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2. Monitoring of Venturia inaequalis harbouring the QoI resistance G143A mutation in French orchards as revealed by PCR assays

Author

Fontaine, Séverine, Remuson, Florent, Fraissinet-Tachet, Laurence, Marmeisse, Roland, Melayah, Delphine, DRAF-SRPV Rhône Alpes, Ministère de l'Agriculture et de la Pêche, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-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), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS )

Subjects
molecular diagnostics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, allele-specific PCR, apple scab, QoI, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [ SDV.MP.MYC ] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Venturia inaequalis, fungicide resistance
Abstract

International audience; BACKGROUND:Genetic resistance to QoI fungicidesmay account for recent failures tocontrol Venturia inaequalis (Cooke) Winter in French orchards. Two PCR-based assays were developed to detect the G143A point mutation in the fungal mitochondrial cytochrome b gene. The mutation is known to confer a high level of resistance to QoI fungicides. Occurrence of the G143A mutation in French field isolates collected from 2004 to 2007 wasmonitored. RESULTS: The QoI-resistant cytochrome b allele was specifically detected either following the cleavage of the amplified marker by a restriction endonuclease (CAPS assay) or its amplification using an allele-specific PCR primer. Using either method, the G143A mutation was found in 42% of the 291 field samples originating from French orchards in which apple scab proved difficult to be controlled. Monitoring of the G143A mutation in orchards located in 15 French administrative regions indicated that the mutation was detected at least once in nine of the regions, and its presence ranged from 33% to 64% of the orchards analysed in 2004 and in 2007 respectively. CONCLUSION: The PCR-basedmethods developed in this study efficiently reveal the presence of the G143A mutation in French V. inaequalis field populations.

Published
2008
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3. A tale of four stories: soil ecology, theory, evolution and the publication system

Author

Pascal Jouquet, Sébastien Barot, Jérôme Mathieu, Manuel Blouin, Jean-Christophe Lata, Sébastien Fontaine, Biodiversité et fonctionnement du sol (BIOSOL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Department of Zoology, Oregon State University (OSU), Biologie et écologie tropicale et méditerranéenne [2007-2010] (BETM), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), DRAF-SRPV Rhône Alpes, Ministère de l'Agriculture et de la Pêche, Unité d'Agronomie de Clermont Ferrand, Institut National de la Recherche Agronomique (INRA), Laboratoire de Physique et Mécanique Textiles (LPMT), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biogéochimie et écologie des milieux continentaux (Bioemco), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Laboratoire Ecologie et évolution, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Supported by the programme ‘‘jeune chercheur 2005' of the ANR (SolEcoEvo project, JC05_52230), ANR-05-JCJC-0189,SolEcoEvo,Vers une écologie évolutive des sols : évolution de la relation faune du sol - plante(2005), Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Perpignan Via Domitia (UPVD), ENSITM-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École normale supérieure - Paris (ENS Paris), Biologie et écologie tropicale et méditerranéenne (BETM), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-ENSITM-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-ENSITM-Matériaux et nanosciences d'Alsace (FMNGE), Lata, Jean-Christophe, Jeunes chercheuses et jeunes chercheurs - Vers une écologie évolutive des sols : évolution de la relation faune du sol - plante - - SolEcoEvo2005 - ANR-05-JCJC-0189 - JCJC - VALID, and Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-ENSITM-Matériaux et Nanosciences Grand-Est (MNGE)

Subjects
0106 biological sciences, BIBLIOMETRIE, Biodiversité et Ecologie, Applied ecology, Ecology (disciplines), PEDOLOGIE, lcsh:Medicine, RECHERCHE SCIENTIFIQUE, Biology, Theoretical ecology, 010603 evolutionary biology, 01 natural sciences, Biodiversity and Ecology, Soil, Ecology/Evolutionary Ecology, Systems ecology, Soil ecology, lcsh:Science, Publishing, Functional ecology, Multidisciplinary, Ecology, lcsh:R, Environmental ethics, 04 agricultural and veterinary sciences, 15. Life on land, MODELISATION, Biological Evolution, EVOLUTION, Quantitative ecology, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Ecology/Theoretical Ecology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, lcsh:Q, BIBLIOGRAPHIE, Evolutionary ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology/Ecosystem Ecology, ECOLOGIE, METHODOLOGIE, Research Article
Abstract

International audience; BACKGROUND: Soil ecology has produced a huge corpus of results on relations between soil organisms, ecosystem processes controlled by these organisms and links between belowground and aboveground processes. However, some soil scientists think that soil ecology is short of modelling and evolutionary approaches and has developed too independently from general ecology. We have tested quantitatively these hypotheses through a bibliographic study (about 23000 articles) comparing soil ecology journals, generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. FINDINGS: We have shown that soil ecology is not well represented in generalist ecology journals and that soil ecologists poorly use modelling and evolutionary approaches. Moreover, the articles published by a typical soil ecology journal (Soil Biology and Biochemistry) are cited by and cite low percentages of articles published in generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. CONCLUSION: This confirms our hypotheses and suggests that soil ecology would benefit from an effort towards modelling and evolutionary approaches. This effort should promote the building of a general conceptual framework for soil ecology and bridges between soil ecology and general ecology. We give some historical reasons for the parsimonious use of modelling and evolutionary approaches by soil ecologists. We finally suggest that a publication system that classifies journals according to their Impact Factors and their level of generality is probably inadequate to integrate "particularity" (empirical observations) and "generality" (general theories), which is the goal of all natural sciences. Such a system might also be particularly detrimental to the development of a science such as ecology that is intrinsically multidisciplinary.

Published
2007
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4. Ostrinia nubilalis parasitism and the field abundance of non-target insects in transgenic Bacillus thuringiensis corn ( Zea mays )

Author

Carine Pagliari, Denis Bourguet, Annie Micoud, Bernard Naïbo, Marc Delos, Josette Chaufaux, Nathalie Eychenne, Fany Bombarde, Gilles Marque, Centre de Biologie pour la Gestion des Populations (UMR CBGP), 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), Unité de recherches en Lutte biologique, Institut National de la Recherche Agronomique (INRA), DRAF-SRPV Rhône Alpes, Ministère de l'Agriculture et de la Pêche, SRPV Midi-Pyrénnées, Partenaires INRAE, and FREDEC Midi-Pyrénées

Subjects
0106 biological sciences, Insecta, predators, Population Dynamics, Ostrinia nubilalis, Metopolophium dirhodum, 01 natural sciences, Ostrinia, Rhopalosiphum padi, Hemolysin Proteins, Sitobion avenae, Aphididae, Bacillus thuringiensis, Chrysoperla carnea, Lydella thompsoni, Safety, Risk, Reliability and Quality, Syrphus corollae, General Environmental Science, 2. Zero hunger, education.field_of_study, biology, Plants, Genetically Modified, [SDE]Environmental Sciences, Seasons, Safety, General Agricultural and Biological Sciences, Safety Research, Biotechnology, Coccinella septempunctata, Population, Bacterial Toxins, Biomedical Engineering, Insect Control, Risk Assessment, Zea mays, Orius insidiosus, Bacterial Proteins, Animals, non-target insects, education, Genetically modified maize, Bacillus thuringiensis Toxins, Pseudoperichaeta nigrolineata, transgenic corn, biology.organism_classification, parasitoids, Endotoxins, 010602 entomology, Agronomy, 010606 plant biology & botany
Abstract

International audience; In this study, we evaluated in field trials the effects on non-target species, of transgenic corn producing the Cry1Ab toxin of Bacillus thuringiensis (Bt). In 1998, we collected Ostrinia nubilalis (Hübner) larvae from transgenic Bt corn (Novartis Hybrid 176) and non-Bt corn at four geographical sites. We found a significant variation in parasitism by the tachinids Lydella thompsoni (Herting) and Pseudoperichaeta nigrolineata (Walker) among sites, and more parasitism in non-Bt than in Bt fields. The Bt effect did not vary significantly among fields. In 1999, we performed a field experiment at two sites, comparing the temporal abundance of non-target arthropods in Bt corn (Monsanto Hybrid MON810) and non-Bt corn. The non-target insects studied included the aphids Metopolophium dirhodum (Walker), Rhopalosiphum padi (L.) and Sitobion avenae (F.), the bug Orius insidiosus (Say), the syrphid Syrphus corollae (Meigen), the ladybird Coccinella septempunctata (L.), the lacewing Chrysoperla carnea (Stephens), thrips and hymenopteran parasitoids. For all species but one, the number of individuals varied greatly over the season but did not differ between the types of corn. The only exception was thrips which, at one site, was significantly more abundant in Bt corn than in non-Bt corn. However this difference did not remain significant when we took the multiple tests into account. Implications for pest resistance management, population dynamics and risk assessment are discussed.

Published
2002
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5. Monitoring of Venturia inaequalis harbouring the QoI resistance G143A mutation in French orchards as revealed by PCR assays.

Author

Fontaine S, Remuson F, Fraissinet-Tachet L, Micoud A, Marmeisse R, and Melayah D

Subjects
Alleles, Base Sequence, Cytochromes b genetics, France, Mutation, Polymerase Chain Reaction, Time Factors, Drug Resistance, Fungal, Fungi drug effects, Fungi genetics, Fungicides, Industrial pharmacology, Malus microbiology
Abstract

Background: Genetic resistance to QoI fungicides may account for recent failures to control Venturia inaequalis (Cooke) Winter in French orchards. Two PCR-based assays were developed to detect the G143A point mutation in the fungal mitochondrial cytochrome b gene. The mutation is known to confer a high level of resistance to QoI fungicides. Occurrence of the G143A mutation in French field isolates collected from 2004 to 2007 was monitored., Results: The QoI-resistant cytochrome b allele was specifically detected either following the cleavage of the amplified marker by a restriction endonuclease (CAPS assay) or its amplification using an allele-specific PCR primer. Using either method, the G143A mutation was found in 42% of the 291 field samples originating from French orchards in which apple scab proved difficult to be controlled. Monitoring of the G143A mutation in orchards located in 15 French administrative regions indicated that the mutation was detected at least once in nine of the regions, and its presence ranged from 33% to 64% of the orchards analysed in 2004 and in 2007 respectively., Conclusion: The PCR-based methods developed in this study efficiently reveal the presence of the G143A mutation in French V. inaequalis field populations.

Published
2009
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