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Investigating Biofumigation for the Control of Plant-Parasitic Nematodes

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Investigating Biofumigation for the Control of Plant-Parasitic Nematodes Investigating Biofumigation for the Control of Plant-Parasitic Nematodes John William Harry Lennon Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds School of Biology September 2018 The candidate confirms that the work submitted is his own and that appropriate credit has been given where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. The right of John William Harry Lennon to be identified as Author of this work has been asserted by him in accordance with the Copyright, Designs and Patents Act 1988. Dedicated to my grandfather, Harry Graham Wallace. i Acknowledgements First and foremost I would like to thank my supervisor, Professor Urwin, for giving me the opportunity to undertake my PhD and for providing guidance and support over the years. I would also like to thank my co-supervisor Dr Kelly Redeker for his support and expertise, which proved invaluable. Thanks go to Dr Catherine Lilley for her words of wisdom and wealth of knowledge. The Plant Nematology group, past and present, earn thanks not only through the support and assistance offered in the lab, but for creating a fantastic, friendly environment to work in. Friday cakes will be missed! I’d like to thank Chris Bell for being a great lab mate and mate in general, and all the friends I’ve made over the past 4 years, both within university walls and without. Finally, I’d like to thank my family for spurring me on over the years, and for inspiring me to begin with. ii ABSTRACT The white potato cyst nematode, Globodera pallida, is an important pest of potato in all potato-growing regions of the world and is of particular importance to UK agriculture, found in 48-64 % of UK potato fields and incurring costs related to management and yield losses. Biofumigation is a pest management practice that seeks to exploit the production of bioactive compounds, isothiocyanates, from disrupted brassica tissues incorporated into soil. Aspects of biofumigation as they relate to control of G. pallida were investigated. The xenobiotic metabolism of G. pallida juveniles in response to contact with isothiocyanates was investigated through RNAseq analysis of nematodes exposed to Dazomet, an isothiocyanate generator. The roles of genes implicated in this response were investigated and their up-regulation confirmed, identifying several genes directly implicated in detoxification of xenobiotic compounds, presenting targets for development of future controls. A screening system for evaluation of novel biofumigant crops was developed, utilising Caenorhabditis elegans reporter lines that indicated the presence of isothiocyanates through induced expression of green fluorescent protein (GFP). Attempts to generate novel C. elegans reporters for G. pallida genes were unsuccessful, but progress was made towards generation of transgenic root-knot nematodes, a step towards a plant- parasitic nematode model system. The volatile emissions given off by brassicas as they grow were measured and a number of bioactive compounds were identified. New estimates of the contributions of brassicas to atmospheric methyl bromide concentrations were generated. A system was developed to test the toxicity of volatile compounds as given off by the above- and belowground biomass of brassicas, and toxicity was observed in C. elegans adults and G. pallida juveniles and encysted eggs. The approaches taken to investigate biofumigation are novel and support expansion of the scope of future biofumigation research in line with the findings presented. iii Table of Contents Acknowledgements ............................................................................................................ i ABSTRACT .......................................................................................................................... ii Table of Contents ............................................................................................................. iii List of Figures ................................................................................................................. viii List of Tables ..................................................................................................................... xi Glossary ........................................................................................................................... xii Chapter 1 Introduction ............................................................................................... 1 1.1 The potato .......................................................................................................... 1 1.2 Plant-parasitic nematodes ................................................................................. 2 1.2.1 Cyst nematodes ........................................................................................... 2 1.2.3 Potato cyst nematodes ............................................................................... 3 1.2.4 The life cycle of potato cyst nematodes ..................................................... 5 1.2.5 The syncytium ........................................................................................... 10 1.2.6 Potato cyst nematode genomics .............................................................. 11 1.3 Control of potato cyst nematodes ................................................................... 15 1.3.1 Resistant potato cultivars ......................................................................... 15 1.3.2 Chemical control of nematode pests of potato ........................................ 16 1.4 Biofumigation ................................................................................................... 20 1.4.1 Glucosinolates and the production of isothiocyanates ............................ 20 1.4.2 The glucosinolate-myrosinase defence system ........................................ 24 1.4.3 Biofumigation in agricultural practice ....................................................... 25 1.5 Aims .................................................................................................................. 32 Chapter 2 General Materials & Methods .................................................................. 33 2.1 Biological Materials .......................................................................................... 33 iv 2.2 Cultivation of nematodes ................................................................................. 33 2.2.1 Cultivation of cyst nematode populations ................................................ 33 2.2.2 Extraction of cysts from soil ...................................................................... 34 2.2.3 Performing egg counts .............................................................................. 34 2.2.4 Hatching Globodera pallida cysts .............................................................. 34 2.2.5 Plate cultivation of Caenorhabditis elegans ............................................. 35 2.2.6 Caenorhabditis elegans liquid cultures ..................................................... 35 2.3 Bacterial cultivation .......................................................................................... 36 2.3.1 Preparation of E. coli HT115 as a food source for C. elegans liquid culture 36 2.3.2 Preparation of ultra-competent E. coli DH5α ........................................... 36 2.4 Molecular Biological Techniques ...................................................................... 37 2.4.1 Transformation of ultra-competent cells .................................................. 37 2.4.2 Extraction of plasmid DNA from bacterial cultures .................................. 37 2.4.3 Extraction of nematode genomic DNA ..................................................... 38 2.4.4 Phenol-chloroform extraction of nucleic acids ......................................... 39 2.4.5 Ethanol precipitation of nucleic acids ....................................................... 39 2.4.6 Polymerase chain reaction ........................................................................ 39 2.4.7 Colony PCR ................................................................................................ 42 2.4.8 Agarose gel electrophoresis ...................................................................... 43 Chapter 3 Globodera pallida xenobiotic metabolism in the context of biofumigation 44 3.1 Introduction ...................................................................................................... 44 3.2 Aims .................................................................................................................. 48 3.3 Materials & methods ........................................................................................ 49 3.3.1 RNAseq analysis of Globodera pallida xenobiotic metabolism ................ 49 v 3.3.2 Confirming gene models and cloning promoter regions .......................... 49 3.3.3 Bioinformatic analysis of genes ................................................................ 50 3.3.4 RNA extraction and reverse transcription ................................................ 50 3.3.5 Quantitative PCR ....................................................................................... 51 3.4 Results .............................................................................................................. 54 3.4.1 RNAseq
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