Take home messages

• Outbreaks of sclerotinia stem rot are sporadic and dependent on the growing season conditions, presence of sclerotes and susceptible crop host. Saturated canopy conditions for more than 48 hours during flowering favour the development of disease epidemics in canola paddocks with a history of disease
• Development of sclerotinia stem rot was variable across NSW in spring 2024 depending on winter and spring rainfall patterns. This will have implications for Sclerotinia development in 2025
• The frequency of canola or narrowleaf lupin in a paddock is very important in determining the risk of a sclerotinia outbreak, as these crops are susceptible hosts for the disease and can quickly build up levels of soil borne sclerotia
• Foliar fungicides for management of the disease in canola are best applied at 20 – 30% bloom (15–20 open flowers on the main stem) for main stem protection
• Double break crop rotations pose an increased risk of Sclerotinia disease development and need to be managed carefully. This includes management of Sclerotinia in other broadleaf phases of the cropping rotation.

Background

Changes within farming systems over the last decade have favoured the development of Sclerotinia disease within crop rotations. With improvements in blackleg resistance and broader adaptation in newer cultivars, canola is now grown in high frequency across a wide range of rainfall zones in NSW. The emergence of canola as a major component of rotations has resulted in Sclerotinia disease becoming a more frequent problem for producers and an important consideration for many. However, the sporadic nature of disease outbreaks can prove challenging with application of foliar fungicides and seasonal irregularity in disease severity making yield loss and economic returns highly variable between seasons.

Where did Sclerotinia stem rot develop in 2024

Rainfall patterns across NSW were highly variable in 2024, with above average rainfall totals in northern, central and western districts, while southern districts received below average winter and spring rainfall. In many western and central districts high levels of Sclerotinia disease developed within crops where the disease had previously been rarely observed. Unfortunately, the high level of disease development means increased Sclerotinia pressure for the next few seasons due to the legacy effect of sclerotes, the small, hard, black survival structures of the Sclerotinia pathogens. In southern districts low levels of disease were observed in canola, driven by warmer and drier conditions in August and September. Despite this there were isolated reports of infection within commercial crops, including basal infections. Surveys of commercial canola crops in central and southern NSW found the disease to be present in 66% of crops assessed, indicating the widespread presence of the pathogen across the region in 2024. Infection incidence ranged from 0 – 76% plants infected within crops.

What drives Sclerotinia development?

Outbreaks of Sclerotinia are driven by the size and viability of the sclerote population in soil in combination with favourable weather conditions for infection and host susceptibility. The buildup and maintenance of sclerotes in soil is dependent on the frequency of host crops in the rotation and the opportunity for new sclerotes to be produced, to replenish the population of viable sclerotes in the soil. The history of previous Sclerotinia outbreaks is important in determining the size of sclerote populations.

The combination of a viable sclerote population and favourable soil moisture conditions enable sclerotes to imbibe water, soften, and produce apothecia fruiting structures that will release ascospores. Ascospores are dispersed over short distances and land on canola petals, subsequently germinating and colonising the petal tissue. The senescing of petals into the crop canopy in combination with long periods of canopy wetness enable the Sclerotinia fungus to transfer from the petal to canola stems and lower leaves, resulting in potentially damaging infections and yield loss (see Figure 1). Under some conditions, sclerotes will also germinate and produce mycelium, that will grow in the upper soil surface and can directly infect stem bases and upper roots. This pathway of infection appears to be becoming more common in recent years.

The disease pressure from both infection pathways (ascospores and mycelium) is driven by the density of the sclerote population in soil. The more viable sclerotes present, the greater the risk of disease development.

Figure 1. Disease triangle showing the factors favouring Sclerotinia stem rot of canola.

What favours the build-up of sclerotes?

Canola is notorious for being an excellent host for Sclerotinia and can rapidly build up levels of sclerotes in soil. It is not coincidental that damaging outbreaks of Sclerotinia are often associated with a history of canola in the paddock. In other regions, pulse crops (including narrowleaf lupin, chickpea and lentil) grown in close rotation can also build up sclerotes in soil. Canola is unique in the size and large number of sclerotes produced when plants become infected. The size of sclerotes directly influences the period of survival, with large sclerotes able to survive for much longer periods (up to 10 years) compared to smaller sclerotes (typically up to 5 years) often produced by other crops.

Sclerotinia spp. fungi are naturally opportunistic and will take every opportunity to colonise and feed upon plant material to survive. Once established in a paddock, the sclerote population needs to be replenished regularly to stay viable. At any point in time the sclerote population in soil will be made up of sclerotes of varying sizes and ranging in age from less than 12 months up to 10 years old. This results in a readily available pathogen population capable of causing damaging levels of infection annually.

The most effective means of building up and maintaining sclerotes is to plant host crops regularly. Frequent planting of canola within crop rotation is an effective means of maintaining a viable and long-lived sclerote population. The emergence of Sclerotinia disease across many regions in the last decade is testament to this. A rotation including canola once every four years (or longer) would be highly effective in reducing background levels of sclerotes in soil.

The impact of double breaks

Pulse crops can contribute to the build-up and maintenance of sclerote populations within paddocks. Research conducted at Wagga Wagga has shown that pulse crops vary in the amount of sclerotia produced and therefore present varying levels of disease risk (see Table 1).

Cropping rotations that incorporate a pulse/oilseed ‘double break’ present a greater threat of damaging levels of Sclerotinia development compared to rotations that spread the frequency of host crops (e.g. pulse and oilseed crops). Research has shown that while the amount of sclerotes produced by the pulse crop may be less than a canola crop, the return of viable sclerotes that have the potential to cause infection to the canola crop the following year is significant. The table below shows how sclerote production can vary significantly between pulse crop species and seasons.

Table 1. Comparison of the weight of sclerotia produced by Sclerotinia sclerotiorum following infection of various pulse crop species grown at Wagga Wagga NSW.

Rotation of host and non-host crops (e.g. broadleaf and cereal) allows for a portion of the sclerote population to breakdown in those years sown to non-host (cereal) crops. The growing of two host crops in succession allows for the quick build-up of sclerotes numbers in soil within several seasons, especially if one of those seasons has a wet spring.

Moving forward – management of sclerotes

Management of Sclerotinia disease in the longer term must include a strategy to manage sclerote populations in soil, both in size and viability.

Management of sclerotes in soil should consider:

1. Avoiding ‘blow out’ epidemics of Sclerotinia disease in crops. The production and return of high numbers of sclerotes to soil will increase disease pressure and the likelihood of future Sclerotinia outbreaks
2. Managing Sclerotinia disease in all broadleaf crops in the rotation. Use every opportunity to avoid Sclerotinia development in broadleaf crops in the rotation. This may include the strategic use of foliar fungicides. Research at Wagga Wagga has shown that sclerote production can be significantly reduced with a single timely application of foliar fungicide
3. Maintain microbial activity in soils. The breakdown of sclerotes is through microbial activity within soils. Practices such as minimum tillage and stubble retention (where possible) promote microbial activity on the soil surface and the breakdown of sclerotes over time
4. Appropriate crop rotations. Where possible rotate with non-host crops frequently. Growing two broadleaf crops in succession increases the risk of disease development and a blow out in disease outbreaks
5. Canopy management. Large crop canopies that develop early in the season are more prone to developing early Sclerotinia infections that result in large numbers of sclerotes. Consider time of sowing, target plant population and crop variety maturity when planting broadleaf crops within the rotation
6. Burning and cultivation do not significantly reduce survival of sclerotia.

Use of fungicides to manage Sclerotinia stem rot of canola

Currently there are no canola cultivars available with resistance to sclerotinia stem rot. Whilst there are agronomic practices that can decrease disease risk, many producers’ aim to manage the disease via foliar fungicide application. Foliar fungicides can be highly effective at reducing the incidence of Sclerotinia disease when applied at the correct crop growth stage.  However, some infection may still develop under conditions of high disease pressure.

Please consider the following when using foliar fungicides:

• Always use fungicide products that are currently registered for use in your state
• New generation fungicides for management of Sclerotinia don’t require mixing with other fungicide products and are highly effective as stand-alone products
• There are consequences from using fungicide application rates below the recommended (registered) rate range, including reduced fungicide efficacy and increasing the risk of resistance
• Timing of foliar fungicide application is more important than choice of fungicide product to reduce potential levels of stem infection
• Foliar fungicide application is most effective when applied before an infection event.
• Application of foliar fungicide at 20–30% bloom stage (15–20 open flowers on the main stem) is most essential in reducing main stem infection. Yield loss and sclerote production can be significantly reduced by protecting early petals from infection and maximising penetration of fungicide product into the crop canopy to protect potential infection sites from senescing petals
• Multiple foliar fungicide applications may be beneficial in some high-risk-disease situations to protect high yield potential but are rarely required. Applications at both 10–20% and 50% bloom provide critical early and follow up protection from multiple infection events. It should be remembered that fungicide applications during full bloom have limited penetration into the crop canopy and will not protect main stems from infection
• Use high water rates (at least 100 litres per hectare) to achieve adequate coverage and penetration into the crop canopy
• Be aware of the protection period provided by the foliar fungicide being applied. The current effective protection period offered by registered products ranges from 2 to 5 weeks. The protection provided may wear off during the critical infection period or in situations where crops have an extended flowering period
• Foliar fungicides will have no effect on managing basal infections, as these occur below the soil surface and beyond the activity of foliar fungicides.  This is due to foliar fungicides being unable to travel down plant vascular tissue towards the roots.

Useful resources

NSW DPI Winter Crop Variety Sowing Guide (Disease updates, fungicide products)

SclerotiniaCM App for iPad and android tablets

Acknowledgements

The authors wish to thank NSW DPIRD and GRDC for co-investment into this research. In addition, the research undertaken as part of this project is made possible by the significant contributions of growers through both trial cooperation and the support of the GRDC.

Contact details

Kurt Lindbeck (Senior Pulse and Oilseed Pathologist)
NSW Department of Primary Industries, Wagga Wagga Agricultural Institute
Ph: 02 69 381 608
Email: kurt.lindbeck@dpi.nsw.gov.au

Date published
February 2025