Managing canola diseases blackleg and sclerotinia

Take home messages

  • Impacts on yield due to blackleg of canola are likely to be lower in northern NSW compared to southern NSW.
  • Growers should still be vigilant in managing this disease and an integrated approach should be adopted by growers that utilises variety resistance, cultural control and the strategic use of fungicides.
  • 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.
  • 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.
  • 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.
  • Extended periods of leaf wetness (at least 48 hours) are ideal for triggering epidemics of stem rot.

Sclerotinia stem rot – 2016 Update

Seasonal overview

Growing season conditions in winter and early spring were highly conducive for the development of sclerotinia stem rot in 2016.  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
  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.  For the third year in a row, 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 in southern 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 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 in research from 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?

Traditionally sclerotinia outbreaks are sporadic 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 was widespread and in districts that rarely see the disease develop.  Damaging levels of sclerotinia were 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?

  • Spring rainfall.  Epidemics of sclerotinia stem rot generally occur in districts with reliable spring rainfall and long flowering periods for canola.  Consider rainfall predictions for spring and canola crop growth stage.
  • 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.
  • 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.

If I had sclerotinia in my canola crop last year, what should I do this season?

There are a number of steps that can be taken to reduce the risk of sclerotinia:

  1. 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.
  2. Rotate canola crops. Continual wheat/canola rotations are excellent for building up levels of viable sclerotia in the soil. A 12 month break from canola is not effective at reducing sclerotia survival. Consider other low risk crops break crops such as cereals, field pea or faba bean.
  3. Follow recommended sowing dates and rates for your district.  BE AWARE OF THE MATURITY RATING OF THE VARIETY AND TIME OF SOWING. 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.
  4. 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.
  5. 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. 

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 and produce little or no yield.
  2. Plants become susceptible to infection once flowering commences.  Research in Australia and Canada has shown that an application of foliar fungicide around the 20% - 30% bloom  stage (20% bloom is 14 – 16 flowers on the main stem, 30% bloom is approx. 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[EM1] .
  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 fine droplet sizes for good canopy penetration and coverage.

Consult the Sclerotinia stem rot in canola factsheet for further information.  This publication is available from the GRDC website.


Blackleg, caused by the pathogen Leptosphaeria maculans, is the most damaging disease of canola and juncea-canola in Australia.  In southern NSW this disease is a major concern for producers, mainly due to the high intensity of canola production in the region.  In northern NSW the level of blackleg observed in commercial crops has been significantly lower where production of the crop is not as concentrated.

Despite the lower levels of blackleg observed in the north growers and advisors should still be vigilant in the management of this disease.  Blackleg is present in all canola paddocks and experience from southern NSW shows higher levels of blackleg development in canola crops with increasing intensity of production in the region.

Symptoms of blackleg

Blackleg most commonly causes distinct lesions on the cotyledons and leaves of canola plants early in the growing season. The lesions are generally pale grey with a dark border and develop distinct pycnida within the lesion.  These appear as “pepper like” spots within the lesion.

The blackleg fungus then grows without symptoms through the vascular tissues to the crown where it causes a necrosis resulting in a crown canker at the base of the plant. The crown canker appears as a dry rot at ground level and causes plants to lodge. This crown canker causes yield loss as it restricts water and nutrient uptake by the plant. Blackleg can occur on all plant parts, however, leaf lesions and crown cankers are the most commonly observed symptoms.

How do we best manage blackleg?

The most effective approach to reduce the impact of blackleg is to use an integrated strategy that utilises cultivar resistance, cultural control and the strategic use of fungicides.  The most effective management practices that can reduce the impact of blackleg include:

  1. Sowing canola cultivars with appropriate levels of blackleg resistance. This is particularly important in districts with a high intensity of canola production where cultivars should be sown with high levels of blackleg resistance.  Plant resistance is the first line of defence against blackleg.
  2. Avoid canola stubble, especially from the previous season’s crop. The distance from last season’s canola stubble will largely determine the severity of blackleg in this season’s canola crop.  Where possible a distance of at least 500m will significantly reduce the disease pressure from blackleg on this season’s crop.  Spores of the blackleg pathogen are released from old canola stubble onto emerging canola crops.  The greater the distance from this inoculum source the better.
  3. Apply seed dressing or fungicide-amended fertiliser. Application of a fungicide seed dressing or use of fungicide amended fertiliser will provide extra protection from blackleg in the critical early stages of crop emergence and establishment.  In high blackleg pressure situations this is very important.
  4. Foliar fungicides.  In certain situations it may be economical to apply a foliar fungicide to extend the length of protection from blackleg, such as if disease severity is very high, if genetic resistance is inadequate or has been overcome by the fungus. Results of field experiments indicated that use of a fungicide seed dressing in combination with the application of a foliar fungicide gives good levels of protection. However, the benefits are only found in those canola cultivars with a low level of resistance to blackleg and in situations of high disease pressure. 
  5. Canola resistance groups. The blackleg fungus has a high propensity to overcome resistance in Brassica napus (canola) cultivars as it is sexually reproducing, resulting in enormously diverse populations. Therefore, the fungal population evolves very rapidly and responds quickly to selection pressures such as wide-scale sowing of cultivars with specific resistance genes. This will lead to resistance being overcome when cultivars of the same resistance gene are sown for 3 or more years. However, we can use the fungal life traits to manipulate the fungal population, by changing cultivars with different sources of resistance, the selection pressure on the fungal population is constantly changing. All canola cultivars and NVT lines have been classified for blackleg resistance genes and placed into resistance groups.  This now allows producers to change or rotate canola cultivars after every 2 to 3 years and prevents the build up of isolates that can overcome resistance. By changing canola cultivars at least every 3 years to a cultivar containing different resistance genes, you are likely to reduce yield losses and reduce the probability of resistance breakdown occurring.

Be sure to check the GRDC website for the latest version of the Blackleg management guide, which will give the latest blackleg disease ratings and resistance groups.

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 account

GRDC Blackleg management guide


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

GRDC Project code: DAN00177, UM0051