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.

Use of genetics to identify novel fungal disease resistance mechanisms in wheat

Project outline: Septoria nodorum blotch (SNB) is a major disease of wheat caused by the fungus Parastagonospora nodorum. Resistance in wheat is mediated by complex interactions of multiple wheat quantitative trait loci. In this study, you will have the opportunity to use biparental populations as well as wheat diversity panels to identify novel sources of resistance to SNB. Association mapping will be performed to identify the underlying mechanism of genetic resistance in wheat when infected with P. nodorum.

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.

Barley net blotch epidemiology, population genetics and gene flow

(Available as top up)

Project Outline: This project aims to examine the relative diversity of Net blotch isolates in Western Australia and the genetic structure of populations and their origin. You will be doing this through population genetics and gene flow analyses.

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.

Genetic screening for barley Net blotch virulence factors

(Available as top up)

Project Outline: Using forward genetics this project aims to find genes which are responsible for the onset and progression of barley Net blotch disease. You will be working to achieve this by generating mutant libraries and the subsequent screen for loss or gain of pathogenicity.

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.

Identification of exotic resistance genes to powdery mildew in barley

(Available as top up)

Project Outline: The goal of this project is to identify new resistance genes in wild barley by genetic mapping or GWAS (genome wide association mapping) to molecularly characterise and understand the interaction of resistance genes.

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.

Molecular processes underlying penetration resistance to powdery mildew in barley

(Available as top up)

Project Outline: This project will explore global gene expression between different mlo lines (a mutation in the negative regulator of host resistance) to understand how mlo affects downstream resistance mechanisms.

Exploring pathogen resistance in lentil

Project outline: Some current lentil varieties differ in their response to the important plant fungal pathogen, Ascochyta lentis. We have characterised isolates that can infect one variety but not another and are producing a genetic mapping population for lentil genes that confer these pathogen resistance traits. You will use GFP-labelled fungal isolates and microscopy to investigate the colonisation of different lentil hosts, screen the mapping population to evaluate resistance and susceptibility traits and produce QTL mapping data using genotyping-by-sequencing methods

Find out more

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