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Coffea Arabica L.) À La Rouille (Hemileia Vastatrix

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Coffea Arabica L.) À La Rouille (Hemileia Vastatrix MINISTERE DE L’AGRICULTURE ET DE LA PÊCHE CENTRE INTERNATIONAL D’ETUDES SUPERIEURES EN SCIENCES AGRONOMIQUES - MONTPELLIER SUP AGRO - THÈSE Présentée pour l‘obtention du titre de DOCTEUR EN SCIENCES École doctorale: Biologie des Systèmes Intégrés, Agronomie et Environnement Spécialité: Ressources Phytogénétiques et Interactions Biologiques Par MAHÉ Laetitia Titre de la thèse Contribution à l'amélioration génétique de la résistance des caféiers (Coffea arabica L.) à la rouille (Hemileia vastatrix) De l'étude des hybrides interspécifiques naturels de Nouvelle-Calédonie à la cartographie d'un locus de résistance Soutenue le mardi 9 janvier 2007 devant le jury composé de Rapporteur Véronique LEBFÈVRE, Directeur de Recherche, INRA Avignon Rapporteur Daniel PRAT, Professeur, Université Claude Bernard Lyon 1 Examinateur Claire NEEMA, Professeur, INA/PG laboratoire de pathologie végétale Examinateur André CHARRIER, Professeur, SupAgro de Montpellier Examinateur Michel DELSENY, Directeur de Recherche, CNRS Perpignan Directeur de thèse Philippe LASHERMES, Directeur de Recherche, IRD Montpellier Remerciements - A Philippe Lashermes, pour son soutien durant ces trois années de recherche, son encadrement, nos discussions scientifiques, pour m’avoir permis de me rendre à des conférences et présenter mon travail de recherche. Je lui suis infiniment reconnaissante pour avoir partagé ses connaissances, son expérience, et pour sa disponibilité. - A Daniel Le Pierrès, pour m’avoir appris la biologie des caféiers et à reconnaître les hybrides interspécifiques de Nouvelle-Calédonie. - A Marie-Christine Combes, l’arme secrète de cette équipe qui porte sur ses épaules la matière de tous projets, qui m’a apportée aide et amitié. Marie-Christine ne fait pas partie de l’organigramme des officiels de la thèse mais sa présence, son investissement ont fait beaucoup pour mon travail. - A l’ensemble des personnes de l’équipe de Véronique Lefebvre de l’INRA d’Avignon et en particulier à Patrick Signoret pour son aide précieuse. - Aux membres de l’équipe de Nouvelle-Calédonie pour leur investissement et leur financement. J’y associe Vitor Varzéa du CIFC du Portugal, grâce à lui l’évaluation des plantes à la rouille a été possible. - Aux membres de l’équipe « résistance des plantes », notamment, Michel Nicole, Diana Fernandez, Benoît Bertrand, Philippe Marmey, Anne-Sophie Petitot, Anne-Claire Lecouls, Agnès Galzi, Sylvie Pounhet et Claire Guilhaumon pour les moments de détente ou de travail que nous avons partagés. - Et, quelque soit l’humeur du jour pendant ces trois années, étaient présents: Myriam R. (pour l’aide à la bibliographie)., Juan-Carlos, Elijha, Sorho, Romain, Arnaud, Myriam C (pour les chocolats), Christine, Laurence, Valérie, Léandro, Edgardo. - Aux membres de la petite entreprise: l’association CONTACT avec lesquels nombre de projets se sont montés. - A ma famille pour son soutien. - Enfin je dédie ce travail à celui qui m’a permis de réaliser cette thèse et qui m’a accompagné et soutenu chaque jour: Hervé Masson. Avant-Propos_______________________________________________________________ 6 CHAPITRE I Revue bibliographique ____________________________________________ 9 1 LE CAFEIER ___________________________________________________________ 10 1.1 Les caféiers : une grande famille_________________________________________________10 1.1.1 Phylogénie des caféiers du genre Coffea_______________________________________10 1.1.2 Caractéristique et origine des caféiers_________________________________________10 1.2 C. arabica, génétique et amélioration _____________________________________________12 1.2.1 Les ressources génétiques chez C. arabica _____________________________________13 1.2.2 Les ressources génétiques chez les espèces diploïdes_____________________________13 1.2.3 Les hybrides interspécifiques _______________________________________________14 1.3 Les objectifs de l’amélioration __________________________________________________14 2 LA RESISTANCE A LA ROUILLE ORANGÉE______________________________ 15 2.1 Biologie et physiologie des rouilles orangée du caféier _______________________________16 2.1.1 Le genre Hemileia vastatrix ________________________________________________16 2.1.2 Caractérisation de la résistance du caféier à la rouille orangée ______________________17 2.2 La lutte contre la rouille _______________________________________________________18 2.2.1 La lutte chimique_________________________________________________________18 2.2.2 Les sources de résistance naturelles et artificielles _______________________________18 2.2.3 Les recherches génétiques sur la résistance à la rouille____________________________20 3 POLYPLOIDIE ET INTROGRESSION _____________________________________ 21 3.1 Les polyploïdes ______________________________________________________________21 3.1.1 Généralités sur les polyploïdes ______________________________________________21 3.1.2 Formation des polyploïdes _________________________________________________21 3.2 L’hybridation introgressive comme source de diversité _______________________________23 3.2.1 L’introgression entre espèces _______________________________________________24 3.2.2 L’introgression entre C. arabica et les espèces diploïdes __________________________24 4 COMPARAISON DES GENOMES _________________________________________ 27 4.1 La comparaison des génomes ___________________________________________________27 4.2 L’histoire des études comparatives _______________________________________________28 4.3 Le synténie : implications et utilisations ___________________________________________29 4.3.1 Evolution de la structure des génomes ________________________________________29 4.3.2 Connaissance sur l’évolution des génomes _____________________________________30 4.3.3 Amélioration de la cartographie génétique et physique ___________________________30 4.3.4 Clonage d’un gène par utilisation de l’orthologie ________________________________31 4.4 De nouvelles plantes modèles pour la synténie______________________________________32 4.4.1 Synténie entre la tomate et Arabidopsis _______________________________________32 4.4.2 Utilisation de la cartographie comparée pour le clonage de gène de résistance _________33 4.4.3 Les défis de la génomique comparative _______________________________________36 5 LES OBJECTIFS DU TRAVAIL DE RECHERCHE __________________________ 37 CHAPITRE II _____________________________________________________________ 39 6 Introgressive hybridization between the allotetraploid Coffea arabica and one of its diploid ancestors C. canephora in an exceptional sympatric zone in New Caledonia_____ 41 6.1 Abstract ____________________________________________________________________41 6.2 Introduction_________________________________________________________________41 6.3 Materials and Methods ________________________________________________________43 6.3.1 Sampling _______________________________________________________________43 6.3.2 Determination of nuclear DNA content _______________________________________43 6.3.3 AFLP assay _____________________________________________________________43 6.3.4 Microsatellite assay_______________________________________________________44 6.3.5 DNA chloroplast identification ______________________________________________44 6.3.6 Data analysis ____________________________________________________________44 6.4 Results_____________________________________________________________________45 6.4.1 Molecular authentication of interspecific hybrid plants collected in New Caledonia _____45 6.4.2 Gene flow between C. arabica and C. canephora _______________________________47 3 6.4.3 Genetic variation of hybrid plants____________________________________________48 6.5 Discussion __________________________________________________________________48 7 A new source of resistance against coffee leaf rust from New-Caledonian natural interspecific hybrids between Coffea arabica and C. canephora _____________________ 54 7.1 Abstract ____________________________________________________________________54 7.2 Introduction_________________________________________________________________54 7.3 Materials and methods ________________________________________________________55 7.3.1 Plant material ___________________________________________________________55 7.3.2 Molecular marker analysis _________________________________________________56 7.3.3 Rust inoculation test ______________________________________________________56 7.4 Results and discussion_________________________________________________________57 CHAPITRE III ____________________________________________________________ 59 8 Development of sequence characterized DNA markers linked to leaf rust (Hemileia vastatrix) resistance in coffee (Coffea arabica L.) _________________________________ 61 8.1 Abstract ____________________________________________________________________61 8.2 Introduction_________________________________________________________________61 8.3 Materials and methods ________________________________________________________63 8.3.1 Plant material ___________________________________________________________63 8.3.2 Evaluation of rust resistance ________________________________________________64 8.3.3 Development of SCARs from AFLP markers___________________________________64 8.3.4 BAC library analysis ______________________________________________________65 8.3.5 Analysis of SCAR and SSR markers__________________________________________65 8.4 Results_____________________________________________________________________66
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