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1. Leaf Microbiome Data for European Cultivated Grapevine (Vitis vinifera) During Downy Mildew (Plasmopara viticola) Epidemics in Three Wine-Producing Regions in France

Author

Didac Barroso-Bergadà, François Delmotte, Julie Faivre d'Arcier, Marie Massot, Emilie Chancerel, Isabelle Demeaux, Soizic Guimier, Erwan Guichoux, David A. Bohan, and Corinne Vacher

Subjects
bacteria, fungi, holobiont, metabarcoding, microbial community, microbiota, Plant culture, SB1-1110, Botany, QK1-989
Abstract

Grapevine downy mildew (Plasmopara viticola) is a major disease of European cultivated grapevine (Vitis vinifera L.) against which a large amount of synthetic pesticides are used. Developing microbial biocontrol of P. viticola could reduce the use of pesticides in viticulture and preserve human and environmental health. To achieve this goal, the ecological interactions that develop during infection between P. viticola and the vine foliar microbiome need to be explored. Here, we present metabarcoding datasets describing the bacterial and fungal communities of pairs of symptomatic and asymptomatic leaf samples collected during downy mildew epidemics in three major wine-producing regions of France. Fungal and bacterial communities were sequenced on a MiSeq Illumina platform, and the abundance of the oomycete P. viticola was quantified using qPCR. We provide the raw metabarcoding datasets, the amplicon sequence variant tables obtained after bioinformatic processing, the metadata describing sampling sites and tissue health conditions, and the code used for bioinformatic analysis. These datasets will enable microbiome comparison within pairs of symptomatic and asymptomatic samples collected at the same time on the same leaf. Such a comparison could help describe the ecological interactions between P. viticola and the grapevine foliar microbiome. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Published
2023
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2. An observer design for Takagi-Sugeno fuzzy bilinear control systems

Author

François Delmotte, Nizar Hadj Taieb, Mohamed Ali Hammami, and Houria Meghnafi

Subjects
fuzzy systems, bilinear systems, stability analysis, observer design, Information technology, T58.5-58.64, Mathematics, QA1-939
Abstract

In this paper, the observer design problem for a T-S fuzzy bilinear control system is investigated. First, an observer of Kalman type is designed to estimate the system states for the linear case. Then, some new sufficient conditions are derived to show the exponential convergence of the solutions of the error equation for fuzzy bilinear systems. Furthermore, we consider some uncertainties of the system that are bounded and satisfy a certain condition where an observer is designed. Moreover, an application to Van de Vusse system is given.

Published
2023
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3. Stability analysis and design of state estimated controller for delay fuzzy systems with parameter

Author

Nizar Hadj Taieb, Mohamed Ali Hammami, and François Delmotte

Subjects
time-delay systems, observer, stabilization, Information technology, T58.5-58.64, Mathematics, QA1-939
Abstract

This paper deals with the problem of stabilization by an estimated state feedback for a family of nonlinear time-delay Takagi-Sugeno fuzzy parameterized systems. The delay is supposed to be constant where the parameter-dependent controls laws are used to compensate the nonlinearities which are formulated in terms of linear matrix inequalities (LMIs). Based on the Lyapunov- Krasovskii functionals, global exponential stability of the closed-loop systems is achieved. The controller and observer gains are able to be separately designed even in the presence of modeling uncertainty and state delay. Finally, a numerical example is given to show the applicability of the main result.

Published
2022
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4. Fungal Metabarcoding Data for Two Grapevine Varieties (Regent and Vitis vinifera ‘Cabernet-Sauvignon’) Inoculated with Powdery Mildew (Erysiphe necator) Under Drought Conditions

Author

Corinne Vacher, Claire Francioni, Marion Michel, Tania Fort, Julie Faivre d'Arcier, Emilie Chancerel, François Delmotte, and Chloé E. L. Delmas

Subjects
disease, drought stress, Erysiphe necator, fungal communities, grapevine, metabarcoding, Plant culture, SB1-1110, Microbial ecology, QR100-130, Plant ecology, QK900-989
Published
2022
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5. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author

Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps, Carole Couture, Laurent Delière, Angela E. Douglas, Keith Dufault-Thompson, Paula Escuer, Honglin Feng, Astrid Forneck, Toni Gabaldón, Roderic Guigó, Frédérique Hilliou, Silvia Hinojosa-Alvarez, Yi-min Hsiao, Sylvie Hudaverdian, Emmanuelle Jacquin-Joly, Edward B. James, Spencer Johnston, Benjamin Joubard, Gaëlle Le Goff, Gaël Le Trionnaire, Pablo Librado, Shanlin Liu, Eric Lombaert, Hsiao-ling Lu, Martine Maïbèche, Mohamed Makni, Marina Marcet-Houben, David Martínez-Torres, Camille Meslin, Nicolas Montagné, Nancy A. Moran, Daciana Papura, Nicolas Parisot, Yvan Rahbé, Mélanie Ribeiro Lopes, Aida Ripoll-Cladellas, Stéphanie Robin, Céline Roques, Pascale Roux, Julio Rozas, Alejandro Sánchez-Gracia, Jose F. Sánchez-Herrero, Didac Santesmasses, Iris Scatoni, Rémy-Félix Serre, Ming Tang, Wenhua Tian, Paul A. Umina, Manuella van Munster, Carole Vincent-Monégat, Joshua Wemmer, Alex C. C. Wilson, Ying Zhang, Chaoyang Zhao, Jing Zhao, Serena Zhao, Xin Zhou, François Delmotte, and Denis Tagu

Subjects
Arthropod genomes, Daktulosphaira vitifoliae, Gene duplications, Host plant interactions, Effectors, Biological invasions, Biology (General), QH301-705.5
Abstract

Abstract Background Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. Results Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. Conclusions The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.

Published
2020
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6. Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author

Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps, Carole Couture, Laurent Delière, Angela E. Douglas, Keith Dufault-Thompson, Paula Escuer, Honglin Feng, Astrid Forneck, Toni Gabaldón, Roderic Guigó, Frédérique Hilliou, Silvia Hinojosa-Alvarez, Yi-min Hsiao, Sylvie Hudaverdian, Emmanuelle Jacquin-Joly, Edward B. James, Spencer Johnston, Benjamin Joubard, Gaëlle Le Goff, Gaël Le Trionnaire, Pablo Librado, Shanlin Liu, Eric Lombaert, Hsiao-ling Lu, Martine Maïbèche, Mohamed Makni, Marina Marcet-Houben, David Martínez-Torres, Camille Meslin, Nicolas Montagné, Nancy A. Moran, Daciana Papura, Nicolas Parisot, Yvan Rahbé, Mélanie Ribeiro Lopes, Aida Ripoll-Cladellas, Stéphanie Robin, Céline Roques, Pascale Roux, Julio Rozas, Alejandro Sánchez-Gracia, Jose F. Sánchez-Herrero, Didac Santesmasses, Iris Scatoni, Rémy-Félix Serre, Ming Tang, Wenhua Tian, Paul A. Umina, Manuella van Munster, Carole Vincent-Monégat, Joshua Wemmer, Alex C. C. Wilson, Ying Zhang, Chaoyang Zhao, Jing Zhao, Serena Zhao, Xin Zhou, François Delmotte, and Denis Tagu

Subjects
Biology (General), QH301-705.5
Abstract

An amendment to this paper has been published and can be accessed via the original article.

Published
2020
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7. Downy mildew is able to carry out its sexual cycle on resistant grape varieties

Author

Lionel Delbac, Laurent Delière, Christophe Schneider, and François Delmotte

Subjects
Agriculture (General), S1-972, Plant culture, SB1-1110
Abstract

Previous studies have shown that new resistant grape cultivars limit epidemics caused by asexual reproduction of downy mildew. However, until now, there was a lack of knowledge on the sexual phase of the pathogen. This study demonstrates that host resistance has little effect on the sexual cycle of downy mildew. Thus, the pathogen can complete its life cycle (asexual and sexual phases) on partially resistant grapevine varieties. The persistence of pathogen populations on partially resistant varieties from one year to the next represents a major challenge for the sustainability of genetic resistance of grapevines.

Published
2020
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8. Continuous Stability TS Fuzzy Systems Novel Frame Controlled by a Discrete Approach and Based on SOS Methodology

Author

Ameni Ellouze, Omar Kahouli, Mohamed Ksantini, Ali Rebhi, Nidhal Hnaien, and François Delmotte

Subjects
discretization, continuous Takagi Sugeno (TS) fuzzy models, Euler approximation, non quadratic Lyapunov function, sum of square approach (SOS), polynomial Lyapunov function, Mathematics, QA1-939
Abstract

Generally, the continuous and discrete TS fuzzy systems’ control is studied independently. Unlike the discrete systems, stability results for the continuous systems suffer from conservatism because it is still quite difficult to apply non-quadratic Lyapunov functions, something which is much easier for the discrete systems. In this paper and in order to obtain new results for the continuous case, we proposed to connect the continuous with the discrete cases and then check the stability of the continuous TS fuzzy systems by means of the discrete design approach. To this end, a novel frame was proposed using the sum of square approach (SOS) to check the stability of the continuous Takagi Sugeno (TS) fuzzy models based on the discrete controller. Indeed, the control of the continuous TS fuzzy models is ensured by the discrete gains obtained from the Euler discrete form and based on the non-quadratic Lyapunov function. The simulation examples applied for various models, by modifying the order of the Euler discrete fuzzy system, are presented to show the effectiveness of the proposed methodology.

Published
2021
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18. LAMP for in-field quantitative assessments of airborne grapevine downy mildew inoculum

Author

Antonin Douillet, Benoit Laurent, Jessie Beslay, Marie Massot, Marc Raynal, and François Delmotte

Subjects
Peronospora, Oomycetes, Vitis, General Medicine, Applied Microbiology and Biotechnology, Plant Diseases, Biotechnology
Abstract

Aims Cheap, rapid tools for measuring emissions of Plasmopara viticola sporangia directly in the field are required to protect grapevines efficiently and sustainably against downy mildew. To this end, we adapted an existing loop-mediated isothermal amplification (LAMP) protocol based on ITS2 sequences, coupled with a rotating-arm sampler and simple cell lysis, for the in-field measurement of airborne sporangia of P. viticola. Methods and Results We estimated the sensitivity and specificity of the molecular reaction with an unpurified DNA template in controlled conditions, using the droplet digital PCR (ddPCR) as a reference. We show that the LAMP lower limit of quantification is 3.3 sporangia.m−3 air sampled. Cell lysis in KOH solution was less efficient than CTAB for DNA extraction, but the repeatability of the method was good. We tested this protocol directly in a plot at Chateau Dillon (Blanquefort, France) in which we monitored P. viticola sporangia concentrations from March to October 2020 (88 samples which revealed concentrations ranging from 0 to 243 sporangia.m−3). There was a significant quantitative correlation (R2 = 0.52) between ddPCR and LAMP results. Conclusion LAMP analysis of an unpurified DNA matrix is a simple and reliable method for in-field estimations of the concentration of airborne P. viticola sporangia. Significance and Impact of the Study This study constitutes a first step towards the development of a regional grapevine downy mildew monitoring network in the vineyards of Bordeaux.

Published
2022
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20. The Characterization of Pathotypes in Grapevine Downy Mildew Provides Insights into the Breakdown of Rpv3, Rpv10, and Rpv12 Factors in Grapevines

Author

Manon Paineau, Isabelle D. Mazet, Sabine Wiedemann-Merdinoglu, Frédéric Fabre, and François Delmotte

Subjects
Peronospora, Oomycetes, Vitis, Plant Science, Agronomy and Crop Science, Disease Resistance, Plant Diseases
Abstract

We describe a standard method for characterizing the virulence profile of Plasmopara viticola, the causal agent of grapevine downy mildew. We used 33 European strains to inoculate six grapevine varieties carrying the principal factors for resistance to downy mildew (Rpv1, Rpv3.1, Rpv3.2, Rpv5, Rpv6, Rpv10, and Rpv12) and the susceptible Vitis vinifera ‘Chardonnay’. For each interaction, we characterized the level of sporulation by image analysis and the intensity of the grapevine hypersensitive response by visual score. We propose a definition for the breakdown of grapevine quantitative resistances combining these two traits. Among the 33 strains analyzed, 28 are virulent on at least one resistance factor. We identified five different pathotypes across the 33 strains analyzed: two pathotypes overcoming a single resistance factor (vir3.1 and vir3.2) and three complex pathotypes overcoming multiple resistance factors (vir3.1,3.2; vir3.2,12; vir3.1,3.2,10). Our findings confirm the widespread occurrence of P. viticola strains overcoming the Rpv3 haplotypes (28 strains). We also detected the first breakdown of resistance to the Rpv10 by a strain from Germany and the breakdown of Rpv12 factors by a strain from Hungary. The pathotyping method proposed here and the associated differential host range lay the groundwork for the early detection of resistance breakdown in grapevines. This approach will also facilitate the monitoring of the evolution of P. viticola populations at large spatial scales. This is an essential step forward to promoting durable management of the resistant grapevine varieties currently available.

Published
2022
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37. Exponential stabilization of fuzzy systems with perturbations by using state estimation

Author

Mohamed Hammami, A. Jellouli, and François Delmotte

Subjects
Output feedback, 0209 industrial biotechnology, Computer science, 02 engineering and technology, Fuzzy control system, Computer Science::Artificial Intelligence, Fuzzy logic, Computer Science Applications, Theoretical Computer Science, 020901 industrial engineering & automation, Exponential stabilization, Exponential stability, Computer Science::Systems and Control, Control and Systems Engineering, Control theory, Modeling and Simulation, 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, State (computer science), Information Systems
Abstract

In this paper, the concept of practical output feedback controller for Takagi-Sugeno fuzzy models is introduced. Some new sufficient conditions are obtained to ensure the exponential stability usin...

Published
2021
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45. The quasi-universality of nestedness in the structure of quantitative plant-parasite interactions

Author

Boissot N, Marcel T, Dogimont C, Marie-Laure Pilet-Nayel, Juliette Doumayrou, S. Perrot, Josselin Montarry, Caffier, Chanéac S, Cantet M, Cindy E. Morris, Justafré I, Audergon J, M. Buisson, Paineau M, François Delmotte, Ben Krima S, Frédéric Fabre, Grimault, C. Constant, Omrani M, Sylvain Fournet, Benoît Moury, Losdat D, Baudracco-Arnas S, Ruellan Y, Jaunet T, Bertrand F, Lefebvre, Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Amélioration des Fruits et Légumes (GAFL), Laboratoires ASL, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Bayer seeds SAS, Gautier semences, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Takii France SAS, Sakata Vegetables Europe, Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 0971 Gip Geves SNES Angers, Institut National de la Recherche Agronomique (INRA)-Accueil GEVES (Accueil GEVES)-Groupe d'étude et de controle des variétés et des semences (GEVES)-Gip Geves SNES Angers (Gip Geves SNES Angers), HM. CLAUSE [France], Vilmorin, Rijk Zwaan, Partenaires INRAE, PROGRAILIVE project (grant 808 RBRE160116CR0530019), Institut Carnot PLANT2PRO, Comité Interprofessionnel des Vins de Bordeaux 810 (CIVB), the INRAE departments 'Santé des Plantes et Environnement' (project APÔGÉ and PhD thesis of Safa Ben Krima) and 'Génétique et Amélioration des Plantes', the INRAE métaprogramme SMaCH (Sustainable Management of Crop Health), the French Ministry of Agriculture and Food for projects 'Recherche et mise au point de méthodes pour évaluer des résistances variétales durables à des agents pathogènes' (CTPS project C2008-29), 'Nouvelles sources de résistance à Aphis gossypii chez le melon' (CTPS project C06/02) and 'Caractérisation de la virulence de Podosphaera xanthii, agent causal de l’oïdium du melon, et développement d’un système de codification des races' (CTPS project C-2012-10)., ANR-12-ADAP-0009,GANDALF,Génomique et adaptation des traits de vie des champignons impliqués dans les interactions plante-pathogène(2012), ANR-18-CE32-0004,ArchiV,Architecture génétique des caractères quantitatifs dans les interactions plante-virus: conséquences pour la gestion des variétés résistantes et/ou tolérantes à l'échelle du paysage.(2018), ANR-11-BTBR-0002,PeaMUST,Adaptation multistress et régulations biologiques pour l'amélioration du rendement et de la stabilité du pois protéagineux(2011), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), ANR-05-PADD-0005,CEDRE,Exploitation durable de résistances aux maladies chez les végétaux(2005), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, PROGRAILIVE project (grant RBRE160116CR0530019) funded by the Bretagne region, France, INRAE departments 'Santé des Plantes et Environnement' (project APÔGÉ and PhD thesis of Safa Ben Krima) and 'Génétique et Amélioration des Plantes', INRAE métaprogramme SMaCH (Sustainable Management of Crop Health), French Ministry of Agriculture and Food for projects 'Recherche et mise au point de méthodes pour évaluer des résistances variétales durables à des agents pathogènes' (CTPS project C2008-29), 'Nouvelles sources de résistance à Aphis gossypii chez le melon' (CTPS project C06/02) and 'Caractérisation de la virulence de Podosphaera xanthii, agent causal de l’oïdium du melon, et développement d’un système de codification des races' (CTPS project C-2012-10)., and Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, bipartite network, Plant resistance, pathogenicity, plant parasite, bipartite network, nestedness, modularity, nestedness, Plant Immunity, Plant resistance, Context (language use), Biology, Quantitative trait locus, 01 natural sciences, 03 medical and health sciences, pathogenicity, plant parasite, modularity, 030304 developmental biology, 2. Zero hunger, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Modularity (networks), Resistance (ecology), Host (biology), fungi, food and beverages, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Evolutionary biology, Trait, Nestedness, 010606 plant biology & botany
Abstract

A previous version of this article has been peer-reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100132); International audience; Understanding the relationships between host range and pathogenicity for parasites, and between the efficiency and scope of immunity for hosts are essential to implement efficient disease control strategies. In the case of plant parasites, most studies have focused on describing qualitative interactions and a variety of genetic and evolutionary models has been proposed in this context. Although plant quantitative resistance benefits from advantages in terms of durability, we presently lack models that account for quantitative interactions between plants and their parasites and the evolution of these interactions. Nestedness and modularity are important features to unravel the overall structure of host-parasite interaction matrices. Here, we analysed these two features on 32 matrices of quantitative pathogenicity trait data gathered from 15 plant-parasite pathosystems consisting of either annual or perennial plants along with fungi or oomycetes, bacteria, nematodes, insects and viruses. The performance of several nestedness and modularity algorithms was evaluated through a simulation approach, which helped interpretation of the results. We observed significant modularity in only six of the 32 matrices, with two or three modules detected. For three of these matrices, modules could be related to resistance quantitative trait loci present in the host. In contrast, we found high and significant nestedness in 30 of the 32 matrices. Nestedness was linked to other properties of plant-parasite interactions. First, pathogenicity trait values were explained in majority by a parasite strain effect and a plant accession effect, with no or minor parasite-plant interaction term. Second, correlations between the efficiency and scope of the resistance of plant genotypes, and between the host range breadth and pathogenicity level of parasite strains were overall positive. This latter result questions the efficiency of strategies based on the deployment of several genetically-differentiated cultivars of a given crop species in the case of quantitative plant immunity.

Published
2021
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46. Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola

Author

Yann Dussert, Tatiana Giraud, Sylvie Richart-Cervera, François Delmotte, Frédéric Labbé, Michael C. Fontaine, Laurent Delière, Fontaine lab, Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), 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]), Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, AgroParisTech, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-07-BDIV-0003,EMERFUNDIS,Comprendre les émergences de maladies fongiques de plantes : vers une estimation des risques liés aux changements globaux(2007), ANR-12-ADAP-0009,GANDALF,Génomique et adaptation des traits de vie des champignons impliqués dans les interactions plante-pathogène(2012), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])

Subjects
0301 basic medicine, microsatellite, [SDV]Life Sciences [q-bio], Population, [SDV.BID]Life Sciences [q-bio]/Biodiversity, emerging crop disease, General Biochemistry, Genetics and Molecular Biology, law.invention, approximate Bayesian computation, 03 medical and health sciences, 0302 clinical medicine, law, Quarantine, Vitis, education, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Disease Resistance, Plant Diseases, 2. Zero hunger, Oomycete, recent introduction, education.field_of_study, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Ecology, population genetics, food and beverages, Bayes Theorem, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Europe, Genetics, Population, 030104 developmental biology, Oomycetes, Vitis vinifera, Plasmopara viticola, Threatened species, Biological dispersal, Downy mildew, invasive plant pathogen, fungi, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery, Microsatellite Repeats
Abstract

International audience; Europe is the historical cradle of viticulture, but grapevines (Vitis vinifera) have been increasingly threatened by pathogens of American origin. The invasive oomycete Plasmopara viticola causes downy mildew, one of the most devastating grapevine diseases worldwide. Despite major economic consequences, its invasion history remains poorly understood. We analyzed a comprehensive dataset of ∼2,000 samples, collected from the most important wine-producing countries, using nuclear and mitochondrial gene sequences and microsatellite markers. Population genetic analyses revealed very low genetic diversity in invasive downy mildew populations worldwide and little evidence of admixture. All the invasive populations originated from only one of the five native North American lineages, the one parasitizing wild summer grape (V. aestivalis). An approximate Bayesian computation-random forest approach allowed inferring the worldwide invasion scenario of P. viticola. After an initial introduction into Europe, invasive European populations served as a secondary source of introduction into vineyards worldwide, including China, South Africa, and twice independently, Australia. Only the invasion of Argentina probably represents a tertiary introduction, from Australia. Our findings provide a striking example of a global pathogen invasion resulting from secondary dispersal of a successful invasive population. Our study will also help designing quarantine regulations and efficient breeding for resistance against grapevine downy mildew.

Published
2021
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47. Des vignes, des invasions et des résistances

Author

François Delmotte, Frédéric Fabre, Anne-Sophie Miclot, Manon Paineau, Christophe Schneider, Laurent Deliere, Fabre, Frédéric, Christian Lannou, Dominique Roby, Virginie Ravigné, Mourad Hannachi, Benoît Moury, Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Santé de la vigne et qualité du vin (SVQV), and Université de Strasbourg (UNISTRA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

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

International audience; Des vignes, des invasions et des résistances Chapitre tiré de l'ouvrage « L'immunité des plantes » Edition Quae, 2021.

Published
2021

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

Author

Benoît, Moury, primary, Jean-Marc, Audergon, additional, Sylvie, Baudracco-Arnas, additional, Safa, Ben Krima, additional, François, Bertrand, additional, Nathalie, Boissot, additional, Mireille, Buisson, additional, Valérie, Caffier, additional, Mélissa, Cantet, additional, Sylvia, Chanéac, additional, Carole, Constant, additional, François, Delmotte, additional, Catherine, Dogimont, additional, Juliette, Doumayrou, additional, Frédéric, Fabre, additional, Sylvain, Fournet, additional, Valérie, Grimault, additional, Thierry, Jaunet, additional, Isabelle, Justafré, additional, Véronique, Lefebvre, additional, Denis, Losdat, additional, Marcel Thierry, C., additional, Josselin, Montarry, additional, Morris Cindy, E., additional, Mariem, Omrani, additional, Manon, Paineau, additional, Sophie, Perrot, additional, Marie-Laure, Pilet-Nayel, additional, and Youna, Ruellan, additional

Published
2021
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49. A New MIP Model and Machine Learning Approach for Home Health Care: Optimization of Cancer Treatment Process by Chemotherapy

Author

Abderrazak Jemai, Adnen El-Amraoui, Mariem Belhor, and François Delmotte

Subjects
Service (systems architecture), Computer science, business.industry, Process (engineering), media_common.quotation_subject, medicine.disease, Scheduling (computing), Cancer treatment, Information and Communications Technology, Home health, Health care, medicine, Quality (business), Medical emergency, business, media_common
Abstract

For several decades, New Information and Communication Technologies (NICTs) have been developing rapidly in the healthcare sector. They are now more and more present in the healthcare system and in particular in Home Health Care (HHC). Our study focuses on oncology which is among the most commonly treated diseases in HHC. Oncology techniques are ranked second in terms of stays in HHC, of which cancer chemotherapy is a part. Cancer treatment with chemotherapy is complex, cumbersome and very expensive. It requires drugs that are very expensive and they are very chemically unstable with usually a lifetime of a few hours, so any prolonged delay between the time of their preparation and the time of injection to the patient involves their destruction. This implies safe transport and administration of the drug within a time frame compatible with the validity of the drug. In this paper, we are interested in improving the quality of treatment service of chemotherapy in HHC by optimizing the delivery of anticancer drugs to patients. Our work is divided into two parts, first, we propose a new MIP Model for nurses scheduling. Our model aims to minimize the delivery time of drugs. In the second part, we propose a new learning approach based on Genetic Fuzzy System. It is applied for the first time in the field of health care and in particular in HHC. This approach is used to deal with the problem of uncertainty for the quantity of drug to be delivered.

Published
2020
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50. A reliable version of choquistic regression based on evidence theory

Author

Sébastien Ramel, François Delmotte, Frédéric Pichon, Laboratoire de Génie Informatique et d'Automatique de l'Artois (LGI2A), and Université d'Artois (UA)

Subjects
Information Systems and Management, Computer science, Monotonic function, 02 engineering and technology, 16. Peace & justice, Logistic regression, Regression, Management Information Systems, Artificial Intelligence, 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, Statistical inference, Econometrics, 020201 artificial intelligence & image processing, [INFO]Computer Science [cs], Uncertainty quantification, Classifier (UML), Software
Abstract

Choquistic regression is an elegant generalisation of logistic regression, which preserves its monotonicity whilst alleviating its linearity. However, much as logistic regression, it lacks self-awareness, that is, an ability to represent the ignorance (aka epistemic uncertainty) involved in its predictions, which is crucial in safety-critical classification problems. Recently, an extension of logistic regression was introduced to remedy this issue for this latter classifier. This extension is formalised within evidence theory and relies in particular on a sound method for statistical inference and prediction developed in this framework. In this paper, a similar extension is derived for choquistic regression. The usefulness of the obtained approach is confirmed empirically in classification problems where cautiousness in decision-making is allowed.

Published
2020
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