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Caractérisation Génétique De Phytophthora Alni Brasier & S.A Caractérisation génétique de Phytophthora alni Brasier & S.A. Kirk, hybride interspécifique agent du dépérissement de l’aulne en Europe Renaud Ioos To cite this version: Renaud Ioos. Caractérisation génétique de Phytophthora alni Brasier & S.A. Kirk, hybride interspé- cifique agent du dépérissement de l’aulne en Europe. Sciences de la Terre. Université Henri Poincaré - Nancy 1, 2006. Français. NNT : 2006NAN10105. tel-01754315 HAL Id: tel-01754315 https://hal.univ-lorraine.fr/tel-01754315 Submitted on 30 Mar 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. AVERTISSEMENT Ce document est le fruit d'un long travail approuvé par le jury de soutenance et mis à disposition de l'ensemble de la communauté universitaire élargie. Il est soumis à la propriété intellectuelle de l'auteur. Ceci implique une obligation de citation et de référencement lors de l’utilisation de ce document. D'autre part, toute contrefaçon, plagiat, reproduction illicite encourt une poursuite pénale. Contact : [email protected] LIENS Code de la Propriété Intellectuelle. articles L 122. 4 Code de la Propriété Intellectuelle. articles L 335.2- L 335.10 http://www.cfcopies.com/V2/leg/leg_droi.php http://www.culture.gouv.fr/culture/infos-pratiques/droits/protection.htm Faculté des Sciences V.F.R. Sciences et Techniques Biologiques Ecole Doctorale Ressources Procédés Produits Environnement Département de Formation Doctorale Sciences Agronomiques et Forestières, Biologie et Ecologie, Biotechnologie Thèse Présentée pour l'obtention du titre de Docteur de l'Université Henri Poincaré, Nancy 1 en Biologie Végétale et Forestière par Renaud 100S Caractérisation génétique de Phytophthora alni Brasier & S.A. Kirk, hybride interspécifique agent du dépérissement de l'aulne en Europe Soutenue publiquement le 6 novembre 2006 devant la commission d'examen M. Franck PANABIERES Directeur de Recherche, INRA Sophia-Antipolis Rapporteur M. Jean-Loup NOTTEGHEM Professeur, ENSAMlINRA Montpellier Rapporteur M. Pierre LEBLOND Professeur, Université Henri Poincaré, Nancy l Président du Jury Mme Anne CHANDELIER Attachée Scientifique, CRA Gembloux (Belgique) Examinatrice M. Pascal FREY Chargé de Recherche, INRA Nancy Examinateur M. Jean PINON Directeur de Recherche, INRA Nancy Directeur de Thèse UMR 1136 INRA!UHP, Interactions Arbres/Microorganismes, Pathologie forestière Centre INRA de Nancy, Champenoux Remerciements Cette thèse a pu être réalisée dans le cadre de laformation complémentaire par la recherche, mis en place pour les corps d'ingénieurs du Ministère de l'Agriculture et de la Pêche. Elle s'est initiée après un premier parcours professionnel de 6 ans à l'Unité de Mycologie Agricole et Forestière du Laboratoire National de la Protection des Végétaux (LNPV-UMAF). Je tiens donc tout d'abord à remercier les personnes qui m'ont permis de saisir cette opportunité: MM Durand et Mathurin, Sous-Directeurs successifs de la Protection des Végétaux à lil Direction Générale de l'Alimentation, Mme Lecoeur, MM Bain et Caffier, en charge de la direction et de l'orientation du LNPV durant ma thèse. Je remercie de même MM Dumont et Bouchot, Directeurs de l'Agriculture et de la Forêt de la région Lorraine d'avoir soutenu la possibilité de formation par la recherche pour l'un de leurs agents. Enfin, je tiens à remercier particulièrement J-D. Bayart, Chef du Service la Protection des Végétaux de Lorraine et P. Loevenbruck, responsable du LNPV-UMAF, de m'avoir permis de m'organiser au mieux matériellement et administrativement afin de me permettre de concilier au mieux mon activité professionnelle au LNPV et mon travail de thèse à l'INRA. Le LNPV-UMAF entretient depuis de longues années de fructueuses relations scientifiques avec l'équipe de pathologie forestière de l'INRA de Champenoux, désormais membre de l'UMR INRAIUHP Nancy l « Interactions Arbres-Microorganismes )~. Cette même équipe, qui m'accueillait déjà ponctuellement lors de travaux de recherche communs, a accepté la charge de m'accueillir pendant trois ans en tant que thésard. La réalisation de cette thèse, conciliant recherche cognitive et appliquée a permis à mon sens de renforcer un peu plus'encore les liens entre les deux institutions autour de la discipline de la mycologie. Je tiens à souligner à cet égard le volontarisme sans faille de Jean Pinon, ancien directeur de l'Unité de Recherche de pathologie forestière et directeur de ma thèse et de Benoît Marçais, actuel responsable de l'équipe. D'un point de vue plus scientifique, mes remerciements vont en premier lieu vers mes deux « mentors» mycologues: Pierre Chandelier, ancien responsable du LNPV-UMAF, pour m'avoir fait découvrir cette discipline complexe par le prisme des objectifs de son microscope et Pascal Frey, chargé de recherche à l'INRA de Champenoux, de m'avoir permis de passer du « côté obscur» pour me/ permettre de traduire les imprononçables noms latins de champignons en jonglant avec seulement quatre lettres de l'alphabet. Pascal a de plus accepté de m'encadrer pendant ces trois années. Je tiens à lui témoigner mon infinie reconnaissance pour son altruisme, sa patience, sa pédagogie, son état d'esprit toujours positifet toutes les autres qualités qui font de lui un encadrant de thèse commeje ne pourrais qu'en souhaiter à tous les étudiants. J'adresse mes remerciements aux membres du jury qui ont bien voulu évaluer mon travail: Mme Chandelier ainsi que MM Leblond, Panabières et Notteghem. Les comités de pilotage ont été par ailleurs des occasions privilégiées quant à l'analyse critique de mes résultats etje tiens à remercier sincèrement les personnes qui ont véritablement contribué à enrichir ce travail passionnant: Yves Brygoo, Franck Panabières, Sylvain Jeandroz, ainsi que Cécile Robin. J'aurai une pensée pour les collègues du LNPV que j'abandonnais à hauteur de 4 jours par semaine et qui l'ont plutôt très bien supporté (c'est plutôt vexant d'ailleurs) et tiens ici à remercier Valérie, Gabriela, et particulièrement Lise et Sylvie, qui ont été, à distance, des collaboratrices d'une efficacité et d'une fiabilité impressionnante. Evidemment, l'ensemble des collègues de l'équipe de pathologieforestière recueillera la plus grosse part de mes remerciements, puisque c'est à elle qu'il a été imposé de me supporter la plupart du temps. J'ai, en compensation, dû supporter le légendaire et mystérieux « café de la patho» pour lesquels les premiers symptômes n'apparaissent parait-il qu'après quelques mois de consommation (çà c'estfait) et un sevrage brutal (çà va être bon aussi). Je profite donc de mes derniers instants de lucidité pour remercier Axelle pour son appui technique lors des manips « high- throughput» (ou plutôt utilisons le terme français de «aillesroupout», puisque cette thèse va tout de même finir peut être à la bibliothèque de France, voire en bonne place dans les rayonnages du bibliobus communal de Champenoux), Claude pour nos tournées de prélèvements dans la jungle Lorraine (interprète très utile lors de nos rencontres avec certains autochtones), Béranger et Olivier pour leur aide technique en serre, et tous les autres collègues de l'équipe de patho pour leur bonne humeur et leur disponibilité: Gilberte, Bénédicte, Marie-Christine et Marie-Claude. Une pensée particulière pour Benoît avec qui j'ai partagé ce bureau si convoité, au carrefour des sons et fragrances du fond du couloir du rez-de­ chaussée (interprétations libres au lecteur), et qui a réussi à démontrer à toutes les pauses café qu'il était possible d'être systématiquement pas d'accord sur tout ou sur rien, tout en affirmant nejamais avoir dit çà. Bon courage enfin à Fabrice pour sa thèse (et pas seulement parce qu'il hérite de notre bureau.. .) et à Fabien qui arrive et quijinira bien par admettre qu'une oogone ornementée çà a quand même plus de classe qu'un vulgaire hémiptère. Mes penséesjinales vont bien sûr à Carole, et à mes deux petites zoospores, Mina et Florica... Sommaire Lexique 3 Introduction 5 1. - L'aulne en Europe 7 1.1. - Les différentes espèces d'aulnes en Europe 7 1.1.1. - L'aulne glutineux 7 1.1.2. - L'aulne blanc 7 1.1.3. - L'aulne vert 7 1.1.4. - L'aulne de Corse 8 1.2. -Intérêts écologiques de l'aulne en Europe 8 2. - Problèmes sanitaires décrits sur l'aulne 9 2.1. - Dommages abiotiques 9 2.2. - Problèmes liés aux maladies ou aux ravageurs 9 2.2.1. - Ravageurs 9 2.2.2. - Dommages d'origine bactérienne 9 2.2.3. - Les maladies cryptogamiques 10 2.3. - Dépérissements d'origine complexe 10 3. - Emergence récente d'une nouvelle maladie sur les aulnes en Europe Il 3.1. - Mise en évidence de dépérissements massifs à travers l'Europe Il 3.2. - Caractéristiques de la maladie 13 3.3. - Une nouvelle espèce de Phytophthora est responsable de cette maladie émergente 13 4. - Etat de l'art sur les caractéristiques de Phytophthora alni agent du dépérissement de l'aulne 14 4.1. - Le Phytophthora de l'aulne est un hybride interspécifique 14 4.1.1. - Le Phytophthora de l'aulne est un complexe de différentes entités 14 4.1.2. - Le Phytophthora de l'aulne de type « standard» : P. alni subsp. alni (Paa) 15 4.1.3. - Les types « variants allemand, anglais et néerlandais)} : P. alni subsp. multiformis (Pam) 15 4.1.4. - Le type « variant suédois)} : P. alni subsp. uniformis (Pau) 16 4.1.5.
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