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National project to advance Australian virus management

DPIRD researcher Dr Ben Congdon in the field with technical officer Jono Baulch.
Photo: DPIRD

GRDC has launched a $12 million, five-year national research project to help growers better prevent and manage virus infections in their crops. The project aims to monitor virus and vector prevalence, better understand the impact of the major grain-associated viruses on yields and develop methods for rating the virus resistance of different grain varieties in sowing guides.

GRDC’s previous national project ran from 2015 to 2019, and while each state has continued to work on its own issues, the launch of the ‘Effective virus management in grain crops’ project in mid-2023 will provide a more-coordinated national approach.

Collaborators include the Western Australian Department of Primary Industries and Regional Development (DPIRD), the Queensland Department of Agriculture and Fisheries, Agriculture Victoria Research, Macquarie University, the New South Wales Department of Primary Industries, the South Australian Research and Development Institute and the University of Western Australia.

The project is being supported with $9.2 million from GRDC and $2.8 million of in-kind contributions from partners.

Project leader Dr Ben Congdon, at DPIRD, says it is a welcome investment that will help build virus research capacity and provide the grains industry with new surveillance and diagnostic tools. It will also provide practical outcomes directly to growers to help improve their yields.


Surveillance is an important part of the project, to better understand the prevalence of different viruses, and the likely impact on crops each year.

“Sometimes, with viruses, there are no obvious symptoms associated with the yield losses they cause,” Dr Congdon says. Trials have shown that virus-infected crops can suffer yield losses of up to 40 per cent with no visual signs of infection.

“So raising awareness about the potential impacts of virus infections is a high priority for the project. And surveillance testing each year will help us to better assess what viruses are spreading out there and provide some explanations for yield losses so that growers can take action in future,” he says.

Researchers will gather crop samples from a minimum of 50 sites across the country each year, testing for many different viruses with a range of diagnostic techniques.

Different diagnostics

Viruses being tested for will depend on the crop type and the location from which samples are collected. For example, canola crops will be tested for the two most-common viruses, but pulse crops will be tested for eight or more viruses. High-throughput quantitative PCR and next-generation genome sequencing protocols are being developed to improve detection of viruses in seed, leaf or insect vector tissue.

Genome sequencing will be applied to selected samples, helping to identify different strains of the same virus, as well as viruses that researchers might not be testing for using other techniques.

“The genome sequencing approach we are taking doesn’t make assumptions about what is in the crop, unlike standard tests for specific viruses. It analyses everything that is present,” Dr Congdon says.

This allows us to get an understanding of the diversity of each virus species and what that might mean in terms of its likely or potential impact. Different variants of viruses we have already explored have different levels of virulence and severity and are also spread by different vectors. The virulence of viruses can also evolve over time.”

Crop and seed sampling

Crop sampling for viruses early in the season will help to provide virus alerts for growers.

Growers will also be encouraged to make use of diagnostic services when crops fail to yield as expected, to identify whether viruses might have contributed to this, and inform their future crop management.

The project will also promote and conduct tests for seed-borne viruses, with a limited number of free tests available to growers in coming seasons .

“For seed-borne viruses, the fundamental management strategy is to sow clean seed – whether that is commercially produced seed, or seed growers have grown themselves. If you get that right, you greatly reduce the risk of aphids spreading infection because there’s little to no source of virus to spread,” Dr Congdon says.

Pulses are particularly susceptible to seed-borne viruses, including alfalfa mosaic virus, bean yellow mosaic virus, cucumber mosaic virus and pea seed-borne mosaic virus.

“Seed testing is a really good way for us to understand virus levels in seed stocks and will also provide direct value to growers within the project.”

Normally, the testing costs up to $900 for a 400 seed test, so the program is a great opportunity for growers who are concerned about virus levels in their seed.

Aphid trapping

In assessing the prevalence of viruses, the project will be trapping aphids, while Queensland will also trap thrips – both common vectors in spreading many viruses.

“We have found that there is value in monitoring aphid movement for particular crop/virus combinations. We’ve used yellow sticky traps to test the green peach aphid and turnip yellows virus (previously known as beet western yellows virusin canola in WA and Victoria, and we’re looking to examine their effectiveness in other regions,” Dr Congdon says.

Identifying tools and strategies to optimise trapping for different aphid species across the country is one of the anticipated outcomes of the project. For example, yellow sticky traps work for green peach aphid, but oat aphids, which spread yellow dwarf viruses, are more attracted to green than yellow. And traps on fencelines will only catch airborne aphids, while wingless aphids in crops can continue to spread infection.

Economic impacts

A major focus of research will be evaluating the impact of viruses on crops to help growers determine the economic thresholds for action.

“We want to update or fill knowledge gaps in terms of yield loss data. There are a few crop/virus combinations for which we either don’t have data or the data is old. Over time, new crop varieties are introduced, viruses mutate and evolve, and climate and agronomic practices change, which means that you can’t always rely on old data.

“The impact of infection on the plant is also highly dependent on a range of factors, just as with human viral infections. This includes the presence of other stresses, the crop variety, the virus strain, the health of the crop, and at what stage in the crop’s growth infection occurs.

“We want to figure out how these different factors impact the magnitude of crop losses, and better assess the annual impact of virus infections.”

alfalfa mosaic virus in faba beansAlfalfa mosaic virus and bean yellow mosaic virus in faba beans. Photo: Joop van Leur

Evaluating the economic impact of viruses is expected to help growers decide on what virus control strategies to implement. On a larger scale, it will also help plant breeding companies decide whether to prioritise breeding virus-resistant varieties.

This latest national project builds on virus management research spanning several decades, including breeding for resistance, and well-established crop management strategies for many viruses. Ongoing work has also identified entirely new strains of virus that will now be considered as part of this research.

Dr Congdon says uncovering the vast diversity within the viruses that cause disease presents a major challenge in developing virus resistance ratings for commercial varieties and breeding programs.

“We have found evidence that resistant lines or varieties are often resistant to particular strains of a virus but not others, so we really need to think about how we are characterising and communicating what resistance means.

“For example, the canola variety Stingray has good resistance to turnip yellows virus. But we know that it is resistant to a certain common strain. We have tested other strains of the same virus, some of which are more virulent, and the resistance completely breaks down.

“So, do we present growers with information on resistance for the most common strain? Will growing varieties resistant to just one strain actually select for other strains of the virus?”

He says these and other questions will be the focus of glasshouse experiments to help develop resistance rating protocols that can be used to screen commercial varieties in the National Variety Trials program. The ratings will support the development of commercially available resistant varieties and assist growers with their crop selections.

Overall, the project aims to lift grower profits by at least one per cent. Understanding the impact of viruses will be an important part of that.

“There is currently no agreed-upon annual impact in Australia of viruses on our grain yields. We know globally that there’s an estimated $40 billion impact of virus diseases. This project will provide the kind of surveillance coupled with the yield loss data to estimate their impact. And that will put us in a better position to identify and prioritise management of the most damaging viruses.”

For more information on free seed testing see the Western Australian October 2023 Pestfacts newsletter online

More information: Ben Congdon,

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