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GRDC ups ante in race to manage oat crown rust

Watched over by Professor Melania Figueroa’s previous rust team from the US and new team in Australia, Eva Henningsen presented her paper ‘A chromosome level genome reference for oat crown rust’ at the 11th International Oat Conference in Perth.
Photo: Dr Sue Knights

Key points

  • Oat crown rust populations evolve rapidly, necessitating durable plant genetic resistance for sustained management
  • New technologies, resources and collaborations are being applied to develop management solutions for oat crown rust

Plant genetic resistance is the key to managing diseases caused by fungal pathogens, but it is often an ongoing race between plant breeders and evolving pathogens. For oat crown rust, the race is a particularly challenging one and can be likened to a steeplechase – full of obstacles.

Oat crown rust, caused by Puccinia coronata f. sp. avenae, is a significant leaf disease of oats worldwide. It not only causes reductions in grain yield and quality, but also reduces the yield and quality of fodder and hay.

Although fungicides can be used to control the pathogen, there is a risk of the pathogen developing insensitivity to these chemicals, as well as additional management requirements, particularly for fodder and hay due to withholding periods. Control through varieties with durable genetic resistance is the most economical and environmentally friendly method.

GRDC has long-standing investments with the University of Sydney rust team, managed by Professor Robert Park. Park and his team have not only provided a valuable industry support through their oat crown rust surveillance service, but also applied significant effort to identifying possible sources of genetic resistance towards developing crown rust-resistant oat cultivars.

However, oat crown rust is a very complex, variable and adaptable fungus that has been quite successful in breaking down many resistance sources in oat varieties. To improve our ability to combat oat crown rust and develop effective resistant oat varieties, we need new innovative approaches.

In 2022, GRDC upped the ante against oat crown rust by enlisting new expertise and technologies to improve ways of achieving effective oat genetic resistance. This includes getting to know more about the fungus itself by decoding its genetic make-up.

Know the foe

Professor Melania Figueroa’s work is at the forefront of understanding the molecular basis of plant-microbe interactions and developing durable resistance in crops. In 2018 her team at the University of Minnesota in the US published the first genome assembly – a sequence that reflects DNA content – for oat crown rust, which set a milestone in rust research and fungal biology.

In 2019 Professor Figueroa relocated to Australia to join CSIRO and worked towards positioning the team to battle oat crown rust, which is also a significant problem in Australia. Professor Figueroa’s graduate master’s student Eva Henningsen also relocated from the US and to date she continues her postgraduate studies at the Australian National University and CSIRO addressing the oat crown rust problem with an Australian view.

In 2022 Professor Figueroa’s team released the complete DNA make-up of the entire chromosome set of the pathogen – with no gaps.

Rusts are amazing organisms; their two nuclei can be genetically very different. We first noticed this for oat crown rust, and since it has been noticed in other rusts as well. This is partly why rusts evolve so quickly.

The high degree of fungal variability is likely also due to the existence of an ancillary host for the fungus – wild oats, which are an extensive fungal reservoir that enables a large number of mutations to occur.

The provision of a high-quality genome reference for the oat crown rust fungus is essential to thoroughly investigate the virulence evolution and diversity of the fungus in Australia and around the world.

With co-investment from CSIRO, Professor Figueroa successfully tendered for a GRDC investment call to provide genetic resources to the industry and control oat crown rust.

Oat defence

Breeding for resistance to oat crown rust began in the 1950s and has been based mainly on all-stage resistance (ASR), often referred to as seeding or major gene resistance. Although providing complete immunity, ASR genes are generally short-lived and overcome by the rapidly evolving fungus in only a few years. Alternatively, adult plant resistance (APR), or minor gene resistance, does not confer complete immunity, but is often far more durable than ASR. Combining ASR and APR could create very efficient, long-lived, broad-spectrum resistance.

New technology is increasing the rate at which researchers can identify valuable ASR and APR genes, with efforts to be bolstered by the complete sequencing of 30 diverse oat genomes by the International Oat Pan-genome Project (PanOat).

New technologies and approaches

At present the only way to profile rust pathotypes is greenhouse virulence tests using oat varieties or ‘differentials’ with different resistance genes and challenging them with rust samples sent in by growers. However, genomic tools are beginning to provide information on the pathogen that could lead to faster diagnostics and also inform genetic improvement of oats.

New technologies and resources are becoming available in the race to develop durable genetic resistance to oat crown rust. Photo: CSIRO

Prof Figueroa points out that “Genetic sequencing used to be expensive, but as the technologies have advanced these costs are reducing and it is time for oats to capitalise on these developments”.

“On the pathogen side, we were able to take a data-intensive approach to genomic sequencing and develop an artificial intelligence model to help predict virulence of the pathogen on oats with a high accuracy for North America,” says Professor Figueroa. Now her team are exploring the expansion of this model to help Australia.

“Implementation of next-generation sequencing and high-throughput pipelines also provide an opportunity to take a deeper look into the causes of disease at a molecular level. This work will help reduce and refine the number of differentials required for field surveillance of the pathogen.”

In parallel, the CSIRO team is using novel sequencing platforms to genotype oats with sources of disease resistance and identify markers for key resistance genes with a focus on delivering durable genetic control for Australian conditions.

We are looking for gene combinations that can help us manage the disease in the field and applying lessons we learned from other cereals like wheat.

Resistance genes, together with access to new genomic breeding technologies being implemented by InterGrain for oats, will remove obstacles and accelerate developing oat varieties more resistant to oat crown rust.

Professor Figueroa encourages growers to inspect crops and nearby weeds for rust diseases, and if rust is found to send freshly collected samples in paper to: Melania Figueroa, GPO Box 1700, Canberra, ACT 2601.

More information: Melania Figueroa, 0408 876 255,

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