Know thine enemy

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Fungal diseases are major constraints to canola (Brassica napus) and juncea canola (B. juncea) production in Australia. Two projects led by scientists from the University of Melbourne are taking a ‘genome to paddock’ approach to deliver improved disease management to canola growers across Australia.

In crop protection, much attention is usually given to identifying genes and markers in the genome of crops to assist in the breeding of cultivars with improved disease resistance. The University of Melbourne team is taking the complementary approach by examining the genomes of the pathogen to identify the genes involved in disease progression.

With a French team, the genome sequence of Leptosphaeria maculans was published in February 2011 (see Ground Cover Issue 91, March–April 2011). This important breakthrough enabled researchers to identify gene-rich and gene-poor blocks in the 12,500-gene genome. The gene-poor regions contain much ‘junk’ DNA, but disease-related genes are embedded in these areas. Such genes include the all-important avirulence effector genes. If these genes are deleted or inactivated the fungus has the ability to break down canola’s resistance to blackleg.

(From left) Rohan Lowe, David Dubois and Angela van de Wouw from the University of Melbourne and Vicki Elliot from Marcroft Grains Pathology collect the stubble of different canola cultivars as part of the 'genome to paddock' approach to improved disease management of canola for Australian growers.In collaboration with Dr Steve Marcroft from Marcroft Grains Pathology and scientists in agricultural departments in South Australia, New South Wales and Western Australia, the severity of blackleg across Australia is being determined and the risk of blackleg resistance breakdown predicted. To assist in these endeavours high-throughput screening techniques have been developed and are being used to analyse fungal populations from blackleg-infested stubble.

Stubble is collected from the previous year’s crop from across Australia and stored under chicken wire until sexual fruiting bodies of the blackleg fungus have matured (see photo). This stubble is taken to the lab and placed in a wind tunnel where sexual spores are released onto tape. DNA on the tape is then analysed with molecular markers to determine the frequency of virulence in the population. The risk of breakdown of resistance of a particular cultivar can then be determined.

This population monitoring is crucial as L. maculans reproduces sexually, producing billions of spores, thus allowing it to evolve much faster than most other fungi and greatly increasing the risk that blackleg resistance will be broken down.

Blackleg severity and virulence of fungal populations are being monitored at 33 National Variety Trials sites. Growers can access these results via the website ( These results provide details of cultivar resistance to blackleg on a regional basis, as the virulence of blackleg populations varies depending on which cultivars have been sown extensively. With this information growers can select cultivars with the most appropriate resistance for their region. Results from last year’s trials support the concept that rotating cultivars with different resistances to blackleg minimises the risk of disease resistance breakdown.

By taking knowledge of the genome of the blackleg fungus to the paddock, a proactive rather than reactive approach to matching cultivar resistance to regional variation in populations of the blackleg pathogen is being pursued. Information generated by these trials is fed into the Blackleg Risk Assessor (see fact sheet on the GRDC website:

Researchers also have access to the genome sequences of two other fungal pathogens of canola: Sclerotinia sclerotiorum, which causes stem rot, and Leptosphaeria bigobosa ‘canadensis’, discovered in Australia in 2008. Disease-related genes in these three fungi are being sought as well as the identification of genes that can be exploited as targets for novel fungicides.

When the genome sequence of the plant partner, canola, becomes available researchers will have another key piece in the jigsaw puzzle that will provide further information on the tricks that these fungi use to cause disease and how the canola plant defends itself. So not only will they ‘know thine enemies’ but ‘know thyself’, which will greatly enhance our ability to manage these devastating diseases.

More information: Professor Barbara Howlett, Univesity of Melbourne, 03 8344 5062,;;

GRDC Project Code UM00038, UM00042

Region National