PhD Projects

CCDM offers a wide range of PhD Projects and our available ones are listed below. If you would like more information on the projects or the application process, please contact, clearly stating the name of the project and the nature of your query.

Using molecular biology to dissect the mechanism of fungal pathogenicity

Project outline: Parastagonospora nodorum is a serious necrotrophic fungal pathogen of wheat. In Australia, the pathogen is responsible for $108 million in yield loss of wheat per annum. In a recent study, we have identified a group of genes that are strongly expressed during infection. These genes are implicated in plant cell wall degradation, nutrient assimilation, effector function and signal transduction. The aim of project is to deduce the role of these genes in fungal pathogenicity using a molecular approach to generate gene knockout mutants. Mutants will be assessed for pathogenicity and developmental defects using a wide range of molecular techniques. The project will provide the candidate with excellent training in molecular biology, bioinformatics, biochemistry, proteomics, metabolomics, microbiology, histology and plant pathology.

Characterisation of candidate pathogenicity gene targets regulated by the transcription factor PnPf2 in Parastagonospora nodorum

Project outline: The fungus Parastagonospora nodorum orchestrate the expression of pathogenicity genes during host infection through complex intracellular signal transduction. We have recently identified a putative transcription factor called PnPf2 that function as a key regulator of fungal virulence gene expression. In this project, you will use characterise genes regulated by PnPf2 using reverse genetics and assess virulence of loss-of-function mutants through infection assays on wheat.

Investigating genome evolution and adaptation mechanisms of fungal pathogens of agricultural crops with comparative genomics

Project outline: Fungi are the major cause of crop disease, with the 5 major species destroying food stocks capable of feeding >600 million people.  You could play an important role in research aimed at combatting this disease by getting involved in research looking at the genomes of fungal plant pathogens. Your role will be to compare hundreds of genomes to identify genes responsible for causing crop disease.

Pathogenicity effector discovery via large-scale protein sequence and structure similarity searches

Project outline: Proteins that interact with a plant host and cause disease are called “effectors” and although some are known, their prediction remains one of the major goals of plant pathology.

This is your chance to get involved in a project that uses supercomputing resources (through HMM-based search algorithms) to detect sequence and structural homology that will help us discover distinctly-related protein families. This knowledge can then be translated into protecting crops from microbial diseases.

Hunting for viral sequences and viral remnants in fungal genomes and RNA-seq next-generation sequencing data

Project outline: Viruses of fungi, or mycoviruses, are capable of either reducing or increasing the virulence of fungal pathogens that cause crop disease, but are still relatively poorly studied. This is your chance to make a difference in this field.  Using enhanced sequence similarity search algorithms, you will search across multiple genome and RNA datasets to enable discovery of novel mycoviruses.

Comparative genomics of fungal pathogens of an emerging crop, narrow-leaf lupin

Project outline: Lupin is an emerging crop of significance in agriculture, livestock and human health.  It is used in crop rotations where over a period of years it can improve the profitability of wheat and other crops.  Crop disease though is still an issue for lupins, with two major fungal pathogens causing significant yield and quality losses. Your role in this project will be to help establish genomic resources and perform comparative genomics in relation to these pathogens, in order to help improve this crop’s potential to be widely adopted across the agriculture industry.

Establishing bioinformatic database resources for pathogenicity effectors that will help improve crop resistance to fungal and bacterial pathogens

Project outline: Bioinformatic databases are fundamental to advancing modern biology, the best known example being GenBank – the database of almost all known DNA/RNA/protein sequences which underlies the extremely popular sequence similarity search tool BLAST.

In this project you will ensure our bioinformatics database is up to date and relevant by curating a database of plant “cell-killing” protein toxins. You will then mine the new database to discover novel patterns and signatures common to effector proteins, which are a major influence in crop disease.

Host resistance to Net blotch of barley

(Available as top up)

Project Outline: In studying host resistance, this project will see you concentrate on phenotypic characterisation and genetic mapping of new resistance genes, along with transient gene expression and complimentary studies of resistance pathway mutants to define fundamental elements of host resistance.

Reverse genetics of virulence factors from barley net blotch

(Available as top up)

Project outline: While a forward genetics approach looks for the gene responsible for a specific phenotype, reverse genetics looks for the phenotype produced by a particular gene when changed or removed.  As a part of this project you will use reverse genetics to identify the function of effectors from barley Net blotch.

Origin of WA barley powdery mildew isolates

(Available as top up)

Project Outline: Western Australian powdery mildew isolates are genetically distinct from isolates in Europe and the USA. To determine their origin, this project will examine the relatedness and genetic structure of Australian and overseas powdery mildew populations together with mildews from wild grasses. The project also seeks to clarify the role of conserved avirulence genes and their targets among different grass species.

Fluorescent labelling of Botrytis and histology of plant infection in pulses

Stipend amount – available on enquiry

Project outline: Botrytis cinerea and B. fabae infect faba beans and lentils to cause the major plant disease, Chocolate Spot and Botrytis Grey Mould, respectively. You will use existing protocols and develop new ones, for the production of transgenic fungal isolates that produce Green Fluorescent Protein (GFP). GFP-labelled fungi will then be used to observe patterns of plant colonisation by fungi during infection, using confocal microscopy.

Secondary metabolite clusters of Botrytis and plant infection in pulses

Stipend amount – available on enquiry

Project outline: Botrytis cinerea and B. fabae infect faba beans and lentils to cause the major plant diseases and there are differences between pathogen species in the complement of secondary metabolites produced. You will use gene knockout methods to manipulate the production of specific secondary metabolite synthetic genes to determine their role in pathogenicity. Microscopy will also be used to observe differences in the mode of infection for Botrytis in which specific secondary metabolite genes have been disabled.

Genetic mechanisms of resistance and virulence of Ascochyta blight in chickpea

Stipend amount – available on enquiry

Project outline: Ascochyta blight is a major plant disease of chickpea and we have identified several candidate virulence genes in the causal organism, Ascochyta rabiei. You will develop knockout fungal strains for three candidate effector genes and characterise the mutant strains using plant pathology assays, and light and confocal microscopy.

Find out more

Interested? If you would like to know more or talk through ideas and options for these projects please contact