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3. The Challenge of Biocontrol Deployment

Author

Bertrand, Cédric, Malausa, Thibaut, Nicot, Philippe C., Fauvergue, Xavier, editor, Rusch, Adrien, editor, Barret, Matthieu, editor, Bardin, Marc, editor, Jacquin-Joly, Emmanuelle, editor, Malausa, Thibaut, editor, and Lannou, Christian, editor

Published
2022
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4. Zéro pesticide

Author

Jacquet, Florence, primary, Jeuffroy, Marie-Hélène, additional, Jouan, Julia, additional, Le Cadre, Edith, additional, Malausa, Thibaut, additional, Reboud, Xavier, additional, and Huyghe, Christian, additional

Published
2022
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9. Bilan et Analyse du mandat 2019-2022 du CSO R&I (Ecophyto II+)

Author

Reboud, Xavier, De Tarlé, Sibylle, Lequin, Sonia, Bonato, Olivier, Bordin, Thierry, De Lapeyre de Bellaire, Luc, Durlin, Christian, Fontaine, Laurence, Galindo, Sabine, Le Bellec, Fabrice, Malausa, Thibaut, Messéan, Antoine, Moreau, Jérôme, Nicot, Philippe, Ranjard, Lionel, Thibierge, Jérôme, Van Baaren, John, Baldi, Isabelle, Bemadac, Gérard, Gallien, Marc, Payrastre, Laurence, Mortaud, Stéphane, Salles, Bernard, Goutte, Aurélie, Graber, Marianne, Kammerer, Martine, Le Gall, Philippe, Richard, Freddie-Jeanne, Rouïl, Laurence, Barthélémy, Carole, Bureau-Point, Eve, Carpentier, Alain, Dumat, Camille, Fleury-Bahi, Ghozlane, Gibert, Caroline, Jourjon, Frédérique, Miralles, André, Temple, Ludovic, Marchand, Philippe, Cousinié, Philippe, Bottou, Caroline, Reboud, Xavier, De Tarlé, Sibylle, Lequin, Sonia, Bonato, Olivier, Bordin, Thierry, De Lapeyre de Bellaire, Luc, Durlin, Christian, Fontaine, Laurence, Galindo, Sabine, Le Bellec, Fabrice, Malausa, Thibaut, Messéan, Antoine, Moreau, Jérôme, Nicot, Philippe, Ranjard, Lionel, Thibierge, Jérôme, Van Baaren, John, Baldi, Isabelle, Bemadac, Gérard, Gallien, Marc, Payrastre, Laurence, Mortaud, Stéphane, Salles, Bernard, Goutte, Aurélie, Graber, Marianne, Kammerer, Martine, Le Gall, Philippe, Richard, Freddie-Jeanne, Rouïl, Laurence, Barthélémy, Carole, Bureau-Point, Eve, Carpentier, Alain, Dumat, Camille, Fleury-Bahi, Ghozlane, Gibert, Caroline, Jourjon, Frédérique, Miralles, André, Temple, Ludovic, Marchand, Philippe, Cousinié, Philippe, and Bottou, Caroline

Abstract

Les objectifs de réduction des produits phytopharmaceutiques portés par le plan Ecophyto Il+ apportent de nouveaux défis à I' Agriculture. L'enjeu de l'Axe 2 Recherche & Innovation est de mobiliser l'ensemble du système de recherche-innovation afin d'apporter les connaissances nécessaires pour les relever et d'appuyer les politiques publiques dans la transition vers un modèle agroécologique des cultures. Cet axe est piloté et orienté par un Comité Scientifique d'Orientation {CSO R&I). Le document " Héritage CSO R&I " dresse un bilan et une analyse synthétiques des actions conduites par les membres du CSO R&I lors du mandat 2019-2022. Il met en perspective les réflexions scientifiques stratégiques, leurs concrétisations en actions (appels à projets, animation scientifique, valorisation ... ), les freins rencontrés et les perspectives pour le prochain mandat 2023-2026.

Published
2023

13. Zéro pesticide

Author

Jacquet, Florence, Jeuffroy, Marie-Hélène, Jouan, Julia, Le Cadre, Edith, Malausa, Thibaut, Reboud, Xavier, and Huyghe, Christian

Subjects
farmer, agriculture, organic farming, agronomy, nitrogen, sustainable development, industry, herbicide, biological control, pest control, nitrate, GMO, pesticide, public policy, pollution, regulation, cropping system, bic Book Industry Communication::T Technology, engineering, agriculture::TV Agriculture & farming::TVP Pest control
Abstract

The use of chemical pesticides is a major societal concern because of their negative impacts on the environment and health. The Priority Research Programme (PPR) "Cultiver et Protéger Autrement" (Growing and Protecting Differently), led by INRAE, plays a structuring role in the evolution of scientific communities and in the emergence of scientific fronts allowing for pesticide-free crop protection. The aim of the book is to explain the foundations of this strategy and the principles of action. By setting itself a zero pesticide course, research is attempting to overcome the current obstacles and produce breakthrough innovations in the biotechnical and socio-economic fields. In addition to research, teaching and the agricultural sector, this book also targets innovation, development and advisory actors.

Published
2022
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14. Consistent variations in personality traits and their potential for genetic improvement in biocontrol agents: Trichogramma evanescens as a case study

Author

Lartigue, Silène, primary, Yalaoui, Myriam, additional, Belliard, Jean, additional, Caravel, Claire, additional, Jeandroz, Louise, additional, Groussier, Géraldine, additional, Calcagno, Vincent, additional, Louâpre, Philippe, additional, Dechaume‐Moncharmont, François‐Xavier, additional, Malausa, Thibaut, additional, and Moreau, Jérôme, additional

Published
2022
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15. Zéro pesticide : un nouveau paradigme de recherche pour une agriculture durable

Author

Jacquet, Florence, Jeuffroy, Marie-Helene, Jouan, Julia, Le Cadre-Barthélemy, Edith, Malausa, Thibaut, Reboud, Xavier, Huyghe, Christian, Perez, Isabelle, Montpellier Interdisciplinary center on Sustainable Agri-food systems (Social and nutritional sciences) (UMR MoISA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département agronomie et sciences de l'environnement pour les agroécosystèmes (AgroEcoSystem), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AGROCAMPUS OUEST, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Programme prioritaire de recherche (PPR) : Cultiver et Protéger Autrement, Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-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), Sol Agro et hydrosystème Spatialisation (SAS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, and Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
[SDE.ES] Environmental Sciences/Environmental and Society, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, [SHS.ECO] Humanities and Social Sciences/Economics and Finance, [SDE.ES]Environmental Sciences/Environmental and Society
Abstract

Disponible gratuitement en ebook; International audience; L’usage des pesticides chimiques est une préoccupation sociétale majeure en raison de leurs impacts négatifs sur l’environnement et la santé. Le Programme prioritaire de recherche (PPR) « Cultiver et Protéger Autrement », piloté par INRAE, joue un rôle structurant dans l’évolution des communautés scientifiques et dans l’émergence de fronts de science permettant une protection des cultures sans pesticides. L’objectif de l’ouvrage est d’expliquer les bases de cette stratégie et les principes d’actions. En se fixant un cap zéro pesticide, la recherche tente de dépasser les verrous actuels et de produire des innovations de rupture dans les champs biotechniques et socio-économiques.Au-delà de la recherche, de l’enseignement et du secteur agricole, cet ouvrage vise également les acteurs de l’innovation, du développement et du conseil.

Published
2022

18. Additional file of Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

Author

Castagnone-Sereno, Philippe, Danchin, Etienne GJ, Deleury, Emeline, Guillemaud, Thomas, Malausa, Thibaut, and Abad, Pierre

Subjects
food and beverages
Abstract

Additional file of Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

Published
2021
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19. Additional file of Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing

Author

Jean-Francois Martin, Pech, Nicolas, Meglécz, Emese, Ferreira, Stéphanie, Costedoat, Caroline, Dubut, Vincent, Malausa, Thibaut, and Gilles, André

Subjects
animal structures
Abstract

Additional file of Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing

Published
2021
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22. Additional file 4 of Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing

Author

Jean-Francois Martin, Pech, Nicolas, Meglécz, Emese, Ferreira, Stéphanie, Costedoat, Caroline, Dubut, Vincent, Malausa, Thibaut, and Gilles, André

Abstract

Additional file 4: Representativeness of genome features using the equiprobability model. Representativeness of genome features using the equiprobability model in the case of Apis mellifera (A) and Danio rerio (B) for each of the six considered two-way tables chromosome × chromosomic region, chromosome × length of sequences, chromosome × microsatellite motifs, chromosomic region × length of sequences, chromosomic region × microsatellite motifs and length of sequences × microsatellite motifs. "Stat" refers to the overall χ2 statistic for the test of independence between the two variables defining the table. For each cell of the table: a red dot corresponds to an observed number significantly higher than expected under the hypothesis of independence between the two variables defining the table; a blue dot corresponds to an observed number significantly lower than expected under the hypothesis of independence between the two variables defining the table; absence of circle means a non-significant deviation. The size of the dot is inversely-proportional to the P-value, the scaling being made to the six considered tables so that the comparison of sizes between tables is meaningful. For cell tests, Benjamini-Hochberg20 correction for multiple tests was performed. (PDF 4 MB)

Published
2021
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27. Additional file 2 of Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing

Author

Jean-Francois Martin, Pech, Nicolas, Meglécz, Emese, Ferreira, Stéphanie, Costedoat, Caroline, Dubut, Vincent, Malausa, Thibaut, and Gilles, André

Abstract

Additional file 2: Representativeness of genome distribution after digestion with Rsa I. Representativeness of genome distribution after digestion with Rsa I in the case of Apis mellifera (A) and Danio rerio (B) for each of the six considered two-way tables: chromosome × chromosomic region, chromosome × length of sequences, chromosome × microsatellite motifs, chromosomic region × length of sequences, chromosomic region × microsatellite motifs and length of sequences × microsatellite motifs. "Stat" refers to the overall χ2 statistic for the test of independence between the two variables defining the table. For each cell of the table: a red dot corresponds to an observed number significantly higher than expected under the hypothesis of independence between the two variables defining the table, a blue dot corresponds to an observed number significantly lower than expected under the hypothesis of independence between the two variables defining the table; absence of dot means a non-significant deviation. The size of the dot is inversely-proportional to the P-value. The scaling is computed for the six considered tables so comparison of significance between tables is meaningful. For cell tests, Benjamini-Hochberg20 correction for multiple tests was performed. (PDF 3 MB)

Published
2021
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28. Additional file 3 of Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing

Author

Jean-Francois Martin, Pech, Nicolas, Meglécz, Emese, Ferreira, Stéphanie, Costedoat, Caroline, Dubut, Vincent, Malausa, Thibaut, and Gilles, André

Abstract

Additional file 3: Comparison of genome features using the equiprobability model Comparison of genome features using the equiprobability model in the case of Apis mellifera (A) and Danio rerio (B) for each of the four considered one-way tables: chromosome, chromosomic region, length of sequences and microsatellite motifs. For each table is figured in red the 95% confidence interval of the expected number of microsatellites under the equiprobability hypothesis, in black are figured observed numbers (genome distribution after digestion in silico with Rsa I). (PDF 2 MB)

Published
2021
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29. Shifts from pulled to pushed range expansions caused by reduction of landscape connectivity

Author

Dahirel, Maxime, Bertin, Aline, Haond, Marjorie, Blin, Aurélie, Lombaert, Eric, Calcagno, Vincent, Fellous, Simon, Malausa, Thibaut, and Vercken, Elodie

Subjects
Trichogramma, biological invasions, biological control, density-dependent dispersal, individual-based model, range shifts
Abstract

Range expansions are key processes shaping the distribution of species; their ecological and evolutionary dynamics have become especially relevant today, as human influence reshapes ecosystems worldwide. Many attempts to explain and predict range expansions assume, explicitly or implicitly, so-called "pulled" expansion dynamics, in which the low-density edge populations provide most of the "fuel" for the species advance. Some expansions, however, exhibit very different dynamics, with high-density populations behind the front "pushing" the expansion forward. These two types of expansions are predicted to have different effects on e.g. genetic diversity and habitat quality sensitivity. However, empirical studies are lacking due to the challenge of generating reliably pushed vs. pulled expansions in the laboratory, or discriminating them in the field. We here propose that manipulating the degree of connectivity among populations may prove a more generalizable way to create pushed expansions. We demonstrate this with individual-based simulations as well as replicated experimental range expansions (using the parasitoid wasp Trichogramma brassicae as model). By analyzing expansion velocities and neutral genetic diversity, we showed that reducing connectivity led to pushed dynamics. Low connectivity alone, i.e. without density-dependent dispersal, can only lead to "weakly pushed" expansions, where invasion speed conforms to pushed expectations, but the decline in genetic diversity does not. In empirical expansions however, low connectivity may in some cases also lead to adjustments to the dispersal-density function, recreating "classical" pushed expansions. In the current context of habitat loss and fragmentation, we need to better account for this relationship between connectivity and expansion regimes to successfully predict the ecological and evolutionary consequences of range expansions. Version 4 has been peer-reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100118). This version (version 4.1) is identical except one correction to the Discussion: "dispersal was density-independent in Tribolium castaneum metapopulations with low connectivity, density-dependent in metapopulations with high connectivity " in v4 should have been "dispersal was density-dependent in Tribolium castaneum metapopulations with low connectivity, density-independent in metapopulations with high connectivity " &nbsp

Published
2020

34. Additional file 3 of Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

Author

Gilles, André, Meglécz, Emese, Pech, Nicolas, Ferreira, Stéphanie, Malausa, Thibaut, and Jean-François Martin

Abstract

Additional file 3: Breakdown of error rate variation using all available variables. For each plate, we used a logistic model to decipher the role of each selected variable in explaining the variation of error rate (see materials and methods). The figure is broken down by error type: a) insertions, b) deletions, c) mismatches and d) ambiguous base calls. We tested the deviance from the complete model by breaking down the model into the sum of three terms: the first exclusive to the single effect of the variable considered (in black), the second exclusive effect of the rest of the variables without the variable of interest (in gray) and the last expressing the sum of the effects of interactions between the variable considered and the other variables (in white). The contribution of each term (the proportion) for a considered variable can be viewed on the y-axis. Additional file 3 displays the results for plates #2 and #3 (results from the plate #1 are presented as Figure 2). (PDF 117 KB)

Published
2020
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35. Additional file 2 of Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

Author

Gilles, André, Meglécz, Emese, Pech, Nicolas, Ferreira, Stéphanie, Malausa, Thibaut, and Jean-François Martin

Abstract

Additional file 2: Distribution of errors along the reference sequences. The blue line represents the proportion of sequences generated (y-axis) according to the sequence position (x-axis), using data obtained from the analysis of reference 5 reference sequences (excluding reference #3, which is displayed in Figure 1). The error rate for each type of error (insertions, deletions, mismatches and ambiguous base calls) is presented as a function of the sequence position (x-axis) and specific position on the y-axis. The position and length of homopolymers for each base is given on the x-axis to facilitate interpretation (green: A, red: T, black: G, blue: C). (PDF 265 KB)

Published
2020
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36. Biocontrôle: Éléments pour une protection agroécologique des cultures

Author

Fauvergue, Xavier, Rusch, Adrien, Barret, Matthieu, Bardin, Marc, Jacquin-Joly, Emmanuelle, Malausa, Thibaut, Lannou, Christian, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), 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 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), Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Département Santé des Plantes et Environnement (DPT SPE)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract

National audience; Protéger les cultures par des moyens naturels est une nécessité pour la transition vers une agriculture respectueuse de l’environnement. Un effort de recherche et développement sans précédent est aujourd’hui mis en œuvre dans le domaine du biocontrôle, qui rassemble des approches basées sur l’usage d’organismes vivants et de produits d’origine biologique. Cet ouvrage en présente un panorama exhaustif et en explique les fondements théoriques et les applications pratiques. L’histoire du biocontrôle débute à la fin du XIXe siècle avec les premiers travaux sur la lutte biologique, qui utilise les ennemis naturels des insectes nuisibles. Puis les progrès scientifiques en écologie, en génomique, en modélisation, vont étendre les possibilités. On cherche maintenant à reconstruire des équilibres biologiques à l’échelle des paysages cultivés. En manipulant leur sens olfactif, on attire les insectes dans un piège, ou on brouille la piste qui les conduit au partenaire sexuel. En étudiant le microbiote végétal, on espère améliorer la santé des plantes. On découvre également que certaines molécules synthétisées par des microorganismes ou par des végétaux sont utilisables en biocontrôle. Réalisée par des chercheurs de réputation internationale, cette synthèse très complète s’adresse à un public professionnel, mais aussi à tout lecteur désireux de s’informer sur la révolution agroécologique de l’agriculture.

Published
2020

39. Biocontrôle

Author

Fauvergue, Xavier, Rusch, Adrien, Barret, Matthieu, Bardin, Marc, Jacquin-Joly, Emmanuelle, Malausa, Thibaut, Lannou, Christian, and ProdInra, Migration

Subjects
[SDV.SA] Life Sciences [q-bio]/Agricultural sciences, [SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract

Protéger les cultures par des moyens naturels est une nécessité pour la transition vers une agriculture respectueuse de l’environnement. Un effort de recherche et développement sans précédent est aujourd’hui mis en œuvre dans le domaine du biocontrôle, qui rassemble des approches basées sur l’usage d’organismes vivants et de produits d’origine biologique. Cet ouvrage en présente un panorama exhaustif et en explique les fondements théoriques et les applications pratiques. L’histoire du biocontrôle débute à la fin du XIXe siècle avec les premiers travaux sur la lutte biologique, qui utilise les ennemis naturels des insectes nuisibles. Puis les progrès scientifiques en écologie, en génomique, en modélisation, vont étendre les possibilités. On cherche maintenant à reconstruire des équilibres biologiques à l’échelle des paysages cultivés. En manipulant leur sens olfactif, on attire les insectes dans un piège, ou on brouille la piste qui les conduit au partenaire sexuel. En étudiant le microbiote végétal, on espère améliorer la santé des plantes. On découvre également que certaines molécules synthétisées par des microorganismes ou par des végétaux sont utilisables en biocontrôle. Réalisée par des chercheurs de réputation internationale, cette synthèse très complète s’adresse à un public professionnel, mais aussi à tout lecteur désireux de s’informer sur la révolution agroécologique de l’agriculture.

Published
2020

40. Additional file 1 of Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

Author

Gilles, André, Meglécz, Emese, Pech, Nicolas, Ferreira, Stéphanie, Malausa, Thibaut, and Jean-François Martin

Abstract

Additional file 1: Number of sequences to correct erroneous positions. 1a: this file illustrates the number of sequences necessary to obtain a majority of correct sequences. The x-axis shows the error rate and the y-axis shows the number of sequences needed, according to three possible probabilities: 0.001 0.01 and 0.05. 1b the x-axis shows the error rate for a given position (ranging from 0 to 0.5); the y-axis shows the cumulative proportion of erroneous sequences sampled (ranging from 0 to 0.5) in the total sample. Sample size varies from 10 to 100, 500 and 1,000 sequences. For a given error rate and a cumulative proportion of erroneous sequences in the sample of size N, the probability of observing this combination is indicated in color: green: 1 to 0.95, blue: 0.95 to 0.8, yellow: 0.8 to 0.6, orange: 0.6 to 0.5, red: 0.5 to 0.4, gray: 0.4 to 0.2 and white: below 0.2. For example, if the error rate is 0.2, the probability of observing a cumulative proportion of erroneous sequences in the sample of between 0 and 0.2 ranges between 0.4 and 0.5 (red envelope). In this case, the probability of there being 20% erroneous sequences in the sample is between 0.4 and 0.5. If we consider the same error rate (0.2) with 40% erroneous sequences, then the probability ranges from 0.8 to 0.95 (blue envelope). If N increases, the variance of the probability envelopes decreases. (PDF 5 MB)

Published
2020
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41. Consistent variations in personality traits and their potential for genetic improvement of biocontrol agents: Trichogramma evanescens as a case study

Author

Louâpre Philippe, Calcagno Vincent, Dechaume-Moncharmont François-Xavier, Malausa Thibaut, Belliard Jean, Lartigue Silène, Jeandroz Louise, Groussier Géraldine, Moreau Jérôme, Caravel Claire, Yalaoui Myriam, Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF), AgroParisTech, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
2. Zero hunger, 0106 biological sciences, biology, Boldness, business.industry, media_common.quotation_subject, Biological pest control, Trichogramma evanescens, Heritability, Fecundity, Affect (psychology), biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Biotechnology, biocontrol, animal personality, Trichogramma, genetic improvement, intraspecific variation, behavioural ecology, behavioural syndrome, genetic correlations, pace-of-life, 010602 entomology, Personality, Big Five personality traits, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, media_common
Abstract

Improvements in the biological control of agricultural pests require improvements in the phenotyping methods used by practitioners to select efficient biological control agent (BCA) populations in industrial rearing or field conditions. Consistent inter-individual variations in behaviour (i.e. animal personality) probably affect BCA efficiency, but have never been taken into account in the development of phenotyping methods, despite having characteristics useful for phenotyping: repeatable (by definition), often heritable, etc. We developed a video-tracking method targeting animal personality traits and evaluated the feasibility of its use for genetic improvement in the BCATrichogramma evanescens, by phenotyping 1,049 individuals from 24 isogenic lines. We found consistent individual variations in boldness, activity and exploration. Personality differences between the 24 isogenic lines suggested a genetic origin of the variations in activity and exploration (broad-sense heritability estimates of 0.06 to 0.11) and revealed a trade-off between exploration and fecundity.

Published
2020

42. Additional file 4 of Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

Author

Gilles, André, Meglécz, Emese, Pech, Nicolas, Ferreira, Stéphanie, Malausa, Thibaut, and Jean-François Martin

Abstract

Additional file 4: Spatial localization of error rate variation. For each error type and the sequence length, the x-axis represents the spatial localization of 454 reads as x-coordinates and the y-axis represents the y-coordinates on the PT plate. The results presented in this additional data file 4 correspond to plates #2 and #3. The strips represent the regions. We display separately the four types of error (insertions, deletions, mismatches and ambiguous base calls) and the length of the generated sequences. Colors represent the ranges of error rates from 0 to 1 (or the length of the sequences from 0 to 500), using a sliding window (see materials and methods). (PDF 550 KB)

Published
2020
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43. Molecular differentiation at nuclear loci in French host races of the European corn borer (Ostrinia nubilalis)

Author

Malausa, Thibaut, Leniaud, Laurianne, Martin, Jean-Francois, Audiot, Philippe, Bourguet, Denis, Ponsard, Sergine, Lee, Siu-Fai, Harrison, Richard G., and Dopman, Erik

Subjects
Molecular genetics -- Research, European corn borer -- Genetic aspects, Divergent evolution -- Research, Plant-pathogen relationships -- Genetic aspects, Biological sciences
Abstract

French populations of the European corn borer consist of two sympatric and genetically differentiated host races. As such, they are well suited to study processes that could be involved in sympatric speciation, but the initial conditions of host-race divergence need to be elucidated. Gene genealogies can provide insight into the processes involved in speciation. We used DNA sequences of four nuclear genes to (1) document the genetic structure of the two French host races previously delineated with allozyme markers, (2) find genes directly or indirectly involved in reproductive isolation between host races, and (3) estimate the time since divergence of the two taxa and see whether this estimate is compatible with this divergence being the result of a host shift onto maize after its introduction into Europe ~500 years ago. Gene genealogies revealed extensive shared polymorphism, but confirmed the previously observed genetic differentiation between the two host races. Significant departures from the predictions of neutral molecular evolution models were detected at three loci but were apparently unrelated to reproductive isolation between host races. Estimates of time since divergence between French host races varied from ~75,000 to ~150,000 years, suggesting that the two taxa diverged recently but probably long before the introduction of maize into Europe.

Published
2007

48. Propositions pour un programme prioritaire de recherche. Cultiver et protéger autrement

Author

Jacquet, Florence, Huyghe, Christian, Barouki, Robert, Barraquand, Frédéric, Bertrand, Cédric, Côte, François, Cravedi, Jean-Pierre, Fontaine, Laurence, Jeuffroy, Marie-Helene, Labarthe, Pierre, Lebeau, Frédéric, Le Cadre, Edith, Lesprit, Emmanuel, Litrico, Isabelle, Malausa, Thibaut, Profizi, Camille, Reboud, Xavier, Roth, Chris, Vissac, Philippe, Watteyne, Thomas, Marchés, Organisations, Institutions et Stratégies d'Acteurs (UMR MOISA), 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 de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-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), Services déconcentrés d'appui à la recherche Nouvelle-Aquitaine-Poitiers, Institut National de la Recherche Agronomique (INRA), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université de Perpignan Via Domitia (UPVD), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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 Technique de l'Agriculture Biologique (ITAB), Agronomie, AgroParisTech-Institut National de la Recherche Agronomique (INRA), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Union Française des Semenciers (UFS), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), 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), Agrauxine, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Association de Coordination Technique Agricole (ACTA), Wireless Networking for Evolving & Adaptive Applications (EVA), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), inra, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM)

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, santé des plantes et environnement, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SHS]Humanities and Social Sciences
Published
2019
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49. Propositions pour un programme prioritaire de recherche. Cultiver et protéger autrement - Rapport d’étape

Author

Jacquet, Florence, Huyghe, Christian, Barouki, Robert, Barraquand, Frédéric, Bertrand, Cédric, Cote, Francois, Cravedi, Jean Pierre, Fontaine, Laurence, Jeuffroy, Marie-Helene, Labarthe, Pierre, Lebeau, Frédéric, Le Cadre-Barthélemy, Edith, Lesprit, Emmanuel, Litrico-Chiarelli, Isabelle, Malausa, Thibaut, Profizi, Camille, Reboud, Xavier, Roth, Chris, Vissac, Philippe, Watteyne, Thomas, ProdInra, Migration, Marchés, Organisations, Institutions et Stratégies d'Acteurs (UMR MOISA), 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)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Services déconcentrés d'appui à la recherche Nouvelle-Aquitaine-Poitiers, Institut National de la Recherche Agronomique (INRA), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université de Perpignan Via Domitia (UPVD), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ToxAlim (ToxAlim), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut Technique de l'Agriculture Biologique (ITAB), Agronomie, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Sol Agro et hydrosystème Spatialisation (SAS), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Union Française des Semenciers (UFS), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Agrauxine, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Association de Coordination Technique Agricole (ACTA), Wireless Networking for Evolving & Adaptive Applications (EVA), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), INRA, ANR, Ministère de l’enseignement supérieur, de la recherche et de l’innovation, Secrétariat général pour l’investissement, 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 (INPT - EI Purpan), Université de Toulouse (UT)-Université de Toulouse (UT), and Les instituts techniques agricoles (Acta)

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [SHS] Humanities and Social Sciences, [SHS]Humanities and Social Sciences
Published
2019

50. Natural enemies of armored scales (hemiptera: diaspididae) and soft scales (hemiptera: coccidae) in chile: molecular and morphological identification

Author

Crochard, Didier, Correa Gutierrez, Margarita, Groussier, Geraldine, Kreiter, Philippe, Roman, Carola, Guerrieri, Emilio, Garonna, Antonio, Malausa, Thibaut, Zaviezo, Tania, and Amouroux, Paul

Subjects
markers, sequence, discovery, encyrtidae, parasitoids, hymenoptera
Abstract

Scale insects (Hemiptera: Sternorrhyncha: Coccomorpha) are key pests of agricultural crops and ornamental plants worldwide. Their populations are difficult to control, even with insecticides, due to their cryptic habits. Moreover, there is growing concern over the use of synthetic pesticides for their control, due to deleterious environmental effects and the emergence of resistant populations of target pests. In this context, biological control may be an effective and sustainable approach. Hymenoptera Chalcidoidea includes natural enemies of scale insects that have been successfully used in many biological control programs. However, the correct identification of pest scale species and their natural enemies is particularly challenging because these insects are very small and highly specialized. Integrative taxonomy, coupling DNA barcoding and morphological analysis, has been successfully used to characterize pests and natural enemy species. In this study, we performed a survey of parasitoids and predators of armored and soft scales in Chile, based on 28S and COI barcodes. Fifty-three populations of Diaspididae and 79 populations of Coccidae were sampled over the entire length of the country, from Arica (18 degrees S) to Frutillar (41 degrees S), between January 2015 and February 2016. The phylogenetic relationships obtained by Bayesian inference from multilocus haplotypes revealed 41 putative species of Chalcidoidea, five Coccinellidae and three Neuroptera. Species delimitation was confirmed using ABGD, GMYC and PTP model. In Chalcidoidea, 23 species were identified morphologically, resulting in new COI barcodes for 12 species and new 28S barcodes for 14 species. Two predator species (Rhyzobius lophantae and Coccidophilus transandinus) were identified morphologically, and two parasitoid species, Chartocerus niger and Signiphora bifasciata, were recorded for the first time in Chile.

Published
2019

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