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Youssef ABU AHMAD Diversité Génétique Et Variabilité Du Pouvoir

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Youssef ABU AHMAD Diversité Génétique Et Variabilité Du Pouvoir ÉCOLE NATIONALE SUPERIEURE AGRONOMIQUE DE MONTPELLIER THESE Pour obtenir le grade de DOCTEUR De l’École Nationale Supérieure Agronomique de Montpellier Discipline : Biologie des organismes École Doctorale : Biologie des Systèmes Intégrés, Agronomie-Environnement (BSIAE) Présentée et soutenue publiquement Par Youssef ABU AHMAD Le 22 septembre 2006 Titre : Diversité génétique et variabilité du pouvoir pathogène du Sugarcane yellow leaf virus, agent causal de la feuille jaune de la canne à sucre JURY M. Jean-Loup NOTTEGHEM Président du jury Mme Véronique BRAULT Rapporteur M. Olivier LEGALL Rapporteur M. Emmanuel JACQUOT Examinateur M. Philippe ROTT Directeur de thèse Avant propos Tout d'abord, je tiens à préciser que c’est avec beaucoup de reconnaissance et une émotion certaine que j'ai tracé ce parcours de thèse avec des travaux de recherche, des collaborations et des découvertes au sein du Cirad à Montpellier, à la Réunion et en Guadeloupe, ainsi que de l’UMR BGPI à Montpellier. En premier lieu, c'est grâce à Philippe ROTT, mon directeur de thèse, que je me suis lancé dans cette grande aventure. Je le remercie très particulièrement de m'avoir proposé, d’avoir encadré et laissé développer ce sujet de cette thèse qu'il m'a confié vers des zones inexplorées, mais aussi pour sa bonne humeur et sa gentillesse, la pertinence de ses réflexions, sa rigueur scientifique et professionnelle, ainsi que pour son optimisme, sa passion, sa détermination et le courage et la grande disponibilité dont il a fait part pendant la rédaction et les heures passées à lire et relire ce manuscrit, et bien d'autres. Je tiens également à remercier Monique ROYER pour son accueil au sein du laboratoire de bactériologie moléculaire et le développement, avec acharnement, de la biologie moléculaire et évolutive du SCYLV, ainsi que pour son soutien et sa disponibilité tout au long de ce travail. Un grand merci est adressé à Jean-Claude GIRARD pour son accueil au sein de l’équipe « Quarantaine », pour ses conseils, son aide au repérage des fautes à la lecture de nombreux manuscrits, ainsi que pour le partage de son savoir, son soutien et ses encouragements tout au long de ma thèse. Un grand merci également à Benoît MOURY qui a accepté de me faire partager son expérience de l’étude de l’évolution des virus, ainsi que pour ses conseils enrichissants et utiles. Je remercie Jean-Heinrich DAUGROIS et Laurent COSTET pour leur accueil en Guadeloupe et à La Réunion, et de m'avoir permis de réaliser des expériences uniques à ce jour. Mes remerciements s'adressent aux membres de jury : Madame Véronique BRAULT, Monsieur Olivier LE GALL, Monsieur Jean-Loup NOTTEGHEM et Monsieur Emmanuel JACQUOT qui ont accepté d'évaluer et dejuger le travail présenté dans ce manuscrit. Je remercie Olivier LEMAIRE, Michel PETERSCHMITT, Hervé LECOQ et Ben LOCKHART qui ont participé aux réunions de mon comité de thèse et qui m'ont permis d'élargir ma vision de la virologie végétale. Merci aussi à Gérard LABONNE, Jean-Michel LETT, Samuel NIBOUCHE et Nicolas SAUVION pour leurs conseils, les nombreuses discussions et la mise en place des méthodes d'élevage des pucerons. Je remercie très chaleureusement les membres de l’équipe « Quarantaine canne à sucre » de Montpellier, Michèle CHATENET, Marie-Josée DARROUSSAT, Jean-François BOUSQUET, Emmanuel FERNANDEZ, Rémy HABAS et Marc MULLER, pour la grande sympathie qu’ils m'ont témoignée et leur aide précieuse à la réalisation des essais de phytopathologie, pour les bons moments passés ensemble, les sorties de ski dans les Pyrénées, les matchs de volley, les escalades de l'Hortus et du Pic Saint-Loup! Merci aussi à Philippe LETOURMY pour ses précieux conseils concernant la mise en place des essais expérimentaux et l’analyse statistique des données. Je remercie également les membres de l'UMR BGPI, permanents ou de passage, pour les échanges scientifiques et amicaux durant cette thèse. Un grand merci notamment à Marie-Line CARUANA, Emmanuelle MULLER, Véronique MARIE-JEANE, Stéphane BLANC et Rémy FROISSART pour leur sympathie et leurs bons et précieux conseils en virologie, ainsi qu'à Daniel GARGANI pour les heures passées sous le microscopie électronique et à la purification du SCYLV. Un énorme merci à Philippe GAYRAL pour sa très grande patience dans mon apprentissage au fonctionnement du logiciel PAML. Je tiens à remercier Robert DOMAINGUE et Jean-Loup NOTTEGHEM de m'avoir permis de réaliser cette thèse au sein de leurs unités, ainsi que leur suivi scientifique et administratif. Mes remerciements s'adressent aussi à Rosiane BOISNE-NOC, Sandrine DUPLAN, Nathalie LABOUREAU, Magali PAYET, Isabelle PIERETTI et Steeve JOSEPH pour leur aide précieuse au laboratoire, pour leur bonne humeur et leur amitié. Je n’oublierai pas de remercier Florence BARTHOD, Geneviève BOURELLY, Janine CAMMAL, Dominique HERAULT, Dominique LAGRENEE, Marie-Ange ROGER et Catherine REMONDAT pour leur support administratif, leur bonne humeur et leur amitié. Ma liste est très longue et non exhaustive, mais je pense aussi à tous ceux qui n’ont pas été cités ci-dessus. Pour ne pas faire de jaloux je ne citerai aucun nom mais ils vont certainement se reconnaître. Qu’ils sachent queje les remercie du fond du cœur. Un chaleureux merci à tous les thésards, les stagiaires, les amis, d’ici et d’ailleurs, rencontrés à Montpellier, en Guadeloupe et à la Réunion, pour leur sympathie, leur bonne humeur et le partage de mon quotidien. Enfin un immense merci à mon épouse pour son soutien et sa patience, à mes parents pour leurs encouragements, leur humilité, et leur goût de la vie. Je sais qu’ils sont tous fiers de moi. Ils ! ont toujours été présents, même quand ils étaient loin. Cette thèse a été financée par le gouvernement de la République Arabe de Syrie, ainsi que par le Cirad et la compagnie sucrière Cenicaña en Colombie. Je les remercie bien vivement de m’avoir permis de réaliser ce travail dans les meilleures conditions. TABLE DES MATIERES Avant propos................................................................................................................................................. i TABLE DES MATIERES........................................................................................................................ iii ABREVIATIONS ET ACRONYMES.........................................................................................................vi INTRODUCTION GENERALE............................................................................................................... 1 CHAPITRE 1................................................................................................................................................ 4 Revue bibliographique : ..............................................................................................................................4 Présentation du pathosystème canne à sucre-SCYLV et définition de la problématique................. 4 1. LA CANNE A SUCRE.......................................................................................................................... 5 1.1. Historique..................................................................................................................................5 1.2. Position taxonomique.............................................................................................................. 6 1.3. Morphologie..............................................................................................................................7 1.4. Physiologie et cycle du développement................................................................................7 1.5. Distribution géographique et importance économique...................................................... 9 1.6. Les débouchés de la canne à sucre........................................................................................ 9 1.7. Les principales maladies de la canne à sucre.....................................................................10 ! 2. LA MALADIE DE LA FEUILLE JAUNE DE LA CANNE A SUCRE.....................................11 2.1 Historique et distribution géographique..............................................................................11 2.2 Symptomatologie...................................................................................................................11 2.3. L’agent causal........................................................................................................................12 3. LE SCYLV, SES HOTES ET SES VECTEURS..............................................................................13 3.1. Caractéristiques, structure et expression de génome du SCYLV....................................13 3.2. Structure des virions.............................................................................................................. 15 3.3. Caractéristiques sérologiques...............................................................................................15 3.4. La gamme d’hôtes et les vecteurs du SCYLV...................................................................16 3.5. Histologie et physiopathologie.............................................................................................16 3.6. Impact du SCYLV sur le rendement...................................................................................17 3.7. Dynamique du SCYLV au champ et dans la plante de canne à sucre........................... 18 3.8. Épidémiologie du SCYLV..................................................................................................
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