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Population Genetics of the Maize Foliar Pathogen Cercospora Zeina Crous & U

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Population Genetics of the Maize Foliar Pathogen Cercospora Zeina Crous & U Population genetics of the maize foliar pathogen Cercospora zeina Crous & U. Braun in five countries of sub-Saharan Africa by David Livingstone Nsibo Submitted in partial fulfilment of the requirements for the degree Philosophiae Doctor In the Faculty of Natural and Agricultural Sciences Department of Plant and Soil Sciences Forestry and Agricultural Biotechnology Institute (FABI) University of Pretoria September 2019 Under the supervision of Prof. Dave K. Berger and co-supervision of Prof. Irene Barnes . TABLE OF CONTENT Declaration ................................................................................................................. vi Acknowledgements ................................................................................................... vii Preface ..................................................................................................................... viii Summary ................................................................................................................... xii List of Figures ........................................................................................................... xiii List of Tables ............................................................................................................ xiv CHAPTER 1 Recent advances in the population biology and management of maize foliar fungal pathogens Exserohilum turcicum, Cercospora zeina and Bipolaris maydis in Africa. 1.1 INTRODUCTION .................................................................................................... 2 1.2 GLOBAL DISTRIBUTION AND CAUSAL AGENTS OF NCLB, GLS, AND SCLB.... 3 1.2.1 Northern corn leaf blight ................................................................................... 3 1.2.2 Gray leaf spot .................................................................................................. 6 1.2.3 Southern corn leaf blight .................................................................................. 6 1.3 DISEASE EPIDEMIOLOGY AND ECONOMIC IMPACT OF NCLB, GLS, AND SCLB ON MAIZE ......................................................................................................................... 9 1.3.1 Northern corn leaf blight ................................................................................... 9 1.3.2 Gray leaf spot ................................................................................................ 10 1.3.3 Southern corn leaf blight ................................................................................ 10 1.4 DIAGNOSIS OF NCLB, GLS, SCLB AND IDENTIFICATION OF THEIR CAUSAL PATHOGENS .................................................................................................................. 11 1.4.1 Field diagnosis of NCLB, GLS, and SCLB ..................................................... 14 1.4.2 Morphological and physiological diagnosis and detection .............................. 18 1.4.3 Molecular identification .................................................................................. 19 1.5 MANAGEMENT OF NCLB, GLS, AND SCLB ....................................................... 21 1.5.1 Cultural control of NCLB, GLS, and SCLB ..................................................... 21 1.5.2 Chemical control of NCLB, GLS and SCLB .................................................... 22 1.5.3 Breeding for resistance against NCLB, GLS and SCLB ................................. 23 1.5.4 Qualitative breeding for resistance ................................................................. 23 1.5.5 Quantitative breeding for resistance ............................................................... 25 i 1.6 RECENT ADVANCES IN POPULATION GENETICS OF NCLB, GLS AND SCLB CAUSAL PATHOGENS. .................................................................................................. 29 1.6.1 Population genetics of Exserohilum turcicum ................................................. 29 1.6.2 Population genetics of Cercospora zeina ....................................................... 30 1.6.3 Population genetics of Bipolaris maydis ......................................................... 31 1.7 POPULATION GENETICS AND BREEDING FOR RESISTANCE AGAINST NCLB, GLS AND SCLB .............................................................................................................. 32 1.8 CONCLUSION ...................................................................................................... 34 1.9 ACKNOWLEDGEMENTS ..................................................................................... 35 1.10 REFERENCES ..................................................................................................... 36 CHAPTER 2 Influence of farming practices on the population genetics of the maize pathogen Cercospora zeina in South Africa. 2.1 ABSTRACT........................................................................................................... 51 2.2 INTRODUCTION .................................................................................................. 52 2.3 MATERIALS AND METHODS .............................................................................. 55 2.3.1 Fungal isolates and DNA extraction ............................................................... 55 2.3.2 PCR amplification and microsatellite genotyping ............................................ 55 2.3.3 Measures of genetic diversity ......................................................................... 56 2.3.4 Linkage disequilibrium and mating type frequencies ...................................... 57 2.3.5 Population genetic differentiation, gene and genotypic flow ........................... 57 2.3.6 Population genetic structure ........................................................................... 59 2.4 RESULTS ............................................................................................................. 59 2.4.1 Cercospora zeina identification and microsatellite genotyping ....................... 59 2.4.2 Population genetic diversity ........................................................................... 62 2.4.3 Mating type frequencies and linkage disequilibrium ....................................... 62 2.4.4 Population genetic differentiation and gene flow ............................................ 66 2.4.5 Population genetic structure ........................................................................... 66 2.5 DISCUSSION ....................................................................................................... 67 2.5.1 High genetic diversity in smallholder farms .................................................... 67 2.5.2 Partial population structure between smallholder and commercial farms ....... 70 ii 2.5.3 Reasons for partial population structure between smallholder and commercial farms 70 2.5.4 Higher clonality in commercial farms .............................................................. 72 2.5.5 Evidence for sexual recombination in Cercospora zeina populations ............. 72 2.6 CONCLUSIONS ................................................................................................... 74 2.7 ACKNOWLEDGEMENTS ..................................................................................... 75 2.8 SUPPLEMENTARY DATA .................................................................................... 76 2.9 REFERENCES ..................................................................................................... 76 CHAPTER 3 Population genetic structure and migration patterns of a maize pathogenic fungus, Cercospora zeina, in Africa. 3.1 ABSTRACT........................................................................................................... 82 3.2 INTRODUCTION .................................................................................................. 82 3.3 MATERIALS AND METHODS .............................................................................. 85 3.3.1 Sample location and isolation of Cercospora zeina ........................................ 85 3.3.2 Species identification and molecular genotyping ............................................ 86 3.3.3 Genetic diversity among populations of Cercospora zeina ............................. 87 3.3.4 Population structure and distribution of genetic variation ............................... 88 3.3.5 Population differentiation ............................................................................... 88 3.3.6 Mating type gene analysis and tests for recombination .................................. 89 3.3.7 Migration events of Cercospora zeina populations ......................................... 91 3.4 RESULTS ............................................................................................................. 91 3.4.1 Species identification ..................................................................................... 91 3.4.2 Genetic diversity among populations of Cercospora zeina ............................. 92 3.4.3 Population structure and distribution of genetic variation ............................... 93 3.4.4 Population differentiation ............................................................................... 94 3.4.5 Mating types and linkage disequilibrium ......................................................... 98 3.4.6 Migration patterns and the effect of geographic distance ............................... 99 3.5 DISCUSSION ....................................................................................................
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