Increasing canola sowing across Western Australia’s grainbelt has increased the prevalence of Sclerotinia stem rot in lupins.

Caused by the fungus Sclerotinia sclerotiorum, the disease is now becoming more common in regions beyond the Geraldton Port Zone (GPZ).

The GPZ is where the disease has traditionally been recorded. It is also where plant pathologist Ciara Beard from the WA Department of Primary Industries and Regional Development (DPIRD) is working on a multifaceted research approach.

Ms Beard says canola serves as a significant fungal host. “This has led to more widespread infection in other broadleaf crops, like lupins, when grown in close rotation with canola, particularly in wetter growing seasons.”

Multifaceted approach

Extensive research on lupin Sclerotinia began in 2021. It includes laboratory, glasshouse and field trials, and paddock-scale trials conducted by growers impacted by the disease.

At the GRDC Grains Research Updates in Perth, Ms Beard presented results from a four-year GRDC co-investment with research partners – DPIRD, the Centre for Crop and Disease Management (CCDM), Mingenew-Irwin Group (MIG) and lupin growers.

She says an integrated disease management (IDM) strategy is being developed. It is part of a broader approach that includes understanding the infection process, yield loss modelling, a risk assessment guide and ongoing research.

IDM strategy

The IDM strategy for canopy Sclerotinia uses data from 2021 to 2024 field trials conducted across the WA grainbelt and an approach that captures agronomic, cultural and chemical control options.

This includes a risk assessment approach, such as paddock, crop and seasonal factors, delayed sowing, wider row spacing, lower seeding rates, and applying a registered foliar fungicide from full flower to early pod emergence on the main spike.

Further research is needed for basal infection management. In most cases, it is not reduced by applying a foliar fungicide at this growth stage.

Lupin leaves spreading basal Sclerotinia on the soil surface. Photo: Evan Collis

Assess risk first

Disease severity is highly variable across properties and growing seasons. That means the IDM strategy would not be needed in all cropping scenarios. The first step is a risk assessment. (See Lupin Sclerotinia disease risk assessment guide, released in 2023.)

“Research in the last four years shows management is more economically viable in the medium to high-rainfall zones of the GPZ, followed by the Kwinana North Port Zone (KNPZ),” Ms Beard says.

“In contrast, the Albany Port Zone had limited disease incidence from 2021 to 2024, resulting in few significant responses to management.”

Risk factors

Field trials have confirmed that Sclerotinia risk is higher in lupin crops grown in paddocks with:

• a history of the disease
• a high plant density
• a loamy soil type
• early canopy closure
• good yield potential, especially in seasons with ongoing moisture during winter and spring.

The greatest yield impact occurs in the GPZ and KNPZ, where infection is more likely to occur earlier in the growing season and reach higher incidence levels.

High infection rates and greater severity are more likely in these northern regions when lupins are grown in close rotation with previously infected canola and when winter temperatures are warmer, as is typical in the GPZ and KWPZ.

Agronomic and cultural strategies

Ms Beard outlined several non-chemical strategies that may reduce the risk or impact of Sclerotinia, including:

• crop rotation – reducing the frequency of broadleaf crops in high-risk paddocks
• sowing clean seed and grading out sclerotia after harvest
• delaying time of sowing
• reducing crop density through wider row spacing and/or a lower seed rate.

Time of sowing trials near Geraldton found earlier-sown lupins were more at risk.

“Three out of four trials found lupins sown in April and May (2021–24) developed infection earlier and had significantly higher rates of canopy Sclerotinia and yield penalty than the lupins sown in June.”

Three out of five plant density trials across the GPZ from 2022 to 2024 showed a higher seed rate significantly increased canopy infection. One trial also showed that basal infection increased at higher seeding rates.

These findings suggest that reducing seed rate could be beneficial in WA paddock areas with high Sclerotinia risk.

Lowering the seed rate improves airflow under the crop canopy, disrupting the prolonged periods of high humidity often observed under dense canopies of crops with high seed rates, which can trigger infection.

Ms Beard notes that further research is needed to assess the economic and agronomic impacts from significantly reducing seeding rate and widening row spacing.

“One 2024 GPZ trial found that a low seed rate combined with wide row spacing significantly reduced canopy infection compared to denser and narrower plots.

“Additionally, wide row spacing improved fungicide effectiveness. However, further research is also needed to confirm this,”  she says.

Chemical management strategies

In lupin, fungicide applications should focus on protecting the emerging main spike pods, which is a vulnerable lupin development stage for Sclerotinia infection.

But while fungicide can be effective, it  does not always result in a yield response  or a positive economic return.

Yield responses were variable as confirmed by DPIRD field trials, as well as those run by MIG and growers.

Breaking this down, Ms Beard says that  24 foliar fungicide application trials were run  in years conducive to disease – 2021, 2022 and 2024.

Where a single foliar fungicide was applied and Sclerotinia was the dominant disease, 10 trials (42 per cent of all trials) showed a statistically significant yield gain. Of those 10 trials, nine were in the GPZ and one in  the KNPZ.

The average yield gain was 10 per cent (0.3t/ha) – a profit of $20 to $75/ha. This assumes a lupin price of $375/t and fungicide application costs ranging from $38 to $93/ha, depending on the product used.

Site-specific weather and canopy conditions significantly influence disease development. There is a higher chance of significant disease levels and yield gain from fungicide application in the GPZ followed by the high-rainfall KNPZ.

Sclerotes forming on the outside of lupin pods (left). Sclerotes forming on the inside of lupin pods (right). Photos: Ciara Beard

Field observations showed a significant yield response to foliar fungicide was more common in paddocks with at least 30 per cent Sclerotinia incidence at crop maturity and other foliar diseases present.

Ms Beard says the challenge with managing Sclerotinia is that foliar fungicide treatment is most effective when applied before infection becomes visible. “Lupin growers will know which paddocks consistently experience high infection levels – there should be plans in place to prioritise these paddocks for earlier-season treatment as crops are flowering.”

A yield loss estimator has been developed based on WA field trials. In the future, it will be incorporated into a decision support tool (app) that will be developed for lupin growers.

Basal infection

Whether basal Sclerotinia infection can  be reduced by fungicide application is  being researched in pot experiments at  DPIRD Northam.

While there are no products that currently target basal Sclerotinia infection in lupins, researchers are investigating the value of fungicide seed treatments and soil application of foliar fungicides.

Further research is required to determine potential management options for basal Sclerotinia. Possible options include innovative fungicide application techniques, the use of biological agents and the development of resistant varieties.

Ongoing research

Sclerotinia resistance in more than 500 lupin wild types and breeding lines is being assessed in glasshouse and field experiments. Researchers at CCDM are conducting this work as part of a new project and are using a new phenotyping method.

Supported by GRDC and the WA Agricultural Research Collaboration, with DPIRD, Murdoch University and Australian Grains Technologies breeding, the aim is to deliver new narrow-leaf lupin varieties with improved resistance  to Sclerotinia.

More information: Ciara Beard, ciara.beard@dpird.wa.gov.au

What is Sclerotinia?

Sclerotinia stem rot is an economically significant disease caused by the fungus Sclerotinia sclerotiorum. It can cause significant yield losses in canola and lupins.

Sclerotinia infects narrow-leaf lupins via two pathways: canopy and basal infection.

Since 2020, commercial crop surveys in WA have found basal – or ground-level – Sclerotinia infection is more common in lupins than in canola, and it is difficult to manage. It can cause up to 60 per cent yield loss in infected plants. However, infections are patchy across a paddock.

Canopy infection typically causes around 10 per cent yield loss in WA, increasing to 25 per cent in growing seasons with a wet spring and/or high disease pressure.

Canopy infection development

The Sclerotinia pathogen survives in the soil as hard,  black structures called sclerotia. The disease cycle starts when cool, moist conditions after crop canopy closure prompt sclerotia germination.

Germination presents as small, mushroom-like structures called apothecia, they release Sclerotinia spores into the air, which infect petals on flowering lupin crops. Under warm and wet conditions, Sclerotinia canopy infection can develop rapidly.

In lupins, symptoms can be seen within seven days in crops when relative humidity is greater than 80 per cent and temperatures are warm (20°C to 25°C).

Experiments in the laboratory and glasshouse at the Centre for Crop and Disease Management (CCDM) also confirmed the speed with which the disease has an impact.

CCDM determined that under high humidity in a laboratory, fungal spore germination of lupin tissues can occur within  24 hours, with visible symptoms in two to five days.

CCDM experiments also showed that lupin pods usually developed necrosis before leaves due to infection in senescing flowers.

“This infection process usually started at the pod base. It correlates with the Department of Primary Industries and Regional Development’s field observations,” Ciara Beard, a plant pathologist at DPIRD, says. “Infected lupin petals often remain in situ, directly infecting emerging pods.”

Yield and grain quality impact

The main spike pods are the most commonly infected plant part causing significant yield loss in lupins.

This differs from canola, where the stems are most commonly infected.

Infected petals can also drop onto leaves, which then wrap around lupin stems and pods, causing further infection.

In 2024, surveyed commercial crops in Kwinana North and Geraldton Port Zones showed an average dry seed weight loss of 26 per cent in plants infected with canopy Sclerotinia.

Grain quality can be reduced by sclerotia, which can contaminate grain at harvest. Research has found sclerotia form inside and outside pods and branches, and growers often need to grade out sclerotia to meet delivery standards. No consistently effective management strategies have been identified to date to reduce sclerotia grain contamination.

How does basal infection occur?

Basal Sclerotinia is usually first identified by wilting plants and fungal hyphae/mycelium at the plant’s base. Basal Sclerotinia in lupins may be caused by one of two infection routes – directly from sclerotia in the soil or canopy infection via infected plant parts falling to the ground.

CCDM laboratory research found that germination of sclerotia to form fungal hyphae can occur on relatively dry soil. However, nearly saturated soil is needed for the fungal hyphae to persist, expand and cause direct basal Sclerotinia infection in lupins.

In WA, this is typically first seen during crop flowering when leaf drop is underway. In northern port zones, this is about three months after crop emergence. Research is investigating the role of leaf matter on the soil surface in the spread of Sclerotinia infection to the base of plants.

Basal Sclerotinia can cause early maturation and even plant death, reducing pod formation and grain fill.

The disease often spreads to nearby plants, leading to patchy infection areas. Field observations have found crops that lodge are more susceptible to infection spread.

In 2024, Kwinana North Port Zone and Geraldton Port Zone crops showed an average 57 per cent dry seed weight loss in infected plants, which is a great concern for growers.

More information: Coastal conditions favour disease.