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Elicitation of Grapevine Defense Responses Against Plasmopara Viticola , the Causal Agent of Downy Mildew

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Elicitation of Grapevine Defense Responses Against Plasmopara Viticola , the Causal Agent of Downy Mildew Elicitation of grapevine defense responses against Plasmopara viticola , the causal agent of downy mildew Dissertation zur Erlangung des Doktorgrades (Dr. rer. nat.) der Naturwissenschaftlichen Fachbereiche der Justus-Liebig-Universität Gießen Durchgeführt am Institut für Phytopathologie und Angewandte Zoologie Vorgelegt von M.Sc. Moustafa Selim aus Kairo, Ägypten Dekan: Prof. Dr. Peter Kämpfer 1. Gutachter: Prof. Dr. Karl-Heinz Kogel 2. Gutachterin: Prof. Dr. Tina Trenczek Dedication / Widmung I. DEDICATION / WIDMUNG: Für alle, die nach Wissen streben Und ihren Horizont erweitern möchten bereit sind, alles zu geben Und das Unbekannte nicht fürchten Für alle, die bereit sind, sich zu schlagen In der Wissenschaftsschlacht keine Angst haben Wissen ist Macht **************** For all who seek knowledge And want to expand their horizon Who are ready to give everything And do not fear the unknown For all who are willing to fight In the science battle Who have no fear Because Knowledge is power I Declaration / Erklärung II. DECLARATION I hereby declare that the submitted work was made by myself. I also declare that I did not use any other auxiliary material than that indicated in this work and that work of others has been always cited. This work was not either as such or similarly submitted to any other academic authority. ERKLÄRUNG Hiermit erklare ich, dass ich die vorliegende Arbeit selbststandig angefertigt und nur die angegebenen Quellen and Hilfsmittel verwendet habe und die Arbeit der anderen wurde immer zitiert. Die Arbeit lag in gleicher oder ahnlicher Form noch keiner anderen Prufungsbehorde vor. II Contents III. CONTENTS I. DEDICATION / WIDMUNG……………...............................................................I II. ERKLÄRUNG / DECLARATION .…………………….........................................II III. CONTENTS ………………….............................................................................III IV. SUMMARY …………………..............................................................................VI V. ZUSAMMENFASSUNG ..................................................................................VII 1. INTRODUCTION ……............................................................................................... 1 1.1 General introduction…........................................................................................1 1.2 Grapevine downy mildew....................................................................................3 1.2.1 History…………….....................................................................................3 1.2.2 Economic importance……..........…….......................................................3 1.2.3 Biology and life style of Plasmopara viticola ….……...…..……..................4 1.2.4 Disease development and symptoms…………….…….............................5 1.2.5 Chemical control of P. viticola ..……..........................................................7 1.2.5.1 Side effects of chemical control…..................................................9 1.2.5.2 Resistance of P. viticola to some fungicides…………..……..........9 1.2.5.3 Reducing fungicides by different means…...................................10 1.3 Induced resistance……………….……..............................................................11 1.3.1 History of induced resistance…………....................................................11 1.3.2 Concept of induced resistance................................................................12 1.3.3 Local cellular events………………………………….................................14 1.3.4 Systemic cellular events………………………...…...................................16 1.3.4.1 Systemic acquired resistance (SAR)..........................................16 1.3.4.2 Induced systemic resistance (ISR).............................................17 1.4 Induced resistance in viticulture………….....…………….………..…..………...18 1.4.1 Allocation (fitness) cost of induced resistance.……….........………….....20 1.4.2 Induced resistance in combination with fungicides…..............................20 1.5 Aim of the work................................................................................................ 22 2. MATERIAL AND METHODS ……………………………..………….....………….…. 23 2.1 Greenhouse experiments.................................................................................23 2.1.1 Grapevine varieties ………………...........................................................23 2.1.2 Plant cultivation ……………….................................................................23 2.1.3 Preparing the pathogen ( P. viticola )……...….……….…..........................24 2.1.3.1 Maintaining and inoculum preparation .......................................24 2.1.3.2 Inoculation…………………………..............................................24 2.1.3.3 Assessment of disease severity………………………..…..…..…25 2.1.4 Resistance inducers and elicitation….....................................................26 2.1.5 Application of the elicitors (protectively – curatively)...............................28 2.1.5.1 Greenhouse experiments for (2009)….....…..…………………...28 2.1.5.2 Greenhouse experiments for (2010 – 2011)..……………….......28 2.1.5.3 Greenhouse experiments for (2012)….....…..……………………28 III Contents 2.2 Microscopic investigation……………………………………………....…..……...32 2.2.1 Leaf discs sampling and bleaching………………..……...……….............32 2.2.2 Leaf discs staining………….…................................................................32 2.3 Assessment of stilbene content…………………………………………………...32 2.4 Gene expression analysis using qPCR…….……….................…..….…..........33 2.4.1 Total RNA extraction……………………….…….…….…..……….............33 2.4.2 cDNA synthesis…….…….…...................................................................34 2.4.3 Real-time RT-PCR (qPCR)……………………….……………….…..........35 2.5 Gene expression analysis using microarray…..…...........................................37 2.5.1 Total RNA extraction…..…......................................................................37 2.5.2 cDNA synthesis and labeling…..….........................................................37 2.5.3 Hybridization and scanning…..…............................................................39 2.6 Identification of reference genes…..…............................................................40 2.7 Statistical analyses…..….................................................................................41 2.8 Chemicals, devices and software....................................................................42 3. RESULTS ……………………………………………………………..…….…………… 43 3.1 Disease severity assessment and efficiency of the elicitors..............................43 3.1.1 Efficiency of the elicitors on susceptible varieties……………..……..……43 3.1.2 Efficiency of the elicitors on tolerant varieties…………...…………..….…50 3.2 Assessment of stilbenes in tolerant varieties…….…………….……..………..…52 3.3 Epifluorescence microscopy observations …………………………...…......……54 3.3.1 Pathogen development…………………...………………………….……....54 3.3.2 Plant response (callose deposition, hypersensitivity response)…..…..…58 3.4 Investigating the time course of the infection by qPCR………….………..….….62 3.4.1 Expression of the gene coding for stilbenes synthase……………...…....62 3.4.2 Expression of the gene coding for lipoxygenase………..…………………63 3.4.3 Expression of the gene coding for chitinase………………………….....…63 3.4.4 Selecting the suitable sampling point for microarray analysis………..….64 3.5 Differential expression after elicitation and/or inoculation by microarray………68 3.5.1 Differentially expressed genes (DEGs) upon inoculation...……………....70 3.5.2 DEGs upon elicitation with phosphonate and phosphate………………...88 3.5.2.1 Common DEGs after phosphonate and phosphate treatments.…...93 3.5.2.2 Specific DEGs after phosphonate treatment……………………......100 3.5.2.3 Specific DEGs after phosphate treatment………………..……….…104 3.5.3 DEGs after phosphate and phosphonate treatment and inoculation..…107 3.5.3.1 Common DEGs after elicitation and inoculation………………..…..111 3.5.3.2 Specific DEGs after phosphonate treatment and inoculation…......122 3.5.3.3 Specific DEGs after phosphate treatment and inoculation……..….128 3.5.4 DEGs after Frutogard ® treatment…..……………..………………..……..138 3.5.5 DEGs after Frutogard ® treatment and inoculation………..……………...139 IV Contents 4. DISCUSSION …………………………………….…………………..……………...… 146 4.1 Control of P. viticola in the greenhouse using resistance inducers…………...146 4.1.1 Efficiency of the elicitors in susceptible grapevine varieties……….…..146 4.1.2 Efficiency of the elicitors in tolerant grapevine varieties………………..153 4.2 Defense related genes are induced after elicitation and/or inoculation……….155 4.2.1 Stilbene synthase (STS)…….…… …………………………………….…155 4.2.2 9-Lipoxygenase (9-LOX)……………….…….……………….……………156 4.2.3 Chitinase (CHIT_1b)………………………..........……………..………….158 4.3 Microarrays as a method to investigate differentially expressed genes...........160 4.3.1 Transcriptional changes during P. viticola -grapevine interaction…...…160 4.3.2 Elicitation with phosphonate and phosphate led to similar changes..…171 4.3.3 Elicitation and subsequent inoculation led to similar changes…………178 4.3.4 Elicitation with Frutogard ® induced few transcriptional changes….…...185 4.3.5 Elicitation with Frutogard ® and inoculation induced very few genes…..187 5. REFERENCES ………………………………………………..……………………..… 188 6. ACKNOWLEDGEMENT ……………………………………………………………… 237 V Summary IV. SUMMARY: The aim of the present study was to investigate the mechanisms of induced resistance after the application of specific elicitors
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