Research Collection Doctoral Thesis Global population genetics of Spongospora subterranea F. SP. subterranea, the plasmodiophorid pathogen causing powdery scab of potato and its impact on disease management Author(s): Gau, Rebecca D. Publication Date: 2012 Permanent Link: https://doi.org/10.3929/ethz-a-007593856 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH No. 20653 GLOBAL POPULATION GENETICS OF SPONGOSPORA SUBTERRANEA F. SP. SUBTERRANEA, THE PLASMODIOPHORID PATHOGEN CAUSING POWDERY SCAB OF POTATO AND ITS IMPACT ON DISEASE MANAGEMENT REBECCA DOROTHEA GAU Zürich, 2012 Diss. ETH No. 20653 GLOBAL POPULATION GENETICS OF SPONGOSPORA SUBTERRANEA F. SP. SUBTERRANEA, THE PLASMODIOPHORID PATHOGEN CAUSING POWDERY SCAB OF POTATO AND ITS IMPACT ON DISEASE MANAGEMENT A dissertation submitted to the ETH ZURICH for the degree of DOCTOR OF SCIENCES presented by REBECCA DOROTHEA GAU MSc in Genome Based Systems Biology, Bielefeld University, Germany Born on December 28th, 1982 Citizen of Germany Accepted on the recommendation of Prof. Dr Bruce A. McDonald, examiner Dr Ueli Merz, co-examiner Prof. Dr Richard E. Falloon, co-examiner Dr Patrick C. Brunner, co-examiner Zürich, 2012 TABLE OF CONTENTS ABSTRACT ................................................................................................................................................ 9 ZUSAMMENFASSUNG............................................................................................................................ 11 CHAPTER 1: GENERAL INTRODUCTION ................................................................................................. 13 1.1 PREFACE....................................................................................................................................... 15 1.2 INVASIVE PLANT PATHOGENS ..................................................................................................... 21 1.3 THE POTATO ................................................................................................................................ 25 1.3.1 History of the potato ............................................................................................................ 28 1.3.2 Economic importance ........................................................................................................... 33 1.3.3. Origin of the potato, major subspecies, and cultivars ........................................................ 35 1.3.4 Potato diseases ..................................................................................................................... 37 1.4 THE PATHOGEN: SPONGOSPORA SUBTERRANEA F. SP. SUBTERRANEA ..................................... 43 1.4.1 Life cycle ............................................................................................................................... 43 1.4.2 Phylogeny of Spongospora subterranea f. sp. subterranea ................................................. 45 1.4.3 Spongospora genetics........................................................................................................... 45 1.4.4 Cultivation ............................................................................................................................ 47 1.4.5 Host range ............................................................................................................................ 47 1.4.6 Environmental factors .......................................................................................................... 47 1.4.7 Propagation and economic impact of the disease ............................................................... 48 1.4.8 Diagnostics and control methods ......................................................................................... 49 1.4.9 Resistance against powdery scab in potato ......................................................................... 53 1.5 AIM OF THE PRESENTED STUDY .................................................................................................. 55 1.6 REFERENCES ................................................................................................................................ 57 CHAPTER 2: GLOBAL GENETICS AND INVASION HISTORY OF THE POWDERY SCAB PATHOGEN, SPONGOSPORA SUBTERRANEA F. SP. SUBTERRANEA ........................................................................... 69 2.1 ABSTRACT .................................................................................................................................... 71 2.2 INTRODUCTION ........................................................................................................................... 73 2.3 MATERIALS AND METHODS......................................................................................................... 79 2.3.1 Samples and DNA extraction ................................................................................................ 79 2.3.2 Nucleotide sequences and phylogenetic reconstruction ..................................................... 80 2.3.3 Microsatellite library construction ....................................................................................... 81 2.3.4 Microsatellite analyses and population structure ................................................................ 81 2.3.5 Inferring migration history ................................................................................................... 83 2.4 RESULTS ....................................................................................................................................... 85 5 2.4.1 Phylogeny ............................................................................................................................. 85 2.4.2 Clonal and genetic diversity ................................................................................................. 86 2.4.3 Population structure ............................................................................................................. 89 2.4.4 Inferred migration history .................................................................................................... 91 2.5 DISCUSSION ................................................................................................................................. 93 2.5.1 Role of hosts, inoculum and the potential of cryptic taxa ................................................... 93 2.5.2 Invasion scenario of Sss and evidence for a bridgehead effect ........................................... 94 2.5.3 Global trade of seed potatoes reflects recent migration patterns of the pathogen ........... 96 2.5.4 Risk assessment for Sss, and comparison with P. infestans ................................................. 96 2.5.5 Strategies for controlling Sss and potato breeding .............................................................. 97 2.6 ACKNOWLEDGEMENTS ............................................................................................................... 99 2.7 SUPPLEMENTARY MATERIAL ..................................................................................................... 101 2.8 REFERENCES .............................................................................................................................. 113 CHAPTER 3: CROSS-INFECTION POTENTIAL OF SPONGOSPORA SUBTERRANEA F. SP. SUBTERRANEA ROOT GALL AND TUBER LESION INOCULUM FROM DIFFERENT POTATO (SOLANUM SPP.) HOSTS ... 119 3.1 ABSTRACT .................................................................................................................................. 121 3.2 INTRODUCTION ......................................................................................................................... 123 3.3 MATERIAL AND METHODS ........................................................................................................ 127 3.3.1 Cultivation and preparation of tissue cultured potato plantlets ....................................... 127 3.3.2 Nutrient solution (NS) ........................................................................................................ 127 3.3.3 Preparation of inoculum ..................................................................................................... 128 3.3.4 Cross-inoculation experiment ............................................................................................ 128 3.3.5 Molecular methods ............................................................................................................ 128 3.4 RESULTS ..................................................................................................................................... 131 3.4.1 Cross inoculation experiment ............................................................................................. 131 3.4.2 Molecular analyses ............................................................................................................. 132 3.5 DISCUSSION ............................................................................................................................... 135 3.6 ACKNOWLEDGEMENTS ............................................................................................................. 139 3.7 REFERENCES .............................................................................................................................. 141 CHAPTER