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Theobroma Cacao L REPUBLIQUE DE CÔTE D’IVOIRE Union-Discipline-Travail Ministère de l’Enseignement Supérieur et de la Recherche Scientifique UFR AGROFORESTERIE THESE DE DOCTORAT ANNEE : 2019-2020 Mention : Agriculture et foresterie tropicale N° D’ORDRE : 024 Spécialité : Microbiologie des sols Isolement et sélection de bactéries endophytes natives du cacaoyer (Theobroma cacao L.) efficientes dans le biocontrôle de Phytophthora spp., agent causal de la pourriture brune des cabosses CANDIDAT Nom : OUATTARA JURY Prénom : Adama Président : M. KONE Tidiani, Professeur Titulaire, Université Jean Lorougnon GUEDE Co-Directeurs : M. KONATE Ibrahim, Maître de Conférences, Université Jean Lorougnon GUEDE M. KEBE Boubacar Ismaël, Directeur de Recherche, Centre National de Recherche Agronomique (CNRA) Rapporteur : M. ALLOU Kouassi, Directeur de Recherche CAMES, Centre National de Recherche Agronomique (CNRA) Examinateurs : M. AKAFFOU Doffou Sélastique, Professeur Titulaire, Soutenue publiquement le : 28 Novembre 2020 Université Jean Lorougnon GUEDE M. CAMARA Brahima, Maître de Conférences, Université Félix HOUPHOUËT-BOIGNY TABLE DES MATIÈRES DEDICACE ...................................................................................................................................... x REMERCIEMENTS ....................................................................................................................... xi SIGLES ET ABREVIATIONS ...................................................................................................... xv LISTE DES TABLEAUX ........................................................................................................... xvii LISTES DES FIGURES................................................................................................................ xix LISTES DES ANNEXES........................................................................................................... xxiii INTRODUCTION ............................................................................................................................ 1 PRÉMIÈRE PARTIE : REVUE BIBLIOGRAPHIQUE ................................................................. 7 Chapitre 1 : Généralités sur le cacaoyer (Theobroma cacao L.) ...................................................... 7 1-1- Origine et historique ................................................................................................................. 7 1-2- Classification botanique et taxonomique .................................................................................. 7 1-2-1- Diversité des cacaoyers ......................................................................................................... 7 1-2-2- Groupes de cacaoyers ............................................................................................................ 8 1-2-2-1- Groupe des Criollo ............................................................................................................. 8 1-2-2-2- Groupe des Forastero amazoniens .................................................................................... 9 1-2-2-3- Groupe des Trinitario ......................................................................................................... 9 1-3- Morphologie et biologie du cacaoyer ..................................................................................... 11 1-3-1- Système racinaire ................................................................................................................ 12 1-3-2- Parties aériennes .................................................................................................................. 13 1-3-2-1- Tronc ................................................................................................................................ 13 1-3-2-2- Feuilles ............................................................................................................................. 13 1-3-2-3- Inflorescences et fleurs .................................................................................................... 13 1-3-2-4- Fruits ............................................................................................................................... 14 i 1-4- Ecophysiologie du cacaoyer ................................................................................................... 14 1-4-1- Exigences climatiques ......................................................................................................... 14 1-4-2- Sols favorables à la cacaoculture ........................................................................................ 15 1-5- Importance de la cacaoculture ................................................................................................ 15 1-5-1- Importance nutritionnelle et médicinale du cacao ............................................................... 15 1-5-2- Importance de la cacaoculture dans l’économie ivoirienne ................................................ 16 1-5-3- Importances écologiques des agroforêts à base de cacaoyers ............................................. 16 1-6- Maladies du cacaoyer ............................................................................................................. 16 1-6-1- Maladies virales ................................................................................................................... 16 1-6-1-1- Swollen shoot ................................................................................................................... 16 1-6-1-2- Nécrose du cacaoyer ........................................................................................................ 19 1-6-1-3- Virus de la mosaïque jaune du cacaoyer .......................................................................... 19 1-6-2- Maladies fongiques ............................................................................................................. 19 1-6-2-1- Balai de sorcière ............................................................................................................... 19 1-6-2-3- Syndrome de dépérissement vasculaire ........................................................................... 24 1-6-2-4- Pourridiés ......................................................................................................................... 26 1-6-2-5- Pourriture brune des cabosses .......................................................................................... 26 Chapitre 2 : Genre Phytophthora ................................................................................................... 27 2-1- Taxonomie .............................................................................................................................. 27 2-1-1- Règne ................................................................................................................................... 27 2-1-2- Ordre des Pythiales .............................................................................................................. 27 2-1-3- Genre Phytophthora ............................................................................................................ 28 2-2- Cycle biologique du genre Phytophthora .............................................................................. 30 2-3- Mode de pénétration du genre Phytophthora dans les organes du cacaoyer .......................... 32 ii 2-4- Espèces du genre Phytophthora sur le cacaoyer .................................................................... 32 2-5- Symptômes de la pourriture brune .......................................................................................... 32 2-6- Méthodes de lutte .................................................................................................................... 35 2-6-1- Mise en quarantaine du matériel végétal ............................................................................. 35 2-6-2- Lutte agronomique .............................................................................................................. 35 2-6-3- Lutte chimique ..................................................................................................................... 36 2-6-4- Lutte génétique .................................................................................................................... 38 2-6-5- Lutte biologique .................................................................................................................. 39 Chapitre 3 : Généralités sur les bactéries endophytes .................................................................... 41 3-1- Diversité microbienne du sol .................................................................................................. 41 3-2- Rhizosphère ............................................................................................................................ 41 3-3- Bactéries endophytes .............................................................................................................. 42 3-3-1- Bactéries endophytes symbiotiques .................................................................................... 42 3-3-1-1- Genre Frankia .................................................................................................................. 43 3-3-1-2- Rhizobia ........................................................................................................................... 43 3-3-2- Diversité des bactéries endophytes associatives ................................................................
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