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At the CCDM, we’re always looking for honours, masters and PhD students to help us achieve our goal in reducing the economic impact of crop disease for Australian growers. Interested in working in a vibrant, modern research centre? Then apply now!

NEW! PhD Scholarship Program to improve digital agriculture. Click here for details.


Honours Projects

Measuring the effect of SSR on the photosynthetic capacity of Canola
Stipend amount – $10,000 for one year

Project outline: A recent report suggests that Sclerotinia sclerotiorum spreads along canola stems by penetrating and growing within xylem vessels (Uloth et al., 2015).  The growth of S. sclerotiorum within the xylem would negatively affect a canola plant’s ability to transpire and photosynthesize. The aim of this project is to test whether differences in the transpiration and photosynthetic rates of canola plants correlate with SSR incidence and severity. We would use gas-exchange measuring instruments, thermal imaging and environmental sensors to detect differences in transpiration and photosynthetic rate of infected plants. Ultimately a selection of these techniques would be developed for detecting SSR incidence and severity in the field.

Interested? Contact Dr Mark Derbyshire for more information.

Determining the diversity of Sclerotinia sclerotiorum across Australia
Stipend amount – $10,000 for one year

Project outline: Population studies of S. sclerotiorum have previously relied on a small number of molecular markers to distinguish relationships between isolates. The aim of this project is to compare the genomic sequences of more than 10 Australian isolates with isolates from around the world. By comparing genomic sequences we hope to answer questions about S. sclerotiorum evolution in Australia, the potential for fungicide resistance to develop in S. sclerotiorum, and whether differences in isolate virulence can be correlated with changes to particular genes.

Interested? Contact Dr Mark Derbyshire for more information.

 

Masters Projects

What abiotic factors influence the germination of Western Australian Sclerotinia sclerotiorum sclerotia?
Stipend amount – $20,000 p.a. for two years

Project outline: The majority of hybrid canola grown in Western Australia (WA) has a genetic modification that allows it to persist in the presence of the herbicide glyphosate. This technology is becoming ever more popular in WA as it allows for better weed control in broad acre agriculture. We are interested in investigating the interaction between glyphosate and the soil-borne plant pathogen Sclerotinia sclerotiorum. The specific aims of this project are:

  • To determine the environmental variables that promote/inhibit carpogenic germination of Western Australian sclerotiorum isolates.
  • To test the effect of glyphosate in the germination of Western Australian sclerotiorum isolates.
  • To use genomic and metagenomic data to investigate the interaction between glyphosate and sclerotiorum.

Interested? Contact Dr Matt Denton-Giles for more information.

 

PhD Projects

Geographic monitoring for agricultural crop disease

Project outline: Spatial and temporal information relating to pathogen distribution and risk of outbreak will enhance farm management and increase profitability. Using cutting edge computational biology techniques to identify unique DNA sequences specific to individual microbial species and/or subspecies, you will apply this unique data resource to novel DNA detection technologies and explore development of on-farm sensor prototypes for field-based pathogen detection.  Integrating species presence data within a national GIS framework, you will also identify trends in pathogen distribution, spread, evolution, etc. This will fortify national and international efforts to safeguard our future food security from the emergence of new and fungicide resistant pathogen species.

Interested? Contact Dr James Hane for more information.

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 a handful are known, their prediction remains one of the major goals of plant pathology.  One of the most successful methods of widely assigning or predicting the function of related proteins has been sequence similarity (similar sequence = similar biological function).  However many proteins have similar functions and yet have different sequences.  But in some cases these are still similar in their 3D structure (similar shape = similar biological function). This project uses highly sensitive HMM-based search algorithms capable of detecting both sequence and structural homology.  Through use of supercomputing resources you will apply this method to discover distantly related protein families of relevance to agriculture and protection of valuable crops from microbial diseases.

Interested? Contact Dr James Hane for more information.

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.  They integrate into host genomes, and may be detected through sensitive homology searches, or may also be detected within fungal RNA degradomes.  Using enhanced sequence similarity search algorithms, you will search across multiple genome and RNA datasets to enable discovery of novel mycoviruses.  Mycoviruses are believed to be common to fungal habitats, and may be responsible for otherwise unexplained variability between both crop-growing regions and experimental replicates.

Interested? Contact Dr James Hane for more information.

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.  Its ability to fix atmospheric nitrogen is also useful for soil improvement and its rotation also provides a ‘disease break’.  It is also used as livestock and aquaculture feed and is growing as a human health food.  Yet there are a number of limitations that hold back this crop’s potential to be widely adopted, one of which is risk of crop disease.  Its two major fungal pathogens, commonly known as anthracnose and phomopsis (Colletotrichum lupini and Diaporthe toxica) cause significant yield and quality losses.  They also produce toxins that are harmful to both livestock and human health. In this project, you will help establish new genomic resources for these pathogens and perform comparative genomics versus related species to identify genes relevant to pathogenicity.

Interested? Contact Dr James Hane for more information.

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.  Scientific knowledge advances quickly and periodically new knowledge from independently published research needs to be aggregated into data repositories so that it can be considered as a whole and inform future research.  Effectors are extremely important proteins in agriculture which cause disease in a host, independently of the pathogen that produced it.  Effector sequences are extremely different from each other, therefore they are still not well understood or easily predicted computationally.  In this project, you will compile a list of plant “cell-killing” protein toxins, and use the newly aggregated dataset to discover novel patterns and signatures common to effector proteins.

Interested? Contact Dr James Hane for more information.

Student Profile: Virginia Wainaina

Undertaking my master’s project with the Fungicide Resistance Group at the CCDM has been both challenging and rewarding.

I left my role working with the Ministry of Agriculture, livestock and fisheries, in Kenya, where I held 10 years working experience, and came to Curtin to pursue a Masters of Science course in dryland agricultural systems. I am passionate about working within the agriculture sector and my interests are in plant pathology, so I jumped at the opportunity to learn more through the Curtin University Master’s course.

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