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Iversidade Técnica De Lisboa Instituto Superior De Agronomia UNIVERSIDADE TÉCNICA DE LISBOA INSTITUTO SUPERIOR DE AGRONOMIA Alternative strategies to fight apple scab Mariana da Silva Gomes Mota ORIENTADOR: Doutora Cristina Maria Moniz Simões Oliveira CO-ORIENTADOR: Doutora Margit Laimer JÚRI: Presidente: Reitor da Universidade Técnica de Lisboa Vogais: Doutora Joana Maria Canelhas Palminha Duclos, professora catedrática do Instituto Superior de Agronomia da Universidade Técnica de Lisboa; Doutora Margit Laimer, professora do Institute of Applied Microbiology da University of Agriculture, Viena, Áustria; Doutora Cristina Maria Moniz Simões Oliveira, professora associada do Instituto Superior de Agronomia da Universidade Técnica de Lisboa; Doutora Maria Luísa Lopes de Castro e Brito, professora auxiliar do Instituto Superior de Agronomia da Universidade Técnica de Lisboa; Doutora Maria Antonieta Piçarra Pereira, professora Adjunta da Escola Superior Agrária de Castelo Branco; Doutora Helene Maria Pühringer, investigadora do Institute of Applied Microbiology da University of Agriculture, Viena, Áustria, na qualidade de especialista. Doutoramento em Engenharia Agronómica Lisboa 2002 UNIVERSIDADE TÉCNICA DE LISBOA INSTITUTO SUPERIOR DE AGRONOMIA Alternative strategies to fight apple scab Mariana da Silva Gomes Mota ORIENTADOR: Doutora Cristina Maria Moniz Simões Oliveira CO-ORIENTADOR: Doutora Margit Laimer JÚRI: Presidente: Reitor da Universidade Técnica de Lisboa Vogais: Doutora Joana Maria Canelhas Palminha Duclos, professora catedrática do Instituto Superior de Agronomia da Universidade Técnica de Lisboa; Doutora Margit Laimer, professora do Institute of Applied Microbiology da University of Agriculture, Viena, Áustria; Doutora Cristina Maria Moniz Simões Oliveira, professora associada do Instituto Superior de Agronomia da Universidade Técnica de Lisboa; Doutora Maria Luísa Lopes de Castro e Brito, professora auxiliar do Instituto Superior de Agronomia da Universidade Técnica de Lisboa; Doutora Maria Antonieta Piçarra Pereira, professora Adjunta da Escola Superior Agrária de Castelo Branco; Doutora Helene Maria Pühringer, investigadora do Institute of Applied Microbiology da University of Agriculture, Viena, Áustria, na qualidade de especialista. "Dissertação apresentada neste Instituto para obtenção do grau de Doutor" Doutoramento em Engenharia Agronómica Lisboa 2002 Table of contents Page Acknowledgements vii Resumo e palavras-chave viii Abstract and key-words ix List of common abbreviations x List of figures xiii List of tables xv I INTRODUCTION 1 1. Fruit production in European Union and Portugal 1 1.1 Apple production 2 1.2 Important limitations to apple production 3 2. The apple scab disease 5 2.1 Importance of apple scab 5 2.2 Hosts 5 2.3 Symptoms 6 2.4 Causal organism 8 2.5 Disease cycle 8 2.6 Interaction plant-fungus 10 2.7 Genetics of the interaction plant-fungus 15 3. Control of apple scab disease 17 3.1 Cultural methods of fight against apple scab 17 3.2 Chemical control 17 3.3 Biological control 20 3.4 Genetic approaches to fight apple scab 21 3.4.1 Natural sources of resistance 21 3.4.2 Breeding based on introgression of resistance trait through backcrossing 22 3.4.3 Efforts towards the identification of integrated resistance mechanism 25 3.4.4 Limitations of this approach and interest of a broad-range mechanism 28 3.4.5 Engineered strategy to impair apple scab development 31 3.4.5.1 Participation of fungal endopolygalacturonases in pathogenesis i and value of pgip promoters as fungus-inducible promoters 31 3.4.5.2 Putative ´defense´ genes 33 3.4.5.2.1 Genes involved in defense responses in resistant types 33 3.4.5.2.2 Genes encoding enzymes degrading fungal cell walls 34 II OBJECTIVES 38 III MATERIAL AND METHODS 40 1. Plant material and tissue culture 40 1.1 Culture media 40 1.2 In vitro plant material 40 1.3 In vivo plant material 41 1.3.1 Nicotiana tabacum 41 1.3.2 Malus x domestica 41 1.4 Leaf discs transformation with Agrobacterium tumefaciens 42 1.4.1 Nicotiana tabacum 42 1.4.2 Malus x domestica 42 1.5 Germination of seeds from transgenic Nicotiana tabacum 43 2. Work with fungi 44 2.1 Fungal isolates and culture of fungi 44 2.2 Infection experiments with apple scab 44 2.2.1 Preparation of a conidial suspension for infection assays 44 2.2.2 Inoculation of plant material with apple scab 45 2.2.2.1 Infection of detached leaves 45 2.2.2.2 Infections in planta 45 2.2.3 Staining of lesions for microscopical examination 46 2.3 Production of supernatants from Botrytis cinerea 46 3. Molecular biology work 48 3.1 Solutions and reagents used in molecular biology 48 3.2 Bacterial strains 48 3.3 Vectors 49 3.4 Primers used 50 3.4.1 Vector primers 50 ii 3.4.2 Anchor primers for reverse-transcription 50 3.4.3 10-mer random primers used in differential display 50 3.4.4 pgip primers 51 3.4.5 chitinase primers 51 3.4.6 Specific primers for differential display fragments 52 3.4.7 CAM primers 52 3.4.8 GUS primers 53 3.5 General molecular biology techniques 53 3.6 Bacteria transformation 53 3.6.1 Transformation of E. coli 53 3.6.1.1 Electroporation 53 3.6.1.2 Heat shock transformation 54 3.6.2 Transformation of Agrobacterium tumefaciens 54 3.6.2.1 Freeze-thaw method 54 3.7 Nucleic acid extractions 55 3.7.1 Bacteriophage DNA extraction 55 3.7.2 Plant DNA extraction 55 3.7.3 Plasmid DNA purification 55 3.7.4 Further DNA purification 55 3.7.5 RNA extraction 56 3.7.6 Quantification of nucleic acids 56 3.8 PCR standard conditions 56 3.9 DDRT-PCR 57 3.10 RT-PCR reaction with fragment-specific primers 58 3.11 Elongation of display fragments using RACE technology 58 3.12 Sequencing and sequence analyses 59 3.13 Non-radioactive hybridisation and detection 59 3.13.1 Synthesis of DIG-labeled probes 59 3.13.2 Hybridisation 60 3.13.3 Chemiluminescent detection 60 3.14 Screening of an apple genomic library 60 3.15 Southern blotting 61 3.16 Northern blotting 61 iii 4. Biochemistry work 62 4.1 Evaluation of polygalacturonase content by 2-cyanoacetamide assay 62 4.2 Elicitation of tobacco explants with fungal supernatants 62 4.3 GUS assays 62 4.3.1 Histochemical test 62 4.3.2 Fluorometric assay 63 IV RESULTS 64 1. Establishment of a scab-infection system under controlled conditions 64 1.1 Culture of Venturia inaequalis 64 1.2 Infection of plant material with a conidial suspension of Venturia inaequalis 64 2. Isolation of pgip promoters and characterisation of pgip family in apple 67 2.1 Cloning and identification of apple pgip genes and their regulating sequences 67 2.2 Characterisation of pgip family in apple 69 2.3 Analysis of isolated pgip promoters in Nicotiana tabacum 70 2.3.1 Generation of pgip promoter-reporter gene constructs 70 2.3.2 Transformation of Nicotiana tabacum with pgip::GUS constructs 71 2.3.3 Synthesis and evaluation of fungal elicitors for elicitation assays 72 2.3.4 Establishment of the elicitation assay 75 2.3.5 Selection of transgenic lines for generation of F1 progenies 78 2.3.6 Analysis of promoter features in tobacco plants upon elicitation with fungal products 80 3. Investigation of interaction ´Florina´- Venturia inaequalis 83 3.1 Analysis of altered gene expression by DDRT-PCR 83 3.2 Verification of the differential expression of the corresponding genes 87 3.2.1 RT-PCR reaction with fragment-specific primers 87 3.2.2 Northern analysis 89 3.3 Elongation of display fragments using RACE technology 89 4. Isolation of apple chitinase genes 92 4.1 Cloning and identification of chitinase genes 92 4.2 Characterisation of acidic chitinase genes in apple 92 4.2.1 Sequence analysis 92 iv 4.2.2 Genomic organisation 95 4.2.3 Inducibility upon fungal infection 96 4.3 Overexpression of the isolated chitinase gene in apple 96 4.3.1 Generation of a CaMV 35S::Chitinase construct 96 4.3.2 Transformation of apple leaf discs with a CaMV 35S::Chitinase construct 97 4.3.2.1 Control regeneration experiment 97 4.3.2.2 Transformation experiment 98 V DISCUSSION 100 1. Establishment of an infection system under controlled conditions 100 2. Isolation and characterisation of apple pgip promoters 101 2.1 Advantage of a fungus-inducible promoter 101 2.2 Characteristics of pgip genes in apple 102 2.3 Characterisation of the isolated pgip promoter sequences in transgenic tobaccos 104 3. Identification of putative defense genes 107 3.1 Isolation of putative defense genes from a scab-resistant apple cultivar 107 3.1.1 Differential display as a tool to analyse the interaction ´Florina´- V. inaequalis 108 3.1.2 Methodological aspects of the differential display 108 3.1.3 Putative function of the genes corresponding to the isolated fragments 110 3.1.3.1 Homologies observed with proteins involved in biosynthesis of plant cell walls and cuticle layer 110 3.1.3.2 Homology observed with a probable menaquinone biosynthesis protein 111 3.1.3.3 Proteins involved in plant cell defense 112 3.2 Identification of apple genes encoding class III chitinases 112 3.2.1 Use of chitinases as putative factor for protection against apple scab 112 3.2.2 Isolation from genes encoding class III chitinases from apple 113 3.2.3 Overexpression of genes encoding class III chitinases in transgenic apples 115 v VI GENERAL DISCUSSION 118 VII REFERENCES 125 Appendix 1: Composition of culture media used 144 Appendix 2: Composition of solutions and buffers used 145 Appendix 3: DNA sequences from isolated clones 148 vi Acknowledgements At the end of this work, I would like to express my gratitude to all the people that contributed with their encouragement, advise, help and support to the accomplishment of this project.
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