Saving grains

November 11, 2015

Communication, genetics expertise and on-the-ground knowledge help distinguish the research outcomes of Curtin’s Centre for Crop and Disease Management.

tan spot

Each year, the fungal disease tan spot costs the Australian economy more than half a billion dollars. Tan spot, also known as yellow spot, is the most damaging disease to our wheat crops, annually causing an estimated $212 million in lost production and requiring about $463 million worth of control measures. Fungal disease also causes huge damage to barley, Australia’s second biggest cereal crop export after wheat. It should come as no surprise, then, that the nation’s newest major agricultural research facility, Curtin University’s Centre for Crop and Disease Management (CCDM), is focusing heavily on the fungal pathogens of wheat and barley.

Launched in early 2014, with the announcement of an inaugural bilateral research agreement between Curtin and the Australian Government’s Grains Research and Development Corporation (GRDC), the CCDM already has a team of about 40 scientists, with that number expected to double by 2016.

“We are examining the interactions of plants and fungal pathogens, and ways and means of predicting how the pathogen species are going to evolve so that we might be better prepared,” says CCDM Director, Professor Mark Gibberd.

An important point of difference for the centre is that, along with a strongly relevant R&D agenda, its researchers will be working directly with growers to advise on farm practices. Influencing the development and use of faster-acting and more effective treatments is part of the CCDM’s big-picture approach, says Gibberd. This encompasses both agronomy (in-field activities and practices) and agribusiness (the commercial side of operations).

“We want to know more about the issues that challenge farmers on a day-to-day basis,” explains Curtin Business School’s John Noonan, who is overseeing the extension of the CCDM’s R&D programs and their engagement with the public. The CCDM, he explains, is also focused on showing impact and return on investment in a broader context.

Two initiatives already making a significant impact on growers’ pockets include the tan spot and Septoria nodorum blotch programs. Tan spot, Australia’s most economically significant wheat disease, is caused by the fungus Pyrenophora tritici-repentis. Septoria nodorum blotch is a similar fungal infection and Western Australia’s second most significant wheat disease.

Curtin University researchers were 2014 finalists in the Australian Museum Eureka Prize for Sustainable Agriculture for their work on wheat disease. Their research included the development of a test that enables plant breeders to screen germinated seeds for resistance to these pathogens and subsequently breed disease-resistant varieties. It’s a two-week test that replaces three years of field-testing and reduces both yield loss and fungicide use.

When fungi infect plants, they secrete toxins to kill the leaves so they can feed on the dead tissue (toxins: ToxA for tan spot, and ToxA, Tox1 and Tox3 for Septoria nodorum blotch). The test for plant sensitivity involves injecting a purified form of these toxins – 30,000 doses of which the CCDM is supplying to Australian wheat breeders annually.

“We have seen the average tan spot disease resistance rating increase over the last year or so,” says Dr Caroline Moffat, tan spot program leader. This means the impact of the disease is being reduced. “Yet there are no wheat varieties in Australia that are totally resistant to tan spot.”

“The development of fungicide resistance is one of the greatest threats to our food biosecurity, comparable to water shortage and climate change.”

Worldwide, there are eight variants of the tan spot pathogen P. tritici-repentis. Only half of them produce ToxA, suggesting there are other factors that enable the pathogen to infiltrate a plant’s defences and take hold. To investigate this, Moffat and her colleagues have deleted the ToxA gene in samples of P. tritici-repentis and are studying how it affects the plant-pathogen interaction.

During the winter wheat-cropping season, Moffat embarks on field trips across Australia to sample for P. tritici-repentis to get a ‘snapshot’ of the pathogen’s genetic diversity and how this is changing over time. Growers also send her team samples as part of a national ‘Stop the Spot’ campaign, which was launched in June 2014 and runs in collaboration with the GRDC. Of particular interest is whether the pathogen is becoming more virulent, which could mean the decimation of popular commercial wheat varieties.


Wheat fungal diseases can regularly cause a yield loss of about 15–20%. But for legumes – such as field pea, chickpea, lentil and faba bean – fungal infections can be even more devastating. The fungal disease ascochyta blight, for example, readily causes yield losses of about 75% in pulses. It makes growing pulses inherently risky, explains ascochyta blight program leader, Dr Judith Lichtenzveig.

In 1999, Western Australia’s chickpea industry was almost wiped out by the disease and has never fully recovered. With yield reliability and confidence in pulses still low, few growers include them in their crop rotations – to the detriment of soil health.

Pulse crops provide significant benefit to subsequent cereals and oilseeds in the rotation, says Lichtenzveig, because they add nitrogen and reduce the impact of soil and stubble-borne diseases. The benefits are seen immediately in the first year after the pulse is planted. The chickpea situation highlights the need to develop new profitable varieties with traits desired by growers and that suit the Australian climate.

The CCDM also runs two programs concerned with barley, both headed by Dr Simon Ellwood. His research group is looking to develop crops with genetic resistance to two diseases that account for more than half of all yield losses in this important Australian crop – net blotch and powdery mildew.

Details of the barley genome were published in the journal Nature in 2012. The grain contains about 32,000 genes, including ‘dominant R-genes’ that provide mildew resistance. The dominant R-genes allow barley plants to recognise corresponding avirulence (Avr) genes in mildew; if there’s a match between a plant R-gene and pathogen Avr genes, the plant mounts a defence response and the pathogen is unable to establish an infection. It’s relatively commonplace, however, for the mildew to alter its Avr gene so that it’s no longer recognised by the plant R-gene.

“This is highly likely when a particular barley variety with a given R-gene is grown over a wide area where mildew is prevalent, as there is a high selection pressure on mutations to the Avr gene,” explains Ellwood. This means the mildew may become a form that is unrecognised by the barley.

Many of the malting barley varieties grown in Western Australia, with the exception of Buloke, are susceptible to mildew. This contrasts with spring barley varieties being planted in Europe and the USA that have been bred to contain a gene called mlo, which provides resistance to all forms of powdery mildew.

Resistance to net blotch also occurs on two levels in barley. “As with mildew, on the first level, barley can recognise net blotch Avr genes early on through the interaction with dominant R-genes. But again, because resistance is based on a single dominant gene interaction, it can be readily lost,” says Ellwood. “If the net blotch goes unrecognised, it secretes toxins that allow the disease to take hold.”

On the second level, these toxins interact with certain gene products so that the plant cells become hypersensitised and die. By selecting for barley lines without the sections of genes that make these products, the crop will have a durable form of resistance. Indeed, Ellwood says his team has found barley lines with these characteristics. The next step is to determine how many genes control this durable resistance. “Breeding for host resistance is cheaper and more environmentally friendly than applying fungicides,” Ellwood adds.

“This is a massive achievement, and we have already shown that the use of more expensive chemicals can be justified on the basis of an increase in crop yield.”


Numerous fungicides are used to prevent and control fungal pathogens, and they can be costly. Some have a common mode of action, and history tells us there’s a good chance they’ll become less effective the more they’re used. “The development of fungicide resistance is one of the greatest threats to our food biosecurity ahead of water shortage and climate change,” says Gibberd. “It’s a very real and current problem for us.”

Fungicides are to grain growers what antibiotics are to doctors, explains Dr Fran Lopez-Ruiz, head of the CCDM’s fungicide resistance program. “The broad-spectrum fungicides are effective when used properly, but if the pathogens they are meant to control start to develop resistance, their value is lost.” Of the three main types of leaf-based fungicides used for cereal crops, demethylation inhibitors (DMIs) are the oldest, cheapest and most commonly used.

Lopez-Ruiz says that to minimise the chance of fungi becoming resistant, sprays should not be used year-in, year-out without a break. The message hasn’t completely penetrated the farming community and DMI-resistance is spreading in Australia. A major aim within Lopez-Ruiz’s program is to produce a geographical map of fungicide resistance. “Not every disease has developed resistance to the available fungicides yet, which is a good thing,” says Lopez-Ruiz.

DMIs target an enzyme called CYP51, which makes a cholesterol-like compound called ergosterol that is essential for fungal cell survival. Resistance develops when the pathogens accumulate several mutations in their DNA that change the structure of CYP51 so it’s not affected by DMIs.

In the barley disease powdery mildew in WA, a completely new set of mutations has evolved, resulting in the emergence of fungicide-resistant populations. The first of these mutations has just been identified in powdery mildew in Australia’s eastern states, making it essential that growers change their management tactics to prevent the development of full-blown resistance. Critical messages such as these are significant components of John Noonan’s communications programs.

tan spot

tan spot

tan spot
The CCDM is researching solutions to plant diseases such as powdery mildew in barley (above top), and Septoria nodorum blotch (above middle) in wheat, with Dr Caroline Moffat (above bottom) leading a program to tackle the wheat tan spot fungus.

Resistance to another group of fungicides, Qols, began to appear within two years of their availability here. They are, however, still widely used in a mixed treatment, which hinders the development of resistance. Lopez-Ruiz says it’s important we don’t end up in a situation where there’s no solution: “It’s not easy to develop new compounds every time we need them, and it’s expensive – more than $200 million to get it to the growers”.

The high cost of testing and registering products can deter companies from offering their products to Australian growers – particularly if, as in the case of legumes, the market is small.

To help convince the Australian Pesticides and Veterinary Medicines Authority that it should support the import and use of chemicals that are already being safely used overseas, the CCDM team runs a fungicide-testing project for companies to trial their products at sites where disease pressures differ – for example, because of climate. This scheme helps provide infrastructure and data to fast-track chemical registrations.

“This is a massive achievement, and we have already shown that the use of more expensive chemicals can be justified on the basis of an increase in crop yield.”


A global problem

More than half of Australia’s land area is used for agriculture – 8% of this is used for cropping, and much of the rest for activities such as forestry and livestock farming. Although Australia’s agricultural land area has decreased by 15% during the past decade, from about 470 million to 397 million ha, it’s more than enough to meet current local demand and contribute to international markets.

Nevertheless, the world’s population continues to grow at a rapid rate, increasing demands for staple food crops and exacerbating food shortages. Australia is committed to contributing to global need and ensuring the sustained viability of agriculture. To this end, Professor Richard Oliver, Chief Scientist of Curtin’s Centre for Crop and Disease Management (CCDM), has established formal relationships with overseas institutions sharing common goals (see page 26). This helps CCDM researchers access a wider range of relevant biological resources and keep open international funding opportunities, particularly in Europe.

“The major grant bodies have a very good policy around cereal research where the results are freely available,” says Oliver. “There’s also the possibility to conduct large experiments requiring lots of space – either within glasshouses or in-field – which would be restricted or impossible in Australia.” It’s a win-win situation.

Branwen Morgan

 

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