Protecting WA crops

Sclerotinia stem rot

Sclerotinia Stem Rot

What is it?

Sclerotinia stem rot (SSR), caused by the fungus Sclerotinia sclerotiorum, is a disease that attacks canola and other broadleaf plants including lupins, chickpeas, lentils, sunflowers and soybeans. Over 400 species can act as a host for sclerotinia including capeweed and wild radish. Previously it was most commonly found in parts of the northern WA wheatbelt but more recently it has extended to most of the canola growing regions in the state.

Agriculture and Food at the Department of Primary Industries and Regional Development (DPIRD) are at the forefront of research into sclerotinia in canola to minimise yield losses to WA growers. From when the disease first started becoming an issue near Geraldton in 2008, DPIRD plant pathologists have been working on all aspects of the disease. From understanding the lifecycle, to cultural management, fungicide application, and developing a forecasting tool, we are providing the grains industry with information and strategies to help combat this disease.

Life cycle of sclerotinia and how to assess disease risk

The fungus survives as sclerotia (fruiting bodies that look like rat droppings) in the soil for 6 years or more or by colonising other host plants. 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 and conducive weather conditions during the season. For sclerotinia stem rot to develop in crop, there are 3 factors that need to occur.

  • Frequent rainfall events combined with temperatures of 10-20°C and high humidity are required for sclerotes to germinate and produce apothecia (small, cream, mushroom-like bodies). Apothecia release large numbers of ascopores into the air which can infect petals.
  • Humid moist weather during flowering and while ascopores are being released leads to petal infection.
  • Infected petals drop down into the crop canopy after 30% bloom and stick to leaf axils where, if weather remains humid and moist, the fungus invades the leaves or branches and ultimately the stems.
Life Cycle of Sclerotinia in canola in the WA grainbelt
Life Cycle of Sclerotinia in canola in the WA grainbelt

Diagnosing sclerotinia stem rot in canola

Symptoms of sclerotinia on the stem appear as bleached greyish white, or brownish with white fluffy fungal growth. Advanced infections have sclerotia (hard, black irregular shaped to rounded bodies) on the inside and bleached parts of the stem. In moist weather, sclerotia can also form on the outside of infected stems and roots. Canola pods can also become infected and will appear creamish white and seeds can be mouldy.

early stages of development of sclerotinia stem rot
Early stages of development of sclerotinia stem rot
Progression of Sclerotinia stem rot on the main stem and a secondary branch
Progression of Sclerotinia stem rot on the main stem and a secondary branch

Sclerote germination experiments

To better understand the lifecycle of Sclerotinia sclerotiorum and why some years or in some regions it is more of a problem than others, sclerote germination experiments are being conducted in Geraldton by DPIRD plant pathologist Ciara Beard and technical officer Anne Smith. In controlled environment conditions in the laboratory, investigations compare the germination of sclerotes sourced from different regions, currently Esperance and Geraldton, under two different temperature regimes (10-22°C/16-29°C) and two soil types (sand/loam). Research is supported by GRDC under the National canola pathology project and the National pathogen management modelling project. Sclerotes are watered regularly to keep them moist. As per past experiments, sclerotes in the current experiment have germinated after 40 days of being kept moist and in day/night temperatures of 10-22°C. This simulates the autumn conditions often found in the southern region such as Albany and Esperance.

Sclerote germination experiments being conducted in Geraldton with different temperatures and soil types.
Sclerote germination experiments being conducted in Geraldton with different temperatures and soil types.

In comparison, preliminary results show that no sclerotes germinated in day/night temperatures of 16-29°C despite regular watering. These temperatures simulate the autumn conditions in the northern wheatbelt such as Geraldton. This research assists our understanding of factors that affect sclerote germination in the different regions of the wheatbelt.

Work done by DPIRD Plant Pathologist Dr Ravjit Khangura in the field has shown that sclerotes can produce apothecia as early as 23 days. Further work is needed to understand why the sclerotes take longer to germinate in lab conditions than they do in the field.

Management options in canola

Sclerotinia in canola is currently being managed through the use of fungicides and some cultural practices.

Cultural practices

Some cultural practices that could be useful in reducing sclerotinia risks include:

  • Having a 1 in 5 year rotation of susceptible crops to prevent sclerote build up
  • Separating susceptible crops by at least 500m from last year’s susceptible crop stubbles or paddocks that have a history of sclerotinia in the previous 4 years
  • Using seed free of sclerotes to prevent spread of disease in disease free areas/paddocks
  • Burning windrows. During his honours project at the Centre for Crop Disease Management (CCDM), Kyran Brooks found that sclerotes can be destroyed by burning windrows if consistently high temperatures are reached. Earlier investigations by Tamrika Lanoiselet (DPIRD) during her PhD found that at lower temperatures sub-lethal burns were occurring. The sub-lethal burns resulted in sclerotes germinating early than unburnt sclerotes. This could lead to an extended window of sclerotinia risk making control more difficult.
  • Avoiding sowing early maturing varieties in March/April in high risk areas. This may result in crops flowering in June and July where conditions might be suitable for apothecia germination.
Sclerotes to be buried at depth
Sclerotes to be buried at depth

With mouldboard ploughing being used in some areas to reduce the weed seed bank and ameliorate non-wetting, could this also be used as a method of controlling sclerotinia? At the Esperance Downs Research Station, DPIRD plant pathologist Andrea Hills has established a trial where five different sized sclerotia have been buried at three depths (15, 20 and 30cm). The 825 sclerotia used were from a paddock at Scaddan and reflect the wide range of sizes (from 2mm to >15mm) which are produced by the fungus in the southern region (see attached photo for an example). They will remain buried for five years before being dug up to assess whether they are still intact and can germinate. There are some additional sclerotia buried that can be dug up in seven years if the others do manage to survive for five. To simulate the mouldboarding result, the soil was inverted on top of the sclerote pockets that were buried. This GRDC supported research is being funded as part of the National Canola Pathology Project.

Occasionally deep buried sclerotia can germinate and produce apothecia as shown by this sclerote found near Hopetoun in 2015.
Occasionally deep buried sclerotia can germinate and produce apothecia as shown by this sclerote found near Hopetoun in 2015.


Research over the past seven years has identified several products effective against Sclerotinia. Currently iprodione, promcymidone and prothioconazole + tebuconozole and more recently prothioconazole + bixafen based products are registered for sclerotinia control. With reports of fungicide resistance in sclerotinia overseas, the rotation of different fungicide groups will help to reduce the risk of this occurring here.

Since 2012, seventeen trials have been done by DPIRD across WA to compare fungicide timings from 10 to 50% flowering including double application scenarios. Nine of these trials had disease levels of 3% or more main stem infection and were taken through to harvest. Double applications (eg at 10 and 50% flowering) consistently reduced disease and increased grain yields. Single applications of fungicide reduced lesion development in approximately 80% of situations while yield responses varied, with two thirds of fungicides that were applied in the 20 -50% flowering window significantly increasing grain yields. It must be remembered that these trials had fungicides applied regardless of the outlook in weather conditions.

In a recent trial in 2016 at Moonyoonooka, in the Northern grainbelt, DPIRD plant pathologist Ravjit Khangura conducted trials to compare fungicide efficacy and timing for optimum economical return. Hyola 400 was sown under a good disease presence. Three different fungicides (Prosaro®, Sumisclex® and Product C) were applied at various bloom stages. All of the fungicides decreased the disease incidence resulting in increased yields in comparison to the untreated plants. There was no difference in disease incidence between the fungicide product or the timing of fungicide application. A double spray application at 10 and 50% proved to have the best yield response due to prolonged growing season that year.  Generally a well-timed single spray application is quite effective in controlling the disease and providing economic returns. However, an economic response from late fungicide applications (50% bloom) may be achieved if the disease epidemics start late in the season as occurred in many areas in 2013. Late spray applications past 50% bloom are not recommended.

Main effect of fungicide timing averaged over fungicides on disease incidence (percent plants infected) of Sclerotinia and grain yield (t/ha) of canola. Lsd (5%) for disease incidence = 7 and for yield = 0.170. Values above bars represent net return/ha ($
Main effect of fungicide timing averaged over fungicides on disease incidence (percent plants infected) of Sclerotinia and grain yield (t/ha) of canola. Lsd (5%) for disease incidence = 7 and for yield = 0.170. This is experimental trial work you will need to check labels for recommended timings of registered products.

Registered foliar fungicides for canola in Western Australia

Dr Khangura also investigated the effect of row spacing, plant density, variety and fungicide application on disease incidence and control in the NAR in 2016. Two varieties were sown (IH30RR and HR600RR) at two different row spacings (44 and 22cm) and two targeted plant densities (30 and 15 plants/m2) with or without Prosaro® applied at 30% bloom at the recommended rate of 450ml/ha. As expected, application of fungicide reduced disease but there was no effect of row spacing or plant densities, Hyola 600RR had less disease incidence than IH30RR. While there are no known resistant canola varieties to sclerotinia, some varieties have shown lower levels of incidence to the disease, most likely due to timing of flowering.

Table 1. Main effect of fungicide on disease incidence (DI) of sclerorinia stem rot and yield of canola.
Main factor Fungicide DI Yield (Kg/ha)
Fungicide + 6* 3393*
Fungicide - 17.2 3130
Lsd (5%) 4.8 176
Table 2. Main effect of row spacing on disease incidence (DI) of sclerorinia stem rot and yield of canola.
Main factor Row Spacing DI Yield (Kg/ha)
22cm 10 3244
44cm 13 3279
Lsd (5%) 5.7 176
Table 3. Main effect of plant density on disease incidence(DI) of sclerorinia stem rot and yield of canola.
Main factor Plant Density DI Yield (Kg/ha)
15 plants/m2 11.5 3150
30 plants/m2 11.6 3372*
Lsd (5%) 4.9 204
Table 4. Main effect of variety on disease incidence (DI) of sclerorinia stem rot and yield of canola.
Main factor Variety* DI Yield (Kg/ha)
IH30 RR 16 3015
GT 50 8* 3508*
Lsd (5%) 5.7 212

Letters in bold indicate significant treatment effects. * = significant treatments

For more information refer to Sclerotinia in canola - ground infections, effect of row spacings. Is it worth spraying after you see the disease?

Managing sclerotinia stem rot in canola

Sclerotinia stem rot in canola GRDC fact sheet

Seasonal variability

Every season is different which means there are no steadfast rules for managing sclerotinia year in year out. Growers need instead to be flexible and assess their risk and best time for fungicide application based on the current season considering:

  • Timing of sclerote germination- varies depending on autumn rainfall/the break of the season and temperatures being cool enough.
  • Flowering window (affected by variety and time of sowing) 
  • Weather conditions (humid moist weather) 3 weeks prior to flowering and during flowering favours petal infection and similar weather conditions after full bloom favours stem rot development.

Pathogenic diversity of WA sclerotinia field isolates

Dr Ravjit Khangura inspecting canola plants.
Dr Ravjit Khangura inspecting canola plants.

Preliminary work done by Dr Ravjit Khangura indicates that there are variations among WA isolates with some isolates more aggressive on certain host varieties; the pathogenicity of 20 different isolates was tested on a range  of canola varieties. CCDM is also investigating the genetic diversity to better understand how isolates differ from one another and how fast they can adapt to potentially new resistant canola varieties or commonly used fungicides. There is potential for collaboration between DPIRD and CCDM in this area in the future.

Sclerotinia forecast model

A forecast model that can predict when sclerotes are likely to germinate and produce apothecia (the small mushrooms) has been developed by researchers at DPIRD using epidemiology data generated in WA and NSW.  Jean Galloway, a plant pathologist with DPIRD is currently testing this model to see how accurate it is.  As part of this testing process sclerote depots have been established at nine locations next to weather stations in the wheatbelt this season.  These depots are equipped with smart technology that takes pictures of the sclerotes twice daily.  The images are sent to DPIRD, are scanned and the number of sclerotes that have germinated are recorded. The sclerote depot photographs identified apothecia germination occurred at Northam in mid-July and at Wickepin in the first week of August this year. The depot at Wickepin has had apothecia present for the entire four week period between early August through to early September.

Sclerotes can be seen germinating in the depot at Wickepin in this photograph taken on the 4 August 2017 and digitally sent to our computers for analysis and data recording.
Sclerotes can be seen germinating in the depot at Wickepin in this photograph taken on the 4 August 2017 and digitally sent to our computers for analysis and data recording.

The detailed information provided by the ‘Smart Sclerotinia Depots’ will be used to refine the apothecia forecast model. This work is being supported by GRDC, the National Modelling Project (led by Jean Galloway) and a Boosting Grains Research and Development Flagship project.

To spray or not to spray?

A sclerotinia decision support tool that will be available on tablets is in development.  The tool will estimate the net return from spraying to control sclerotinia, including minimum and maximum estimates.  The following are the current inputs that growers and consultants can adjust in the tool using the sliders (circles) on the left in the picture below:

  • Are you considering a first or second spray?
  • What is the target yield of the crop?
  • What is the anticipated grain price?
  • What are the costs of production other than sclerotinia management?
  • Is it a heavy or sandy soil type?
  • How frequently have broadleaf crops been grown in the paddock?
  • How frequently has sclerotinia loss been observed in past seasons?
  • What is the bloom stage of the crop?
  • How many wet days have there been in the past 3 weeks?
  • How many wet days are expected next week and in the week after?
  • What is the cost of the spray?
Sclerotinia decision support tool example
Sclerotinia decision support tool example

After entering your situation-specific inputs, the decision support tool produces a table (shown at the right of the screen) for the economic returns for spraying to control sclerotinia versus not doing anything (no spray).  It is planned that the sclerotinia tool will be available as a beta (test) version later this season. This tool is being developed by Art Diggle (DPIRD) in the National Pathogen Modelling Project, supported by GRDC, with input from canola pathologists and agronomists in WA, NSW, Victoria and SA. 

Sclerotinia in lupins

Sclerotinia stem rot in lupins

Sclerotinia stem rot (SSR) is also a damaging disease of crops other than canola. In Western Australia it has historically been a sporadic concern in lupins crops, causing stem and branch lesions as well as infecting individual pods or the whole main stem flower spike. However through the 2015 and 2016 seasons there have been increasing reports of damaging levels of SSR in lupin crops, most likely a result of highly favourable seasons and increasing inoculum pressure contributed by infected canola. In lupins, SSR causes both a yield reduction and considerable additional grain cleaning costs to remove sclerotia from the harvested sample prior to delivery.

A 2016 survey, conducted by Anne Smith from DPIRD, of lupin paddocks in the Geraldton port zone, found that 7/15 crops had SSR present, with incidence of infected plants ranging from 1-10%.

A lack of registered fungicides leaves growers without options for management of the disease. Preliminary field trials, with unregistered products, have demonstrated reduced sclerotinia infection and given a positive yield response in albus lupin (4 – 15%) and narrow-leaf lupin (0 – 14%).

Limited variety screening for sclerotinia has been conducted in lupins. Preliminary testing of released varieties has not detected any significant difference in susceptibility of stem tissue to infection. Paddock observations suggest that crop canopy development, flowering date and regional weather conditions influence incidence and severity of infection more than variety. Research into managing sclerotinia in lupins is supported by GRDC through the Improving grower surveillance, management, epidemiology knowledge and tools to manage crop disease project.


Sclerotinia in canola

Dr Ravjit Khangura
Research Officer
Ph: +61 (0)8 9368 3374

Andrea Hills
Research Officer
Ph: +61 (0)8 9083 1144

Sclerotinia forecast model

Jean Galloway
Research Officer
Ph: +61 (0)8 9690 2172

Sclerotinia spray decision tool

Dr Art Diggle
Senior Research Officer
Ph: +61 (0)8 9368 3563

Sclerotinia in lupins

Geoff Thomas
Research Officer
Ph: +61 (0)8 9368 3262