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Reaping the benefits of monitoring cereal rust pathotypes

A widespread epidemic of stripe rust in eastern Australian wheat crops in 2022 resulted in significant costs to the industry through yield loss and the need to use fungicide.
Photo: Robert Park

Efforts are made to monitor the pathotypes (strains, races) of cereal rust pathogens that occur in many of the world’s cereal growing regions. In Australia, for example, the University of Sydney initiated nationwide monitoring of the pathotypes of cereal rust pathogens in 1921 and has continued this work ever since.

Growers can only reap the full benefit of this work if it underpins resistance pre-breeding, breeding and post-release management of cereal varieties. This has been the philosophy behind the approach developed and used by staff at the University of Sydney over many years. How does it work?

Sample collection

The success of rust monitoring depends entirely on the samples received for analysis. As always, growers and other stakeholders are encouraged to monitor cereal crops and vulnerable weeds (for example, barley grass, wild oats etc) closely for rust, and to forward freshly collected samples in paper only to the Australian Cereal Rust Survey, University of Sydney, Reply Paid 88076, Narellan, NSW, 2567.

Senders of all samples are notified of the results, usually between two to three weeks of receipt, and results are added to a regularly updated online interactive map.

Detecting new pathotypes – the earlier the better

Can this be done with a DNA test? Simple answer – not yet. Pathotypes are identified by infecting seedlings of cereals with known resistance genes with rust from a crop under greenhouse conditions.

In some laboratories, crop rust samples are first used to infect rust-susceptible seedlings, from which subsamples are taken for pathotype identification. However, quite often a crop rust sample will comprise more than one pathotype in unequal frequencies, and in these cases, subsampling more often than not results in excluding pathotypes present at low frequencies.

University of Sydney staff use all of a rust sample to ensure all pathotypes present are identified. This also shaves about two to three weeks off the time taken for pathotype identification.

Capturing all pathotypes present in a crop sample is particularly important in ensuring the earliest-possible detection of new pathotypes, well before they become common.

Detecting a new pathotype marks the beginning of the most-important aspect of monitoring rust pathogens.

Will a new pathotype threaten current varieties?

Without an understanding of the risk posed to industry by a new rust pathotype, rust monitoring is of almost zero value to cereal growers. The earlier an understanding of risk is known, the more agile industry can be in responding.

Assessing risk can only be done with a sound understanding of the genetic basis of resistance in cereal varieties, and an understanding of what resistance genes a new pathotype can overcome. This involves extensive greenhouse tests in which cereal genetic stocks plus current and past cereal varieties are infected with historical reference rust pathotypes and the new pathotype.

Should a threat to any current variety be identified, advisories are issued recommending close monitoring of at-risk varieties, and information is provided to assist with future varietal selection. Advisories are sent out by email (please contact Ms Jo Geist, details below, if you would like to be added to our email list).

Will a new pathotype threaten future varieties?

A delay in identifying a significant new pathotype extends the time breeders have to select for effective resistance, at best slowing genetic gain and at worst resulting in the release of varieties with inadequate rust resistance.

Any new rust pathotype that is found to be significant is used by University of Sydney staff to test cereal lines at all stages of the breeding pipeline, from early generation (under a fee-for-service program) all the way through to entries in the National Variety Trials.

Managing in-crop risk

Monitoring the occurrence, frequency and distribution of all cereal rust pathotypes, old and new, is foundational in genetic approaches to control these diseases. Linking this information with varietal response allows informed decisions to be made on the need and benefit of chemical intervention if rust is found in a crop.

More information: Jo Geist,

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