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Against the Brown Spot Pathogen Cochliobolus Miyabeanus

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Against the Brown Spot Pathogen Cochliobolus Miyabeanus the brown the brown spot pathogen Silicon - induced induced resistance in rice ( / Magnum Photos Vink © John John © Cochliobolus Cochliobolus miyabeanus Oryza Oryza sativa L.) against Jonas Van Bockhaven Van Jonas Jonas Van Bockhaven Silicon-induced resistance in rice (Oryza sativa L.) against the brown spot pathogen Cochliobolus miyabeanus 2014 ISBN 978-90-5989-721-2 Silicon-induced resistance in rice (Oryza sativa L.) against the brown spot pathogen Cochliobolus miyabeanus Jonas VAN BOCKHAVEN Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences: Agricultural Sciences "We are all in the gutter, but some of us are looking at the stars" Oscar Wilde Promotor: Prof. Dr. ir. Monica H¨ofte Co-promotor: Dr. ir. David De Vleesschauwer Laboratory of Phytopathology Department of Crop Protection Ghent University Dean: Prof. Dr. Ir. Guido Van Huylenbroeck Rector: Prof. Dr. Anne De Paepe Dutch translation of the title: Silicium-ge¨ınduceerderesistentie tegen Cochliobolus miyabeanus in rijst (Oryza sativa L.) Cover illustration: The cover picture is made by John Vink (www.johnvink.com/JohnVinkSite), a Belgian photographer who is a member of the renowned photographic cooperative Magnum Photos. He took the cover picture in Myanmar showing rice fields and an elderly Palaung woman carrying rice stems to her house, some 3 kilometers away. I cropped the picture to make it fit the cover, the original picture is displayed below. There are several reasons why I chose this picture. First of all, I think this image is beautiful and one can not overestimate the importance of aesthetics. Second and more importantly, this picture represents the main motivations for starting my PhD project. Even though my research is quite fundamental, the potential social and environmental implications of it have always been more important to me than impact factors and amount of citations. Cite as: Van Bockhaven J (2014) Silicon-induced resistance in rice (Oryza sativa L.) against the brown spot pathogen Cochliobolus miyabeanus. PhD thesis, Ghent University, Belgium ISBN number: 978-90-5989-721-2 The author and the promotor give the authorization to consult and to copy parts of this work for personal use only. Every other use is subject to the copyright laws. Permission to reproduce any material contained in this work should be obtained from the author. i Members of the jury Prof. dr. ir. Monica H¨ofte(Promotor) Department of Crop Protection Ghent University Dr. ir. David De Vleesschauwer (Co-promoter) Department of Crop Protection Ghent University Prof. dr. Els Van Damme (Chairman) Department of Molecular Biotechnology Ghent University Dr. ir. Kris Audenaert (Secretary) Department of Applied Biosciences Ghent University Dr. ir. Simona M. Cristescu Department of Molecular and Laser Physics Radboud University Nijmegen, NL Prof. dr. Sofie Goormachtig Department of Plant Systems Biology VIB, Gent, Belgium Prof. dr. ir. Anne Legr`eve Applied Microbiology (ELIM) Universit´ecatholique de Louvain Prof. Luis Mur Institute of Biological, Environmental and Rural Sciences Aberystwyth University, UK ii Acknowledgements / Dankwoord A PhD is many things, both good and bad, but most of all it is teamwork. I would not have survived the five years of research alone. Therefore, I would like to thank the people who played a significant role during my research. First of all, my jury members. Up to now, I never realized how much time and effort a jury member invests in a PhD. Your useful comments greatly helped to improve this manuscript. Especially the chairman of the jury, Els Van Damme deserves a special mention. I know I gave you a hard time with all sorts of last minute problems and administrative changes. Thank you very much for your time and effort. My promoter, Monica, deserves a special thanks, first of all for giving me the opportunity to start my PhD research at this lab. I can imagine I was not the easiest PhD student to supervise, but I really enjoyed brainstorming with you and I have learned a great deal from you during these five years of research. David, the period during which I was applying for my scholarship was very difficult for me. I am very grateful you were there to help me, because otherwise I would never have made it. During My PhD as well, you were always there for me. Even though we have different styles of working, I really enjoyed our collaboration. Thanks for everything. I would also like to thank the people we collaborated with and who greatly contributed to my PhD research. Simona, I have great memories of my stay in Nijmegen. Not only did we generate a lot of essential data on short time with the help of Denys and Holger, I also enjoyed the brainstorm sessions via Skype to discuss the results and new experiments. The role of microbial ET in plant-pathogen interactions appears to be an interesting topic and I hope that our collaboration will guide novel research. Kathy Steppe and Ingvar Bauweraerts, I really enjoyed collaborating on the leaf gas exchange measurements. I am sure that there are more of interesting links between plant metabolism and disease resistance. Hopefully this will not be the last collaboration between our labs. Shoshi Kikuchi and Takayuki Asano from NIAS in Japan, thanks for having me at your lab and for all the help with the microarray experiment. Big thanks to Tim De Meyer for the help with the processing and statistical analysis of the microarray data. Bernd Mueller-Roeber and Salma Balazadeh from the Max Planck institute Molecu- iii lar Plant Physiology for the performance for the high-throughput transcription factor expression analysis. Luk´aˇsSp´ıchal, OndˇrejNov´ak and Miroslav Strnad from Palack´yuniversity, Czech Republic for the help on the cytokinin story. Of course I should not forget my lovely (ex-)colleagues who made my PhD research so much more than conducting experiments and working in the lab. I appreciated your critical thinking, useful comments and of course the many nice moments we spent together. A special thanks for my office co-workers and the members of the rice team. Ilse, I don't know what I would have done without you. Not only did you often save the day with a smart-ass solution, what I appreciated the most were the lunch and coffee breaks. I often passed by to ask random stuff just so I could just have a 5 min chat or persuade you to have a short coffee break. Last but not least, I would like to thank my two thesis students Dieneke and Lien.I am really happy with your results and I hope you'll be glad to see that your work was not in vain and really contributed to my PhD. Vervolgens is het de beurt aan mijn familie, al mijn broers en zussen, neefjes, nichtjes, nonkels en tantes, grootouders, buren en kennissen. Ik kan jullie zeggen dat ik nu volledig ben afgestudeerd en ik ben blij dat ik jullie kan tonen waar ik mij vijf jaar mee heb bezig gehouden. Bedankt voor jullie steun en interesse. Speciale vermelding voor mijn petekind Emma, hopelijk lees je dit ooit eens. En natuurlijk wil ik ook mijn ouders in het bijzonder bedanken. Het is niet evident om een kroostrijk gezin als het onze op te voeden. Jullie hebben vooral veel moeite gedaan om al jullie kinderen de kans te geven om te gaan studeren wat ze wouden, waarvoor bedankt. Ik zou hier al mijn vrienden willen opsommen, maar uit vrees iemand te vergeten zal ik het algemeen houden. Ik wil niet te melig worden, maar ik weet niet wat ik zou doen zonder jullie. Bedankt om er te zijn. Vooral de mensen waarmee ik heb samengewoond verdienen een speciale vermelding: Antigone, Astrid, C´eline,Jasmien, Louise, Reyes, Rob, Sofie en Thomas. Jullie kregen toch net iets meer geklaag over jullie wanneer het niet iets minder ging, of net een heel lange uitleg over waarom een bepaald experiment toch zo interessant was. Daarvoor alleen al verdienen jullie een medaille, of iets dergelijks. De grootste fan van mijn onderzoek, Milene, de enige persoon die al 5 jaar kan onthouden iv dat ik werk rond 'brown spot disease'. Lien, samen uit, samen thuis. Je was een zeer gewaardeerde collega en je hulp, vooral met LaTeX, was dikwijls van onschatbare waarde. Na de trappist die we dronken op een terras in Brussel vlak na het indienen van ons IWT projectvoorstel, wist ik dat we vrienden gingen worden. En kijk. Jasmien, de ideale doctoraatspauze. Wat hebben we gelachen tijdens die lunchpauzes bij Annick, ergens ten velde of gewoon tijdens het passeren in de gang. Ik zie het niet direct stoppen en dat is maar goed ook. Rob, waarschijnlijk de persoon die mijn doctoraat het meest verwenst heeft. Je hebt het mooi opgelost door op de momenten dat de werkdruk piekte, te vertrekken naar Afrika om daar de wereld te gaan redden. Ondanks je milde aversie jegens mijn project, vooral in het weekend, stond je toch altijd klaar, waarvoor bedankt. Er zijn ook twee personen die ik er enorm graag bij had willen hebben op mijn verdediging, maar waar het lot anders over heeft beslist. Katelijne, ik heb je pas onlangs leren kennen, maar het klikte meteen. Ik denk graag aan jou in je gouden rok die zich een weg danst door het leven. Dan denk ik "Life is gold!" en plotsklaps smelten de problemen als sneeuw voor de zon. An, mijn doctoraat kon niet slechter starten, ik kan me nog herinneren dat ik op weg was naar Monica om te praten over mijn projectvoorstel wanneer Ellen en Jasmien mij het trieste nieuws kwamen brengen. Ik denk dikwijls aan hoe we ooit, ietwat lacherig, in groep beslist hadden om van "Carpe diem" onze leuze te maken.
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