Fusarium disease of wheat - exploring tissue specific host-pathogen interactions using a systems biology approach

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Fusarium graminearum is the causative agent of the highly destructive fungal disease Fusarium Head Blight (FHB), which infects wheat and other cereals. It causes devastating crop losses by dramatically decreasing grain quality before harvest. Furthermore, the pathogen produces harmful toxins which deem grains unfit for human or animal consumption. Faced with a growing population, climate change, environmental pressures, and fungicide resistance; the ability to control fungal plant pathogens has become a global concern requiring urgent solutions. With F. graminearum being one of the most economically important plant pathogenic fungi, developing our understanding of its ability to infect and inflict disease is paramount. Following the advances of fungal genomics and sequencing technologies, there have been a substantial number of studies investigating the genetic interaction between F. graminearum and its cereal hosts during infection. There has also been progress in the development of bioinformatic pipelines and network analyses to predict and identify disease-related genes in microorganisms. In this project, the student will work with experts in both fields of F. graminearum microbiology and emerging bioinformatic analysis technologies to develop different bioinformatic pipelines to study the host-pathogen interaction between F. graminearum and wheat. To predict and identify key disease-related genes and gene complexes a transcriptomic expression network will be developed. Initially a network will be generated to solely study the expression of F. graminearum genes during in planta infections and compare this with expression during in vitro growth. However, this project also aims to develop a dual pathogen-host combined expression network. This will illustrate genetic interactions between F. graminearum and Wheat. The F. graminearum networks will be generated using both unpublished in-house and published public RNA-sequencing (RNA-seq) datasets. Additional RNA-seq datasets may be generated to study unique aspects of the infection process. Predicted virulence and disease-related genes identified through the network analyses or other pipelines, will be deleted in the fungus using a split-marker deletion strategy. The mutants will then be inoculated onto wheat heads at anthesis to assay for changes in virulence levels and undergo a range of phenotypic tests. Genes involved in virulence will then be further functionally characterised to understand their involvement in cellular processes. Selected potential resistance or susceptibility genes in wheat could also be tested using overexpression and virus induce gene silencing. Overall, this project will generate novel insight on the infection process of F. graminearum, which is imperative for developing chemical and biological means of crop protection. The network analysis and other bioinformatics pipelines can also be used by other researchers to further advance research in the field.