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MOLECULAR CHARACTERISATION of Peronospora Parasitica INFECTING Brassica SPECIES

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MOLECULAR CHARACTERISATION of Peronospora Parasitica INFECTING Brassica SPECIES MOLECULAR CHARACTERISATION OF Peronospora parasitica INFECTING Brassica SPECIES by Manesbree Jugmoban Submitted in partial fulfilment of the requirements for the degree Doctor of Philosophy in the Department of Microbiology in the Faculty of Science and Engineering at the University of Durban-Westville, Durban, South Africa. Promoters: Professor John A Lucas, Institute of Arable Crops Research (IACR), Long Ashton, UK Professor P.N. Achar, Department of Microbiology, University of Durban-Westville, Durban Date submitted: June 2002 DECLARATION The Registrar (Academic) University of Durban-Westville Dear Sir I, Maneshree Jugmohan, Reg. No., 9509660, hereby declare that the thesis entitled: Molecular Characterisation of Peronospora parasitica infecting Brassica species, is the result of my own investigation and research and that it has not been submitted in part or in full for any other degree or to any other University. Maneshree Jugmohan June 2002 Dedicated to the memory of my father Mr Jugmohan Ramdan for his inspiration and altruism CONTENTS Page PREFACE ............................................................................................................. i ACKNOWLEDGEMENTS ........................................................................................ ii ABSTRACT ............................................................................................................v LIST OF ABBREVIATIONS ...................................................................................... vi LIST OF FIGURES ................................................................................................. vii LIST OF TABLES ................................................................................................... xiv CHAPTER ONE: LITERATURE REVIEW 1.1 INTRODUCTION ......................................................................... 1 1.1.1 Downy mildew of crucifers ....................................................3 1.2 Peronospora parasitica ..................................................................... 4 1.2.1 Symptoms ..........................................................' .............. 4 1.2.2 Morphology and life cycle ..................................................... 6 1.2.2.1 Asexual reproduction ...................................................... 6 1.2.2.2 Sexual reproduction ......................................................... 8 1.2.3 Taxonomy ............................................................................. 12 1.3 HOST SPECIFICITY AND HOST RESISTANCE ................................. 13 1.3.1 Host specificity ................................................................... 13 1.3.2 Host resistance ................................................................... 17 1.3.2.1 Plant defence mechanisms ................................................ 17 1.3.2.2 Resistance genes ............................................................ 20 1.4 APPLICATION OF MOLECULAR TECHNIQUES FOR POPULATION DIVERSITY ANALYSIS ........................................... 26 1.5 SCOPE OF PRESENT STUDy ......................................................... 34 1.6 HYPOTHESIS TO BE TESTED ....................................................... 38 1.7 APPROACHES ADOPTED ............................................................. 38 Phase I: Establishment of a culture collection of Peronospora parasitica ....... 38 Phase II:To analyse the phylogeny of Peronospora parasitica by amplification of rDNA ........................................................ 38 Phase III:Use of microsatellite markers to determine the relationships between Peronospora parasitica isolates ................................. 39 CHAPTER TWO: ESTABLISHMENT OF A CULTURE COLLECTION OF Peronospora Parasitica 2.1 INTRODUCTION .............................................................. ·.········· 40 2.2 MATERIALS AN"D METHODS ........................................................ 43 2.2.1 Culturing Peronospora parasitica in the laboratory ......................43 2.2.2 Derivation of single spore isolates of Peronospora parasitica ......... .45 2.2.3 Axenic cultures of Peronospora parasitica .......••.•.........••..........• 46 2.2.4 Isolation and purification of genomic DNA from isolates of Peronospora parasitica .............................................................47 2.2.5 Extraction and purification of Brassica host DNA ....................... 48 2.3 RESULTS .................................................................................... 48 2.3.1 Representative culture collection of Peronospora parasitica ..•......•.. 48 2.3.2 Maintenance of Peronospora parasitica field and "single spore" isolates ............................................................................. 49 2.3.3 Genomic DNA isolation of Peronospora parasitica ..................•..... 53 2.4 DISCUSSION .............................................................................. 59 CHAPTER THREE: MOLECULAR PHYLOGENY OF PATHOTYPES OF Peronospora parasitica 3.1 INTRODUCTION ......................................................................... 61 3.2 MATERIALS AND METHODS ....................................................... 68 3.2.1 Isolation and purification of genomic DNA ................................ 68 3.2.2 PCR amplification of thew ITS1~ITS4 region of the rRNA operon.70 3.2.3 Sequencing of the ITSI ~ITS4 PCR products ............................ 71 3.2.3.1 Cloning PCR products into the pPCR-Script CAM SK (+) cloning vector ................................................................71 3.2.3.1.1 Purification of PCR products ................................. 71 3.2.3.1.2 Polishing of purified PCR products ......................... 72 3.2.3.1.3 Ligation to the pPCR-Script CAM SK (+) cloning vector .................................................... 72 3.2.1.3.4 Transformation .................................................. 73 3.2.1.3.5 Preparation of plasmid DNA ................................. 73 3.2.3.2 Purification ofpeR products for direct sequencing .................. 75 3.2.3.2.1 Purification of PCR products with ExoSAP-IT TM ........75 3.2.3.2.1 Qiagen purification ............................................. 75 3.2.3.3 Direct sequencing using the ABI Prism cycle sequencing kit .......76 3.2.4 Sequence analysis ............................................................... 77 3.3 RESULTS ................................................................................ 77 3.3.1 PCR amplification of the ITS1 ~ITS4 rDNA operon of Peronospora parasitica ........................................................ 77 3.3.1 Direct sequencing of ITS-PCR products .................................. 78 3.3.2 Alignment ofITS1~ITS4 sequences of the rRNA operon of Peronospora parasitica and related Oomycetes ..........................82 3.3.3 Statistical Analysis of ITS1 ~ITS4 aligned sequences of the rDNA operon of isolates of Peronospora parasitica and related Oomycetes ............................................................ 91 3.4 DISCUSSION ............................................................................... 96 CHAPTER FOUR: ISOLATION OF MICROSATELLITES FROM Peronospora parasitica 4.1 INTRODUCTION ......................................................................... 100 4.2 MATERIALS AND METHODS ........................................................ 109 4.2.1 Axenic cultures of Peronospora parasitica and extraction of genomic DNA ..................................................................... 112 4.2.2 Preparation of filters for micro satellite enrichment ..................... 112 4.2.3 Digestion of genomic DNA with restriction enzymes ..................... 112 4.2.4 Pre-amplification of DNA ...................................................... 113 4.2.5 Enrichment for microsatellites ............................................... 113 4.2.6 Cloning of Enriched DNA into PJVl. ....................................... 114 4.2.7 Plasmid preparation ............................................................. 115 4.2.8 Sequencing of positive clones .................................................115 4.2.9 Pre-screening of microsatellite library ...................................... 116 4.3 RESULTS .................................................................................... 117 4.3.1 Digestion of Peronospora parasitica genomic DNA with restriction enzymes, ligation to adapters and pre-amplification .....................117 4.3.2 Amplification of enriched DNA sequences ................................. 117 4.3.3 Cloning of enriched DNA into PJV1 .........................................119 4.3.4 Selective hybridisation of positive transformed colonies ................ 119 4.3.5 Plasmid preparation and sequencing ....................................... 121 4.3.6 Design of amplification primers .............................................. 122 4.3.7 Pre-screening of the microsatellite library................................. 127 4.4 DISCUSSION .............................................................................. 130 CHAPTER FIVE: ASSESSMENT OF MICROSATELLITE DIVERSITY IN PATHOTYPES OF Peronospora parasitica 5.1 INTRODUCTION ......................................................................... 135 5.2 MATERIALS AND METHODS ........................................................ 146 5.2.1 DNA isolation from isolates of Peronospora parasitica .................. 146 5.2.2 Pre-screening of a genomic DNA library of Peronospora parasitica enriched for microsatellites,by
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