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Three-pronged strategy to beat oat leaf blotch

Dr Judith Atieno (left) and Dr Tara Garrard inspecting the Septoria leaf blotch nursery at Manjimup, Western Australia.
Photo: Dr Judith Atieno, SARDI

An infection of Septoria leaf blotch of oats can significantly decrease grain yield and downgrade oaten hay quality, particularly in high-rainfall zones.

The disease is caused by the fungus Parastagonospora avenae f. sp. avenaria. Commonly managed by rotations or stubble burning, foliar fungicides can also be applied for in-season control, but the most cost-effective way to manage the disease is the development of resistant oat varieties.

Since 2012, Australian oat breeding germplasm has been evaluated every year for reaction to Septoria inoculum at a nursery in Manjimup, Western Australia. Despite this sustained screening effort, only moderate resistance has been identified and current Australian oat varieties are predominantly susceptible.

In 2020, GRDC commenced a partnership with the South Australian Research and Development Institute (SARDI) using a three-pronged strategy to better understand the disease virulence and diversity of the fungus, to identify potential new sources of resistance in international germplasm sets and to develop molecular markers to fast-track breeding efforts.

This is the first research to look at improving Septoria leaf blotch in oat by seeking to understand the genetic drivers of the pathogen’s virulence and the host’s resistance and involves combining skills in plant pathology and molecular genetics.

SARDI researchers collaborated with Dr Manisha Shankar, plant pathologist with Department of Primary Industries and Regional Development WA, to enable assessment of the Manjimup nursery during the 2020–21 COVID-19 border closures.

Assessing virulence of the pathogen

Assessing the observable traits of a fungus is known as ‘phenotypic pathotyping’ and provides researchers with a method to gauge the variability of the pathogen and understand the fungus’ ability to cause disease.

In this project, a total of 37 Septoria leaf blotchisolates were pathotyped from diseased oat leaves collected in 2020 and 2021 throughout WA and SA.

The pathotyping was conducted at SARDI on a differential set of 24 adult Australian oat varieties and breeding lines to capture virulence at the advanced crop growth stage. A high degree of diversity was observed in both the virulence and aggressiveness of the fungal isolates, likely due to active sexual reproduction of the Septoria leaf blotch pathogen in Australia.

The virulence and aggressiveness traits of isolates from the pathotyping dataset was used to select appropriate isolates for screening oat germplasm under controlled environment conditions for sources of resistance.

Sources of resistance

The diversity in Septoria leaf blotch isolates complicates breeding for durable resistance in oat. To date, limited research has been undertaken to seek sources of resistance to Septoria leaf blotch from international oat germplasm. This project addresses this gap by screening diverse US, Canadian and Scandinavian oat germplasm collections.

Using these diverse sources of germplasm, SARDI researchers undertook screening in controlled environment growth rooms with isolates selected from pathotyping. The lines were also screened in the field at the Manjimup nursery with naturally occurring isolates. Using a combination of screening methods ensured that the lines were exposed to multiple pathotypes and enabled comparison between response to SA and WA isolates.

Genetic variation for Septoria leaf blotch resistance in the international oat germplasm was observed in the field nursery, with 102 lines found to be more resistant than the moderately resistant check variety, Koorabup . Australian oat varieties Tammar , Tungoo  and Glider also exhibited moderate levels of Septoria leaf blotch resistance.

Development of breeding tools

Genotyping of 376 oat lines was conducted to detect small genetic differences that could influence the host disease reaction. Genotyping is the process of determining the genetic make-up (genotype) using DNA sequences. These DNA sequences are compared to identify unique (polymorphic) markers. In total around 29,000 polymorphic DNA-based markers were identified and mapped to the latest version of the oat reference genome.

Relatedness of the different lines was investigated using DNA marker analysis. The majority of Australian varieties and advanced lines were found to be closely related and were distinct from the global germplasm. This suggests that the international germplasm has the potential to provide new resistance genes that will support genetic gain in the breeding of Septoria leaf blotch-resistant oat for the Australian environment.

The use of many minor genes for resistance, commonly known as Adult Plant Resistance, is expected to be necessary to create resistance in oats to Septoria leaf blotch that will be more durable for the Australian industry. The three-pronged approach undertaken by SARDI researchers will be the key to deliver multiple sources of resistance to Septoria leaf blotch to the breeding program.

Further work

Further research will:

  • obtain whole genome sequences of SARDI’s collection of Septoria leaf blotch isolates to understand the factors driving the pathogen’s virulence;
  • develop and validate genetic markers for Septoria leaf blotch resistance in oat and provide these markers to oat breeders for selection of resistance; and
  • incorporate resistance genes into Australian adapted oat varieties.

More information: Dr Tara Garrard,, Dr Judith Atieno,

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