Research projects

Here are some links to research projects we work on and partners we are involved with.

Resistance management in crop disease control

Effective genetic resistance for the control of diseases in crops (i.e. R-genes) is often short-lived. This is because of evolution: Genetic changes in the pathogen population mean that control measures can partially or completely lose efficacy.  Controlling such unwanted evolution is important. The emergence of new pathogen genotypes results in an ongoing need for investment in R&D for breeding and pesticides, increased use of pesticides, loss of genetic resources and crop losses in seasons when control measures become ineffective. Currently, little thought is given to how to deploy resistance genes in a way that slows or prevents pathogens evolving in response.  The consequence is ongoing rapid erosion of genetically based disease resistance. This is concerning, given that novel sources of crop resistance are hard to identify and represent a limited genetic resource.

A description of the multiple scales at which pathogen evolution and epidemiology occur, and influence the evolution of resistance

We address the factors that influence pathogen evolution and epidemiology across multiple scales, ranging from genes through to landscapes.

Our research in this space focuses on understanding how to control unwanted evolution in populations of plant pathogens infecting grains crops, particularly wheat and canola. It is already well established that the way in which varieties are deployed across landscapes in space and time (e.g. mixtures, mosaics, rotations) influence both the likelihood of disease outbreaks and the potential for pathogens to evolve. However, while breeders and farmers can choose how varieties are deployed and used, we currently lack the ability to predict which deployment strategy is likely to be best for a given host–pathogen combination.

We use simulation modelling, in combination with controlled glasshouse experiments and field trials, to better understand how different approaches to deploying resistant crop (wheat and canola) cultivars influence the rate at which pathogens evolve and the severity of disease outbreaks. The models allow us to identify feasible options to improve the durability of resistant crop cultivars in the field, while the experimental work provides parameters to feed into the model and also test aspects of the model predictions.

For farmers, our results so far indicate that varying resistance genes in space and time can help control disease, even when resistance has been overcome. However, to get uptake by breeders and farmers, it is clear that we must treat resistance breakdown it as a “wicked problem,” in the sense that there are social, economic, and biological uncertainties and complexities interacting in ways that decrease incentives for actions aimed at promoting stewardship.


Evaluating the use of gene drives to control agricultural pests

Recent progress in gene editing technologies have opened the door to novel strategies of genetic control in a wide range of species. In particular, there is now much interest in the use of gene drives to control pest species in many environments. Gene drives are based on specific genetic elements that have the ability to be preferentially inherited beyond the simple rules of Mendelian genetics, independently of, or even against, natural selection. These elements can be harnessed to drive traits of interest into natural populations, or to carry heavy fitness loads that would reduce populations of undesirable pests.

A figure illustrating results from the modelling project, showing how the existence of seed banks slow the spread of gene drives

With this modelling framework we can investigate the importance of specific aspects of a target’s biology. For instance, the presence of a seed bank, a common feature in many plant species, is shown here to significantly slow down the spread of a recessive lethal gene drive in a population of an annual plant target.

With modern gene editing tools like CRISPR-Cas9, these techniques could, in theory, be developed in virtually any species of interest, including disease vectors, agricultural pests or harmful invasive species. This is only in theory, however, and there are a lot of factors that will impact the ability of a gene drive to be successfully implemented as a control measure in a new target species. Some of those are technical hurdles, as gene drives might be difficult to engineer in novel species like plants for example. Other factors also relate to the biological and ecological characteristics of the target species. For example, the dispersal patterns of an insect pest will influence the ability of a gene drive to spread across populations and landscapes, whether that is a desired outcome or not.

The decision to research and develop gene drives in a new target species will likely involve a significant scientific and financial investment, and the ability to evaluate these species-specific challenges early in the decision process would provide significant value to stakeholders around gene drive technologies. To that end, we decided to develop a decision support tool that would inform decisions around gene drive technologies in any novel target species.

This modelling tool has several important characteristics that will make it valuable to decision makers. First, it is a stochastic spatial model that can examine the fate of a gene drive at the landscape scale. Second, it is a modular tool that can be applied to a wide range of species, and can accommodate a variety of biological and ecological features that would be relevant to virtually any species of interest, including animals, plants and fungi. With this model, we can ultimately provide various stakeholders with an objective tool to define the potential value of gene drives as a genetic control method for any given application. Researchers can use this tool to define the main areas of uncertainty around a given gene drive and guide future science accordingly. Funders and pest control boards can rely on this evidence-based process to make decisions around gene drives. Regulatory authorities can be informed by theoretical results to define a roadmap for the potential deployment of gene drives in a safe and controlled manner.

This project is funded by the CSIRO Synthetic Biology Future Science Platform. Please contact Mathieu Legros and Luke Barrett for more information.

New knowledge about some of our most under-studied pest and beneficial invertebrates

Predicting when and where invertebrate pests will reach high densities and cause damage to result in yield loss in grain crops is a challenging task. This is partly due to a lack of fundamental knowledge on where each species is common, when they are likely to attack crop plants, and the seasonal factors that influence outbreaks. This project, involving partners in CSIRO, state governments, and the University of Melbourne, will generate new knowledge about the life-cycle and biology of pest and beneficial species across southern and western regions, to better manage these species into the future.

Portuguese Millipede; a new pest of grain crops

Portuguese Millipede; a new pest of grain crops

The project team will deliver recommendations around timing of monitoring and management for certain pest species, and scenarios where beneficials are likely to provide a real benefit to pest management. This project is funded by GRDC (CSE00059).

The main questions we are addressing are:

  1. When do I need to watch out for these pest species?
  2. When do I need to control them?
  3. What can I do on my farm to protect and support beneficial invertebrates?

More information


Africa cassava whitefly project: Identify factors driving cassava whitefly (Bemisia tabaci) outbreaks in East Africa

Over the last 20 years there has been a marked increase in frequency of outbreaks of the invertebrate pest, whitefly complex, Bemisia tabaci, in the cassava growing regions of East Africa.  The cassava whitefly vectors a range of plant viruses that have caused widespread damage to cassava, a staple food in many households. Whilst significant effort has gone into developing virus-resistant cassava varieties, there has been no effort focused on the vector which alone is able to reduce yields by 40%. This failure threatens the current USD$50 million that is being invested in cassava variety improvement in Africa. Solving the whitefly problem will therefore have a substantial direct bearing on the successful development, application and long term sustainability of cassava production in Africa.

cassava is a staple food for families in East Africa

A new project is investigating an damaging pest of cassava which is a staple food for families in East Africa

A team of CSIRO researchers, in partnership with scientists in East Africa, will carry out ecological field work in cassava production landscapes to elucidate factor(s) that are driving this marked increase in cassava whitefly abundance. Our team is part of an international project funded by the Bill and Melinda Gates Foundation through the Natural Resources Institute, University of Greenwich (that will run from 2015 to 2019). We will examine the relationships between host plants, cassava disease incidence, B. tabaci species and their natural enemies across contrasting cassava production landscapes. We will test if the amount, temporal availability and sequence of host plants in a landscape influence the abundance of whitefly in cassava. Contact Sarina Macfadyen if you would like more information.


Defining the rules governing crop microbiome assembly

Plants are host to a complex and interconnected assembly of microbes that provide essential services.

Recent advances in DNA and RNA sequencing technologies have provided an unprecedented view of the complex microbial communities that populate our bodies and surroundings. For plants, these microbial communities (microbiomes) provide essential services, such as sourcing and mobilising hard-to-find nutrients; deterring disease-causing pests; and bolstering the plant’s tolerance to environmental stresses. Despite this, the rules governing the assembly of these microbiomes in natural environments is still poorly understood. 

As part of the Microbiomes for One Systems Health (MOSH) Future Science Platform, we are bringing together several Omics technologies to define this dynamic and complex process in important Australian crop species. We hope that this work will prove foundational in guiding the strategic management of this invisible–but vital–aspect of agricultural management.