Canola Disease Update - Sclerotinia

Author: | Date: 25 Jul 2017

NSW Department of Primary Industries

Take home message

  1. Sclerotinia stem rot is a production issue where spring rainfall is adequate to provide long periods of leaf wetness in the presence of flowering canola crops.
  2. If there is a history of sclerotinia stem rot in your district causing yield loss, be prepared to use a foliar fungicide to reduce yield loss.
  3. Sclerotinia stem rot occurred in those districts with a frequent history of the disease in 2016.  Wet conditions in spring were ideal for disease development.
  4. Extended periods of leaf wetness (approximately 48 hours) are ideal for triggering epidemics of stem rot.
  5. Foliar fungicides for management of the disease are best applied at 20% to 30% bloom for main stem protection.

Sclerotinia Stem Rot – 2016 in Review

Seasonal overview

Growing season conditions in winter and early spring were highly conducive for the development of sclerotinia stem rot in 2016 in southern and central NSW.  Prolonged wet weather in winter was ideal for the germination and development of apothecia, the fruiting structures of the sclerotinia fungus.  The first warning signs appeared in early July with apothecia being observed within canola crops in southern NSW, with flowering commencing shortly afterwards in some early sown crops.  Continued wet weather throughout August and September provided periods of extended leaf wetness and opportunities for disease epidemics to develop in many districts.

In general, disease levels were low across southern NSW despite the wet conditions.  Widespread use of foliar fungicides in high disease risk districts was effective in managing the disease.

How does the disease develop?

The complexity of the disease cycle of sclerotinia stem rot results in disease outbreaks being sporadic compared to other diseases. There are several key stages that must be synchronised and completed in order for plant infection to occur.  Weather conditions must be suitable for the pathogen at each stage. These stages of development include:

  1. Softening and germination of soil borne sclerotia;
  2. Apothecia development and release of ascospores;
  3. Infection of petals by air-borne ascospores; and
  4. Senescence of infected petals in the presence of moisture and subsequent stem infection.

Weather conditions during flowering play a major role in determining the development of the disease. The presence of moisture during flowering and petal fall will determine if sclerotinia stem rot develops. Dry conditions during this time can quickly prevent development of the disease, hence even if flower petals are infected, dry conditions during petal fall will prevent stem infection development.

Research findings in 2016

Commercial canola crops and trial sites were monitored for the development of sclerotinia stem rot in high sclerotinia risk districts in 2016.  These crops were located in southern NSW and northern Victoria where the disease is an annual problem.  Consistent with the previous year’s results, observations within these crops found a very strong relationship between prolonged periods of leaf wetness and stem rot development.

In addition, a small scale petal survey was conducted across southern NSW and northern Victoria in 2016.  The aim of this survey was to investigate the relationship between petal infestation with the sclerotinia fungus and stem rot development.

Stem infection

Infection levels at disease monitoring sites were generally low (<10%). Despite above average rainfall, foliar fungicides applied by growers were effective at keeping potential disease levels low.  However, some reports were received of higher levels of stem infection in some commercial crops, depending on where rainfall events occurred and crop growth stage.  Consistent with previous seasons, results showed that extended periods of leaf wetness of at least 48 hours were most effective for the development of stem infection within crops.

Petal testing

For the second year a petal survey was conducted across NSW and northern Victoria. The highest levels of petal infestation (>90%) were detected in crops grown in higher rainfall districts with a high frequency of canola crops.  Crops further west had reduced levels of infestation in general (<60%), with levels of infestation fluctuating with environmental conditions. These results are consistent with the previous year’s findings.

Once again the results confirm findings that were observed 10 years ago which found no direct correlation between the numbers of canola petals infested with the sclerotinia pathogen and stem rot development within the crop. This confirms the importance of leaf wetness within the crop canopy as the driving factor behind development of stem rot.

Where did the disease occur in 2016 in NSW?

Traditionally sclerotinia outbreaks are more frequent in southern NSW and northern Victoria and usually restricted to those districts with a history of sclerotinia, high intensity of canola and reliable spring rainfall. Due to above average spring rainfall in 2016 outbreaks of the disease where widespread and in districts that rarely see the disease develop.  Damaging levels of sclerotinia where largely restricted to the ‘traditional’ districts that frequently see the disease, while in lower rainfall districts the disease was observed but didn’t significantly affect canola yields.

What are the indicators that sclerotinia stem rot could be a problem in 2017?

  1. Spring rainfall.  Epidemics of sclerotinia stem rot generally occur in districts with reliable spring rainfall and long flowering periods for canola.
  2. Frequency of sclerotinia outbreaks. Use the past frequency of sclerotinia stem rot outbreaks in the district as a guide to the likelihood of a sclerotinia outbreak.  Paddocks with a recent history of sclerotinia are a good indicator of potential risk, as well as those paddocks that are adjacent.  Also consider the frequency of canola in the paddock.  Canola is a very good host for the disease and can quickly build up levels of soil-borne sclerotia.
  3. Commencement of flowering. The commencement of flowering can determine the severity of a sclerotinia outbreak.  Spore release, petal infection and stem infection have a better chance of occurring when conditions are wet for extended periods, especially for more than 48 hours.  Canola crops which flower earlier in winter, when conditions are cooler and wetter, are more prone to disease development.

Sclerotinia in lower rainfall areas

In lower rainfall regions sclerotinia stem rot is generally not a canola production issue. The disease may appear sporadically in some years, but often at levels that cause negligible yield loss. In these regions disease control would focus on blackleg, rather than sclerotinia stem rot.

To manage sclerotinia stem rot in lower rainfall regions use prevention measures such as:

  • Paddock selection. Sow this year’s crop away from last year’s canola stubble to prevent airborne spore movement between paddocks.
  • Crop rotation. Canola is an excellent host for the Sclerotinia stem rot fungus, the more frequently that canola is grown in a paddock, the more opportunities for sclerotia to develop and build up.  In addition avoid sowing two consecutive broadleaf crops, such as lupin/canola.
  • Follow recommended sowing dates and rates for your district.


Early flowering crops are more prone to developing sclerotinia stem rot by increasing opportunities for infected petals to lodge in a wet crop canopy.  In addition, early sown crops will most likely develop bulky crop canopies which retain moisture and increase the likelihood of infection.  Wider row spacings can also help by increasing air flow through the crop canopy to some degree and delaying the onset of canopy closure.

Other disease prevention measures include:

  • Sowing canola seed that is free of sclerotia. This applies to growers retaining seed on farm for sowing.  Consider grading seed to remove sclerotia that would otherwise be sown with the seed and infect this season’s crop.
  • Consider the use of a foliar fungicide. Weigh up yield potential, disease risk and costs of fungicide application when deciding to apply a foliar fungicide.
  • Monitor crops for disease development and identify the type of stem infection. Main stem infections cause the most yield loss and indicate infection events early in the growing season.  Lateral branch infections cause lower levels of yield loss and indicate infection events later in the growing season.

Use of foliar fungicides

At this time there are no commercial canola cultivars available on the Australian market with resistance to sclerotinia stem rot.  Management of the disease relies on the use of cultural and chemical methods of control.  Foliar fungicides should be considered in those districts which are at a high risk of disease development (eg: districts where the disease frequently occurs, long flowering period and reliable spring rainfall).  There are several foliar fungicides currently registered for use in Australia to manage sclerotinia stem rot including Prosaro® and products containing the active ingredients procymidone or iprodione.

Points to consider when using a foliar fungicide to manage sclerotinia stem rot

  1. The most yield loss from sclerotinia occurs from early infection events.  Early infection is likely to result in premature ripening of plants that produce little or no yield.
  2. Plants become highly susceptible to infection once flowering commences.  Research in Australia and Canada has shown that an application of foliar fungicide around the 20% to 30% bloom  stage (20% bloom is 14 – 16 flowers on the main stem, 30% bloom is approximately 20 flowers on the main stem) can be effective in significantly reducing the level of sclerotinia stem infection.  Most registered products can be applied up to the 50% bloom (full bloom) stage.
  3. The objective of the fungicide application is to prevent early infection of petals while ensuring that fungicide also penetrates into the lower crop canopy to protect potential infection sites (such as lower leaves, leaf axils and stems). Timing of fungicide application is critical.
  4. A foliar fungicide application is most effective when applied before an infection event (eg: before a rain event during flowering).  These fungicides are best applied as protectants and have no curative activity.
  5. In general, foliar fungicides offer a period of protection of up to 3 weeks.  After this time the protectant activity of the fungicide is compromised. In some crops development of lateral branch infections later in the season is not uncommon if conditions favourable for the disease continue.  The greatest yield loss occurs when the main stem becomes infected, especially early.  Lateral branch infection does cause yield loss, but at a much reduced level.
  6. Use high water rates and ensure droplet size is optimum for good canopy penetration and coverage (always adhering to any label restraints).
  7. Fungicide choice is often secondary to timing of application.
  8. Be aware the maximum number of applications of Prosaro® in a season is two.

Consult the Sclerotinia Stem Rot in Canola factsheet for further information.

Useful resources

NSW DPI Winter Crop Variety Sowing Guide (Disease updates, variety resistance, fungicide products.)
NSW DPI Southern NSW Research Results 2015
NSW DPI Agronomy Twitter


The authors wish to thank NSW DPI and GRDC for investment into this research.

Contact details

Kurt Lindbeck
NSW Department of Primary Industries, Wagga Wagga Agricultural Institute
Ph: 02 69 381 608

Audrey Leo
NSW Department of Primary Industries, Wagga Wagga Agricultural Institute
Ph: 02 69 381 902

Joop van Leur
NSW Department of Primary Industries, Tamworth Agricultural Institute
Ph: 02 67 631 204

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