Managing sclerotinia stem rot in canola

Page last updated: Monday, 7 September 2020 - 10:04am

Please note: This content may be out of date and is currently under review.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

Contact information


Ravjit Khangura
Ciara Beard
Andrea Hills