Recherche Agronomique ( INRA ) -SFR Condorcet, and 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 )
Subjects: [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: C-MIP: An international model inter-comparison simulating organic carbon dynamics in bare fallow soils. 6th International Symposium on Soil Organic Matter
Published: 2017

8. Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests

Author: Annelies Haegeman, Yoika Foucart, Kris De Jonghe, Thomas Goedefroit, Maher Al Rwahnih, Neil Boonham, Thierry Candresse, Yahya Z. A. Gaafar, Oscar P. Hurtado-Gonzales, Zala Kogej Zwitter, Denis Kutnjak, Janja Lamovšek, Marie Lefebvre, Martha Malapi, Irena Mavrič Pleško, Serkan Önder, Jean-Sébastien Reynard, Ferran Salavert Pamblanco, Olivier Schumpp, Kristian Stevens, Chandan Pal, Lucie Tamisier, Çiğdem Ulubaş Serçe, Inge van Duivenbode, David W. Waite, Xiaojun Hu, Heiko Ziebell, Sébastien Massart, Research Institute for Agricultural, Fisheries and Food (ILVO), University of California [Davis] (UC Davis), University of California (UC), Newcastle University [Newcastle], Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Julius Kühn-Institut (JKI), USDA-APHIS PPQ, National Institute of Biology [Ljubljana] (NIB), Jozef Stefan International Postgraduate School [Ljubljana, Slovenia], Agricultural Institute of Slovenia, USDA-Animal and Plant Health Inspection Service (USDA-APHIS), United States Department of Agriculture (USDA), Department of Plant Protection, Agroscope, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK, Zespri International Limited, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Pathologie Végétale (PV), Niğde Ömer Halisdemir University, Dutch General Inspection Service for Agricultural Seed and Seed Potatoes, Plant Health and Environment Laboratory, Ministry for Primary Industries, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Gembloux Agro-Bio Tech, University of Liege, Belgian Federal Public Service of Health, Food Chain Safety and Environment (FPS Health) through the contract 'RI 18_A-289'., Euphresco project 'Plant Health Bioinformatics Network' (PHBN) (2018-A-289)., Slovenian Research Agency (project and core financing grants No. P4-0072, L7-2632 and P4-0165), and European Project: 2018-A-289,PHBN
Subjects: metagenomics, metatranscriptomics, Ecology, Prevention, plant pathogen, diagnostics, high-throughput sequencing, RNA-seq, Plant Science, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Vaccine Related, Emerging Infectious Diseases, Infectious Diseases, Biodefense, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genetics, Infection, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.
Published: 2023

9. Tannin phenotyping of the Vitaceae reveals a phylogenetic linkage of epigallocatechin in berries and leaves

Author: Jean-Marc Brillouet, Charles Romieu, Roberto Bacilieri, Peter Nick, Anna Trias-Blasi, Erika Maul, Katalin Solymosi, Peter Teszlák, Jiang-Fu Jiang, Lei Sun, Danielle Ortolani, Jason P Londo, Ben Gutierrez, Bernard Prins, Marc Reynders, Frank Van Caekenberghe, David Maghradze, Cecile Marchal, Amir Sultan, Jean-Francois Thomas, Daniel Scherberich, Helene Fulcrand, Laurent Roumeas, Guillaume Billerach, Vugar Salimov, Mirza Musayev, Muhammad Ejaz Ul Islam Dar, Jean-Benoit Peltier, Michel Grisoni, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), 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), 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, Karlsruhe Institute of Technology (KIT), Royal Botanic Gardens [Kew], Julius Kühn-Institut (JKI), Eötvös Loránd University (ELTE), Department of Plant Anatomy, Institute of Biology [Budapest], Faculty of Sciences [Budapest], Eötvös Loránd University (ELTE)-Eötvös Loránd University (ELTE)-Faculty of Sciences [Budapest], Eötvös Loránd University (ELTE)-Eötvös Loránd University (ELTE), University of Pecs, Chinese Academy of Agricultural Sciences (CAAS), Jardin Exotique, USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service, University of California [Davis] (UC Davis), University of California (UC), Meise Botanic Garden [Belgium] (Plantentuin), National Wine Agency of Georgia, Domaine expérimental de Vassal (MONTP DOM VASSAL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Herbarium (Stewart Collection), Jardin Botanique de Lyon, Partenaires INRAE, Azerbaijani Scientific Research Institute of Viticulture and Winemaking, Azerbaijan National Academy of Sciences (ANAS), University of Azad Jammu & Kashmir (UAJ&K), Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: American wild grapevines, leaf, phenotype, [SDV]Life Sciences [q-bio], leaf margin teeth, Original Articles, Plant Science, Asian wild grapevines, Catechin, Plant Leaves, Vitaceae, Vitis vinifera, Fruit, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Condensed tannins, pericarp, Proanthocyanidins, Vitis, epigallocatechin, Tannins, EGC(-) vines, Phylogeny, EGC(+) vines
Abstract: Background and Aims Condensed tannins, responsible for berry and wine astringency, may have been selected during grapevine domestication. This work examines the phylogenetic distribution of condensed tannins throughout the Vitaceae phylogenetic tree. Methods Green berries and mature leaves of representative true-to-type members of the Vitaceae were collected before ‘véraison’, freeze-dried and pulverized, and condensed tannins were measured following depolymerization by nucleophilic addition of 2-mercaptoethanol to the C4 of the flavan-3-ol units in an organic acidic medium. Reaction products were separated and quantified by ultrahigh pressure liquid chromatography/diode array detection/mass spectrometry. Key Results and Conclusions The original ability to incorporate epigallocatechin (EGC) into grapevine condensed tannins was lost independently in both the American and Eurasian/Asian branches of the Vitaceae, with exceptional cases of reversion to the ancestral EGC phenotype. This is particularly true in the genus Vitis, where we now find two radically distinct groups differing with respect to EGC content. While Vitis species from Asia are void of EGC, 50 % of the New World Vitis harbour EGC. Interestingly, the presence of EGC is tightly coupled with the degree of leaf margin serration. Noticeably, the rare Asian EGC-forming species are phylogenetically close to Vitis vinifera, the only remnant representative of Vitis in Eurasia. Both the wild ancestral V. vinifera subsp. sylvestris as well as the domesticated V. vinifera subsp. sativa can accumulate EGC and activate galloylation biosynthesis that compete for photoassimilates and reductive power.
Published: 2022

10. Targeted gene deletion with Sp Cas9 and multiple guide RNAs in Arabidopsis thaliana : four are better than two

Author: Jana Ordon, Niklas Kiel, Dieter Becker, Carola Kretschmer, Paul Schulze-Lefert, Johannes Stuttmann, Max Planck Institute for Plant Breeding Research (MPIPZ), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Martin-Luther-University Halle-Wittenberg, Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), 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)-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), and Julius Kühn-Institut (JKI)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: BackgroundIn plant genome editing, RNA-guided nucleases such as Cas9 fromStreptococcus pyogenes(SpCas9) predominantly induce small insertions or deletions at target sites. This can be used for inactivation of protein-coding genes by frame shift mutations. However, in some cases, it may be advantageous to delete larger chromosomal segments. This is achieved by simultaneously inducing double strand breaks upstream and downstream of the fragment to be deleted. Experimental approaches for deletion induction have not been systematically evaluated.ResultsWe designed three pairs of guide RNAs for deletion of the ArabidopsisWRKY30locus (~2.2 kb). We tested how the combination of guide RNA pairs and co-expression of the exonuclease TREX2 affect the frequency ofwrky30deletions in editing experiments. Our data demonstrate that compared to one pair of guide RNAs, two pairs increase the frequency of chromosomal deletions. The exonuclease TREX2 enhanced mutation frequency at individual target sites and shifted the mutation profile towards larger deletions. However, TREX2 did not elevate the frequency of chromosomal deletions.ConclusionsMultiplex editing with at least two pairs of guide RNAs (four guide RNAs in total) elevates the frequency of chromosomal deletions, and thus simplifies the selection of corresponding mutants. Co-expression of the TREX2 exonuclease can be used as a general strategy to increase editing efficiency in Arabidopsis without obvious negative effects.
Published: 2023

11. Speciation and distribution of chromium (III) in rice root tip and mature zone: The significant impact of root exudation and iron plaque on chromium bioavailability

Author: Peiman Zandi, Xing Xia, Jianjun Yang, Jin Liu, Laurent Remusat, Cornelia Rumpel, Elke Bloem, Beata Barabasz Krasny, Ewald Schnug, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences (CAAS), China Agricultural University (CAU), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Julius Kühn-Institut (JKI), Pedagogical University of Krakow, and Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig]
Subjects: Environmental Engineering, Health, Toxicology and Mutagenesis, Environmental Chemistry, Iron-plaque dissolution, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Cr-speciation, Pollution, Waste Management and Disposal
Abstract: International audience; Evidence on the contribution of root regions with varied maturity levels in iron plaque (IP) formation and root exudation of metabolites and their consequences for uptake and bioavailability of chromium (Cr) remains unknown. Therefore, we applied combined nanoscale secondary ion mass spectrometry (NanoSIMS) and synchrotron-based techniques, micro-X-ray ﬂuorescence (µ-XRF) and micro-X-ray absorption near-edge structure (µ-XANES) to examine the speciation and localisation of Cr and the distribution of (micro-) nutrients in rice root tip and mature region. µ-XRF mapping revealed that the distribution of Cr and (micro-) nutrients varied between root regions. Cr K-edge XANES analysis at Cr hotspots attributed the dominant speciation of Cr in outer (epidermal and sub-epidermal) cell layers of the root tips and mature root to Cr(III)-FA (fulvic acid-like anions) (58–64%) and Cr(III)-Fh (amorphous ferrihydrite) (83–87%) complexes, respectively. The co-occurrence of a high proportion of Cr(III)-FA species and strong co-location signals of 52Cr16O and 13C14N in the mature root epidermis relative to the sub-epidermis indicated an association of Cr with active root surfaces, where the dissolution of IP and release of their associated Cr are likely subject to the mediation of organic anions. The results of NanoSIMS (poor 52Cr16O and 13C14N signals), dissolution (no IP dissolution) and µ-XANES (64% in sub-epidermis >58% in the epidermis for Cr(III)-FA species) analyses of root tips may be indicative of the possible re-uptake of Cr by this region. The results of this research work highlight the significance of IP and organic anions in rice root systems on the bioavailability and dynamics of heavy metals (e.g. Cr).
Published: 2023

12. Serologic Surveillance for SARS-CoV-2 Infection among Wild Rodents, Europe

Author: Vincent Bourret, Lara Dutra, Hussein Alburkat, Sanna Mäki, Ella Lintunen, Marine Wasniewski, Ravi Kant, Maciej Grzybek, Vinaya Venkat, Hayder Asad, Julien Pradel, Marie Bouilloud, Herwig Leirs, Valeria Carolina Colombo, Vincent Sluydts, Peter Stuart, Andrew McManus, Jana A. Eccard, Jasmin Firozpoor, Christian Imholt, Joanna Nowicka, Aleksander Goll, Nathan Ranc, Guillaume Castel, Nathalie Charbonnel, Tarja Sironen, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Medical University of Gdańsk, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Antwerp (UA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), University of Potsdam = Universität Potsdam, Julius Kühn-Institute, Munster Technological University (MTU), Julius Kühn-Institut (JKI), BiodivErsA3, Our research was funded through the European H2020 (WP 2018-2020) call and the 2018–2019 BiodivERsA joint call for research proposals, under the BiodivErsA3 ERA-Net COFUND program and cofunded by Agence Nationale de la Recherche, Research Foundation–Flanders, National Science Centre, Poland, Deutsche Programme 2021–2030. The National Science Centre, Poland, supported M.G., J.N., and A.G. under the BiodivERsA3 program (2019/31/Z/NZ8/04028).Sampling from Thuringia (Germany) was funded by the DFG Priority Program 1374.Trapping data from this study will be available in Germany in the Biodiversity Exploratories Information System (https://doi.org/10.17616/R32P9Q).Forschungsgemeinschaft, and the EPA Research, European Project: 101052342,Biodiversa+, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), funded from Agence Nationale de la Recherche, Research FoundationFlanders, National Science Centre, Poland, Deutsche Forschungsgemeinschaft, and the EPA Research Programme 2021-2030. The National Science Centre, Poland, supported M.G., J.N., and A.G. under the BiodivERsA3 program (2019/31/Z/NZ8/04028). Sampling from Thuringia (Germany) was funded by the DFG Priority Program 1374, European Project: 138572,FCT::,BiodivERsA/2014,BiodivERsA/0001/2014(2015), Medicum, Faculty of Veterinary Medicine, Department of Virology, Emerging Infections Research Group, Faculty Common Matters (Faculty of Medicine), Helsinki One Health (HOH), and Viral Zoonosis Research Unit
Subjects: Microbiology (medical), Epidemiology, serology, Rodentia, serologic tests, Antibodies, Viral, respiratory infections, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, Humans, viruses, severe acute respiratory infection coronavirus 2, 11832 Microbiology and virology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, SARS-CoV-2, COVID-19, zoonoses, Europe, Infectious Diseases, serosurveillance, coronavirus disease, 3121 General medicine, internal medicine and other clinical medicine, rodents, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Human medicine, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: We report results from serologic surveillance for exposure to SARS-CoV-2 among 1,237 wild rodents and small mammals across Europe. All samples were negative, with the possible exception of 1. Despite suspected potential for human-to-rodent spillover, no evidence of widespread SARS-CoV-2 circulation in rodent populations has been reported to date.Esitämme tulokset serologisesta tutkimuksesta, jossa seulottiin SARS-CoV-2 tartuntojen varalta 1,237 luonnonvaraista jyrsijää ja piennisäkästä eri puolilta Eurooppaa. Kaikki näytteet olivat negatiivisia, yhtä näytettä lukuun ottamatta. SARS-CoV-2:n läikkymisen ihmisistä jyrsijöihin on arveltu olevan mahdollista, mutta todisteet viruksen laajamittaisesta leviämisestä jyrsijäpopulaatioissa puuttuvat.
Published: 2022

13. Effect of contamination and adulteration of wax foundations on the brood development of honeybees

Author: Jens Pistorius, Gabriela Bischoff, Abdulrahim T. Alkassab, Malte Frommberger, David Thorbahn, and Julius Kühn-Institut (JKI)
Subjects: 0106 biological sciences, Wax, Biocide, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Wax foundation, Acaricide, Honeybee, 010501 environmental sciences, Contamination, Biology, 01 natural sciences, Beeswax, Brood, Toxicology, 010602 entomology, Residue, Insect Science, visual_art, Stearin, visual_art.visual_art_medium, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Acaricides, 0105 earth and related environmental sciences, Field conditions
Abstract: Various reports recently informed about the effects of contaminated or adulterated wax foundations as a main cause of poor brood and colony development. Beekeepers reported that affected colonies were showing a holey brood pattern and a decline in population size. Twenty-five samples of wax foundations were collected from different sources in Germany. Samples were analyzed using a multi-residue analysis for 147 insecticides, acaricides, and varroacides to investigate the actual load of contamination in beeswax. Furthermore, the effect of selected contaminated and/or adulterated wax foundations on colony and brood development of honeybees was evaluated under field conditions. Our results show that 38 active substances in total were found in the wax samples. Acaricides used in-hive were the most frequently detected contaminants at high concentrations. Trace concentrations of plant protection products and biocides were also found. In the field trials, a significant influence of stearin-adulterated wax on population size, the number of capped brood cells, and termination rate was found compared with the reference. No detectable effects of other treatments on the investigated parameters were observed.
Published: 2020

14. Perception et gestion par les agriculteurs de la biodiversité fonctionnelle dans les vergers à pomme en agriculture biologique

Author: Servane PENVERN, Aurélie CARDONA, Marc TCHAMITCHIAN, Arnaud DUFILS, Weronika SWIERGIEL, Marco TASIN, Maren KORSGAARD, Annette HERZ, Lene SIGSGAARD, Unité de recherche d'Écodéveloppement (ECODEVELOPPEMENT), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Swedish University of Agricultural Sciences (SLU), Ecoadvice, Julius Kühn-Institut (JKI), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Projet 'ECOORCHARD', FP7 ERA-net (618107) et CORE Organic Plus (28698)., and European Project: 618107,EC:FP7:KBBE,FP7-ERANET-2013-RTD,CORE ORGANIC PLUS(2013)
Subjects: enquête auprès des professionnels, [SDV.SA.STA]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of agriculture, agroécologie, General Earth and Planetary Sciences, service écosystémique, General Environmental Science, biodiversité
Abstract: International audience; Les bénéfices de la biodiversité fonctionnelle, notamment en terme de lutte contre les ravageurs, font l'objet de débats entre les praticiens et on sait peu de choses sur les pratiques et les motivations des agriculteurs pour favoriser cette biodiversité. Nous avons supposé que l'utilisation de méthodes de suivi aiderait les agriculteurs à mieux apprécier les bénéfices de la biodiversité fonctionnelle et les inciterait à mettre en œuvre des pratiques qui lui sont favorables. Nous avons mis en œuvre une approche globale combinant des entretiens semi-directifs et des ateliers participatifs pour décrire les pratiques et la perception des agriculteurs vis-à-vis de la biodiversité fonctionnelle et concevoir des méthodes de suivi adaptées à leurs besoins. Nos résultats fournissent des preuves empiriques que la biodiversité fonctionnelle est associée à de multiples services et dis-services. En outre, ils montrent que l'expérience et le temps disponible des agriculteurs sont deux conditions importantes à la mise en œuvre de pratiques favorables à la biodiversité fonctionnelle. Quatre attitudes principales envers la gestion de la biodiversité fonctionnelle ont été caractérisées : attentisme, naturalisme, régulation et multifonctionnalité. La connaissance de ces attitudes fournit un cadre utile pour concevoir des outils de soutien et des programmes de recherche en adéquation avec les besoins des agriculteurs.
Published: 2022

15. 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

16. Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm

Author: Markus Kellerhals, Annalisa Marchese, Daniela Giovannini, Suzanne Litthauer, Marine Blouin-Delmas, Stéphanie Mariette, Edward Venison, Felicidad Fernández-Fernández, Christina Kägi, Monika Höfer, Matthew Ordidge, Hilde Nybom, University of Reading (UOR), National Institute of Agricultural Botany (NIAB), Unité d'arboriculture (BORDX ARBORI UE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Julius Kühn-Institut (JKI), Office Fédéral de l'Agriculture - Federal Office for Agriculture - Bundesamtes für Landwirtschaft [Berne] (OFAG), Agroscope, Università degli studi di Palermo - University of Palermo, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Swedish University of Agricultural Sciences (SLU), Research Centre on Food and Nutrition (CREA), Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), This research was funded by the European Cooperative Program for Plant Genetic Resources: Activity Grant Scheme (Project: Prunus Alignment) and Defra, UK (Project: GC0147 The Long Term Housing, Maintenance and Scientific Curation of the [UK] National Fruit Collections)., Ordidge M., Litthauer S., Venison E., Blouin-Delmas M., Fernandez-Fernandez F., Hofer M., Kagi C., Kellerhals M., Marchese A., Mariette S., Nybom H., and Giovannini D.
Subjects: 0106 biological sciences, 0301 basic medicine, Germplasm, Matching (statistics), microsatellite, Genetics and Breeding, sweet cherry, Plant Science, Prunus avium, 01 natural sciences, Article, 03 medical and health sciences, International database, Genetic resources, Genotype, Allele, Ecology, Evolution, Behavior and Systematics, Ecology, Botany, germplasm, Sequence repeat, SSR, 030104 developmental biology, Geography, QK1-989, [SDE]Environmental Sciences, Microsatellite, genetic resource, Cartography, 010606 plant biology & botany
Abstract: International audience; The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe.
Published: 2021

17. The Durability of Quantitative Host Resistance and Variability in Pathogen Virulence in the Interaction Between European Grapevine Cultivars and Plasmopara viticola

Author: Oliver Trapp, Rebecca Höfle, Lisa Heyman, Reinhard Töpfer, Monica Höfte, Anna Kicherer, Essaid Ait Barka, Faculty of Bioscience Engineering [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT), Julius Kühn-Institut (JKI), Résistance Induite et Bioprotection des Plantes - EA 4707 (RIBP), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, Agriculture and Food Sciences, phenotyping, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Virulence, Introgression, Quantitative trait locus, Rpv, 01 natural sciences, SB1-1110, 03 medical and health sciences, Pathosystem, characterization, Pathogen, Genetics, breakdown, biology, Host (biology), downy mildew, resistance genes, Plant culture, Agriculture, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, virulence, 030104 developmental biology, Plasmopara viticola, Vitis vinifera, Downy mildew, 010606 plant biology & botany
Abstract: European grapevine, Vitis vinifera, carries no major resistances against Plasmopara viticola, the causal agent of grapevine downy mildew. The introgression of quantitative trait loci conferring resistance to P. viticola (Rpv) from American and Asian donor species has resulted in a range of resistant cultivars. In light of the perennial nature of grapevine and the high evolutionary potential of P. viticola, the durability of this quantitative resistance is an important challenge. Durability of host resistance and variability in pathogen virulence may be evaluated by describing interactions between pathogen isolates and grapevine cultivars in terms of Rpv loci. A set of 16 cultivars carrying different combinations of Rpv loci, was challenged with five P. viticola isolates, obtained from susceptible or Rpv3.1+V. vinifera cultivars. Based on the severity of sporulation, different host and pathogen phenotypes might be distinguished, which could be related to the presence of different Rpv loci. The hormonal responses before and during some interactions were compared to assess the resistance mechanisms underlying Rpv3.1, Rpv10, and Rpv12 and the infection mechanisms of the different isolates. This paper reports on the strength of some of the commonly used Rpv loci, single or stacked. The isolates derived from Rpv3.1+ hosts, GREPv1 and GPHPv1, were able to sporulate intensely on cultivars carrying Rpv3.1, without triggering necrosis. Moreover, Rpv10 was not able to efficiently halt the development of the Rpv3.1-breaking isolate GPHPv1. Cultivars carrying Rpv12, however, were resistant to all five P. viticola isolates. Phytohormones might be implicated in the basal resistance against this pathogen, but during the early defense response, no significant hormonal responses to the isolates were observed. The isolate-specificity of the Rpv3- and Rpv10-mediated resistance suggests that these loci do not result in the most sustainable resistance. Furthermore, the isolate-specific behavior of the pathogen emphasizes the need for a characterization system for P. viticola. A standardized phenotyping assay may be used to determine P. viticola pathogen phenotypes or measure the durability, strength, and isolate-specificity of the host quantitative resistances. The characterization of both components of the pathosystem may lead to an increased understanding of the resistance mechanisms, beneficial for a durable deployment of resistance genes.
Published: 2021

18. ICTV Virus Taxonomy Profile: Nanoviridae

Author: Thomas, John E., Gronenborn, Bruno, Harding, Robert M., Mandal, Bikash, Grigoras, Ioana, Randles, John W., Sano, Yoshitaka, Timchenko, Tania, Vetten, H. Josef, Yeh, Hsin-Hung, Ziebell, Heiko, Ictv Report Consortium, null, 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), Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Queensland University of Technology [Brisbane] (QUT), Indian Agricultural Research Institute (IARI), Université d'Évry-Val-d'Essonne (UEVE), University of Adelaide, Niigata University, Julius Kühn-Institut (JKI), 9 Taipei Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC, CEA- Saclay (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute for Integrative Biology of the Cell [Gif-sur-Yvette] (I2BC), and Queensland University of Technology (Queensland University of Technology - Brisbane) (QUT)
Subjects: 0301 basic medicine, biology, [SDV]Life Sciences [q-bio], 030106 microbiology, Nanoviridae, biology.organism_classification, Genome, Virology, Zingiberales, 03 medical and health sciences, taxonomy, 030104 developmental biology, Genus, Plant virus, ICTV Report, Taxonomy (biology), Eudicots, Virus classification
Abstract: Nanoviridae is a family of plant viruses (nanovirids) whose members have small isometric virions and multipartite, circular, single-stranded (css) DNA genomes. Each of the six (genus Babuvirus) or eight (genus Nanovirus) genomic DNAs is 0.9–1.1 kb and is separately encapsidated. Many isolates are associated with satellite-like cssDNAs (alphasatellites) of 1.0–1.1 kb. Hosts are eudicots, predominantly legumes (genus Nanovirus), and monocotyledons, predominantly in the order Zingiberales (genus Babuvirus). Nanovirids require a virus-encoded helper factor for transmission by aphids in a circulative, non-propagative manner. This is a summary of the ICTV Report on the family Nanoviridae, which is available at ictv.global/report/nanoviridae.
Published: 2021

19. Designing the Crops for the Future; The CropBooster Program

Author: Jess Davies, Francesco Loreto, Norbert Rolland, Martin A. J. Parry, René Klein Lankhorst, Ralf Wilhelm, Jeremy Harbinson, Karin Metzlaff, Wageningen University and Research [Wageningen] (WUR), Lancaster Environment Centre, Lancaster University, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Naples Federico II = Università degli studi di Napoli Federico II, Julius Kühn-Institut (JKI), European Plant Science Organisation, European Project: 817690,H2020, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Consiglio Nazionale delle Ricerche (CNR), Università degli studi di Napoli Federico II, Harbinson, Jeremy, Parry, Martin A. J., Davies, Je, Rolland, Norbert, Loreto, Francesco, Wilhelm, Ralf, Metzlaff, Karin, and Klein Lankhorst, René
Subjects: 0106 biological sciences, 0301 basic medicine, Breeding, 01 natural sciences, 7. Clean energy, 11. Sustainability, Climate change, resource use efficiency, Photosynthesis, Biology (General), biodiversity, 2. Zero hunger, education.field_of_study, Food security, BioSolar Cells, Biodiversity, Bioeconomy, sustainability, Natural resource, CO, International Action, Biofysica, climate change, Sustainability, CO2, General Agricultural and Biological Sciences, Opinion, QH301-705.5, Population, Biophysics, Food supply, Biology, General Biochemistry, Genetics and Molecular Biology, 12. Responsible consumption, 03 medical and health sciences, Crop yield, education, Environmental planning, bioeconomy, Sustainable development, photosynthesis, General Immunology and Microbiology, business.industry, [SDV.SA.AEP]Life Sciences [q-bio]/Agricultural sciences/Agriculture, economy and politics, 15. Life on land, crop yield, food supply, 030104 developmental biology, Climate change mitigation, 13. Climate action, Agriculture, breeding, Resource use efficiency, business, 010606 plant biology & botany
Abstract: Simple Summary Our climate is changing and the world population is growing to an estimated 10 billion people by 2050. This may cause serious problems in global food supply, protection of the environment and safeguarding Earth’s biodiversity. To face these challenges, agriculture will have to adapt and a key element in this will be the development of “future-proof” crops. These crops will not only have to be high-yielding, but also should be able to withstand future climate conditions and will have to make very efficient use of scarce resources such as water, phosphorus and minerals. Future crops should not only sustainably give access to sufficient, nutritious, and diverse food to a worldwide growing population, but also support the circular bio-based economy and contribute to a lower atmospheric CO2 concentration to counteract global warming. Future-proofing our crops is an urgent issue and a challenging goal that only can be realized by large-scale, international research cooperation. We call for international action and propose a pan-European research and innovation initiative, the CropBooster Program, to mobilize the European plant research community and all interested actors in agri-food research and innovation to face the challenge. Abstract The realization of the full objectives of international policies targeting global food security and climate change mitigation, including the United Nation’s Sustainable Development Goals, the Paris Climate Agreement COP21 and the European Green Deal, requires that we (i) sustainably increase the yield, nutritional quality and biodiversity of major crop species, (ii) select climate-ready crops that are adapted to future weather dynamic and (iii) increase the resource use efficiency of crops for sustainably preserving natural resources. Ultimately, the grand challenge to be met by agriculture is to sustainably provide access to sufficient, nutritious and diverse food to a worldwide growing population, and to support the circular bio-based economy. Future-proofing our crops is an urgent issue and a challenging goal, involving a diversity of crop species in differing agricultural regimes and under multiple environmental drivers, providing versatile crop-breeding solutions within wider socio-economic-ecological systems. This goal can only be realized by a large-scale, international research cooperation. We call for international action and propose a pan-European research initiative, the CropBooster Program, to mobilize the European plant research community and interconnect it with the interdisciplinary expertise necessary to face the challenge.
Published: 2021

20. Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode

Author: Sebastian Kiewnick, Martine Da Rocha, Abdelnaser Elashry, Juerg E. Frey, Djampa K. L. Kozlowski, Cristina Martin-Jimenez, Etienne Danchin, Georgios Koutsovoulos, Christian H. Ahrens, Laetitia Perfus-Barbeoch, Erika Sallet, Marine Poullet, 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), Strube Research GmbH & Co. KG, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroscope, Julius Kühn-Institut (JKI), ANR-13-JSV7-0006,ASEXEVOL,Un génome fait de multiples copies divergentes permet-il à un animal parasite de plantes d'évoluer en l'absence de reproduction sexuée ?(2013), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), and Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: 0106 biological sciences, Transposable element, Statistics and Probability, Data Descriptor, [SDV]Life Sciences [q-bio], Meloidogyne Enterolobii, Sequence assembly, Biology, Library and Information Sciences, Genome informatics, 01 natural sciences, Genome, Education, 03 medical and health sciences, Animals, Root-knot nematode, Tylenchoidea, lcsh:Science, Author Correction, Gene, Genome size, Plant Diseases, 030304 developmental biology, 2. Zero hunger, Genome, Helminth, 0303 health sciences, Contig, Comparative genomics, Root-knot Nematodes, fungi, food and beverages, biology.organism_classification, Computer Science Applications, Europe, Meloidogyne enterolobii, Evolutionary biology, lcsh:Q, Pathogens, Statistics, Probability and Uncertainty, 010606 plant biology & botany, Information Systems
Abstract: Root-knot nematodes (genus Meloidogyne) are plant parasites causing huge economic loss in the agricultural industry and affecting severely numerous developing countries. Control methods against these plant pests are sparse, the preferred one being the deployment of plant cultivars bearing resistance genes against Meloidogyne species. However, M. enterolobii is not controlled by the resistance genes deployed in the crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Here, we sequenced the genome of M. enterolobii using short and long-read technologies. The genome assembly spans 240 Mbp with contig N50 size of 143 kbp, enabling high-quality annotations of 59,773 coding genes, 4,068 non-coding genes, and 10,944 transposable elements (spanning 8.7% of the genome). We validated the genome size by flow cytometry and the structure, quality and completeness by bioinformatics metrics. This ensemble of resources will fuel future projects aiming at pinpointing the genome singularities, the origin, diversity, and adaptive potential of this emerging plant pest., Measurement(s) genome • sequence_assembly • sequence feature annotation Technology Type(s) DNA sequencing assay • sequence assembly process • sequence annotation Sample Characteristic - Organism Meloidogyne enterolobii Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12410363
Published: 2020
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21. Route of a Multipartite Nanovirus across the Body of Its Aphid Vector

Author: Yannis Michalakis, Jean-Louis Zeddam, Heiko Ziebell, Yahya Z. A. Gaafar, Jeremy Di Mattia, Stéphane Blanc, Mathilde Villegas, Marie-Stéphanie Vernerey, Michel Yvon, Elodie Pirolles, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), 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, 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), Julius Kühn-Institut (JKI), Evolution Théorique et Expérimentale (MIVEGEC-ETE), Perturbations, Evolution, Virulence (PEV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), ANR-14-CE02-0014,Nano,Exploration de la biologie des virus multipartite(2014), ANR-18-CE92-0028,Nanovirus,Aspects moléculaires et cellulaires du cycle de vie des virus multipartites: les nanovirus(2018), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Viral protein, [SDV]Life Sciences [q-bio], Immunology, vector transmission, circulative, plant, Luteoviridae, medicine.disease_cause, 01 natural sciences, Microbiology, Genome, Virus, Plant Viruses, 03 medical and health sciences, Viral Proteins, nanovirus, Viral entry, Virology, Plant virus, medicine, Animals, Geminiviridae, In Situ Hybridization, Fluorescence, 030304 developmental biology, Plant Diseases, Genetics, 0303 health sciences, biology, Nanovirus, DNA Viruses, Virion, biology.organism_classification, 3. Good health, Virus-Cell Interactions, Insect Vectors, aphid, Insect Science, insect vector, Aphids, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, multipartite virus, Nanoviridae, nonpropagative, 010606 plant biology & botany
Abstract: BGPI : Equipe 2 : Interactions Virus Insecte Plante (VIP); International audience; Vector transmission plays a primary role in the life cycle of viruses, and insects are the most common vectors. An important mode of vector transmission, reported only for plant viruses, is circulative nonpropagative transmission whereby the virus cycles within the body of its insect vector, from gut to salivary glands and saliva, without replicating. This mode of transmission has been extensively studied in the viral families Luteoviridae and Geminiviridae and is also reported for Nanoviridae. The biology of viruses within these three families is different, and whether the viruses have evolved similar molecular/cellular virus-vector interactions is unclear. In particular, nanoviruses have a multipartite genome organization, and how the distinct genome segments encapsidated individually transit through the insect body is unknown. Here, using a combination of fluorescent in situ hybridization and immunofluorescence, we monitor distinct proteins and genome segments of the nanovirus Faba bean necrotic stunt virus (FBNSV) during transcytosis through the gut and salivary gland cells of its aphid vector Acyrthosiphon pisum. FBNSV specifically transits through cells of the anterior midgut and principal salivary gland cells, a route similar to that of geminiviruses but distinct from that of luteoviruses. Our results further demonstrate that a large number of virus particles enter every single susceptible cell so that distinct genome segments always remain together. Finally, we confirm that the success of nanovirus-vector interaction depends on a nonstructural helper component, the viral protein nuclear shuttle protein (NSP), which is shown to be mandatory for viral accumulation within gut cells.IMPORTANCE An intriguing mode of vector transmission described only for plant viruses is circulative nonpropagative transmission, whereby the virus passes through the gut and salivary glands of the insect vector without replicating. Three plant virus families are transmitted this way, but details of the molecular/cellular mechanisms of the virus-vector interaction are missing. This is striking for nanoviruses that are believed to interact with aphid vectors in ways similar to those of luteoviruses or geminiviruses but for which empirical evidence is scarce. We here confirm that nanoviruses follow a within-vector route similar to that of geminiviruses but distinct from that of luteoviruses. We show that they produce a nonstructural protein mandatory for viral entry into gut cells, a unique phenomenon for this mode of transmission. Finally, noting that nanoviruses are multipartite viruses, we demonstrate that a large number of viral particles penetrate susceptible cells of the vector, allowing distinct genome segments to remain together.
Published: 2020

22. Advances in Plant Sulfur Research

Author: Jean-Christophe Avice, Dimitris L. Bouranis, Mario Malagoli, Elke Bloem, Agricultural University of Athens, University of Padova [Padova, Italy], Ecophysiologie Végétale, Agronomie et Nutritions NCS (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Julius Kühn-Institut (JKI)
Subjects: 0106 biological sciences, 0301 basic medicine, Sulfur nutrition physiology, Brassica, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, chemistry.chemical_element, Plant Science, Root hair, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Arabidopsis, Botany, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Ecology, biology, Lateral root, fungi, food and beverages, 15. Life on land, Sulfur deficiency, biology.organism_classification, Sulfur, Sulfur interactions, 030104 developmental biology, Editorial, chemistry, Glucosinolate, QK1-989, Phaseolus, 010606 plant biology & botany
Abstract: As an essential nutrient required for plant growth and development, sulfur (S) deficiency in productive systems limits yield and quality. This special issue hosts a collection of original research articles, mainly based on contributions from the 11th International Plant Sulfur Workshop held on 16−20 September 2018 in Conegliano, Italy, focusing on the following topics: (1) The germinative and post-germinative behaviour of Brassica napus seeds when severe S limitation is applied to the parent plants; (2) the independence of S deficiency from the mRNA degradation initiation enzyme PARN in Arabidopsis; (3) the glucosinolate distribution in the aerial parts of sel1-10, a disruption mutant of the sulfate transporter SULTR1;2, in mature Arabidopsis thaliana plants; (4) the accumulation of S-methylcysteine as its γ-glutamyl dipeptide in Phaseolus vulgaris; and (5) the role of ferric iron chelation-strategy components in the leaves and roots of maize, have provided new insights into the effect of S availability on plant functionality. Moreover, the role of S deficiency in root system functionality has been highlighted, focusing on (6) the contribution of root hair development to sulfate uptake in Arabidopsis, and (7) the modulation of lateral root development by the CLE-CLAVATA1 signaling pathway under S deficiency. The role of S in plants grown under drought conditions has been investigated in more detail focusing (8) on the relationship between S-induced stomata closure and the canonical ABA signal transduction machinery. Furthermore, (9) the assessment of S deficiency under field conditions by single measurements of sulfur, chloride, and phosphorus in mature leaves, (10) the effect of fertilizers enriched with elemental S on durum wheat yield, and (11,12) the impact of elemental S on the rhizospheric bacteria of durum wheat contributed to enhance the scientific knowledge on S nutrition under field conditions.
Published: 2020

23. Genetic assessment of the pomological classification of plum Prunus domestica L. accessions sampled across Europe

Author: Kersti Kahu, Marc Lateur, Stein Harald Hjeltnes, Hilde Nybom, Matthew Ordidge, Marine Blouin-Delmas, Pavlina Drogoudi, S. Kovács, Daniela Giovannini, Fuad Gaši, V. Ognjanov, Jasmin Grahić, D. Benedikova, Jasna Sehic, Monika Höfer, Gunārs Lācis, Torben Bo Toldam-Andersen, University of Sarajevo, UNIVERZITET U SARAJEVU, Swedish University of Agricultural Sciences (SLU), University of Reading (UOR), National Agriculture and Food Centre – Research Institute of Plant Production, Unité d'arboriculture (BORDX ARBORI UE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Julius Kühn-Institut (JKI), Estonian University of Life Sciences (EMU), Research Institute of Horticulture, Dept. of Life Sciences, Unit of Breeding & Biodiversity, Centre Wallon de Recherches Agronomiques (CRA-W), and Dept Plant Breeding Balsgard
Subjects: 0106 biological sciences, 0301 basic medicine, Microsatellite markers, Plant Science, Biology, Plant conservation, 01 natural sciences, 03 medical and health sciences, Prunus, Sensu, Genotype, Genebank, Genetics, Cultivar, Allele, Genotyping, Ecology, Evolution, Behavior and Systematics, DNA, SSR, Horticulture, 030104 developmental biology, Genetic structure, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agronomy and Crop Science, Fruit tree, 010606 plant biology & botany
Abstract: The genotyping of European fruit tree collections has helped to identify synonyms, determine parentage, reveal key specimens in the collections and provide information on the development of modern cultivars from one or several progenitors. However, studies on European plum Prunus domestica L. accessions have been lagging behind, mainly because of the hexaploid chromosome number. In this co-operative study, 104 accessions conserved by 14 partners across Europe were phenotyped for 20 descriptors, and genotyped for 8 SSR loci together with 8 reference cultivars. Based on the descriptors and additional information supplied by the partners, as well as the scientific and horticultural literature, each accession was assigned to one of six pomological groups; (1) egg plums sensu lato (E), (2) prunes of the French d’Agen type (P/A), (3) prunes of the Central-Southeast European Zwetschen type (P/Z), (4) greengages (G), (5) mirabelles (M) and (6) bullaces, damsons and var. pomariorum (D/B). A MANOVA conducted on descriptor data revealed significant differentiation among the pomological groups as well as a geographic impact on the differentiation of local plum accessions in Europe. SSR data showed that two trios and seven pairs of genotypes had very similar allele profiles and possibly are genetically identical in spite of different accession names. An AMOVA indicated sparse genetic differentiation when accessions were grouped according to geographic origin whereas significant differences were obtained among pomological groups. A Bayesian analysis of genetic structure, as well as a discriminant analysis of principal components (DAPC), further revealed levels of similarity among and within the different pomological groups, suggesting that egg plums sensu lato (E) and greengages (G) can be referred to subsp. domestica while damsons and bullaces (D/B) but also Central-Southeast European prunes (P/Z) show more affinity to subsp. insititia. The small and possibly heterogeneous groups with mirabelles (M) and prunes of the d’Agen type (P/A) take an intermediate position suggesting a hybridogenic origin.
Published: 2020

24. The Potential for Decision Support Tools to Improve the Management of Root-Feeding Fly Pests of Vegetables in Western Europe

Author: Martin Hommes, Dominique Mazzi, Michael Gaffney, Tor J. Johansen, Richard Meadow, Quentin Schorpp, Annette Schjøll, Nicolai V. Meyling, Gunda Thöming, Rosemary Collier, Ute Vogler, Anne-Marie Cortesero, University of Warwick [Coventry], Agroscope, Norwegian Institute of Bioeconomy Research (NIBIO), Julius Kühn-Institut (JKI), ‎ Norwegian Univ Life Sci, University of Copenhagen = Københavns Universitet (KU), 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), Teagasc - The Agriculture and Food Development Authority (Teagasc), This paper has arisen from a European ERA-NET C-IPM project called FlyIPM (integrated control of root-feeding fly larvae infesting vegetable crops). Participation was funded nationally. National funders were the Danish Environmental Protection Agency (grant no. MST-667-00280), the UK Department for Environment, Food and Rural Affairs (DEFRA), the Research Council of Norway (RCN), project No. 273179/E50, the Swiss Federal Office for Agriculture (FOAG). Ireland through Teagasc, The Agriculture and Food Authority, project No. 0336 and Department of Agriculture, Food and the Marine Stimulus project 14/s/879 and Agence Française pour la Biodiversité (AFB)., Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), University of Copenhagen = Københavns Universitet (UCPH), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, Delia floralis, Integrated pest management, Decision support system, decision support, Delia antiqua, [SDV]Life Sciences [q-bio], forecasting, Review, 010603 evolutionary biology, 01 natural sciences, Delia radicum, Chamaepsila rosae, Delia platura, fly larvae, lcsh:Science, biology, integrated pest management, Agroforestry, Phenology, Delia florilega, biology.organism_classification, 010602 entomology, monitoring, Insect Science, lcsh:Q, PEST analysis
Abstract: Several important vegetable crops grown outdoors in temperate climates in Europe can be damaged by the root-feeding larvae of Diptera (Delia radicum, Delia floralis, Chamaepsila rosae, Delia platura, Delia florilega, Delia antiqua). Knowledge of pest insect phenology is a key component of any Integrated Pest Management (IPM) strategy, and this review considers the methods used to monitor and forecast the occurrence of root-feeding flies as a basis for decision-making by growers and the ways that such information can be applied. It has highlighted some current management approaches where such information is very useful for decision support, for example, the management of C. rosae with insecticidal sprays and the management of all of these pests using crop covers. There are other approaches, particularly those that need to be applied at sowing or transplanting, where knowledge of pest phenology and abundance is less necessary. Going forward, it is likely that the number of insecticidal control options available to European vegetable growers will diminish and they will need to move from a strategy which often involves using a single ‘silver bullet’ to a combination of approaches/tools with partial effects (applied within an IPM framework). For the less-effective, combined methods, accurate information about pest phenology and abundance and reliable decision support are likely to be extremely important.
Published: 2020

25. Genetic and genomic approaches for adaptation of grapevine to climate change

Author: Silvia Vezzulli, Eric Duchêne, Ludger Hausmann, Lorenza Dalla Costa, Nathalie Ollat, Pablo Carbonell-Bejerano, Anna Schwandner, Jérôme Grimplet, Pierre-François Bert, Mario Pecile, Luigi Bavaresco, Gabriele Di Gaspero, Mickael Malnoy, Michele Morgante, Serge Delrot, Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Université Victor Segalen - Bordeaux 2-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Julius Kühn-Institut (JKI), Santé de la vigne et qualité du vin (SVQV), Université de Strasbourg (UNISTRA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università cattolica del Sacro Cuore [Roma] (Unicatt), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Università degli Studi di Udine - University of Udine [Italie], Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Chittaranjan Kole, and KOLE, Chittaranjan
Subjects: 0106 biological sciences, Genotyping, Vitis vinifera L, Climate change, Biology, Terroir, 01 natural sciences, Vineyard, 03 medical and health sciences, Effects of global warming, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Regeneration (ecology), Vitis spp, Genetic resources, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Genetic diversity, business.industry, 15. Life on land, Data bases, Biotechnology, Settore AGR/07 - GENETICA AGRARIA, 13. Climate action, Phenotyping, Settore AGR/03 - ARBORICOLTURA GENERALE E COLTIVAZIONI ARBOREE, Rootstock, Adaptation, Viticulture, business, 010606 plant biology & botany
Abstract: International audience; The necessity to adapt to climate change is even stronger for grapevine than for other crops, because grape berry composition—a key determinant of fruit and wine quality, typicity and market value— highly depends on “terroir” (complete natural environment), on vintage (annual climate variability), and on their interactions. In the same time, there is a strong demand to reduce the use of pesticides. Thus, the equation that breeders and grape growers must solve has three entries that cannot be dissociated: adaptation to climate change, reduction of pesticides, and maintenance of wine typicity. Although vineyard management may cope to some extent to the short–medium-term effects of climate change, genetic improvement is necessary to provide long-term sustainable solutions to these problems. Most vineyards over the world are planted using vines that harbor two grafted plants’ genomes. Although this makes the range of interactions (scion-atmosphere, rootstock-soil, scion-rootstock) more complex, it also opens up wider possibilities for the genetic improvement of either or both the grafted genotypes. Positive aspects related to grapevine breeding are as follows: (a) a wide genetic diversity of rootstocks and scions that has not been thoroughly explored yet; (b) progress in sequencing technologies that allows high-throughput sequencing of entire genomes, faster mapping of targeted traits and easier determination of genetic relationships; (c) progress in new breeding technologies that potentially permit precise modifications on resident genes; (d) automation of phenotyping that allows faster and more complete monitoring of many traits on relatively large plant populations; (e) functional characterization of an increasing number of genes involved in the control of development, berry metabolism, disease resistance, and adaptation to environment. Difficulties involve: (a) the perennial nature and the large size of the plant that makes field testing long and demanding in manpower; (b) the low efficiency of transformation, regeneration and small size of breeding populations; (c) the complexity of the adaptive traits and the need to define more clearly future ideotypes; (d) the lack of shared and integrative platforms allowing a complete appraisal of the genotype-phenotype-environmental links; (e) legal, market and consumer acceptance of new genotypes. The present chapter provides an overview of suitable strategies and challenges linked to the adaptation of viticulture to a changing environment.
Published: 2020

26. Rat feeding trials: A comprehensive assessment of contaminants in both genetically modified maize and resulting pellets

Author: Florence Richard-Forget, Xavier Coumoul, Bérengère Laporte, Pablo Steinberg, Nathalie Priymenko, Joachim Schiemann, Bernard Salles, Ralf Wilhelm, Annick Moing, Sylvain Chéreau, Peter M. Rogowsky, Unité de recherche Mycologie et Sécurité des Aliments (MycSA), Institut National de la Recherche Agronomique (INRA), Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Institut National de la Santé et de la Recherche Médicale (INSERM), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Prévention et promotion de la cancérogénèse par les aliments (ToxAlim-PPCA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), University of Veterinary Medicine Hannover, Department of Animal Nutrition, Julius Kühn-Institut (JKI), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Food, Genetically Modified, Pellets, [SDV.TOX.TVM]Life Sciences [q-bio]/Toxicology/Vegetal toxicology and mycotoxicology, Food Contamination, Toxicology, Fumonisins, Zea mays, 01 natural sciences, Hemolysin Proteins, chemistry.chemical_compound, GM pellets, 0404 agricultural biotechnology, Bacterial Proteins, Toxicity Tests, Fumonisin, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Animals, Food science, Pesticides, Mycotoxin, 2. Zero hunger, GM maize, Genetically modified maize, Bacillus thuringiensis Toxins, [SDV.BA]Life Sciences [q-bio]/Animal biology, 010401 analytical chemistry, food and beverages, 04 agricultural and veterinary sciences, General Medicine, Mycotoxins, Contamination, Pesticide, Plants, Genetically Modified, Animal Feed, 040401 food science, Diet, Rats, 0104 chemical sciences, Genetically modified organism, Endotoxins, Heavy metals, chemistry, 13. Climate action, Glyphosate, Food Science
Abstract: UMR BFP - Equipe Métabolisme; International audience; We analyzed a comprehensive set of contaminants in MON810 and NK603 genetically modified (GM) maize, and their non-GM counterparts, used in a rat feeding study (the GMO90 + project). Both the maize grains and the manufactured pellets were characterized. Only minor differences in contaminant levels between GM and corresponding non-GM harvests were evidenced. Fumonisin and deoxynivalenol mycotoxins were the pollutants present in the highest amounts, with concentrations that were however largely below acceptance reference values. Our data reporting slightly higher levels of fumonisin in MON810 compared to its non-GM counterpart corroborate the lower susceptibility of insect resistant Bt maize to fumonisin-producing fungi. Traces of glyphosate (0.016 mg/kg) were evidenced in grains from NK603 treated crops. Regarding the pellets, analysis of more than 650 potentially toxic substances revealed low amounts of various mycotoxins, pesticides and heavy metals. Concentrations of contaminants quantified in the pellets were however far below the maximum level of residues values set by regulatory agencies, and no substantial differences in contaminants between GM and non-GM pellets were observed. Moreover, when comparing the contamination status of grains and pellets, we demonstrate yet again that characterizing the grains is actually not sufficient to foresee the quality of the produced pellets.
Published: 2018

27. A whole-genome scan for association with invasion success in the fruit fly Drosophila suzukii using contrasts of allele frequencies corrected for population structure

Author: Mathieu Gautier, Marc Kenis, Mathilde Paris, Arnaud Estoup, Nicolas Borowiec, Heiko Vogel, Heidrun Vogt, Lauren M Diepenbrock, Anne Loiseau, Benoit Facon, Benjamin Prud'homme, Donald K. Price, Christelle Guédot, Jinping Zhang, Xiao Chen, Antoine Fraimout, Hugues Parrinello, Laure Olazcuaga, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier 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 de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), University of Wisconsin-Madison, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), Centre for Agricultural and Biosciences International Europe - Switzerland (CABI Europe - Switzerland), Chinese Academy of Agricultural Sciences (CAAS), Yunnan Agricultural University, 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), 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), Julius Kühn-Institut (JKI), University of Nevada [Las Vegas] (WGU Nevada), Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), and Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: 0106 biological sciences, BayPass, [SDV]Life Sciences [q-bio], Genome, Insect, Population, Adaptation, Biological, Genome Scan, Genome-wide association study, Single-nucleotide polymorphism, Biology, AcademicSubjects/SCI01180, 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, Gene Frequency, Drosophila suzukii, Genetics, Animals, GWAS, Biological invasions, education, Molecular Biology, Allele frequency, Drosophila, Discoveries, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, education.field_of_study, Pool-Seq 1, Models, Genetic, Pool-Seq, AcademicSubjects/SCI01130, 15. Life on land, biology.organism_classification, Evolutionary biology, Drosophila melanogaster, Introduced Species
Abstract: Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here we characterized the genome response of the spotted wing drosophilaDrosophila suzukiiduring the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we calledC2, that contrasts allele frequencies corrected for population structure. This new statistical framework has been implemented in an upgraded version of the program BayPass. We identified a relatively small set of single nucleotide polymorphisms (SNPs) that show a highly significant association with the invasive status of populations. In particular, two genesRhoGEF64Candcpo, the latter contributing to natural variation in several life-history traits (including diapause) inDrosophila melanogaster, contained SNPs significantly associated with the invasive status in the two separate main invasion routes ofD. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by non-equilibrium demographic conditions for which binary covariables of interest can be defined at the population level.
Published: 2019
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28. Consistency of impact assessment protocols for non-native species

Author: Johanna Witzell, João Canning-Clode, Alejandro Juárez-Escario, Wolf-Christian Saul, Franz Essl, Paulo A. V. Borges, Marius Skolka, Alberto Maceda-Veiga, Carmen Morales-Rodríguez, Elena Tricarico, Eleni Kytinou, Hélia Marchante, Triya Tessa Ramburn, Pablo González-Moreno, Stefanos Kalogirou, Angeliki F. Martinou, Rumen Tomov, Ciaran Laverty, C. Romeralo, Predrag Simonović, Konstantinos Tsiamis, Giuseppe Brundu, Claudia Giuliani, Ali Serhan Tarkan, Rory Sheehan, Vanessa Lozano, Naida Muhthassim, Jan Pergl, Hugo Verreycken, Carla Rego, António O. Soares, Ahmet Uludag, Greta Srėbalienė, Fabian Reichenbach, Niki Chartosia, Wolfgang Nentwig, Tim Adriaens, Mi-Jung Bae, Lucija Šerić Jelaska, Helen E. Roy, Ana Andjelković, Jonathan M. Jeschke, Gordon H. Copp, Lorenzo Lazzaro, Z. Á. Nagy, Miquel Jover, Marie-Anne Auger-Rozenberg, Stelios Katsanevakis, Montserrat Vilà, Emili García-Berthou, Leif Sundheim, Aleksandra Kočić, Swen Follak, Mário Boieiro, Toril Loennechen Moen, Øystein Wiig, Gritta Schrader, Johan van Valkenburg, Maria Cristina Morais, Elizabeth J. Cottier-Cook, Michel Bariche, Fried Guillaume, Øivind Gammelmo, Dan Minchin, Kęstutis Arbačiauskas, Wolfgang Rabitsch, Fabio Crocetta, Ana Montero-Castaño, Bram D'hondt, Sven Bacher, Nikica Ogris, Andrea Zanetta, Hüseyin Önen, Sylvaine Giakoumi, Sandro Meyer, Frances E. Lucy, Elizabete Marchante, Bruno Foggi, Anna Maria Vettraino, Riikka Puntila, Pieter Boets, Federico Cardigos, Sonia Vanderhoeven, Belinda Gallardo, Marc Kenis, Lluís Vilar, Venche Talgø, Cristina Preda, Centre for Agricultural and Biosciences International (CABI), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Estación Biológica de Doñana (EBD), Department of Biology, Northern Arizona University [Flagstaff], Ovidius University of Constanta, Research Institute for Nature and Forest (INBO), Department of Agriculture, Università degli studi di Napoli Federico II, Salmon & Freshwater Team (SFT), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Bournemouth University [Poole] (BU), Division of Conservation, Vegetation and Landscape Ecology, University of Vienna [Vienna], Universitat de Girona (UdG), Department of Marine Sciences [Aegean], University of the Aegean, Norwegian Biodiversity Information Centre, Partenaires INRAE, Institute of Technology Sligo, Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Natural Environment Research Council (NERC), Klaipėda University [Lituanie] (KU), Norwegian Institute of Bioeconomy Research (NIBIO), Service Public de Wallonie, Institute for Plant Protection and Environment, University of Novi Sad, Nature Research Centre, Unité de recherche Zoologie Forestière (URZF), Institut National de la Recherche Agronomique (INRA), Nakdonggang National Institute of Biological Resources, American University of Beirut [Beyrouth] (AUB), Provincial Centre of Environmental Research, Centre for Ecology, Evolution and Environmental Changes (CE3C), Universidade dos Açores, Marine and Environmental Sciences Centre (MARE UC), Universidade de Coimbra [Coimbra], University of the Azores, Smithsonian Environmental Research Center, University of Cyprus, Scottish Marine Institute, Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn (SZN), Austrian Agency for Health and Food Safety, Applied and Restoration Ecology Group, Pyrenean Institute of Ecology, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Università degli Studi di Milano [Milano] (UNIMI), Plant Health Laboratory, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Department of Biology, Faculty of Science, University of Isfahan, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Freie Universität Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Universitat de Lleida, Hellenic Centre for Marine Research (HCMR), J.J. Strossmayer University of Osijek, Queen's University [Belfast] (QUB), Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Instituto Politécnico de Coimbra, Royal Air Forces, Department of Environmental Sciences, University of California [Los Angeles] (UCLA), University of California-University of California, Marine Organism Investigations, Universidade de Trás-os-Montes e Alto Douro, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Slovenian Forestry Institute, Gaziosmanpaşa University, Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences [Prague] (CAS), Marine Research Centre (CIMA), Regional government of Galicia, Environment Agency Austria, Simon Fraser University (SFU.ca), Sustainable Forest Management Research Institute, Universitad de Valladolid, Swedish University of Agricultural Sciences (SLU), Julius Kühn-Institut (JKI), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Muğla Sıtkı Koçman University, University of Forestry (UF), European Commission's Joint Research Centre, and MÜ
Subjects: 0106 biological sciences, environmental impact, expert judgement, invasive alien species policy, management prioritization, risk assessment, socio-economic impact, Computer science, vaikutukset, PEST RISK ANALYSIS, protocols, Plant Science, Medi ambient -- Anàlisi d'impacte, 01 natural sciences, Environmental impact, udc:630*44:630*44, Socio economic impact, SUPPORT, Statistics, Milieux et Changements globaux, lcsh:QH301-705.5, asiantuntijuus, Risk assessment, CALIBRATION, Introduced organisms, evaluation, Ecology, VDP::Landbruks- og Fiskerifag: 900, Ecological Modeling, tulokaslajit, riskinarviointi, Pest Risk Analysis, humanities, družbeno ekonomski vpliv, yhtenäisyys, ympäristövaikutukset, expertise, invazivne tujerodne vrste, Expert judgement, Espècies introduïdes, politika, tarpeet, [SDE.MCG]Environmental Sciences/Global Changes, education, INVASIVENESS SCREENING TOOL, ukrepanje, Aquatic Science, 010603 evolutionary biology, vpliv na okolje, CLASSIFICATION, Ecology and Environment, ENVIRONMENTAL-IMPACT, ocena tveganja, Invertebrate Zoology, Environmental Impact, lajit, Biological invasions, Invasions biològiques, Ecology, Evolution, Behavior and Systematics, sosioekonomiset tekijät, strokovna ocena, needs, ALIEN PLANTS, Environmental impact, expert judgement, invasive alien species policy, management prioritization, risk assessment, socio-economic impact, consistency, Impact assessment, 010604 marine biology & hydrobiology, Biology and Life Sciences, 500 Naturwissenschaften und Mathematik::590 Tiere (Zoologie)::590 Tiere (Zoologie), types and species, ECOLOGICAL IMPACTS, FRAMEWORK, Zoologie des invertébrés, protokollat, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Environmental impact analysis, lcsh:Biology (General), Insect Science, Animal Science and Zoology, arviointi, SYSTEM
Abstract: Standardized tools are needed to identify and prioritize the most harmful non-native species (NNS). A plethora of assessment protocols have been developed to evaluate the current and potential impacts of non-native species, but consistency among them has received limited attention. To estimate the consistency across impact assessment protocols, 89 specialists in biological invasions used 11 protocols to screen 57 NNS (2614 assessments). We tested if the consistency in the impact scoring across assessors, quantified as the coefficient of variation (CV), was dependent on the characteristics of the protocol, the taxonomic group and the expertise of the assessor. Mean CV across assessors was 40%, with a maximum of 223%. CV was lower for protocols with a low number of score levels, which demanded high levels of expertise, and when the assessors had greater expertise on the assessed species. The similarity among protocols with respect to the final scores was higher when the protocols considered the same impact types. We conclude that all protocols led to considerable inconsistency among assessors. In order to improve consistency, we highlight the importance of selecting assessors with high expertise, providing clear guidelines and adequate training but also deriving final decisions collaboratively by consensus
Published: 2019
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29. The polyploid genome of the mitotic parthenogenetic root-knot nematodeMeloidogyne enterolobii

Author: Georgios D. Koutsovoulos, Marine Poullet, Abdelnaser El Ashry, Djampa K. Kozlowski, Erika Sallet, Martine Da Rocha, Cristina Martin-Jimenez, Laetitia Perfus-Barbeoch, Juerg-Ernst Frey, Christian Ahrens, Sebastian Kiewnick, Etienne G.J. Danchin, 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), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Strube-Dieckmann, Partenaires INRAE, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Agroscope, and Julius Kühn-Institut (JKI)
Subjects: 2. Zero hunger, 0106 biological sciences, 0303 health sciences, 03 medical and health sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, food and beverages, 01 natural sciences, 030304 developmental biology, 010606 plant biology & botany
Abstract: Root-knot nematodes (genusMeloidogyne) are plant parasitic species that cause huge economic loss in the agricultural industry and affect the prosperity of communities in developing countries. Control methods against these plant pests are sparse and the current preferred method is deployment of plant cultivars bearing resistance genes againstMeloidogynespecies. However, some species such asM. enterolobiiare not controlled by the resistance genes deployed in the most important crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Like the other most damaging Meloidogyne species (e.g.M. incognita,M. arenariaandM. javanica),M. enterolobiireproduces by obligatory mitotic parthenogenesis. Genomic singularities such as a duplicated genome structure and a relatively high proportion of transposable elements have previously been described in the above mentioned mitotic parthenogenetic Meloidogyne.To gain a better understanding of the genomic and evolutionary background we sequenced the genome ofM. enterolobiiusing high coverage short and long read technologies. The information contained in the long reads helped produce a highly contiguous genome assembly ofM. enterolobii, thus enabling us to perform high quality annotations of coding and non-coding genes, and transposable elements.The genome assembly and annotation reveals a genome structure similar to the ones described in the other mitotic parthenogenetic Meloidogyne, described as recent hybrids. Most of the genome is present in 3 different copies that show high divergence. Because most of the genes belong to these duplicated regions only few gene losses took place, which suggest a recent polyploidization. The most likely hypothesis to reconcile high divergence between genome copies despite few gene losses and translocations is also a recent hybrid origin. Consistent with this hypothesis, we found an abundance of transposable elements at least as high as the one observed in the mitotic parthenogenetic nematodesM. incognitaandM. javanica.
Published: 2019
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30. Psyllid Vectors

Author: Barbara Jarausch, Rosemarie Tedeschi, Nicolas Sauvion, Jürgen Gross, Wolfgang Jarausch, Julius Kühn-Institut (JKI), Università degli studi di Torino (UNITO), 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), AlPlanta-Institute for Plant research, Assunta Bertaccini, Phyllis G Weintraub, Govind Pratap Rao, and Nicola Mori
Subjects: 0106 biological sciences, 0303 health sciences, pear decline, european stone fruit yellows, 01 natural sciences, 3. Good health, Apple proliferation, Epidemiology, European stone fruit yellows, Pear decline, Phytoplasmas, Psyllid vectors, 03 medical and health sciences, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, apple proliferation, psyllid vectors, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, epidemiology, phytoplasmas, 030304 developmental biology, 010606 plant biology & botany
Abstract: BGPI : équipe 6; International audience; ‘Candidatus Phytoplasma’ species are mostly transmitted from plant to plant by phloem feeding hemipterans, primarily leafhoppers (Cicadellidae) and planthoppers (Fulgoroidea) (Hemiptera, Auchenorrhyncha). However, there is one group of phytoplasmas, the 16SrX or apple proliferation group, whose members are transmitted by psyllid vectors of the superfamily Psylloidea (Hemiptera, Sternorrhyncha). These psyllid-transmitted phytoplasmas are genetically closely related and are associated with economically important diseases of fruit trees such as pear decline, apple proliferation and European stone fruit yellows. The psyllid vector species of these phytoplasmas are also closely related and all belong to the genus Cacopsylla. Both, phytoplasmas and psyllid vectors, are geographically limited to the Palaearctic region, mainly Europe. Only pear decline and peach yellow leaf roll phytoplasmas have probably been introduced to America along with their vectors. As phytoplasma-infected trees cannot be cured and resistant plant material is not available to the growers, preventive control measures such as vector control are of paramount importance to limit the spread of these diseases. Thus, detailed knowledge about the biology and ecology of the vector species, their host plants as well as knowledge about the transmission parameters is crucial.
Published: 2019

31. Sediment Respiration Pulses in Intermittent Rivers and Ephemeral Streams

Author: Robert J. Rolls, Chelsea J. Little, Simone Guareschi, Annamaria Zoppini, R. Vander Vorste, Eduardo J. Martín, Arnaud Foulquier, Núria Cid, Kate S. Boersma, Michael T. Bogan, Björn Gücker, Cleo Woelfle-Erskine, Amina Taleb, V. D. Diaz-Villanueva, Manuela Morais, J. Marshall, Arturo Elosegi, Vladimir Pešić, Lluís Gómez-Gener, S. Kubheka, Marko Miliša, Clara Mendoza-Lera, Florian Altermatt, Rachel Stubbington, Iola G. Boëchat, Ryan M. Burrows, Arnaud Dehedin, Damien Banas, Iñaki Odriozola, Núria Bonada, Roland Corti, Marcos Moleón, R. Gómez, Ricardo J. Albariño, Erin E. Beller, Alex Laini, Pablo Rodríguez-Lozano, Andreas Bruder, Melanie L. Blanchette, Felicitas Hoppeler, Shai Arnon, B. de Freitas Terra, A. Papatheodoulou, Nathan J. Waltham, Christophe Piscart, Rafael Marcé, Catherine M. Febria, A. Uzan, Peter M. Negus, Dev K. Niyogi, Dominik Zak, Sophie Cauvy-Fraunié, Ana Savić, Catherine Leigh, R. Figueroa, Sarig Gafny, Alisha L. Steward, Emile Faye, Elisabeth I. Meyer, Petr Pařil, Daniel C. Allen, Klement Tockner, D. von Schiller, Mark O. Gessner, K. Brintrup, Jason L. Hwan, Fiona Dyer, C. P. Duerdoth, Gonzalo García-Baquero, Michael Danger, Isabel Pardo, Musa C. Mlambo, R. del Campo, Tommaso Cancellario, Brian Four, A. M. De Girolamo, Thibault Datry, Oleksandra Shumilova, María Isabel Arce, M. M. Sánchez-Montoya, Marek Polášek, Nick Bond, Juan F. Blanco-Libreros, Simone D. Langhans, Stephanie M. Carlson, Andy Banegas-Medina, Manuel A. S. Graça, Joanna Blessing, Biel Obrador, Stefan Lorenz, Christiane Zarfl, Angus R. McIntosh, European Commission, Milieux aquatiques, écologie et pollutions (UR MALY), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Leibniz-Institut für Gewässerökologie und Binnenfischerei (IGB), Leibniz Association, Department of Plant Biology and Ecology, University of the Basque Country, Department of Advanced Materials, Cranfield University, Laboratoire d'Ecologie des Hydrosystèmes Fluviaux (EHF), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Purdue University [West Lafayette], Centro de investigaciones biológicas, Spanish National Research Council (CSIC), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Electronique Quantique, Université des Sciences et de la Technologie Houari Boumediene [Alger] (USTHB)-Faculté de Physique, 748625, Horizon 2020 Framework Programme, 603629, European Commission, CGL2017‐86788‐C3‐3‐P, Ministerio de Economía y Competitividad, PP00P3_179089, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, IT‐951‐16, Eusko Jaurlaritza, CA15113, European Cooperation in Science and Technology, Universidad del Pais Vasco / Euskal Herriko Unibertsitatea [Espagne] (UPV/EHU), Universitat de Barcelona (UB), RiverLy (UR Riverly), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Austrian Science Fund (FWF), Instituto Catalán de Investigación del Agua - ICRA (SPAIN) (ICRA), Laboratory of Molecular Structure Characterization [Prague] (MBU / CAS), Institute of Microbiology of the Czech Academy of Sciences (MBU / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), University of Barcelona, Technische Universität Berlin (TU), Nottingham Trent University, Instituto Nacional de Investigaciones en Biodiversidad y Medioambiente [Bariloche] (INIBIOMA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Comahue [Neuquén] (UNCOMA), University of Oklahoma (OU), Universität Zürich [Zürich] = University of Zurich (UZH), Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), The Jacob Blaustein Institutes for Desert Research (BIDR), Ben-Gurion University of the Negev (BGU), Unité de Recherches Animal et Fonctionnalités des Produits Animaux (URAFPA), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Universidad de Concepción - University of Concepcion [Chile], Department of Geography [Berkeley], University of California [Berkeley], University of California-University of California, Edith Cowan University (ECU), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO)-Planning and Transport Research Centre (PATREC), Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Queensland Government, Universidade Federal de São João del-Rei (UFSJ), University of San Diego, University of Arizona, La Trobe University, Scuola universitaria professionale della Svizzera italiana [Manno] (SUPSI), Australian Rivers Institute, Griffith University [Brisbane], Universidad de Navarra [Pamplona] (UNAV), Department of Environmental Science, Policy, and Management [Berkeley] (ESPM), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Universidade Estadual Vale do Acarau, Asconit Consultants, National Research Council, Water Research Institute, Universidad de Murcia, Queen Mary University of London (QMUL), University of Canberra, Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), School of biological Sciences [Christchurch], University of Canterbury [Christchurch], University of Windsor [Ca], Département Ecologie des Forêts, Prairies et milieux Aquatiques (DEPT EFPA), Institut National de la Recherche Agronomique (INRA), Ruppin Academic Center, Department of Ecology and Environmental Science [Umeå], Umeå University, Marine and Environmental Sciences Centre (MARE UC), Universidade de Coimbra [Coimbra], Loughborough University, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Ezemvelo KZN Wildlife, University of Parma = Università degli studi di Parma [Parme, Italie], University of Otago [Dunedin, Nouvelle-Zélande], Basque Centre for Climate Change (BC3), Queensland University of Technology [Brisbane] (QUT), Julius Kühn-Institut (JKI), Institute for Evolution and Biodiversity (IEB), Westfälische Wilhelms-Universität Münster (WWU), University of Zagreb, Rhodes University, Grahamstown, Universidad de Granada (UGR), Universidade de Évora, Missouri University of Science and Technology (Missouri S&T), University of Missouri System, Terra Cypria - Cyprus Conservation Foundation, Universidade de Vigo, Masaryk University [Brno] (MUNI), University of Montenegro (UCG), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), School of Environmental and Rural Science, University of New England (UNE), University of Niš, Freie Universität Berlin, University of Trento [Trento], Université Aboubekr Belkaid - University of Belkaïd Abou Bekr [Tlemcen], Israel Nature and Parks Authority, Partenaires INRAE, Centre for TropicalWater and Aquatic Ecosystem Research (TropWATER), School of Earth and Environmental Sciences [Australia], James Cook University (JCU)-James Cook University (JCU), University of Washington [Seattle], Universität Rostock, Aarhus University [Aarhus], Center for Applied Geoscience [Tübingen] (ZAG), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Short-Term Scientific Mission of the COST Action : CA15113, European Cooperation in Science and Technology (COST), European Commission : 603629 , 748625, Grant for Research Groups of the Basque University System - Basque Government : IT-951-16, Spanish Ministry of Science, Innovation and Universities through project CHYDROCHANGE : CGL2017-86788C3-2-P , CGL2017-86788-C3-3-P, Swiss National Science Foundation (SNSF) - European Commission : PP00P3_150698, PP00P3_179089, EU project LIFE+ TRivers : LIFE13 ENV/ES/000341, INTER-COST project : LTC17017, CONICYT/FONDAT/15130015, European Project: 748625,H2020-MSCA-IF-2016,SABER CULTURAL, European Project: 0934954(2009), Institute of Microbiology of the Czech Academy of Sciences [Prague, Czech Republic] (MBU / CAS), Technical University of Berlin / Technische Universität Berlin (TU), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), University of San Diego (USD), Scuola universitaria professionale della Svizzera italiana = University of Applied Sciences and Arts of Southern Switzerland [Manno] (SUPSI), Università degli studi di Parma = University of Parma (UNIPR), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Universidad de Granada = University of Granada (UGR), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Carbon sequestration, 0106 biological sciences, Atmospheric Science, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, river, CO, 2, intermittent, respiration, stream, temporary, STREAMS, Atmospheric sciences, 01 natural sciences, River sediments, chemistry.chemical_compound, Rivers, Respiration, Environmental Chemistry, Ecosystem, Captura i emmagatzematge de diòxid de carboni, ComputingMilieux_MISCELLANEOUS, Cursos d'aigua, 0105 earth and related environmental sciences, General Environmental Science, Riparian zone, Global and Planetary Change, geography, geography.geographical_feature_category, 010604 marine biology & hydrobiology, Sediments fluvials, fungi, River, Stream, Intermittent, Temporary, CO2, CO2 emissions, C cycling, stream respiration, Sediment, Vegetation, 15. Life on land, 6. Clean water, chemistry, 13. Climate action, CO 2, [SDE]Environmental Sciences, Carbon dioxide, Plant cover, Environmental science
Abstract: The dataset (Data File S1; DOI: 10.6084/m9.figshare.8863721) and the R code used to generate the results (Code S1; DOI: 10.6084/m9.figshare.8863655), including step by step explanations of the statistical tests, have been deposited in Figshare Digital Repository (https://figshare.com/projects/Sediment_Respiration_Pulses_in_Intermittent_Rivers_and_Ephemeral_Streams/66104)., Intermittent rivers and ephemeral streams (IRES) may represent over half the global stream network, but their contribution to respiration and carbon dioxide (CO2) emissions is largely undetermined. In particular, little is known about the variability and drivers of respiration in IRES sediments upon rewetting, which could result in large pulses of CO2. We present a global study examining sediments from 200 dry IRES reaches spanning multiple biomes. Results from standardized assays show that mean respiration increased 32–66-fold upon sediment rewetting. Structural equation modelling indicates that this response was driven by sediment texture and organic matter quantity and quality, which, in turn, were influenced by climate, land use and riparian plant cover. Our estimates suggest that respiration pulses resulting from rewetting of IRES sediments could contribute significantly to annual CO2 emissions from the global stream network, with a single respiration pulse potentially increasing emission by 0.2–0.7%. As the spatial and temporal extent of IRES increases globally, our results highlight the importance of recognizing the influence of wetting-drying cycles on respiration and CO2 emissions in stream networks., We thank Y. Etxeberria, L. Sánchez, C. Gutiérrez, G. LeGoff and B. Launay for laboratory support. DvS was supported by a Short-Term Scientific Mission of the COST Action CA15113 (SMIRES, Science and Management of Intermittent Rivers and Ephemeral Streams, www.smires.eu), supported by COST (European Cooperation in Science and Technology) and received additional funding from the EU’s 7th Framework Programme for research, technological development and demonstration under grant agreement No. 603629 (GLOBAQUA) and a Grant for Research Groups of the Basque University System (IT-951-16) funded by the Basque Government. RM and BO were supported by the Spanish Ministry of Science, Innovation and Universities through project C-HYDROCHANGE (CGL2017-86788-C3-2-P and CGL2017-86788-C3-3-P). FA was funded by the Swiss National Science Foundation grants No. PP00P3_150698 and PP00P3_179089. NC was supported by the EU project LIFE+ TRivers (LIFE13 ENV/ES/000341). SDL received funding from the EU’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 748625. PP and MP were supported by INTER-COST project LTC17017. The authors declare that they have no competing interests.
Published: 2019

32. Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

Author: Jianxiu Liu, Magnus Hertzberg, Zhiyong Chen, Christopher Lyndon Davey, Iris Lewandowski, Danny Awty-Carroll, Kankshita Swaminathan, Elaine Jensen, Salvatore Luciano Cosentino, Paul Robson, Lindsay V. Clark, Tsai Wen Hsu, Antoine Harfouche, Donal Murphy-Bokern, Catherine Bastien, Gancho T. Slavov, Jon P. McCalmont, Anneli Adler, Astley Hastings, Iain Donnison, Kai Uwe Schwarz, Vasile Botnari, Danilo Scordia, Gail Taylor, Chris Ashman, Do-Soon Kim, Junqin Zong, Gerald A. Tuskan, Lawrence B. Smart, Maryse Brancourt-Hulmel, Huw Jones, Oene Dolstra, Xiaoli Jin, Sebastian Bopper, Uffe Jørgensen, Andreas Kiesel, Chang Yeon Yu, Lin Huang, Timothy J. Tschaplinski, Michal Mos, W. J. Macalpine, Anatolii Sandu, Richard Flavell, Susan Dalton, Brian J. Stanton, Andres F. Torres, Joerg Greef, Michael D. Casler, Ronald S. Zalesny, Luisa M. Trindade, Steve J. Hanley, Giovanni Scalici, Ian Shield, Antonella Iurato, Bernard G. McMahon, John Clifton-Brown, Reza Shafiei, Toshihiko Yamada, Erik J. Sacks, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Department for Innovation in Biological, Agro-Food and Forest Systems, Tuscia University, US Dairy Forage Research Center, USDA-ARS : Agricultural Research Service, Rothamsted Research, Chercheur indépendant, Cornell University [New York], SweTree Technol AB, Partenaires INRAE, Swedish University of Agricultural Sciences (SLU), Biologie intégrée pour la valorisation de la diversité des arbres et de la forêt (BioForA), Institut National de la Recherche Agronomique (INRA)-Office National des Forêts (ONF), University of Hohenheim, Academy of Sciences of Moldova (ASM), Agroressources et Impacts environnementaux (AgroImpact), Institut National de la Recherche Agronomique (INRA), Hunan Agricultural University, Department of Crop Sciences, University of Göttingen - Georg-August-Universität Göttingen, University of Illinois at Urbana Champaign (UIUC), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Università degli Studi di Catania (UniCT), Plant Breeding, Wageningen University and Research [Wageningen] (WUR), Independent Artist, Julius Kühn-Institut (JKI), Institute of Biological and Environmental Science, University of Aberdeen, Endemic Species Research Institute, Zhejiang University, Department of Agroecology, Aarhus University [Aarhus], Centre for Circular Bioeconomy, Seoul National University [Seoul] (SNU), Chinese Academy of Sciences (CAS), University of Minnesota [Duluth], University of Minnesota System, Energene, The James Hutton Institute, GreenWood Resources, HudsonAlpha Institute for Biotechnology [Huntsville, AL], Biological Sciences (University of Sydney), The University of Sydney, Oak Ridge National Laboratory, Hokkaido University [Sapporo, Japan], Kangwon National University, Northern Research Station, Forest Research [Great Britain], Italian Ministry of Education, Brain Gain Program (Rientro dei cervelli), US Department of Energy [DE-AC05-00OR22725, DE-SC0006634, DE-SC0012379, DE-SC0018420], Department of Trade and Industry (UK) [B/W6/00599/00/00], Biotechnology and Biological Sciences Research Council [CSP1730/1, BB/N016149/1, N016149, LK0863, K01711X/1, 10963A01, G016216/1, E006833/1, G00580X/1, 000I0410], Department for Environment, Food and Rural Affairs [LK0863, NF0424, NF0426], National Institute of Food and Agriculture, US Department of Agriculture, H2020 Environment [GRACE-745012/Bio-Based Industries Joint Undertaking], European Project: 311929,EC:FP7:KBBE,FP7-KBBE-2012-6-singlestage,WATBIO(2012), Biotechnology and Biological Sciences Research Council (BBSRC)-Aberystwyth University, Università degli studi della Tuscia [Viterbo], Biotechnology and Biological Sciences Research Council (BBSRC), Institut National de la Recherche Agronomique (INRA)-Office national des forêts (ONF), Georg-August-University = Georg-August-Universität Göttingen, University of Illinois System, and Università degli studi di Catania = University of Catania (Unict)
Subjects: Germplasm, Agricultural Biotechnology, Biomass, Populus spp, 010501 environmental sciences, bioenergy, 01 natural sciences, cbio, Laboratorium voor Plantenveredeling, lignocellulose, Platform, salix, feedstocks, M. sacchariflorus, M. sinensis, Miscanthus, Panicum virgatum, perennial biomass crop, Salix spp, TARGETED MUTAGENESIS, Cultivar, AGRONOMIC TRAITS, Waste Management and Disposal, 2. Zero hunger, Molecular breeding, Vegetal Biology, sélection génétique, Forestry, 04 agricultural and veterinary sciences, production de biomasse, M.&nbsp, M. sacchariflorus, M. sinensis, Renewable Energy, Sustainability and the Environment, Agronomy and Crop Science, sélection végétale, Willow, sacchariflorus, PLANT-REGENERATION, populus, Biology, Bioenergy, avancée scientifique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Renewable Energy, POPULATION-STRUCTURE, GENOME-WIDE ASSOCIATION, AGROBACTERIUM-MEDIATED TRANSFORMATION, 0105 earth and related environmental sciences, bioénergie, amélioration génétique, Sustainability and the Environment, Environmental and Society, matériel forestier de reproduction, 15. Life on land, BIOENERGY CROP, biology.organism_classification, matière première végétale, [SDE.ES]Environmental Sciences/Environmental and Society, Plant Breeding, Agronomy, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, SINENSIS ANDERSS, sinensis, Environnement et Société, EPS, Biologie végétale, NATURAL-POPULATIONS, GENETIC-TRANSFORMATION
Abstract: This is the accepted manuscript of the paper "Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar", published as final paper in "Global Change Biology Bioenergy Volume 11, Issue 1, 08 February 2019, Pages 118–151 https://doi.org/10.1111/gcbb.12566”. Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namelyPanicum virgatum(switchgrass), species of the generaMiscanthus(miscanthus),Salix(willow) andPopulus(poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed‐based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass‐scale deployment of PBCs.
Published: 2019

33. Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves

Author: Frank Rabenstein, Victor Golyaev, Mikhail Pooggin, Thierry Candresse, 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), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Julius Kühn-Institut (JKI), INRA SPE department, European Project: 232250,EC:FP7:SME,FP7-SME-2008-1,DIVAS(2009), 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), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)
Subjects: 0106 biological sciences, 0301 basic medicine, Molecular biology, Virologie, lcsh:Medicine, 01 natural sciences, Deep sequencing, Article, Plant Viruses, 03 medical and health sciences, RNA interference, Plant virus, Virology, Human virome, RNA-Seq, Desiccation, RNA, Small Interfering, lcsh:Science, pathologie végétale, Illumina dye sequencing, Furovirus, Genetics, Multidisciplinary, biology, lcsh:R, fungi, RNA, food and beverages, Hordeum, Argonaute, biology.organism_classification, antiviral, Plant Leaves, 030104 developmental biology, RNA, Plant, maladie virale, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, lcsh:Q, Plant sciences, 010606 plant biology & botany
Abstract: In plants, RNA interference (RNAi) generates small interfering (si)RNAs from entire genomes of viruses, satellites and viroids. Therefore, deep small (s)RNA sequencing is a universal approach for virome reconstruction and RNAi characterization. We tested this approach on dried barley leaves from field surveys. Illumina sequencing of sRNAs from 2 plant samples identified in both plants Hordeum vulgare endornavirus (HvEV) and barley yellow mosaic bymovirus (BaYMV) and, additionally in one plant, a novel strain of Japanese soil-borne wheat mosaic furovirus (JSBWMV). De novo and reference-based sRNA assembly yielded complete or near-complete genomic RNAs of these viruses. While plant sRNAs showed broad size distribution, viral sRNAs were predominantly 21 and 22 nucleotides long with 5′-terminal uridine or adenine, and were derived from both genomic strands. These bona fide siRNAs are presumably processed from double-stranded RNA precursors by Dicer-like (DCL) 4 and DCL2, respectively, and associated with Argonaute 1 and 2 proteins. For BaYMV (but not HvEV, or JSBWMV), 24-nucleotide sRNAs represented the third most abundant class, suggesting DCL3 contribution to anti-bymovirus defence. Thus, viral siRNAs are well preserved in dried leaf tissues and not contaminated by non-RNAi degradation products, enabling both complete virome reconstruction and inference of RNAi components mediating antiviral defense.
Published: 2019

34. Simulating rewetting events in intermittent rivers and ephemeral streams: a global analysis of leached nutrients and organic matter

Author: Arnaud Foulquier, Michael T. Bogan, Björn Gücker, Roland Corti, Daniel von Schiller, Pablo Rodríguez-Lozano, Fiona Dyer, Vladimir Pešić, Stefan Lorenz, Klement Tockner, Jonathan C. Marshall, Lluís Gómez-Gener, Ana Savić, Thibault Datry, Dominik Zak, Rubén del Campo, Marcos Moleón, Clara Mendoza-Lera, Elisabeth I. Meyer, Chelsea J. Little, Simone Guareschi, Ross Vander Vorste, Richardo Figueroa, Florian Altermatt, Michael Danger, Oleksandra Shumilova, Musa C. Mlambo, Rosa Gómez Cerezo, Annamaria Zoppini, Joanna Blessing, Kate S. Boersma, Petr Paril, Núria Bonada, Alisha L. Steward, Christiane Zarfl, Amina Taleb, Manuel A. S. Graça, Juan F. Blanco-Libreros, Peter M. Negus, Isabel Pardo, Iola G. Boëchat, Ryan M. Burrows, Stephanie M. Carlson, Angus R. McIntosh, Mark O. Gessner, Andy Banegas-Medina, Simone D. Langhans, María Isabel Arce, Kate Brintrup, Rachel Stubbington, Pierre Gnohossou, Biel Obrador, Athina Papatheodoulou, Erin E. Beller, Nick Bond, Shai Arnon, Robert J. Rolls, Brian Four, Catherine M. Febria, Sophie Cauvy-Fraunié, Bianca de Freitas Terra, Catherine Leigh, Emile Faye, Andreas Bruder, Daniel C. Allan, Jason L. Hwan, Núria Cid, Skhumbuzo Kubheka, Damien Banas, Nathan J. Waltham, M. M. Sánchez-Montoya, Arturo Elosegi, Marko Miliša, Dev K. Niyogi, Anna Maria De Girolamo, Tommaso Cancellario, Melanie L. Blanchette, European Commission, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Freie Universität Berlin, University of Trento, Universität Rostock, Aarhus University, Institut National de Recherche en Sciences et Technologies pour l'Environnement et l'Agriculture (IRSTEA), University of the Basque Country (University of the Basque Country), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), University of Barcelona, Austrian Science Fund (FWF), University of Oklahoma (OU), University of Zurich, Centro de Edafologia y Biologia Aplicada del Segura, Ben-Gurion University of the Negev (BGU), Unité de Recherches Animal et Fonctionnalités des Produits Animaux (URAFPA), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Universidad de Concepción, University of California [Berkeley], University of California, Edith Cowan University, University of Antioquia, Queensland Government, Universidade Federal de São João del-Rei (UFSJ), University of California [San Diego] (UC San Diego), University of Arizona, Universitat Autònoma de Barcelona [Barcelona] (UAB), La Trobe University, University of Applied Sciences and Arts Switzerland, Griffith University [Brisbane], University of Navarra, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Université de Lorraine (UL), Universidade Estadual Vale do Acarau, National Council of Research, Water Research Institute, Universidad de Murcia, University of Canberra, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Canterbury, University of Windsor, Département Ecologie des Forêts, Prairies et milieux Aquatiques (DEPT EFPA), Institut National de la Recherche Agronomique (INRA), Berlin Institute of Technology, Université de Parakou, Umea University, University of Coimbra, Ezemvelo KZN Wildlife, University of Otago [Dunedin, Nouvelle-Zélande], Basque Centre for Climate Change (BC3), Queensland University of Technology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Julius Kühn-Institut (JKI), Brandenburg University of Technology, University of Münster, University of Zagreb, Rhodes University, Universidad de Granada (UGR), Missouri University of Science and Technology (Missouri S&T), University of Missouri System, Terra Cypria - Cyprus Conservation Foundation, Universidate de Vigo, Masaryk University, University of Montenegro (UCG), University of New England (UNE), University of Niš, Nottingham Trent University, Université de Tlemcen, James Cook University (JCU), University of Tübingen, Aarhus University [Aarhus], Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Universitat Autònoma de Barcelona (UAB), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), University of Canterbury [Christchurch], University of Windsor [Ca], Université de Parakou (UP), Department of Ecology and Environmental Science [Umeå], Umeå University, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Rhodes University, Grahamstown, Universidade de Vigo, and Masaryk University [Brno] (MUNI)
Subjects: 0106 biological sciences, Geologic Sediments, sédiment, 010504 meteorology & atmospheric sciences, Climate, rehumectation, 01 natural sciences, Substance nutritive, Klimatforskning, chemistry.chemical_compound, zone humide temporaire, Nutrient, Nitrate, matière organique dissoute, Dissolved organic carbon, Canvi climàtic, Primary Research Article, Organic Chemicals, General Environmental Science, chemistry.chemical_classification, Global and Planetary Change, leaf litter, cycle des nutriments, Ecology, zone climatique, Litière végétale, Sediments fluvials, sediments, Lessivage du sol, 6. Clean water, Lixiviació, biofilms, leaching, rewetting, temporary rivers, climatic region, climate change, Environmental chemistry, Leaching (pedology), Biogeochemical cycle, Climate Research, P40 - Météorologie et climatologie, [SDE.MCG]Environmental Sciences/Global Changes, Cours d'eau, Climate change, Biological Availability, 010603 evolutionary biology, River sediments, Sécheresse, biodisponibilité, Rivers, Environmental Chemistry, Organic matter, litière du sol, Matière organique, P10 - Ressources en eau et leur gestion, variation géographique, 0105 earth and related environmental sciences, Changement climatique, Nitrates, entraînement par lessivage, P35 - Fertilité du sol, Nutrients, 15. Life on land, Primary Research Articles, Arid, Climatic change, Plant Leaves, chemistry, 13. Climate action, Environmental science, bioavailability
Abstract: Climate change and human pressures are changing the global distribution and the extent of intermittent rivers and ephemeral streams (IRES), which comprise half of the global river network area. IRES are characterized by periods of flow cessation, during which channel substrates accumulate and undergo physico‐chemical changes (preconditioning), and periods of flow resumption, when these substrates are rewetted and release pulses of dissolved nutrients and organic matter (OM). However, there are no estimates of the amounts and quality of leached substances, nor is there information on the underlying environmental constraints operating at the global scale. We experimentally simulated, under standard laboratory conditions, rewetting of leaves, riverbed sediments, and epilithic biofilms collected during the dry phase across 205 IRES from five major climate zones. We determined the amounts and qualitative characteristics of the leached nutrients and OM, and estimated their areal fluxes from riverbeds. In addition, we evaluated the variance in leachate characteristics in relation to selected environmental variables and substrate characteristics. We found that sediments, due to their large quantities within riverbeds, contribute most to the overall flux of dissolved substances during rewetting events (56%–98%), and that flux rates distinctly differ among climate zones. Dissolved organic carbon, phenolics, and nitrate contributed most to the areal fluxes. The largest amounts of leached substances were found in the continental climate zone, coinciding with the lowest potential bioavailability of the leached OM. The opposite pattern was found in the arid zone. Environmental variables expected to be modified under climate change (i.e. potential evapotranspiration, aridity, dry period duration, land use) were correlated with the amount of leached substances, with the strongest relationship found for sediments. These results show that the role of IRES should be accounted for in global biogeochemical cycles, especially because prevalence of IRES will increase due to increasing severity of drying events., In this study we experimentally simulated under laboratory conditions rewetting of leaves, riverbed sediments, and epilithic biofilms collected during the dry phase from intermittent rivers and ephemeral streams covering global spatial scale. We determined the amounts and quality of the leached nutrients and dissolved organic matter, assessed their inter‐substrate and cross‐climate differences, and estimated areal fluxes from 1 m2 of riverbeds. In addition, we evaluated the variance in leachate characteristics related to selected environmental variables and substrate characteristics.
Published: 2019

35. Manure and doxycycline affect the bacterial community and its resistome in lettuce rhizosphere and bulk soil

Author: Khald Blau, Samuel Jacquiod, Søren J. Sørensen, Jian-Qiang Su, Yong-Guan Zhu, Kornelia Smalla, Sven Jechalke, Jechalke, Sven, Julius Kühn-Institut (JKI), Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, University of Copenhagen = Københavns Universitet (KU), Chinese Academy of Sciences (CAS), State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences [Changchun Branch] (CAS), and Libyan Government - German Environmental Agency (Umweltbundesamt) [FKZ 3713 63 402]
Subjects: Microbiology (medical), Tetracycline, high-throughput quantitative polymerase chain reaction, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Bulk soil, Microbiology, lcsh:Microbiology, Clostridia, 03 medical and health sciences, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Food science, bulk soil, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Rhizosphere, biology, 030306 microbiology, Chemistry, resistance genes, lettuce rhizosphere, prokaryotic community, biology.organism_classification, Manure, Soil contamination, Resistome, manure, [SDE]Environmental Sciences, Bacteria, medicine.drug
Abstract: International audience; Manure application to agricultural soil introduces antibiotic residues and increases the abundance of antibiotic-resistant bacteria (ARB) carrying antibiotic resistance genes (ARGs), often located on mobile genetic elements (MGEs). The rhizosphere is regarded as a hotspot of microbial activity and gene transfer, which can alter and prolong the effects of organic fertilizers containing antibiotics. However, not much is known about the influence of plants on the effects of doxycycline applied to soil via manure. In this study, the effects of manure spiked with or without doxycycline on the prokaryotic community composition as well as on the relative abundance of ARGs and MGEs in lettuce rhizosphere and bulk soil were investigated by means of a polyphasic cultivation-independent approach. Samples were taken 42 days after manure application, and total community DNA was extracted. Besides a pronounced manure effect, doxycycline spiking caused an additional enrichment of ARGs and MGEs. High-throughput quantitative PCR revealed an increase in tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin B (MLSB) resistance genes associated with the application of manure spiked with doxycycline. This effect was unexpectedly lower in the rhizosphere than in bulk soil, suggesting a faster dissipation of the antibiotic and a more resilient prokaryotic community in the rhizosphere. Interestingly, the tetracycline resistance gene tetA(P) was highly enriched in manure-treated bulk soil and rhizosphere, with highest values observed in doxycycline-treated bulk soil, concurring with an enrichment of Clostridia. Thus, the gene tetA(P) might be a suitable marker of soil contamination by ARB, ARGs, and antibiotics of manure origin. These findings illustrate that the effects of manure and doxycycline on ARGs and MGEs differ between rhizosphere and bulk soil, which needs to be considered when assessing risks for human health connected to the spread of ARGs in the environment.
Published: 2019

36. Advances and challenges in cherry breeding

Author: Mirko Schuster, Amy F. Iezzoni, Gregorio López-Ortega, Cameron Peace, José Quero-Garcia, Elisabeth Dirlewanger, Mathieu Fouché, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Michigan State University [East Lansing], Michigan State University System, Instituto Murciano de Investigación y desarrollo Agrario y Alimentario (IMIDA), Washington State University (WSU), and Julius Kühn-Institut (JKI)
Subjects: 0106 biological sciences, 0303 health sciences, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biology, 01 natural sciences, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience
Published: 2019

37. When a Palearctic bacterium meets a Nearctic insect vector: genetic and ecological insights into the emergence of the grapevine Flavescence dorée epidemics in Europe

Author: Malembic-Maher, Sylvie, Desqué, Delphine, Khalil, Dima, Salar, Pascal, Bergey, Bernard, Danet, Jean-Luc, Duret, Sybille, Dubrana-Ourabah, Marie-Pierre, Beven, Laure, Ember, Ibolya, Acs, Zoltan, Della Bartola, Michele, Materazzi, Alberto, Filippin, Luisa, Krnjajic, Slobodan, Krstić, Oliver, Toševski, Ivo, Lang, Friederike, Jarausch, Barbara, Kölber, Maria, Jović, Jelena, Angelini, Elisa, Arricau-Bouvery, Nathalie, Maixner, Michael, Foissac, Xavier, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Genlogs Biodiagnostika Kft, University of Pisa - Università di Pisa, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Institute for Plant Protection and Environment, Julius Kühn-Institut (JKI), European Project, Genlogs Biodiagnosztika Ltd, Partenaires INRAE, Department of Agriculture, Food and Environment, Center For Viticulture, CREA, CABI Europe Switzerland, Julius Kühn Institut - Institut für Pflanzenschutz in Obst und Weinbau (JKI), ProdInra, Migration, and Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria = Council for Agricultural Research and Economics (CREA)
Subjects: [SDV]Life Sciences [q-bio], Mollicute phytopathogène, Plant Science, Disease Vectors, Vigne Vitis vinifera, Geographical Locations, Animals, Bacteria, Bacterial Proteins, Epidemics, Europe, Genetic Variation, Hemiptera, Insect Vectors, Phylogeny, Phytoplasma, Plant Diseases, Vitis, santé des plantes, Medicine and Health Sciences, Biology (General), Flowering Plants, ComputingMilieux_MISCELLANEOUS, Flavescence dorée de la vigne, Plant Bacterial Pathogens, Eukaryota, Plants, Legumes, Insects, Infectious Diseases, Italy, insect vector, Grapevine, epidemiology, France, Adhesin, Research Article, Arthropoda, QH301-705.5, Beans, Plant Pathogens, Pathologie végétale, Plante fruitière, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, European Union, Grapevine yellows, Bactérie phytopathogène, [SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Organisms, Biology and Life Sciences, Plant Pathology, RC581-607, Invertebrates, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Species Interactions, Phytoplasmas, Fruit, People and Places, Immunologic diseases. Allergy
Abstract: Flavescence dorée (FD) is a European quarantine grapevine disease transmitted by the Deltocephalinae leafhopper Scaphoideus titanus. Whereas this vector had been introduced from North America, the possible European origin of FD phytoplasma needed to be challenged and correlated with ecological and genetic drivers of FD emergence. For that purpose, a survey of genetic diversity of these phytoplasmas in grapevines, S. titanus, black alders, alder leafhoppers and clematis were conducted in five European countries. Out of 132 map genotypes, only 11 were associated to FD outbreaks, three were detected in clematis, whereas 127 were detected in alder trees, alder leafhoppers or in grapevines out of FD outbreaks. Most of the alder trees were found infected, including 8% with FD genotypes M6, M38 and M50, also present in alders neighboring FD-free vineyards and vineyard-free areas. The Macropsinae Oncopsis alni could transmit genotypes unable to achieve transmission by S. titanus, while the Deltocephalinae Allygus spp. and Orientus ishidae transmitted M38 and M50 that proved to be compatible with S. titanus. Variability of vmpA and vmpB adhesin-like genes clearly discriminated 3 genetic clusters. Cluster Vmp-I grouped genotypes only transmitted by O. alni, while clusters Vmp-II and -III grouped genotypes transmitted by Deltocephalinae leafhoppers. Interestingly, adhesin repeated domains evolved independently in cluster Vmp-I, whereas in clusters Vmp-II and–III showed recent duplications. Latex beads coated with various ratio of VmpA of clusters II and I, showed that cluster II VmpA promoted enhanced adhesion to the Deltocephalinae Euscelidius variegatus epithelial cells and were better retained in both E. variegatus and S. titanus midguts. Our data demonstrate that most FD phytoplasmas are endemic to European alders. Their emergence as grapevine epidemic pathogens appeared restricted to some genetic variants pre-existing in alders, whose compatibility to S. titanus correlates with different vmp gene sequences and VmpA binding properties., Author summary Since the first outbreaks, Flavescence dorée epidemics had been associated to the introduction of the North American leafhopper vector Scaphoideus titanus. We hereby show that the associated phytoplasma originated from European alders and that epidemics in grapevine are restricted to some phytoplasma genetic variants pre-existing in this wild asymptomatic plant host. The compatibility of this phytoplasma to the introduced S. titanus insect vector resulted from the adaptation of phytoplasma variable membrane proteins Vmps to leafhoppers of the same subfamily living on alders. Vmps organization is similar to adhesion related proteins (ARP) and seems to allow the duplication of pre-adapted repeated domains. This suggests a key role of the Vmp adhesins in the life-style of phytoplasmas infecting woody hosts that rely on the adaptation to new insect vectors to expand their plant-host range.
Published: 2019

38. Palaeogenomic insights into the origins of French grapevine diversity

Author: Anne Kathrine W. Runge, Roberto Bacilieri, Jasmin Ramos-Madrigal, Thierry Lacombe, Bent O. Petersen, Nathan Wales, Caroline Schaal, Thomas M. P. Gilbert, Isabel Figueiral, Patrice This, José M. Martínez-Zapater, Anne-Françoise Adam-Blondon, Charlotte Hallavant, José Alfredo Samaniego Castruita, Thomas Sicheritz-Pontén, Reinhard Töpfer, Laurent Bouby, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), BioArch, Department f Archeology, University of York, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [Bolivie]), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), Université de Montpellier (UM), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COMUE), Centre National de la Recherche Scientifique (CNRS), UMR5608 (pôle Terrae) Bureau d’études Hadès, laboratoire TRACES, Université Toulouse - Jean Jaurès (UT2J), Instituto de Ciencias de la Vid y del Vino (CSIC-UR-Gobierno de La Rioja), Universidad de la Rioja, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut für Rebenzüchtung Geilweilerhof, Julius Kühn-Institut (JKI), Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, NTNU University Museum [Trondheim], Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), Department of Plant and Microbial Biology, University of California, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, ANR-PLANT-KBBE-2008 GrapeReSeq, ANR-16-CE27-0013,VINICULTURE,Vignes et vins en France du Néolithique au Moyen Age. Approche intégrée en archéosciences(2016), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Université Toulouse Jean Jaurès, UMR 6249 GéoArchEon Sarl, Laboratoire Chrono-Environnement, Université de Franche Comté (UFC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE27-0013 VINICULTURE, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), École Pratique des Hautes Études (EPHE), 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), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement (UMR 6249) (LCE), University of California (UC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT), Danish Council for Independent Research, and Agence Nationale de la Recherche (France)
Subjects: 0106 biological sciences, 0301 basic medicine, Crops, Agricultural, Vegetative reproduction, [SDV]Life Sciences [q-bio], Wine, Plant Science, 01 natural sciences, Polymorphism, Single Nucleotide, Domestication, 03 medical and health sciences, Genetic variation, Middle Ages, Vitis, Cultivar, History, Ancient, Taxonomy, Winemaking, 2. Zero hunger, Genetic diversity, Diversity, Ecology, Genetic Variation, food and beverages, Biodiversity, 15. Life on land, humanities, 030104 developmental biology, Geography, Archaeology, Iron Age, Vitis vinifera, Seeds, Grapevine, France, 010606 plant biology & botany
Abstract: The Eurasian grapevine (Vitis vinifera) has long been important for wine production as well as being a food source. Despite being clonally propagated, modern cultivars exhibit great morphological and genetic diversity, with thousands of varieties described in historic and contemporaneous records. Through historical accounts, some varieties can be traced to the Middle Ages, but the genetic relationships between ancient and modern vines remain unknown. We present target-enriched genome-wide sequencing data from 28 archaeological grape seeds dating to the Iron Age, Roman era and medieval period. When compared with domesticated and wild accessions, we found that the archaeological samples were closely related to western European cultivars used for winemaking today. We identified seeds with identical genetic signatures present at different Roman sites, as well as seeds sharing parent–offspring relationships with varieties grown today. Furthermore, we discovered that one seed dated to ~1100 CE was a genetic match to ‘Savagnin Blanc’, providing evidence for 900 years of uninterrupted vegetative propagation., This project was funded by the Danish Council for Independent Research (10–081390) and the Danish National Research Foundation (DNRF94). L.B. and R.B. were supported by the French National Agency of Research (VINICULTURE project—ANR-16-CE27–0013).
Published: 2019

39. Automatic Flower Number Evaluation in Grapevine Inflorescences Using RGB Images

Author: Katja Herzog, Florian Rist, Javier Tello, Agnes Doligez, Patrice This, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Julius Kühn-Institut (JKI), Federal Ministry of Education & Research (BMBF) [FKZ 031A349E], German Research Foundation (DFG) [TO 152/6-1], European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), 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, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Vine, flowering, business.industry, Reproductive behavior, Pattern recognition, modeling, 04 agricultural and veterinary sciences, Horticulture, segregating population, computer vision, 040501 horticulture, image processing, Set (abstract data type), Inflorescence, Vitis vinifera L, RGB color model, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Segmentation, Cultivar, Artificial intelligence, 0405 other agricultural sciences, business, Variable number, Food Science, Mathematics
Abstract: A precise count of flower number per inflorescence is essential to characterize the reproductive behavior of a vine. Previous efforts to automatize this process by image-based technologies have failed in the development of a universal system that can be applied to multiple grapevine cultivars, or they have been tested in a set of inflorescences of narrow morphological diversity. Here, we have developed an alternative general method in the open-source platform Fiji for the nondestructive counting of visible flowers in red-green-blue (RGB) images, considering inflorescences from 45 different grapevine genotypes from three progenies segregating for inflorescence morphology. The algorithm, based on the segmentation of the image into regions of interest according to their color and morphology, provided counting results highly correlated to manual ones (R2 = 0.91). Similar results were obtained when validating this tool in an external data set of 400 images of four grapevine cultivars. Counting values were used for actual flower number estimation by linear modeling using a subset of 45 images, considering a flower density factor to reduce the adverse effect of the variable number of hidden flowers. Our approach allowed the estimation of flower number with satisfactory results, providing useful information for grapevine breeding and research.
Published: 2019

40. From leaf to continent: The multi-scale distribution of an invasive cryptic pathogen complex on oak

Author: Marie Massot, Julie Faivre d’Arcier, Levente Kiss, Katarína Pastirčáková, Uwe Braun, Slavtcho Slavov, Johanna Boberg, Xavier Capdevielle, Corina Junker, Martin Pastirčák, P. Christova, Olivier Fabreguettes, Tamara Corcobado, Maude Toïgo, Dominique Piou, Funda Oskay, Ayco J. M. Tack, Cyril Dutech, Andrin Gross, Anne Chandelier, Tugba Dogmus, Gilles Saint-Jean, Marie-Laure Desprez-Loustau, Kaloyan Kostov, Jonàs Oliva, Jan Stenlid, Thomas R. Cech, Susumu Takamatsu, Arnaud Sallafranque, Marília Horta Jung, Ayşe Gülden Aday Kaya, A. Lyubenova, Tania Fort, A. Lehtijärvi, Venche Talgø, Thomas Jung, Eugenia Iturritxa, Benoit Marçais, Lehtijaervi, Asko Tapio, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Süleyman Demirel University, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences (SLU), Martin-Luther-University Halle-Wittenberg, Federal Research and Training Centre for Forests Natural Hazards and Landscape, Walloon Agricultural Research Centre, AgroBioInstitute, Mendel University in Brno (MENDELU), Faculty of Forestry, Eidg. Forschungsanstalt WSL, Partenaires INRAE, Universidade do Algarve (UAlg), Instituto Vasco de Investigación y Desarrollo Agrario [Derio] (NEIKER), Julius Kühn-Institut (JKI), Hungarian Academy of Sciences (MTA), University of Southern Queensland (USQ), Bursa Technical University, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Universitat de Lleida, Çankırı Karatekin University, National Agricultural and Food Centre, Soil Science and Conservation Research Institute, Slovak Academy of Sciences (SAS), Ministère de l'Agriculture et de l'Alimentation, Norwegian Institute of Bioeconomy Research (NIBIO), Mie University, and Stockholm University
Subjects: 0106 biological sciences, Scale (anatomy), Species complex, Emission inventory, [SDV]Life Sciences [q-bio], VDP::Landbruks- og Fiskerifag: 900::Landbruksfag: 910::Planteforedling, hagebruk, plantevern, plantepatologi: 911, Distribution (economics), Plant Science, Spatial distribution, 010603 evolutionary biology, 01 natural sciences, Quercus, Powdery mildew, Erysiphe alphitoides, Cryptic invasion, Plant pathogen, Erysiphe, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Ecology, biology, business.industry, Ecological Modeling, Niche differentiation, Species coexistence, 15. Life on land, biology.organism_classification, Oak, Cryptic species, business, 010606 plant biology & botany
Abstract: Marcais, Benoit/0000-0002-8107-644X; Jung, Thomas/0000-0003-2034-0718; Jung, Marilia Horta/0000-0003-2219-8647; Corcobado, Tamara/0000-0001-5762-4728; Lyubenova, Aneta/0000-0001-7414-1808; Pastircak, Martin/0000-0001-5118-9518; Pastircakova, Katarina/0000-0003-0371-428X; Fort, Tomas/0000-0002-4186-0918; Oskay, Funda/0000-0002-8918-5595; Oliva, Jonas/0000-0003-2418-2542; FORT, Tania/0000-0001-6998-5985; Kiss, Levente/0000-0002-4785-4308; Iturritxa, Eugenia/0000-0002-6390-5873; Aday Kaya, Ayse Gulden/0000-0002-5631-6026; Nave, Corina/0000-0003-2290-8282 WOS:000452564900005 The spatial distribution and niche differentiation of three closely related species (Erysiphe alphitoides, Erysiphe quercicola and Erysiphe hypophylla) causing oak powdery mildew was studied at scales ranging from the European continent, where they are invasive, to a single leaf. While E. alphitoides was dominant at all scales, E. quercicola and E. hypophylla had restricted geographic, stand and leaf distributions. The large-scale distributions were likely explained by climatic factors and species environmental tolerances, with E. quercicola being more frequent in warmer climates and E. hypophylla in colder climates. The extensive sampling and molecular analyses revealed the cryptic invasion of E. quercicola in nine countries from which it had not previously been recorded. The presence of the three species was also strongly affected by host factors, such as oak species and developmental stage. Segregation patterns between Erysiphe species were observed at the leaf scale, between and within leaf surfaces, suggesting competitive effects. (C) 2018 Elsevier Ltd and British Mycological Society. All rights reserved. Conseil Regional d'AquitaineRegion Nouvelle-Aquitaine [20030304002FA, 20040305003FA]; European Union FEDEREuropean Commission [2003227]; Investissements d'AvenirFrench National Research Agency (ANR) [ANR-10-EQPX-16-01]; European BiodivERsA project "RESIPATH: Responses of European Forests and Society to Invasive Pathogens"; Portuguese Science and Technology FoundationPortuguese Foundation for Science and Technology [BIODIVERSA/0002/2012, ANR-13-EBID-0005-01]; ANR (France)French National Research Agency (ANR) [ANR-13-BSV7-0011]; Japan Society for the Promotion of ScienceMinistry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of Science [16K07613, 16F16097]; Slovak Research and Development AgencySlovak Research and Development Agency [APVV-15 0210] We thank Adrien Bolay, Caroline Gordon, Banga Grigaliunaite, Gabriela Juhasova, Vasyl Heluta, Seyed Akbar Khodaparast, Eleni Topalidou, Gy-ongyver Nagy, and all other collectors, for providing samples. Part of the analyses were performed at the Genome Transcriptome Facility of Bordeaux (grants from the Conseil Regional d'Aquitaine no 20030304002FA and 20040305003FA, from the European Union FEDER no 2003227 and from Investissements d'Avenir ANR-10-EQPX-16-01). Funding was obtained through the European BiodivERsA project "RESIPATH: Responses of European Forests and Society to Invasive Pathogens" co-financed by national funds (ANR-13-EBID-0005-01 for France, Portuguese Science and Technology Foundation Ref. BIODIVERSA/0002/2012). Other grants came from the ANR (France) Funfit project (ANR-13-BSV7-0011), the Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research (Nos. 16K07613 and16F16097), and the Slovak Research and Development Agency under the contract No. APVV-15 0210.
Published: 2018

41. One‑year oral toxicity study on a genetically modified maize MON810 variety in Wistar Han RCC rats (EU 7th Framework Programme project GRACE)

Author: Nils Bohmer, Zora Krivošíková, Esther J. Kok, Christian Kohl, Miroslava Kuricova, Maria Pla, Pablo Steinberg, Viera Spustova, Dagmar Zeljenková, Gijs Kleter, Zuzana Ševčíková, Elena Szabova, A. Pöting, Marc Bohmer, Anton Kebis, Armin Spök, Ralf Einspanier, Júlia Ondrejková, Maria Corujo, Soňa Wimmerová, Radka Aláčová, Martin Cernak, Ralf Wilhelm, Karine Adel-Patient, Mikuláš Levkut, Jana Tulinska, Joachim Schiemann, Kerstin Schmidt, Eva Rollerova, Katarína Ambrušová, Paul Schmidt, Jevgenij Kovrižnych, Jörg Schmidtke, Maria Bartusova, Jutta Sharbati, Jose Luis La Paz, Aurelia Liskova, Viera Revajová, Faculty of Public Health, Slovak Medical University of Bratislava (SMU), University of Veterinary Medicine and Pharmacy [Košice, Slovakia], GmbH, Center for Research in Agricultural Genomics, Universitat de Girona (UdG), Wageningen University and Research Centre (WUR), Free University of Berlin (FU), Service de Pharmacologie et d'Immunoanalyse (SPI), Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Inter-University Research Centre on Technology, Work and Culture, Partenaires INRAE, Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Julius Kühn-Institut (JKI), University of Veterinary Medicine Hannover, Department of Animal Nutrition, EU, Service de Pharmacologie et Immunoanalyse (SPI), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Male, 0301 basic medicine, Novel Foods & Agrochains, Health Status, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Food, Genetically Modified, Genetically modified crops, Toxicology, Novel Foods & Agroketens, GRACE, Rat feeding trial, BU Toxicology, Novel Foods & Agrochains, Toxicity Tests, Chronic, Blat de moro -- Genètica, 2. Zero hunger, BU Toxicology, 04 agricultural and veterinary sciences, General Medicine, Plants, Genetically Modified, 040401 food science, Genetically modified organism, OECD Test Guideline No. 452-Chronic toxicity studies (2009), Enginyeria genètica vegetal, Food/Feed Guidance Document of the EFSA Scientific Committee (2011), BU Toxicologie, Novel Foods & Agroketens, Genetically modified maize MON810, OECD Test Guideline No. 452– Chronic toxicity studies (2009), Chronic oral toxicity study, Female, Risk assessment, Plant genetic engineering, Wistar Han, Animal feed, BU Toxicologie, Biologics, Biology, Risk Assessment, Zea mays, 03 medical and health sciences, Corn -- Genetics, 0404 agricultural biotechnology, OECD Test Guideline No. 452–Chronic toxicity studies (2009), Animals, Adverse effect, Genetically modified maize, Plantes transgèniques, business.industry, Transgenic plants, Rats, Inbred Strains, Guideline, Animal Feed, Biotechnology, 030104 developmental biology, business
Abstract: The GRACE (GMO Risk Assessment and Communication of Evidence; www.grace-fp7.eu) project was funded by the European Commission within the 7th Framework Programme. A key objective of GRACE was to conduct 90-day animal feeding trials, animal studies with an extended time frame as well as analytical, in vitro and in silico studies on genetically modified (GM) maize in order to comparatively evaluate their use in GM plant risk assessment. In the present study, the results of a 1-year feeding trial with a GM maize MON810 variety, its near-isogenic non-GM comparator and an additional conventional maize variety are presented. The feeding trials were performed by taking into account the guidance for such studies published by the EFSA Scientific Committee in 2011 and the OECD Test Guideline 452. The results obtained show that the MON810 maize at a level of up to 33 % in the diet did not induce adverse effects in male and female Wistar Han RCC rats after a chronic exposure. Electronic supplementary material The online version of this article (doi:10.1007/s00204-016-1798-4) contains supplementary material, which is available to authorized users.
Published: 2016

42. CarrotDiverse: understanding variation in a wild relative of carrot

Author: A. Hägnefelt, Thomas Nothnagel, S. Huet, V. Lopes, Charlotte J. Allender, C. Mallor Gimenez, T. Charpentier, Emmanuel Geoffriau, Ulrike Lohwasser, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Julius Kühn-Institut (JKI), University of Warwick, and Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], plant genetic resources, Wild carrot, Horticulture, genebank, 010603 evolutionary biology, 01 natural sciences, Daucus, Genotype, characterization, music, 2. Zero hunger, Genetic diversity, biology, business.industry, QK, food and beverages, crop wild relative, 15. Life on land, biology.organism_classification, music.songwriter, Biotechnology, Taxon, Crop wild relative, Trait, business, 010606 plant biology & botany, Daucus carota
Abstract: International audience; Genebanks and other ex situ collections have a significant role in the conservation, management and use of crop genetic diversity, including that of crop wild relatives. Efficient management and use depends on insight into the patterning and distribution of genetic diversity as well as obtaining baseline information on phenotypic characters and traits. Wild carrot (Daucus carota L.) is the closest wild relative of cultivated carrot (Daucus carota L. subsp. sativus (Hoffm.) Arcang.), and is a potential source of useful traits for crop improvement. There are over 900 accessions of D. carota described as wild in European genebanks, however associated phenotypic and genotypic characterization data are sparse. The influence of environment on phenotype is also not well understood in this taxon, meaning that it is difficult to ascertain how data collected at different locations can be compiled and collated. We present initial results of CarrotDiverse, a collaborative project in which wild D. carota accessions are undergoing detailed phenotypic and morphological characterization in parallel at three sites of varying latitude across Europe located in Portugal, France and Sweden. This will allow us to understand which traits are affected by environmental variables. Basic phenotypic information is being collected on a further 150 accessions. Furthermore, resistance screening to Alternaria species and polyacetylene profiling will be included in the evaluation. A Genotyping by Sequencing approach will be used to generate knowledge about genetic background and trait associations. The project will result in a significant data set which will facilitate the use of crop wild relatives in carrot breeding and improvement.
Published: 2018

43. Preservation via utilization: minor grape varieties on-farm

Author: Topfer, Reinhard, Maul, Erika, Lacombe, Thierry, Schneider, Anna, Carka, Frida, Cunha, Jorge, Eiras Dias, José, Gardiman, Massimo, Gazivoda, Anita, Ivanisevic, Dragoslav, Maletic, Edi, Mara, Vesna, Munoz Organero, Gregorio, Nikolic, Dragan, Regner, Ferdinand, Rockel, Franco, Zdunic, Goran, Maggioni, Lorenzo, Schreiber, Toni, Julius Kühn-Institut (JKI), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Istituto per la Protezione Sostenibile delle Piante (CNR), Agricultural University of Tirana, Instituto Nacional de Investigaciones Agropecuarias (INIAP), Center For Viticulture, CREA, Partenaires INRAE, Development sector, Faculty of Agriculture, University of Zagreb, Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Université nationale du Rwanda, Federal College and Office of Vineyards and Orchards (HBLAuBA), Institute for Adriatic Crops and Karst Reclamation, and CGIAR
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, niche products, marketing, on-farm preservation, cultural heritage, documentation, ComputingMilieux_MISCELLANEOUS, European Vitis Database, diversity
Abstract: National audience
Published: 2018

44. Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs

Author: Laucou, Valerie, Launay, Amandine, Bacilieri, Roberto, Lacombe, Thierry, Adam-Blondon, Anne-Francoise, Martinez-Zapater, José Miguel, Topfer, Reinhard, Peros, Jean-Pierre, Boursiquot, Jean-Michel, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Instituto de Ciencias de la Vid y el Vino - Institute of Grapevine and Wine Sciences, Partenaires INRAE, and Julius Kühn-Institut (JKI)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, genetic linkage disequilibrium, association studies, parentage analysis, SNP, genetic diversity, structure, ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2018

45. RecQ Helicases Function in Development, DNA Repair, and Gene Targeting in Physcomitrella patens[OPEN]

Author: Eva L. Decker, Lina Maloukh, Katrin Schulze, Fabien Nogué, Fabian Köchl, Lisa Hunn, Ralf Reski, Gertrud Wiedemann, Nico van Gessel, Frank Hartung, Plant Biotechnology, Faculty of Biology, University of Freiburg, Julius Kühn-Institut (JKI), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Excellence Initiative of the State Government [EXC 294], Federal Ministry of Education and Research [GABI-PRECISE 0315057D], Deutsche Forschungsgemeinschaft [TRR 141, project B02], European Union (European Regional Development Fund) in the framework of the program INTERREG IV Upper Rhine [A17 TIP-ITP], LabEx Saclay Plant Sciences-SPS [ANR-10-LABX-0040-SPS], Hartung, Frank, and Reski, Ralf
Subjects: 0301 basic medicine, DNA Repair, DNA repair, Mutant, Arabidopsis, Plant Science, Physcomitrella patens, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Enhancer, Gene, Research Articles, Phylogeny, Plant Proteins, Genetics, Vegetal Biology, biology, RecQ Helicases, Gene targeting, Helicase, food and beverages, Cell Biology, biology.organism_classification, Bryopsida, 030104 developmental biology, biology.protein, Biologie végétale, Genome, Plant
Abstract: International audience; RecQ DNA helicases are genome surveillance proteins found in all kingdoms of life. They are characterized best in humans, as mutations in RecQ genes lead to developmental abnormalities and diseases. To better understand RecQ functions in plants we concentrated on Arabidopsis thaliana and Physcomitrella patens, the model species predominantly used for studies on DNA repair and gene targeting. Phylogenetic analysis of the six P. patens RecQ genes revealed their orthologs in humans and plants. Because Arabidopsis and P. patens differ in their RecQ4 and RecQ6 genes, reporter and deletion moss mutants were generated and gene functions studied in reciprocal cross-species and cross-kingdom approaches. Both proteins can be found in meristematic moss tissues, although at low levels and with distinct expression patterns. PpRecQ4 is involved in embryogenesis and in subsequent development as demonstrated by sterility of ΔPpRecQ4 mutants and by morphological aberrations. Additionally, ΔPpRecQ4 displays an increased sensitivity to DNA damages and an increased rate of gene targeting. Therefore, we conclude that PpRecQ4 acts as a repressor of recombination. In contrast, PpRecQ6 is not obviously important for moss development or DNA repair but does function as a potent enhancer of gene targeting.
Published: 2018

46. Variability and function of Vmp adhesion related proteins give insight into the emergence of phytoplasma epidemics

Author: Malembic-Maher, Sylvie, Desque, Delphine, Salar, Pascal, Danet, Jean-Luc, Duret, Sybille, Dubrana, Marie-Pierre, Batailler, Brigitte, Jovic, Jelena, Krnjajic, Slobodan, Angelini, Elisa, Filippin, Luisa, Monticone, Michela, Bosco, Domenico, Ember, Ibolya, Kölber, Maria, Della Bartola, Michele, Materazzi, Alberto, Maixner, Michael, Beven, Laure, Renaudin, Joel, Arricau-Bouvery, Nathalie, Foissac, Xavier, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Institute for Plant Protection and Environment, Center For Viticulture, CREA, Partenaires INRAE, Università degli studi di Torino (UNITO), Genlogs Biodiagnostika Kft, Universita degli studi di Pisa, Julius Kühn-Institut (JKI), and ProdInra, Migration
Subjects: [SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, ComputingMilieux_MISCELLANEOUS, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: International audience
Published: 2018

47. Advanced spectroscopy-based phenotyping offers a potential solution to the ash dieback epidemic

Author: Rasmus Enderle, Berthold Metzler, Michelle Cleary, Erik Dahl Kjær, Lars-Göran Stener, Vytautas Suchockas, Luis E. Rodriguez-Saona, Pierluigi Bonello, Caterina Villari, Marjan Ghasemkhani, Alfas Pliūra, Lea Vig McKinney, Thomas Kirisits, Arnaud Dowkiw, Diana Marčiulynienė, Lene Rostgaard Nielsen, Facundo Muñoz, Department of Plant Pathology, Ohio State University [Columbus] (OSU), Warnell School of Forestry & Natural Resources, University of Georgia [USA], Biologie intégrée pour la valorisation de la diversité des arbres et de la forêt (BioForA), Institut National de la Recherche Agronomique (INRA)-Office National des Forêts (ONF), Department Forest Protection, Forest Research Institute Baden-Wuerttemberg (FVA), Julius Kühn-Institut (JKI), Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences (SLU), Institute of Forest Entomology - Forest Pathology and Forest Protection (IFFF) - Department of Forest and Soil Sciences, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Department of Geosciences and Natural Resource Management [Copenhagen] (IGN), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, The Forest Research Institute, Skogforsk, Department of Food Science and Technology, and Kasetsart University
Subjects: 0106 biological sciences, 0301 basic medicine, Biodiversité et Ecologie, lcsh:Medicine, Spectroscopie, Fraxinus, 01 natural sciences, phénotypage, Milieux et Changements globaux, lcsh:Science, Multidisciplinary, Geography, biology, Agroforestry, U10 - Informatique, mathématiques et statistiques, Hymenoscyphus fraxineus, Modélisation et simulation, Europe, Population decline, medicine.drug_formulation_ingredient, Phenotype, Natural population growth, Modeling and Simulation, spectrométrie de fourier, Disease Susceptibility, résistance aux maladies, Resource (biology), spectrométrie infrarouge, [SDE.MCG]Environmental Sciences/Global Changes, Dépérissement terminal, Article, chalarose, Biodiversity and Ecology, 03 medical and health sciences, medicine, Epidemics, Keystone species, Plant Diseases, H20 - Maladies des plantes, Resistance (ecology), Spectrum Analysis, lcsh:R, Fraxinus excelsior, 15. Life on land, biology.organism_classification, Champignon pathogène, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 030104 developmental biology, Modélisation, Threatened species, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: Natural and urban forests worldwide are increasingly threatened by global change resulting from human-mediated factors, including invasions by lethal exotic pathogens. Ash dieback (ADB), incited by the alien invasive fungus Hymenoscyphus fraxineus, has caused large-scale population decline of European ash (Fraxinus excelsior) across Europe, and is threatening to functionally extirpate this tree species. Genetically controlled host resistance is a key element to ensure European ash survival and to restore this keystone species where it has been decimated. We know that a low proportion of the natural population of European ash expresses heritable, quantitative resistance that is stable across environments. To exploit this resource for breeding and restoration efforts, tools that allow for effective and efficient, rapid identification and deployment of superior genotypes are now sorely needed. Here we show that Fourier-transform infrared (FT-IR) spectroscopy of phenolic extracts from uninfected bark tissue, coupled with a model based on soft independent modelling of class analogy (SIMCA), can robustly discriminate between ADB-resistant and susceptible European ash. The model was validated with populations of European ash grown across six European countries. Our work demonstrates that this approach can efficiently advance the effort to save such fundamental forest resource in Europe and elsewhere.
Published: 2018

48. Humoral and cellular immune response in Wistar Han RCC rats fed two genetically modified maize MON810 varieties for 90 days (EU 7th Framework Programme project GRACE)

Author: Radka Aláčová, Silvia Ilavska, Eva Rollerova, Aurelia Liskova, Jana Tulinska, Jean-Michel Wal, Hervé Bernard, Anton Kebis, Joachim Schiemann, Ralf Wilhelm, Mira Horvathova, Miroslava Kuricova, Pablo Steinberg, Júlia Babincová, Paul Schmidt, Jörg Schmidtke, Christian Kohl, Karine Adel-Patient, Kerstin Schmidt, Slovak Medical University of Bratislava (SMU), Service de Pharmacologie et Immunoanalyse (SPI), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Faculty of Public Health, GmbH, University of Hohenheim, Julius Kühn-Institut (JKI), University of Veterinary Medicine Hannover, Department of Animal Nutrition, Max Rubner-Institut, Dutch Ministry of Economic Affairs, ITMS Project [26240120033], European Project: 311957,EC:FP7:KBBE,FP7-KBBE-2012-6-singlestage,GRACE(2012), Service de Pharmacologie et d'Immunoanalyse (SPI), and Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay
Subjects: 0301 basic medicine, European corn borer, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Food, Genetically Modified, Toxicology, Immunoglobulin E, 01 natural sciences, Hemolysin Proteins, GRACE, Humoral immune response, Cry1Ab, Toxicity Tests, Chronic, Lymph node, 2. Zero hunger, Immunity, Cellular, food and beverages, General Medicine, Food allergenicity, Native immunity analysis, Plants, Genetically Modified, Respiratory burst, medicine.anatomical_structure, Genetically modified maize MON810, Food Hypersensitivity, Immunoglobulins, Spleen, Biologics, Biology, Zea mays, Microbiology, 03 medical and health sciences, Immune system, Bacterial Proteins, medicine, Animals, Rats, Wistar, OECD Test Guideline no. 408-repeated dose 90-day oral toxicity study in rodents (1998), OECD Test Guideline no. 408—repeated dose 90-day oral toxicity study in rodents (1998), Anti-Cry1Ab antibodies, Genetically modified maize, Acquired immunity analysis, Bacillus thuringiensis Toxins, 010401 analytical chemistry, fungi, Cellular immune response, biology.organism_classification, Animal Feed, In vitro, Immunity, Humoral, 0104 chemical sciences, Endotoxins, 030104 developmental biology, Consumer Product Safety, biology.protein, Anti-maize protein antibodies, Immune cell phenotyping
Abstract: The genetically modified maize event MON810 expresses a Bacillus thuringiensis-derived gene, which encodes the insecticidal protein Cry1Ab to control some lepidopteran insect pests such as the European corn borer. It has been claimed that the immune system may be affected following the oral/intragastric administration of the MON810 maize in various different animal species. In the frame of the EU-funded project GRACE, two 90-day feeding trials, the so-called studies D and E, were performed to analyze the humoral and cellular immune responses of male and female Wistar Han RCC rats fed the MON810 maize. A MON810 maize variety of Monsanto was used in the study D and a MON810 maize variety of Pioneer Hi-Bred was used in the study E. The total as well as the maize protein- and Cry1Ab-serum-specific IgG, IgM, IgA and IgE levels, the proliferative activity of the lymphocytes, the phagocytic activity of the granulocytes and monocytes, the respiratory burst of the phagocytes, a phenotypic analysis of spleen, thymus and lymph node cells as well as the in vitro production of cytokines by spleen cells were analyzed. No specific Cry1Ab immune response was observed in MON810 rats, and anti-maize protein antibody responses were similar in MON810 and control rats. Single parameters were sporadically altered in rats fed the MON810 maize when compared to control rats, but these alterations are considered to be of no immunotoxicological significance. Electronic supplementary material The online version of this article (10.1007/s00204-018-2230-z) contains supplementary material, which is available to authorized users.
Published: 2018

49. Challenges and opportunities for integrated pest management in Europe: A telling example of minor uses

Author: Antoine Messéan, Silke Dachbrodt-Saaydeh, Johan C. Roman, José E.M. van Bijsterveldt-Gels, Per Kudsk, Mario Wick, Wilma Arendse, Jay Ram Lamichhane, Unité Impacts Ecologiques des Innovations en Production Végétale (ECO-INNOV), Institut National de la Recherche Agronomique (INRA), Netherlands Plant Protection Organization, Partenaires INRAE, Julius Kühn-Institut (JKI), Department of Agroecology, and Aarhus University [Aarhus]
Subjects: Integrated pest management, [SDV]Life Sciences [q-bio], minor crops, minor uses, Biology, [SHS]Humanities and Social Sciences, sustainable production, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Economic impact analysis, Agricultural productivity, Stock (geology), 2. Zero hunger, integrated pest management, Agroforestry, business.industry, fungi, Pest control, food and beverages, 15. Life on land, Pesticide, Crop protection, Agronomy, [SDE]Environmental Sciences, Sustainability, business, Agronomy and Crop Science, crop protection
Abstract: International audience; Minor crops include mostly vegetables, fruits, nursery stock and ornamentals. These crops account for an EU production value of over (sic) 60 billion per year, representing more than 20% of the value of EU's total agricultural production. The sustainable production of such crops, from an economic point of view, is vital for both human health and European economies. For minor crops, this sustainability can only be realized by the continued availability of crop protection solutions for pest control. The number of minor crops in Europe without viable solutions for plant protection has increased in recent years. This is mainly due to the lack of pesticides in certain crops, as a number of previously authorized pesticides has not been re-authorized due to a stricter regulation. Also the introduction of tropical or sub-tropical crops and their pests into Europe has contributed to the problem of minor crops without any crop protection solutions as pesticides used elsewhere to protect these crops are not allowed in Europe. The limited range of pesticides available to farmers has increased the risk of resistance development since, in absence of a sufficient number of pesticides with various modes of action, farmers apply repetitively only a narrow spectrum of molecules. The direct economic impact due to the absence of viable plant protection solutions for minor crops has been estimated over a billion Euros per year, impacting 9 million hectares throughout Europe. In light of this, here we discuss the current state of the art of minor crops in Europe and elucidate ongoing efforts to address such problems through Integrated Pest Management (IPM). The information reported is expected to provide relevance of minor crops in Europe and encourage the development and implementation of effective IPM solutions.
Published: 2015

50. Fungal community associated with grapevine wood lesions in Lebanon

Author: Michael Fischer, Paulette Chlela, Elia Choueiri, Gwenaelle Comont, Pascal Lecomte, Valérie Mayet, Lizel Mostert, Jean-Michel Liminana, Fouad Jreijiri, ProdInra, Migration, Lebanese Agricultural Research Institute (LARI), Santé et agroécologie du vignoble (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Stellenbosch University, and Julius Kühn-Institut (JKI)
Subjects: 2. Zero hunger, Veterinary medicine, biology, Fomitiporia mediterranea, biology.plant_disease_cause, [SDV]Life Sciences [q-bio], lcsh:S, 15. Life on land, Horticulture, Botryosphaeriaceae, biology.organism_classification, eutypa dieback, Community associated, lcsh:QK1-989, [SDV] Life Sciences [q-bio], lcsh:Agriculture, trunk diseases, esca, Vitis vinifera, lcsh:Botany, Botany, Botryosphaeria dieback, Family Botryosphaeriaceae, Food Science
Abstract: Aims: To detect and identify the cultivable microorganisms putatively associated with esca disease in representative Lebanese vineyards.Methods and results: Two field surveys were conducted in Lebanon in 2005 and 2007 to study the fungal community associated with grapevine wood lesions. A total of 68 vines showing typical esca symptoms were randomly sampled in 17 vineyards and cross sections were obtained of cordons and trunks. The shape and type of inner necrosis and discoloration were examined and isolations were made from the symptomatic wood. Isolation results showed that inner necrosis and isolated fungi were similar to those previously found elsewhere, namely in Central Europe or Mediterranean countries. Additionally, three methods for numerical evaluation of micro-organisms found were compared.Conclusion: Most fungal pathogens generally associated with grapevine trunk diseases were detected, of which the basidiomycete Fomitiporia mediterranea and species of the ascomycete family Botryosphaeriaceae were the most frequently encountered. Additionally, a large diversity of other wood colonizing micro-organisms was detected. The putative role of some of the obtained micro-organisms in the process of wood degradation related to esca disease is discussed.Significance and impact of the study: This isolation study is presently the most completed that was carried out with grapevine wood samples collected in Lebanon. Besides, it is the first to provide isolation results based on a classification of inner necrosis in five categories and to compare three criteria for numerical evaluation. This study also tends to further highlight that Botryosphaeriaceae species are common wood inhabiting fungi that should be associated with esca.
Published: 2014

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