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Characterization of a Resistance Locus to Coffee Leaf Rust (Hemileia

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Characterization of a Resistance Locus to Coffee Leaf Rust (Hemileia UNIVERSITE MONTPELLIER II SCIENCES ET TECHINIQUES DU LANGUEDOC THESE Présentée pour l‘obtention du titre de Docteur en Sciences de l’Université Montpellier II Formation Doctorale : Biologie Intégrative des Plantes Ecole Doctorale : SIBAGHE – Systèmes Intégrés en Biologie, Agronomie, Géosciences, Hydro sciences et Environnement par Alessandra Ferreira RIBAS Characterization of a resistance locus to coffee leaf rust (Hemileia vastratrix) in coffee trees: genomic organization, diversity and development of tools for functional gene validation Soutenue publiquement devant le jury composé de, Mme Françoise ADAN-BLONDON (INRA), Rapporteur Mme Valérie GEFFROY (INRA), Examinatrice M. Emmanuel DOUZERY (UM2), Examinateur M. Gilles PILATE (INRA), Rapporteur M. Hervé ETIENNE (CIRAD), Co-Directeur de thèse M. Philippe LASHERMES (IRD), Co-Directeur de thèse ABREVIATIONS BAC Bacterial Artificial Chromosome 6-BA: 6-benzylaminopurine CaMV: cauliflower mosaic virus CC Coiled-Coil CGA candidate gene approach CG candidate gene CLR Coffee Leaf Rust CP medium: callus proliferation medium DNA Deoxyribonucleic acid 2,4-D: 2,4-dichlorophenoxyacetic acid ECP medium: embryogenic callus production medium ETI Effector-Triggered Immunity ETS Effector-Triggered Susceptibility GFP Green Fluorescent Protein HR Hypersensitive Response HPTII hygromycin phosphotransferase II i.e. id est Ka non-synonymous substitutions Ks synonymous substitutions LRR Leucine-Rich Repeats LTR Long Terminal Repeat M medium: maturation medium MAMP Microbe-Associated Molecular Pattern MAS market assisted selection NBS Nucleotide-Binding site NPTII Neomycin Phosphotransferase III OD: optical density PAMP Pathogen-Associated Molecular Pattern PCR Polymerase Chain Reaction PEMs: proembryogenic masses PTI PAMP-Triggered Immunity QTL Quantitative-Trait Locus R: regeneration medium RLK Receptor-Like Kinase RLP Receptor-Like Protein SD: standard deviation SNP single nucleotide polymorphism TAIR: the Arabidopsis information resources TIR Toll and Interleukin-1 Receptor SUMMARY LIST OF FIGURES .................................................................................................................... 7 LIST OF TABLES .................................................................................................................... 11 General Introduction ................................................................................................................ 13 CHAPTER I ............................................................................................................................... 14 LITERATURE REVIEW ......................................................................................................... 14 PART I ....................................................................................................................................... 15 1. Generalities about Coffee ................................................................................................. 15 1.1 Coffee consumption, cultivation and economical trade .................................................... 15 1.2 Coffee taxonomy ............................................................................................................... 16 1.3 Characteristics of cultivated coffee species ....................................................................... 19 1.4 Cytological aspects of Coffea ............................................................................................ 22 1.5 Speciation and genome features of C. arabica .................................................................. 22 1.6 Coffee arabica genetic diversity and breeding .................................................................. 23 1.7 Interspecific hybridization and coffee introgression ......................................................... 26 2. Coffee leaf rust: the main coffee disease ............................................................................. 28 2.1 The genus Hemileia ........................................................................................................... 28 2.2 Coffee leaf rust (CLR) symptoms ..................................................................................... 29 2.3 CLR epidemic ................................................................................................................... 31 2.4 Disease Management......................................................................................................... 32 2.4.1 Chemical control ........................................................................................................ 33 2.4.2 Biological control ....................................................................................................... 33 2.5.1 CLR resistance genes ................................................................................................. 35 2.5.2 Physiological races of Hemileia vastatrix .................................................................. 36 3. Identification of molecular markers associated to CLR .................................................... 39 3.1 Partial resistance to CLR ................................................................................................... 41 PART II ...................................................................................................................................... 42 1. Mechanisms of disease resistance in plants ..................................................................... 42 1.1 Non host resistance............................................................................................................ 42 1.1.1 PAMP/MAMP-triggered immunity (PTI/MTI) ......................................................... 44 1.2 Host resistance (Effector-Triggered Immunity (ETI)) ...................................................... 45 2. Modes of plant-pathogen interaction ............................................................................... 49 2.1 Direct Interaction .............................................................................................................. 49 2.2 The Guard Model (indirect R-Avr) interactions ................................................................ 50 2.3 Decoy model ..................................................................................................................... 51 3. Avirulence genes (effectors) .............................................................................................. 53 4. Resistance Genes (R genes) ............................................................................................... 54 4.1 Classes of Resistance Gene ............................................................................................... 58 4.1.1 RLP and RLK class of R genes .................................................................................. 58 4.2.1 The function of main domains in NB-LRR proteins .................................................. 61 5. How NBS-LRR proteins recognize pathogens and activate defense responses? ......... 66 6. Expression of R proteins ................................................................................................... 67 7. Plant-pathogen co evolution ............................................................................................. 68 7.1 Evolution of R genes at plant population level ................................................................. 68 7.2 Evolutionary patterns R genes clusters ............................................................................. 71 8. Wide genome analysis of NBS-LRR encoding genes ...................................................... 72 8.1 Organization of NBS-LRR genes into plant genomes ...................................................... 75 9. Mechanisms of R-genes diversification ........................................................................... 77 9.1 Duplication ........................................................................................................................ 79 9.1.1 Duplication by polyploidization ................................................................................. 79 9.2 Sequence recombination ................................................................................................... 81 9.3 Selection ............................................................................................................................ 82 9.4 Other mechanisms that contributed to generate R gene diversification ............................ 84 10. Patterns of R gene function .......................................................................................... 86 11. Comparative analysis of R genes ................................................................................. 88 PART III .................................................................................................................................... 91 1. Identification of candidate genes...................................................................................... 91 1.1 Identification of CG genes based on genomic synteny ..................................................... 91 1.2 Identification of CG using positional cloning strategy ..................................................... 93 2. Functional validation of CG ............................................................................................. 95 2.1 RNA interference .............................................................................................................. 95 2.2
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