Managing sclerotinia stem rot in canola

Page last updated: Tuesday, 27 February 2024 - 6:12pm

Please note: This content may be out of date and is currently under review.

Sclerotinia stem rot is a fungal disease of canola, that can cause significant yield losses exceeding 20% under conducive conditions.  Initially only common in parts of the Geraldton port zone, it is now a challenge in other areas of Western Australia's wheat belt. It is one of the most variable and unpredictable diseases of canola but incidence of infection varies greatly between paddocks and between years. Yield losses can be severe in years of higher moisture, cool conditions and high humidity which favour disease development. 


Sclerotinia can infect any part of the plant. Visible symptoms are  most commonly found on the stem and branches, and sometimes leaves and pods.

Stem symptoms appear as bleached greyish white, or brownish white, fungal growth covering portions of the canola stem sometimes just above soil level but also at any height in the canopy. After infection is well established, the disease causes plants to wilt and ripen prematurely, resulting in lodging and reduced seed production. Advanced infection will have sclerotia (hard, black, generally irregular-shaped to rounded bodies) growing on the inside of the affected and bleached parts of the stem. Bleached stems can be carefully split to observe the black sclerotia within. The sclerotia, which are larger than 2 millimetres (mm) in diameter, are the survival structure of the fungus. They appear like rat droppings. In moist weather they can also form on the outside of the infected stem or roots.

If the weather is favourable, canola pods also may become infected. Infected pods appear creamish white in colour and usually contain white mouldy seeds. In some instances, these seeds are replaced by sclerotia which contaminate harvested seed samples.

In wet years basal stem infection can occur prior to flowering where sclerotia in the soil germinate to produce mycelium that can directly penetrate canola leaves touching the ground or the stem base of a nearby canola plant. This appears as fluffy white growth on the soil, leaves and the stem base where it touches the soil.

Further information on diagnosis is available on the MyCrop sclerotinia page and you can submit samples for definitive diagnosis to DDLS - Plant pathology services (this is a chargeable service).

Leaf lesion due to sclerotinia appearing as a watermark on canola leaf
Sclerotinia leaf lesions can appear as watermarks on canola leaves
Early stem lesion of sclerotinia stem rot infecting canola
Early stem lesions appear as a bleached oval area on infected stems
Stem bleaching, rotting and lodging due to sclerotinia stem rot in canola
Stem bleaching, rotting and lodging due to sclerotinia stem rot in canola
Sclerotia of sclerotinia stem rot on the outside of an infected canola stem
Severe infection on stem showing fluffy white fungal growth and sclerotes
Creamish white pods that usually contain white mouldy seeds
Sclerotinia infection causes creamish white pods that usually contain white mouldy seeds
Bleached canola stem indicative of sclerotinia stem rot infection
Infected canola stems stand out as looking bleached and maturing early amidst healthy plants
Bleached lodged stems due to sclerotinia stem rot in canola
Infected stems are weak and can lodge
Break open the bleached stem to find black sclerotes inside due to sclerotinia infection
Breaking open the bleached stem may reveal black sclerotes inside, the resting phase of the fungus
Sclerotinia basal infection in a canola crop.
In wet years, sclerotinia mycelium may be observed on leaves on the ground and the very base of the stem prior to crop flowering. This is known as basal infection.

Assessment of sclerotinia risk

Risk factors for sclerotinia stem rot infection include:

  • paddock history
  • rotation with susceptible crops
  • disease incidence in the last affected crop
  • distance from last affected crop
  • rain events during flowering.

For disease to occur, sclerotia or spores must be present to initiate infection. Sclerotinia sclerotia can survive for up to six years or more in the soil, so the disease risk persists for several years. Sclerotinia spores can blow in on the wind from neighbouring paddocks that previously had the disease.

A canola crop is considered at risk of developing sclerotinia stem rot if:

  • Sclerotinia has been present within the past three years in the paddock or an adjacent paddock.
  • An intensive rotation with other broad-leaf crop species has been followed. For example, if a canola or susceptible crop has been grown in the past two years, then the risk is high compared with a paddock where only cereals have been grown for the past five years.

The over-riding determinant of the severity of sclerotinia stem rot that develops on the primary stem in a crop is the weather during flowering. Moisture in the crop canopy is required for infection to occur and develop into stem rot. This usually results from frequent rain events of 5mm or more. Infrequent rain or light showers are unlikely to result in sufficient canopy wetness for yield-limiting infections to occur.

Cause and disease cycle

Sclerotinia stem rot is caused by the fungus Sclerotinia sclerotiorum. It survives as sclerotia in the soil for many years. The fungus may also survive by colonising other host broadleaf plants such as lupins, chickpeas, lentils, faba beans and field peas, and weeds such as wild radish and capeweed. During cool (10-22ºC), moist weather in autumn or winter, sclerotia in the soil (fruiting bodies that look like rat droppings) germinate and produce small, cream/brown/orange, mushroom-like bodies called apothecia. These grow to be about 5mm in diametre and become darker coloured as they age. Sclerote germination usually occurs when the crop canopy has closed over (eg from cabbage stage in canola) as this creates a humid, protected environment. DPIRD research has found that a single sclerote can produce multiple apothecia at a time, and some produce multiple generations over several months if weather conditions are favourable. Most apothecia last at least 2 weeks under optimal conditions and at most 5 weeks, with the average being around 3 weeks.


Healthy/young apothecia of sclerotinia look like tiny white mushrooms and over time they age/dehydrate to turn brown
Healthy/young apothecia of sclerotinia look like tiny white mushrooms (top) and over time they age/dehydrate and turn brown (bottom)

These apothecia produce large numbers of ascospores (millions), which become airborne and blow to nearby crop plants. While the spores rarely infect healthy stems and leaves directly, they readily infect canola petals (illustrated below) if weather conditions are favourable. When infected petals fall into the canopy and stick to leaf axils, the fungus invades healthy leaves and stems using the infected petal as a food source. Cool, wet weather favours the pathogen, and mist, dew and fog provide enough moisture for infection.

In summary there are three trigger points (stages) required for sclerotinia infection to occur in canola and all need specific favourable weather conditions to be successful :

  1. Germination of sclerotia to form apothecia (in autumn/winter) that produce ascospores - cool (10-22ºC), moist weather
  2. During crop flowering, infection of petals by the ascospores - moist humid weather
  3. Infection of the crop as infected petals fall into the crop canopy - cool moist humid weather (temperatures below 25°C)

If the presence of apothecia does not coincide with crop flowering (for petals to be infected) and/or if the weather conditions are not suitable at any of these three points then significant stem infection will not occur. Sclerotinia disease levels are closely related therefore to seasonal rainfall and the disease is mostly a problem in average to above average rainfall seasons.

Under extremely moist conditions, sclerotia resting in the soil can also germinate to produce hyphae or mycelium that can penetrate the stem base of a nearby canola plant and cause basal stem infection. Direct germination of sclerotia is not considered to be a common cause of infection in canola, but has been observed in WA in wet years such as 2016 and 2018.

To keep up to date with sclerotinia reports from across the wheatbelt subscribe to PestFax. If you find apothecia or sclerotinia in your crop please report your find to PestFax reporter to let other growers know, or the PestFax editor via

Lifecycle of sclerotinia stem rot showing how disease develops and spreads
Lifecycle of sclerotinia stem rot showing how disease develops and spreads


Sclerotinia sclerotiorum has a wide host range including more than 400 different plant species. It infects most of the broad-leafed crops. Among these, lupins and chickpeas are commonly infected whereas faba beans and field peas appear to be less susceptible. Broad-leafed weeds, such as wild radish and capeweed are also hosts and play a role in carryover of the fungus.


Rotation and fungicides are currently the best strategies for managing scleronia stem rot, including:

  • long rotations
  • rotating with non-host crops
  • avoiding sowing close to last year’s infected crop
  • using clean seed (that does not contain sclerotia)
  • using foliar fungicide.

Under dry conditions sclerotia can remain viable in the soil for up to ten years, but parasitism and moisture commonly mean they survive 3-6 years on average. Research by CCDM into burning stubble has found that it can prevent germination of sclerotia on the soil surface within the windrows, but buried sclerotia, those in standing stems or outside the windrows remain viable. Research by DPIRD into grinding up sclerotia to simulate the use of a weed seed destructor found that it can provide some reduction in sclerotia germination but would not be a complete solution. We found that finely ground sclerotia could still germinate to form apothecia though there were fewer apothecia formed, they were smaller in size and did not persist as long compared to those germinated from whole sclerotia.   


Crop rotation can help in reducing disease severity. Leave canola out of the rotation for as long as possible (at least three years) to allow sclerotia to decompose, reducing the risk of subsequent infections. Include species unaffected by sclerotinia in rotations, such as cereals. Leave out species such as lupins, chickpeas and lentils, which are very susceptible. Windborne spores may be blown a great distance into susceptible crops. Separate canola crops by 100 metres or more from paddocks that had conspicuous levels of sclerotinia stem rot in the previous year.


Mouldboard ploughing of infected stubble may reduce carryover initially to subsequent crops as deep burial - greater than 15 centimetres - limits germination of sclerotia and development of apothecia. Most sclerotia germinate if they are close (within 2-3cm) to the soil surface but may survive for five or more years when buried at greater depths. If deep tillage is used in following years, viable sclerotia can be brought back to the soil surface continuing the problem. Hence, management with tillage is uncertain.


Registered fungicides

The Registered foliar fungicides for canola in WA page shows current registrations for both sclerotinia and blackleg. It is important to read product labels carefully before applying products. Always use fungicides according to the product label. Some products require addition of a wetter. Take note of application instructions in regards to harvest withholding periods.

The decision to spray should be based on:

  • presence of inoculum (previous sclerotinia infections in paddock or nearby, sightings of apothecia in area)
  • favourable weather conditions for the pathogen
  • crop growth stage - flowering stages are described below
  • frequent showers and humidity within the crop canopy during and after flowering. This is crucial, firstly to enable petal infection to occur, and then secondly, once the petals drop conditions need to be right for them to infect the crop branches/stems.
  • yield potential.

It can be very challenging to decide whether to apply a foliar fungicide for sclerotinia in a given season. In many of the DPIRD trials conducted over many years, sclerotinia did not eventuate, and even when it did, a fungicide application did not always result in a significant yield response. The SclerotiniaCM app can assist with spray decisions and allows the user to enter information specific to their paddock (eg sclerotinia history), crop (eg target yield, flowering stage), and expected local weather conditions. It is free and works on iPad or android tablets so can be used in the paddock to determine the likely economic returns from a spray decision. Further information is available on the SclerotinaCM app page including links to download the app to tablet devices. 

In the webinar below, Ciara Beard and Dr Art Diggle (DPIRD) discuss Sclerotinia stem rot in canola and share some tips for using the SclerotiniaCM App when making fungicide spraying decisions. 

Timing of fungicide application

The timing of fungicide application is extremely important for the effective control of this disease. Timing is heavily dependant on seasonal conditions so can vary year to year.

Western Australian trial data suggests that in the case of early on-set of disease, early applications at 15-30% bloom may give excellent control of the disease whereas late applications (40-50% bloom) may be too late. However, an economic response from late applications may be achieved if the disease epidemic starts late in the season (as occurred in many areas in 2013 with a wet spring). On average in most seasons, application at 20-30% bloom may be a good strategy if only one fungicide spray will be applied. If an early application was applied (10-20% bloom) and the forecast is for a wet spring which will favour the disease, then a second appliction may be required around 40-50% bloom. However, the decision to spray (or not to spray) is determined by the disease risk, the current price of canola and the yield potential of the crop. The SclerotiniaCM app takes all these factors into account for you so is a great tool to help you determine the best timing for fungicide application to your crop. Further information on the app is provided below under 'Decision support tool.'

Application before 10% flowering (10 flowers open on main stem) is usually not economic, and spraying after 50% is not recommended due to harvest witholding period (read product label).

Sclerotinia infection and spread requires moist conditions so if it is dry, or hot (>25ºC) disease progression in the crop will slow. Hence being flexible and monitoring future rainfall patterns is important in the timing of fungicide application; applying close to the next rainfall event is a good strategy. The economics of fungicide applications is discussed in the 'Current research' section below. How to assess the various flowering stages in canola is described in another section below.

Flowering window - varieties and time of sowing

All current commercial canola varieties are considered to have low resistance to sclerotinia. However, some varieties may be less susceptible than others. Risk of infection each year is related to whether a variety's flowering window coincides with spore release or extended humid weather conditions in that particular season. In average years, late flowering/late sown varieties can sometimes escape infection. In other years, if autumn is dry and spore release occurs later than usual, then early flowering or early sown varieties may escape the brunt of infection. Sow only good-quality seed that is free of sclerotia.

All current commercial canola varieties are considered to have low resistance to sclerotinia. Why is it so difficult to breed canola varieties with resistance to sclerotinia stem rot? The reasons are:

  • lack of reliable screening techniques

  • challenges in screening lines under field conditions

  • pathogen variability.

Assessment of flowering stages in canola

Guide to canola bloom stages
Guide to canola bloom stages (© DPIRD 2021).

Flowering (bloom) stages in canola can be challenging to determine so a standard method of assessing them is provided below. Correct determination of flowering stages will enable fungicides to be applied at the correct time.

Flowering stage should be assessed on the main stem:

  • 10% bloom = 10 flowers open on main stem
  • 20% bloom = 14-16 flowers open on main stem
  • 30% bloom = 17-20 flowers open on main stem
  • 50% bloom = more than 20 flowers open on main stem, crop is at its most instense yellow (full flower)
  • 60% bloom = flowering intensity is beginning to decline.

A video guide to determining bloom stages in available in the 'Tips' section of the  SclerotiniaCM app. Click on the lightbulb icon in the app to access the 'Tips' section. 

Decision support tool - the SclerotiniaCM app

SclerotiniaCM is a sclerotinia decision support tool for iPad/android tablet.  The tool estimates the net return from spraying to control sclerotinia, including minimum and maximum estimates, to assist growers in making spray decisions in a given season.  This tool has been developed by DPIRD in the National Pathogen Modelling Project, led by DPIRD research officer Jean Galloway, with input from canola pathologists and agronomists in WA, NSW, Victoria and SA.  The user enters their situation specific inputs (example below) and the tool uses this to produce an economic return for spraying to control sclerotinia vs not doing anything (no spray). In the example below it can be seen that in most years a spray on this crop would result in a $26 net return on investment (highlighted line in the ‘Change due to spray’ box).  In 1 in 10 years this spray might result in a loss of $16 (minimum net return) and/or up to $74 (maximum net return).  The app is available for free from the app/google play stores. 

Sclerotinia decision support tool example
Sclerotinia decision support tool example

Current research

Department of Primary Industries and Regional Development with funding from GRDC is currently undertaking research in the following areas in relation to sclerotinia stem rot:

  • sclerotinia surveys and monitoring
  • epidemiology (sclerote germination and longevity, petal testing and spore trapping) to understand the disease lifecycle in the field
  • epidemiological work assessing sclerote germination under controlled environmental conditions in the laboratory to see how apothecia formation is affected by moisture, temperature, sclerote source and soil type
  • timing of fungicide application, and investigating non-chemical measures for control
  • effect of sowing time, row spacing, crop density and flowering time on sclerotinia development
  • investigating ground-level (basal) infection
  • investigating the influence of abiotic factors on inoculum production and disease development
  • development of an automated imaging system to monitor germinating apothecia from sclerotes in the field
  • conducting field trials and working with industry to validate and improve the SclerotiniaCM app.

Crop Updates papers outlining recent research results are available to download from 'External links' on the right hand side.

Incidence surveys in Western Australia

Survey results have shown high incidence of sclerotinia stem rot (SSR) across canola crops in WA in 2008, 2009, 2011 and 2013 and particularly with significantly higher incidence in the Geraldton port zone in all years except for in 2013 (see Figure 5). This does not mean the disease cannot be a problem in southern areas of the state. Survey results of 71 crops in the southern agricultural region in 2009 showed over 20% exhibiting symptoms of sclerotinia stem rot and in four worst affected crops the incidence ranged between 69-80% (see Figure 6). Also, in 2013, SSR incidence was relatively high in the southern agricultural region and it has been since. In recent years, SSR incidence was high in 2016 and 2018.

Five years of incidence survey results showing a general decline in the incidence of sclerotinia stem rot but with a significantly higher rate in the northern agriculture region of Western Australia
Figure 5 Sclerotinia stem rot incidence in Western Australia (2008-2013).
Three crops from the shires of Cranbrook and the Stirlings in Western Australia showed an incidence of sclerotinia in excess of 70% and one in Mt Barker was nearly 70%
Figure 6 Survey results assessing the prevalence of Sclerotinia stem rot in four crops in the Southern Agriculture Region in Western Australia

Efficacy and economics of fungicide applications

Research activities have shown that in the presence of disease, treatment with fungicides has improved the percent disease index by a significant level and sometimes this results in grain yields showing significant improvements compared to untreated controls. The economics of these treatments, however is largely dependent on the cost of fungicide applied, with more expensive fungicides not improving yields enough to recoup application costs. Table 2 and 3 below provide an indication of the economics of fungicide applications.

Cost return tables

Table 2 Return on fungicide application (dollars per hectare ($/ha)) for a range of crop yield potentials and expected yield response when a single application of fungicide is made by plane ($15/ha) for a total cost of $41/ha. Canola price used was $500/t.
- Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha)
Yield response (%) 0.7 1.0 1.2 1.5 1.8 2.0 2.2 2.5
0 -41 -41 -41 -41 -41 -41 -41 -41
+5 -24 -16 -11 -3 4 9 14 22
+10 -6 9 19 34 49 59 69 84
+15 11 34 49 71 94 109 124 147
+20 29 59 79 109 139 159 179 209
+25 47 84 109 147 184 209 234 272
+30 64 109 139 184 229 259 289 334
+35 82 134 169 222 274 309 344 397
+40 99 159 199 259 319 359 399 459
Table 3 Return on fungicide application ($/ha) for a range of crop yield potentials and expected yield response when a single application of fungicide is made by self-propelled boomspray ($5/ha) for a total cost of $31/ha. Canola price used was $500/t.
- Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha) Crop yield (t/ha)
Yield response (%) 0.7 1.0 1.2 1.5 1.8 2.0 2.2 2.5
0 -31 -31 -31 -31 -31 -31 -31 -31
+5 -14 -6 -1 7 14 19 24 32
+10 4 19 29 44 59 69 79 94
+15 21 44 59 81 104 119 134 157
+20 39 69 89 119 149 169 189 219
+25 57 94 119 157 194 219 244 282
+30 74 119 149 194 239 269 299 344
+35 92 144 179 232 284 319 354 407
+40 109 169 209 269 329 369 409 469

Acknowledgements and disclaimer

The information presented here includes results of two GRDC cofunded projects - the National Canola Pathology Project (DPIRD staff: Ravjit Khangura, Ciara Beard and Andrea Hills), and the National Pathogen Modelling Project (DPIRD staff: Jean Galloway, Art Diggle, Kylie Chambers, and Ciara Beard).

Mention of trade names does not imply endorsement or preference of any company’s product by Department of Primary Industries and Regional Development. Any omission of a trade name is unintentional. Recommendations are current at the time of publication.


Ravjit Khangura
Ciara Beard
Andrea Hills