Sclerotinia in canola update: current understanding, emerging opportunities and knowledge gaps

Key messages

  • As Sclerotinia stem rot in canola is often unpredictable and sporadic with high variability between regions and years, research on the disease and its management is difficult.
  • A new method for rapid, low-cost and consistent screening of canola varieties for Sclerotinia stem rot resistance has been developed, which will reduce dependency on unpredictable field testing.
  • The SclerotiniaCM decision support tool and the research underpinning it can reduce unnecessary fungicide applications and reduce input costs.


This paper summarises the field and lab research done over the past decade by the Department of Primary Industries and Regional Development (DPIRD), the Centre for Crop Disease Management (CCDM) and their collaborators which has investigated the ecology of the pathogen Sclerotinia sclerotiorum, Sclerotinia stem rot infection process and effective management options in canola crops. The paper also includes information on the SclerotiniaCM decision support tool and details a novel method developed at CCDM for producing consistent Sclerotinia infection in canola, which will enable more rapid screening of canola lines for Sclerotinia resistance in the future.


Western Australian canola growers face increasing pressure from Sclerotinia stem rot (caused by the fungus Sclerotinia sclerotiorum). This disease can cause significant yield loss in conducive seasons when the environmental conditions are favourable. Inoculum is now widespread and is known to persist for several years and infect subsequent broadleaf crops. Due to the long-term survival of sclerotia in WA farming systems, growers should assume that paddocks that have had canola or lupins in the past six years have a Sclerotinia risk. Lack of available resistant canola varieties in Australia makes managing this disease particularly challenging.

Summary of historical field and lab research results

Sclerotinia infection process

As the Western Australian environment is distinct from other cropping regions in Australia and overseas, it is important for research to be conducted under local conditions. WA research in both the field and lab has found that S. sclerotiorum sclerotia can survive for at least six growing seasons on the soil surface and that hot, dry summer conditions are required to condition them for germination. S. sclerotiorum isolates collected in WA have been shown to have adapted to local conditions, with temperature requirements for preconditioning and germination varying depending on the environment in which the sclerotia formed. Ongoing observations and measurements in field trials since 2010 have determined that the Sclerotinia disease lifecycle and risk of crop infection are heavily dependent on weather (season break, temperature, moisture and humidity) and crop/paddock conditions (Sclerotinia infection history, soil type, crop density, time of flowering) during the growing season. This makes disease occurrence highly variable, even between paddocks, and management of the disease is therefore complex. Regular rainfall and high humidity (>75%) in the three weeks before and after commencement of flowering are most conducive for damaging levels of canopy Sclerotinia to occur in crops. The temperature range that favours crop infection is 15–25°C, so seasons with cold winters may reduce infection. Research into methods to reduce sclerotia germination (grinding/ burning/ burying/ fungicide-treating sclerotia) has been undertaken and is currently continuing, but no definitive solution has yet been found. Some fungal and bacterial antagonists have also been identified in WA as potential biological control agents for reducing formation or germination of sclerotia and research into this area is currently ongoing.

Sclerotinia management options

Many management strategies have been investigated in WA in different growing seasons and geographical locations but the sporadic incidence of Sclerotinia at damaging levels in the field has hindered progress. If disease risk is considered high, rotating with non-host crops and applying a registered foliar fungicide during crop flowering are currently the best management strategies. A Predicta B soil test may indicate if Sclerotinia DNA is present to identify paddocks at risk, and petal testing (for research purposes only) will identify whether spores of S. sclerotinia are present during canola flowering. However, these methods are only indicators of pathogen presence and do not determine subsequent Sclerotinia disease infection, as this is reliant on conducive environmental conditions.

Timing of fungicide application is extremely important for the effective control of Sclerotinia disease in-canopy but can vary from season to season and even paddock to paddock. While fungicide application reduces levels of canopy infection, it does not necessarily result in a yield response or a positive economic return. Out of 90 Sclerotinia management field trials conducted across WA between 2010–2023, less than a quarter had a statistically significant yield gain following a foliar fungicide application during crop flowering. It is important to consider crop risk and value of disease management carefully each season and identify crops to be prioritised. The use of the SclerotiniaCM app has been demonstrated in on-farm trials and by industry uptake to be a useful tool for determining the likely yield impact and economic return from applying fungicide for Sclerotinia at a specific time during flowering. The decision support tool allows the user to enter information specific to their paddock, crop, and expected local weather conditions, to predict if Sclerotinia may develop and therefore if fungicide management is likely to be beneficial or not.

Field research over many seasons and across all WA port zones has determined that in areas with a history of frequent Sclerotinia infection, a foliar fungicide application at 20–50% bloom may be a good strategy, provided conditions are favourable for infection before and during flowering (use the SclerotiniaCM tool for guidance). A second fungicide application at 50% bloom is generally only useful in seasons when the flowering period is prolonged due to extended wet conditions, and when the first spray was applied early. Fungicides should not be applied after 50% bloom (full bloom or when the crop is at its brightest). Research to date has shown that basal Sclerotinia is very difficult to manage as the fungal infection occurs at or below ground level. Currently no foliar fungicides are registered or recommended for controlling basal Sclerotinia infection.

A new method for future screening of canola lines for Sclerotinia stem rot resistance

A new high-throughput method that leads to reliable and consistent Sclerotinia infection has been developed to screen canola for Sclerotinia disease resistance. Twelve plant-based organic carriers were utilised to infect canola plants, using detached leaf assays, whole plant, and field plot inoculations (with and without misting) to determine the optimum organic carrier, concentration and technique for reliable and consistent Sclerotinia disease progression in plants. The organic carriers were colonised by mycelium from a single local aggressive isolate (CU11.19) of S. sclerotiorum, with both whole seed and granulated treatments of each carrier applied. Granulated red rice and sesame seed were found to be ideal plant-based carriers for the Sclerotinia fungal pathogen, leading to development of Sclerotinia in canola under favourable moist and warm conditions.

Conclusion and research recommendations

Sclerotinia stem rot in canola is a challenging disease for growers to manage. Our expanded understanding of the infection process, risk factors and yield loss from over a decade of lab and field research has resulted in the development of effective management strategies and tools that growers can use in combating the disease. The SclerotiniaCM app incorporates field research results and the expertise of Sclerotinia pathologists from across Australia to accurately predict circumstances in which Sclerotinia stem rot is likely to develop. It is a recommended tool available for growers to use when considering the economics of spray decisions and to reduce unnecessary fungicide applications. A new high-throughput technique will enable breeders to effectively screen new canola lines for Sclerotinia disease resistance faster and more reliably than before, providing screening methods that are not reliant on conducive environmental field conditions.

Despite the significant amount of work to date, significant gaps still exist in the understanding of Sclerotinia stem rot disease and these need to be addressed to identify other potential IDM strategies:

  • Targeted foliar fungicide application for crops based on soil type, current and historical paddock biomass, yield maps and drone imagery.
  • Identification of alternative non-fungicide technologies for reducing sclerotia germination. These technologies include tools such as biological control agents, biofungicides, microwave technology, plasma coating and suppressive soils.
  • The potential of using wider row spacing and lower seeding rates to reduce canopy humidity and thus conducive environmental conditions for Sclerotinia, particularly in areas where growers routinely use two fungicide applications to manage the disease.
  • Germination and longevity of sclerotia following tillage and soil renovation practices.
  • Linking paddock inoculum levels to disease damage potential. Predicta B testing for Sclerotinia is now available to growers, however in-field testing needs ground-truthing.
  • Use of real time weather data loggers and spore detection technologies.
  • Monitoring fungicide resistance and genetic diversity in Sclerotinia sclerotiorum isolates.
  • Combining fungicide and non-fungicide strategies to reduce/delay resistance potential.
  • Understanding basal infection processes and potential interactions with nutrition.
  • Developing canola varieties with increased resistance to both basal and stem rot forms of Sclerotinia.
  • Growers make management decisions about a crop, not a disease, so combining the current suite of canola decision support tools into a single canola disease management strategy is critical.
  • Research is also required on co-infection in canola of Sclerotinia, blackleg and Alternaria to develop recommended management strategies for situations where growers are dealing with infection from more than one pathogen.
  • Regular communication of updated Sclerotinia disease information and current management tools to a wide audience.


Web resources

  1. Managing sclerotinia stem rot in canola, DPIRD webpage covering symptoms, lifecycle and management options and research,
  2. Sclerotinia CM – Sclerotinia in Canola management app, DPIRD webpage providing information on the app and how to download it,
  3. Sclerotinia stem rot in Canola, GRDC Factsheet covering disease cycle, high risk crops and management options,
  4. Registered foliar fungicides for canola in WA, DPIRD webpage

Scientific papers

  1. Han, V-C., Michael, P.J., Crockett, R., Swift, B. & Bennett, S.J. (2024). Effective, consistent, and rapid non-contact methods for seedling basal stem infection by Sclerotinia sclerotiorum. Plant Disease. (Accepted)
  2. Bennett, S.J., Rijal Lamichhane, A. & Michael, P.J. (2024). Thermal time and time of sowing impacts disease development of Brassica napus inoculated with diverse Sclerotinia sclerotiorum isolates. Journal of Plant Pathology (submitted)
  3. Michael, P.J., Rijal Lamichhane, A., Bennett, S.J. (2023). Growing Season Conditions and Isolate Are Important Determinants of Brassica Napus Susceptibility to Aggressive Sclerotinia Sclerotiorum Isolates. Agronomy 13, 1606. Online.
  4. Han, V-C., Michael, P.J., Swift, B. & Bennett, S.J. (2023). Biological control of Sclerotinia sclerotiorum: Modes of action of biocontrol agents, soil organic amendments and soil microbiome manipulation. Biological Control 186, 105346.
  5. Hidayah, BN., Khangura, R., Dell, B. (2022).Biological Control Potential of Trichoderma Species and Bacterial Antagonists against Sclerotinia sclerotiorum on Canola in Western Australia. International Journal of Agriculture and Biology 27:215-227.
  6. Bennett, S.J., Lamichhane, A.R.., Thomson, L.L., Yin, K.L. and Michael, P.J. (2021). Impact of fungicide application and host genotype on susceptibility of Brassica napus to Sclerotinia stem rot across the south-western Australian grain belt: A genotype x environment x management study. Agronomy 11:6 (Online)
  7. Khangura, R., van Burgel, A.J. (2021). Foliar fungicides and their optimum timing reduce sclerotinia stem rot incidence, improve yield and profitability in canola (Brassica napus L.). Indian Phytopathology 74, 549–558.
  8. Michael, P. Lui, K.Y., Thomson, L.L., Lamichhane, A. & Bennett, S.J. (2021). Impact of preconditioning and duration period on carpogenic germination of diverse Sclerotinia sclerotiorum (Lib.) de Bary populations in south-western Australia. Plant Disease (Online
  9. Michael, P. Lui, K.Y., Thomson, L.L., Stefanova, K. & Bennett, S.J. (2020). Carpogenic germinability of diverse Sclerotinia sclerotiorum (Lib.) de Bary populations within the south-western Australian grain belt. Plant Disease 104:2891-2897 (Online
  10. Brooks, K.D, Bennett S.J., Hodgson, L.M & Ashworth, M.B. (2018). Narrow windrow burning canola (Brassica napus L.) residue for Sclerotinia sclerotiorum (Lib.) de Bary sclerotia destruction. Pest Management Science 74:2594-2600.

Conference papers and presentations

  1. Bennett, SJ (2023). Determining yield loss in canola following Sclerotinia stem rot infection – an update. Australian Canola Pathology Workshop (Adelaide).
  2. Galloway, J., Sparks A., Marcroft S., Beard, C., & Chambers, K.R. (2023). How long do Sclerotinia sclerotia survive? SclerotiniaCM tool to help with on-farm management of sclerotinia stem rot. Australian Canola Pathology Workshop (Adelaide).
  3. Bennett, S.J., Lamichhane, A.R. & Michael, P.J. (2022). Using a systems approach to investigate the efficacy of a disease rating system for Sclerotinia stem rot in canola. System Solutions for Complex Problems. Proceedings of the 20th Australian Agronomy Conference. Ed. Bell, L. 18-22 September 2022, Toowoomba, Qld, Australia. (
  4. Michael, P.J., Lamichhane, A.R. & Bennett, S.J. (2022). Sclerotia contamination of canola and lupin grain by the fungal pathogen Sclerotinia in the Western Australian grainbelt. System Solutions for Complex Problems. Proceedings of the 20th Australian Agronomy Conference. Ed. Bell, L.18-22 September 2022, Toowoomba, Qld, Australia.
  5. Bennett, SJ (2022). Determining yield loss in canola following Sclerotinia stem rot infection. Australian Canola Pathology Workshop (Adelaide & online).
  6. Hills (2015) Using grain sclerote levels to study canola Sclerotinia distribution in WA Australasian Plant Pathology Society Conference, 14-16th September, Fremantle, Western Australia. Available at
  7. Hills AL (2018) Sclerotia size and position in post-harvest canola stems Proceedings of the 20th Australian Research Assembly of Brassicas, Perth, Western Australia. Available at
  8. Hills A.L. & Delroy J. (2018) A survey of Sclerotinia stem rot sclerotia in canola stems post-harvest Proceedings of the 20th Australian Research Assembly of Brassicas, Perth, Western Australia. Available at
  9. Michael, P., Lamichhane, A.R., Crockett, R. & Bennett, S. (2022). Effect of soil water content, soil texture and sclerotia conditioning temperature on myceliogenic germination of Australian Sclerotinia sclerotiorum isolates. Botrytis-Sclerotinia Symposium 2022, Avignon, France. (
  10. Bennett, S., Lamichhane, A.R., Crockett, R. & Michael, P. (2022). Sclerotinia sclerotiorum inoculation response on Brassica napus varieties is influenced by environmental conditions. Botrytis-Sclerotinia Symposium 2022, Avignon, France. (
  11. Bennett SJ (2021). Is a disease rating system feasible for Sclerotinia stem rot in canola. Australian Canola Pathology Workshop (Online).
  12. Bennett, S.J., Michael, P.J., Thompson, L.L. & Lui, K.Y. (2019). Increasing our understanding of the impact of management in canola to reduce the incidence of sclerotinia stem rot. 2019 Australian Plant Pathology Society Conference, Melbourne (presentation).
  13. Michael, PJ., Bennett, SJ, Thompson, LL & Lui, KY (2019). Influence of pre-conditioning and germination temperatures on the carpogenic germinability of diverse Sclerotinia sclerotiorum populations within the south-western Australian grain belt. 2019 Australian Plant Pathology Society Conference, Melbourne (presentation).
  14. Lindbeck, K., Khangura, R., Leo, A., Beard, C. & Hills, A (2018) Sclerotinia research 2013-2018 – Summary of major findings and future directions from the national canola pathology project. Australian Canola Pathology Workshop.
  15. Khangura, R., Van Burgel, A., Salam, M. & Aberra, M. (2015). Epidemiology and management of Sclerotinia stem rot in canola. 14th International Rapeseed Congress, Saskatoon, Canada.
  16. Khangura, R., MacLeod, W.L., & Aberra, M. (2011) Dynamics of fungal diseases of canola in Western Australia. 17th Australian Research Assembly on Brassicas (ARAB), Wagga Wagga, NSW.

GRDC Updates

  1. Galloway et al. (2023).  How long do Sclerotinia sclerotia survive in WA? Decision support tools to help with on-farm management of blackleg and sclerotinia in canola, GRDC Grains Research Updates.
  2. Bennett, S.J., Michael, P.J. & Rijal Lamichhane, A. (2022). Determining yield loss in canola following Sclerotinia stem rot infection. GRDC Grains Research Updates, Perth.
  3. Bennett, S.J., Derbyshire, M., Michael, P., Denton-Giles, M., Lui, K.Y., & Thomson, L. (2019). Tackling Sclerotinia – an insight into the factors influencing disease development. GRDC Grains Research Updates 2019, 25-26 Feb 2019. Perth. GRDC.
  4. Diggle, A. et al. (2019). Tailored management of sclerotinia in canola with SclerotiniaCM app. GRDC Grains Research Updates, Perth.
  5. Jupp, B., Butler, A., Beard, C., Smith, A., Wahlsten, L., Swift, B. & Galloway, B. (2019). Validating the SclerotiniaCM app for managing sclerotinia in canola. GRDC Grains Research Updates.
  6. Bennett, S.J., Brooks, K., Ashworth, M., Denton-Giles, M. & Michael, P. (2018). Factors affecting Sclerotinia stem rot infections in canola. Grains Research Updates 2018, 26-27 Feb 2018. Perth. GRDC.
  7. Beard, C. & Smith, A. (2018). Understanding how sclerotinia sclerotiorum initiates stem rot. GRDC Grains Research Updates, Perth.
  8. Khangura, K., Aberra, M., & Vincent, S. (2017). 'Sclerotinia in canola - ground infections, effect of row spacings. Is it worth spraying after you see the disease?' GRDC Grains Research Updates, Perth.
  9. Khangura, R. et al. (2016). Fungicide options and optimal spray timings for effectively managing Sclerotinia stem rot in canola, GRDC Grains Research Updates, Perth.
  10. Khangura, R. (2015). Unravelling factors involved in the development of Sclerotinia stem rot in canola, particularly in the light of making fungicide spray decisions, GRDC Grains Research Updates. Available to view on
  11. Khangura, R., van Burgel, A., Salam, M., Aberra, M., MacLeod, W.J. (2014). Why was sclerotinia so bad in 2013, GRDC Grains Research Updates, Perth.


GRDC for funding the research through the following projects: DAW2112-002RTX, DAW1810-007RTX, DAW00228, DAW2104-002RTX, MGP2307-001RTX, UM00051, CUR000023. We acknowledge the collaborators we have worked with on this research, particularly growers who have hosted trials.

DPIRD staff: Kylie Chambers, Ravjit Khangura, Kith Jayasena, Anne Smith, Debra Donovan, Bec Swift, Bonnie Jupp, Alice Butler, M. Aberra, S. Vincent, DPIRD Field research support staff

Centre for Crop Disease Management staff: Ashmita Lamichhane, Rachael Crockett, Mark Derbyshire, Linda Thompson, King-Yin Lui, Kyran Brooks, Michael Ashworth

Contact details for further information on managing sclerotinia in canola

Geraldton Port Zone – Ciara Beard, DPIRD,, 08 9956 8504

Esperance and Albany port zones – Andrea Hills, DPIRD,, 08 9083 1144

Kwinana Port Zone – Jean Galloway, DPIRD,, 08 9690 2172 and Kylie Chambers, DPIRD,, 08 9690 2151

Centre for Crop Disease Management – Pippa Michael,; and Sarita Bennett,, 08 9266 2740