How long do Sclerotinia sclerotia survive in WA? Decision support tools to help with on-farm management of blackleg and sclerotinia in canola

Key messages

  • Sclerotinia sclerotiorum sclerotia were still producing apothecia after six seasons on the soil surface at Northam.
  • DPIRD and GRDC have developed three tools to support on-farm management decisions for key diseases in canola. BlacklegCM for blackleg stem canker, UCI BlacklegCM for blackleg upper canopy infection (UCI) and SclerotiniaCM for sclerotinia stem rot (SSR) management.
  • UCI BlacklegCM was released in mid-2022. Based on field monitoring of UCI in 2022, the decision support tool has been recently updated to take account of blackleg leaf lesions on canola varieties that are rated as resistant (R).


  • Determine how long Sclerotinia sclerotiorum sclerotia remain viable on the soil surface in WA.
  • Test and update canola disease management decision support tools.


Sclerotia are structures used by a range of fungi to survive adverse environmental conditions. Sclerotinia sclerotiorum causes sclerotinia stem rot (SSR) in canola in WA forms sclerotia within the stems, on the outside of the stems, in pods, on the crown and on the roots of canola plants. These sclerotia germinate the following season producing tiny spore bearing mushrooms called apothecia. Literature searches on survival rates for S. sclerotiorum sclerotia from around the world indicated that they could be surviving for 3-4 years on the soil surface and were able to initiate disease over this period. We set up a series of experiments to monitor sclerotia survival on the soil surface under WA environmental conditions. In this paper we are briefly reporting on the findings of the experiment conducted at Northam from 2017–2022.

GRDC and DPIRD in collaboration with canola pathology experts from across Australia have produced a series of three decision support tools, the CM (Canola Management) series, for management of the two main diseases that impact the yield of canola. SclerotiniaCM was developed and released as an app for tablet devices in 2019. The tool provides disease management decision support for SSR in flowering canola crops. This tool utilised all available data and knowledge on SSR from WA and the eastern states gathered over the last decade and has a model embedded within the tool that predicts the probability of SSR developing within a crop.

The BlacklegCM decision support tool was developed and released as an app for tablet devices in 2018 to help with on-farm disease management decisions for blackleg stem canker at sowing and in the early vegetative stage of canola crops. This tool was built and tested using 20 years of historical data and knowledge of blackleg stem canker management and contains a comprehensive blackleg variety resistance list which is updated twice a year.

With the shift to earlier sowing of canola, blackleg upper canopy infection (UCI) has become more prominent. Research into the management and occurrence of this form of the blackleg disease is ongoing. The UCI BlacklegCM decision support tool was developed and released as an app for both phones and tablet devices in 2022 to help with on-farm disease management decisions for blackleg UCI from first flowers through to early flowering (20–30% bloom stage) of canola crops. This tool was built using the available data and knowledge on UCI from WA and the eastern states.

The UCI BlacklegCM tool utilises the timing of first flowers and disease presence to predict if a crop is flowering in the susceptible window or if the crop is safe. The tool was heavily weighted for the presence of leaf lesions at the time of first flowers in early sown canola crops as available research had shown a strong correlation with this and the subsequent development of blackleg upper canopy infection. No consideration was made within the tool for blackleg varietal resistance levels as only limited data was available. Genetic resistance is a large part of the ongoing research into the management of UCI. It is expected that UCI BlacklegCM will be updated as more knowledge becomes available.


Sclerotia survival in WA

Sclerotia that formed in a canola crop during 2016 near Northam were collected from stubble after harvest that year. Fifty sclerotia were placed on the soil surface in a 10cm diameter PVC ring (depot) at the DPIRD Northam Research Site (-31.650142, 116.696731) in early 2017. The remainder of the collected sclerotia were placed on soil in a well-drained ‘bulk weathering tub’ at the same time. In subsequent years, sclerotia from the bulk weathering tub were used to replace sclerotia that were missing from the depot and the number of sclerotia in the depot was increased to 100 to improve the accuracy of the experiment. The sclerotia in the depot and bulk weathering tub were left in the paddock year-round to weather under natural environmental conditions. Apothecia production by the sclerotia was monitored weekly from May–October for six seasons (2017–2022). This work is ongoing, and these depots will be monitored again in 2023.

Testing the SclerotiniaCM decision support tool

A total of ten on-farm validation trials were conducted across the central and northern regions of WA during 2019, 2020 and 2022. These trials were conducted in growers’ paddocks and compared the decision to apply a fungicide for SSR management with the decision to not apply a fungicide. At all sites petal testing was conducted at the 20–30% bloom stage to confirm the presence of Sclerotinia inoculum in the trials. The incidence of SSR that developed at each trial site was rated before harvest.  The SclerotiniaCM decision support tool was run for each trial and the models’ predictions on the probability of SSR developing at the ten sites was recorded. The outputs from the SclerotiniaCM tool were compared with SSR disease incidence and yield in these trials.

Testing the UCI BlacklegCM decision support tool

In 2022, blackleg UCI was monitored in growers’ paddocks at more than 20 locations in Esperance, Albany, Merredin, and Northam. At all sites, the date of first flowers, the incidence and severity of blackleg leaf lesions, flower infection, and upper canopy stem/branch darkening (an indicator of potential for yield loss) was recorded.


Sclerotia survival in WA

In 2022, after six seasons on the soil surface, the sclerotia that formed in a 2016 canola crop were still producing apothecia. These sclerotia did not produce apothecia every season, and there was no gradual decline in production over the years. In 2022 (a decile 10 winter) these sclerotia produced more apothecia than in any previous season.

Testing the SclerotiniaCM decision support tool

On-farm testing of SclerotiniaCM occurred across locations and seasons with different rainfall patterns. Seasonal rainfall varied from very dry in the Geraldton area, (autumn decile 1 and winter decile 2–3) in 2019. In 2020, the growing season was also dry (decile 2–3), but the rainfall pattern was different from 2019 with small amounts of rain spread at timely intervals through the growing season. The 2022 season in the Northam area was characterised by an extremely wet winter (decile 10 winter).

In all seasons at all sites, petal testing confirmed the presence of sclerotinia inoculum during the early bloom stage with infection levels ranging between 4–90% across trial sites and seasons. Seasonal conditions after this stage determined the levels of SSR that developed. This resulted in differing levels of SSR developing across seasons and trial sites. This made it possible to test the tool under a range of different circumstances. In the dry season of 2019, no SSR developed at any of the four trial sites and the SclerotiniaCM tool was accurate in predicting that conditions were not favourable for the development of SSR at all four sites, suggesting no probability of a positive return from spraying. In 2020, conditions were conducive to the development of varying levels of SSR at four of the five trial sites. The SclerotiniaCM tool was accurate in predicting that conditions were favourable for the development of SSR at these four sites. In 2022, about one third of the canola plants at the trial site developed main stem SSR. The SclerotiniaCM tool was accurate in predicting that conditions were highly favourable for the development of SSR at this site, suggesting a strong probability of a positive return on spraying.

Testing the UCI BlacklegCM decision support tool

In-crop monitoring of blackleg UCI in early sown canola crops at more than 20 locations in WA in 2022 found blackleg leaf lesions at the time of first flowers in most varieties at most locations, including lesions on some resistant (R) varieties. When the UCI BlacklegCM tool was run for these R varieties it predicted a potential for yield limiting levels of blackleg UCI to develop in these crops with a potential for a positive return for fungicide application. Current research data suggested that canola varieties with a high level of resistance to blackleg stem canker (R varieties) may not develop yield limiting UCI. The UCI BlacklegCM tool was updated to take account of R varieties that develop blackleg leaf lesions. The latest version of UCI BlacklegCM now has an additional function that asks the user to input information about the resistance rating of the cultivar being grown.


Sclerotinia sclerotiorum sclerotia can survive for at least six seasons on the soil surface in WA. These experiments demonstrate how hardy sclerotia can be in our environment. Considering that it is known that a single apothecium can produce millions of ascospores, these results demonstrate the potential for sclerotia to survive and potentially cause infection in canola and other broadleaf crops years down the track. The previous history of a paddock in terms of disease presence is therefore a key factor to consider when planning crop rotations and SSR disease management strategies. Most paddocks in WA will by now have some level of Sclerotinia risk associated with them.

SclerotiniaCM has been shown in on-farm trials to be accurate in predicting circumstances in which SSR can develop in canola crops. In 2022, the tool identified the high probability of sever SSR developing in the Northam area, this was supported in the trial located in this area where one third of the crop developed yield limiting SSR. The value of this tool for growers in below average seasons to aid them in avoiding unnecessary fungicide applications was demonstrated in the 2019 season.

The new functionality in UCI BlacklegCM will prevent the tool from predicting a positive return for fungicide application on R varieties that have leaf lesions at the time of flowering. Ongoing upgrades to this tool will occur as new information on the management of this form of the disease become available.


The research undertaken as part of this project is made possible by the significant contributions of growers through both trial cooperation and the support of the GRDC, the author would like to thank them for their continued support.

Research, tool development and testing were supported by the following people (in alphabetical order): David Campbell, Steve Collins, Jenny Davidson, Art Diggle, Deb Donovan, Fumie Horiuchi, Zia Hoque, Alexander Idnurm, Kith Jayasena, Joel Kidd, Ravjit Khangura, Kurt Lindbeck, Audrey Leo, Liz Mackle, Dave Nicholson, Rebecca O’Leary, Pip Payne, Janette Pratt, Anne Smith, Kawsar Salam, Susan Sprague, David Stead, Angela Van de Wouw, Andrew Ware, and Laurie Wahlsten.

Contact details

Jean Galloway
Department of Primary Industries and Regional Development
75 York Road, Northam, WA 6401
Ph: 0475 959 932

GRDC Project Code: DAW2112-002RTX,