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Ugent Biblio ..GiL. t:i\ 111111 \;2) UNIVERSITEIT GENT FACUL TElT BlO-INGENIEURSWETENSCHAPPEN A best friend is like a four leaf clover: hard to find and lucky to have Promotor: Prof. Dr. ir. Erik Van Bockstaele Department of Plant Production, Faculty of Bioscience Engineering, Ghent University Dean FBW: Prof. Dr. ir. Guido Van Huylenbroeck Rector UGent: Prof. Dr. Paul van Cauwenberge ir. Tim Vleugels BREEDING FOR RESISTANCE TO CLOVER ROT (SCLEROTINIA SPP.) IN RED CLOVER (TRIFOLIUM PRATENSE) Thesis submitted in fulfilment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences (Biotechnology) Dutch translation of the title: VEREDELING NAAR RESISTENTIE TEGEN KLAVER ROT (SCLEROTINA SPP.) IN RODE KLAVER (TRIFOLIUM PRATENSE) To refer to the present thesis: Vleugels T. 2013. Breeding for resistance to clover rot (Sclerotinia spp.) in red clover (Trifolium pratense L.). PhD Thesis, Faculty of Bioscience Engineering, Ghent University, Belgium. 192p. ISBN-number: The author and promotor give the authorisation to consult and to copy parts of this work for personal use only. Any other use is limited by the Laws of Copyright. Permission to reproduce any material contained in this work should be obtained from the author. ACKNOWLEDGEMENTS Ik weet nog alsof het gisteren was, toen prof. van Bockstaele me tijdens de cursus “Diepgaande aspecten van de plantenveredeling” wees op de mogelijkheid te doctoreren bij het ILVO. Het bestaan van ILVO was me tot op dat moment niet bekend. Vooral de mogelijkheid om een doctoraat rond fytopathologie te combineren met plantenveredeling sprak me sterk aan. Toen ik de op ILVO aanwezige ervaring rond plantenveredeling en de mogelijkheden tot labowerk en veldwerk zag, was ik helemaal overtuigd om hier mijn doctoraat te beginnen. In november 2008 was het dan eindelijk zo ver. De thesis die hier nu ligt is het resultaat van ruim vier jaar werk met volle overtuiging. Toch was dit niet mogelijk geweest zonder de steun van talrijke mensen. Een woord van dank is dan ook zeker op zijn plaats voor al de mensen van ILVO die de voorbije vier en half jaar mijn pad gekruist hebben. Allereerst wil ik mijn promotor prof. dr. ir. Erik Van Bockstaele bedanken voor de kans die ik kreeg om me te vervolmaken als onderzoeker aan het ILVO. Bedankt voor de vrijheid die ik kreeg binnen mijn onderzoek, het kritisch nalezen van mijn manuscripten en de interessante discussies. Ook mijn wetenschappelijk begeleider ir. Joost Baert wil ik bedanken voor de hulp bij het opstellen van mijn talrijke experimenten, voor het nalezen van mijn manuscripten en voor de interessante discussies. I sincerely want to thank the members of the examination committee for the thorough reading of my manuscript and the useful comments and suggestions that undoubtedly helped to improve my thesis. Bedankt ook aan mijn wetenschappelijk directeur dr. ir. Johan Van Huylenbroeck en mijn afdelingshoofd dr. ir. Kristiaan Van Laecke bedanken voor het geloof dat ze steeds in mij en mijn doctoraat hebben gesteld. Bijzondere dank gaat uit naar Marianne Malengier die me gedurende de eerste jaren alles geleerd heeft over rode klaver veredeling. Bedankt voor de uitleg in de selectievelden, de interessante gesprekken en de ondersteuning bij het uittekenen van mijn experimenten. Bedankt ook Dr. ir. Kurt Heungens en Kris Van Poucke voor de praktische begeleiding, vooral tijdens de eerste jaren van mijn doctoraat. Jullie hebben me geholpen bij het steriel leren werken met schimmelculturen, bij de talloze DNA extracties en bij het produceren van ascosporen. Bedankt ook Kurt voor het nalezen van mijn manuscripten en de interessante opmerkingen. Dr. ir. Jan de Riek wil ik bedanken voor de hulp bij de AFLP reacties, de verwerking van de resultaten en voor de hulp bij mijn vele vragen. Miriam Levenson wil ik bedanken voor het corrigeren van het Engels in mijn thesis. Bedankt ook ir. Hervé De Clercq voor de nuttige opmerkingen op mijn vragen. Uiteraard wil ik ook onze technische medewerkers bedanken. In de eerste plaats Geert Lejeune, Hugo Reyntens en Hilde Carlier voor het helpen onderhouden van mijn schimmelculturen, het scoren van klaverplanten op het veld, het maken van voedingsbodems en het helpen scoren van die eindeloze hoeveelheden geïnfecteerde klaverplantjes. Bedankt ook Filip, Luc, Eddy, Johan, Greta en Kristof voor het onderhouden van mijn talrijke proeven, zowel op het veld als in de serre. Ook de laboranten wil ik bedanken voor hun hulp bij het moleculaire werk en het wegwijs maken in het labo. Graag wou ik ook nog de collega doctoraatstudenten danken waarmee ik de afgelopen jaren een bureau heb gedeeld: eerst Gijs, dan Anna en uiteindelijk Farzaneh. Jullie zijn bedankt voor de leuke gesprekken en de morele steun. Alle mensen die ik hier niet expliciet vernoemd heb en die toch op een of andere manier meegeholpen hebben aan het tot stand komen van dit project wil ik ook nog eens uitdrukkelijk bedanken. Tenslotte wil ik ook mijn ouders bedanken voor de kansen die ze mij hebben gegeven, de onaflatende steun en het geloof in mij, zelfs als ik het niet meer zag zitten. Bedankt ook aan mijn vrienden, met in het bijzonder Dieter, voor de morele steun en de nodige ontspanning tussendoor. Ook Anubis en Aurora wil ik bedanken voor de steun tijdens het langdurige computerwerk in het weekend. En tot slot, aan mijn schatje Frédérique, bedankt voor je steun, voor je begrip voor al de weekends waarin ik geen tijd voor je had, voor je liefde, voor onze vele mooie reizen en voor al die andere gestolen momentjes samen. Tim Vleugels maart 2013 TABLE OF CONTENT LIST OF ABBREVIATIONS 1 THESIS OUTLINE 3 1. CHAPTER 1 GENERAL INTRODUCTION 1.1. Red clover 005 1.1.1. Botanical characteristics 005 1.1.2. History of red clover 007 1.1.3. Agricultural value 008 1.1.3.1. Red clover for silage 010 1.1.3.2. Red clover for fresh herbage 012 1.1.4. Diseases in red clover 013 1.1.5. Persistence 013 1.1.6. Breeding methods 015 1.2. Clover rot 019 1.2.1. Sclerotinia spp. 019 1.2.1.1. Sclerotinia trifoliorum Erikks. 019 1.2.1.2. Sclerotinia sclerotiorum (Lib.) de Bary 022 1.2.2. Difference between S. trifoliorum and S. sclerotiorum 023 1.2.3. Root rot 025 1.2.4. Resistance breeding against clover rot 025 1.2.5. Other strategies to control clover rot 026 1.3. Factors possibly contributing to resistance 027 1.3.1. Prostrate growth habit 027 1.3.2. Phytoalexins 027 2. CHAPTER 2 ANALYSIS OF GENETIC DIVERSITY IN SCLEROTINIA POPULATIONS FROM EUROPEAN RED CLOVER CROPS 2.1. Objectives 031 2.2. Introduction 032 2.2.1. Mycelial compatibility grouping 032 2.2.2. Molecular genetic diversity 033 2.2.3. Genetic diversity in S. trifoliorum 035 2.3. Materials and methods 036 2.3.1. Collecting Sclerotinia isolates 036 2.3.2. Mycelial compatibility grouping 037 2.3.3. Optimising the DNA extraction 038 2.3.4. AFLP analysis 040 2.3.5. Species specific PCR 041 2.4. Results and discussion 043 2.4.1. Collecting Sclerotinia isolates 043 2.4.2. Mycelial compatibility grouping 043 2.4.3. Optimising the DNA extraction 044 2.4.4. Genetic diversity and population structure 047 2.4.5. Species specific PCR 053 2.5. Summary 056 3. CHAPTER 3 DEVELOPMENT OF BIO-TESTS TO ANALYSE PATHOGEN - PLANT INTERACTIONS 3.1. Objectives 057 3.2. Introduction 058 3.2.1. Problem statement 058 3.2.2. Ascospore production in the literature 058 3.2.3. Bio-tests in the literature 059 3.3. Materials and methods 061 3.3.1. Ascospore production 061 3.3.1.1. Production of sclerotia 061 3.3.1.2. Breaking the dormancy 062 3.3.1.3. Induction of apothecia 063 3.3.1.4. Storage of ascospores 063 3.3.2. High-throughput bio-test 064 3.3.2.1. Effect of ascospore concentration 064 3.3.2.2. Effect of plant age 066 3.3.2.3. Effect of cold treatment 066 3.3.2.4. Mycelium inoculation 067 3.3.3. Bio-test on detached leaves 067 3.3.3.1. Effect of inoculation method 067 3.3.3.2. Effect of ascospore concentration 068 3.3.3.3. Effect of the leaves’ growth stage 068 3.3.3.4. Effect of mechanical damage 069 3.3.3.5. Effect of incubation time 069 3.3.3.6. Mycelium inoculation 069 3.3.4. Correlations between both bio-tests and field infection 070 3.4. Results and discussion 071 3.4.1. Ascospore production 071 3.4.1.1. Production of sclerotia 071 3.4.1.2. Breaking the dormancy 073 3.4.1.3. Induction of apothecia 074 3.4.1.4. Storage of ascospores 075 3.4.1.5. Final protocol 075 3.4.2. High-throughput bio-test 076 3.4.2.1. Effect of ascospore concentration 076 3.4.2.2. Effect of plant age 078 3.4.2.3. Effect of cold treatment 079 3.4.2.4. Mycelium inoculation 080 3.4.2.5. Final protocol 081 3.4.3. Bio-test on detached leaves 082 3.4.3.1. Effect of inoculation method 082 3.4.3.2. Effect of ascospore concentration 083 3.4.3.3. Effect of the leaves’ growth stage 084 3.4.3.4. Effect of mechanical damage 085 3.4.3.5. Effect of incubation time 085 3.4.3.6. Mycelium inoculation 086 3.4.3.7. Final protocol 087 3.4.4. Correlations between both bio-tests and field infection 088 3.5. Summary 089 4. CHAPTER 4 MORPHOLOGICAL AND PATHOGENIC VARIATION AMONG SCLEROTINIA ISOLATES FROM RED CLOVER 4.1.
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