Key messages

• Sclerotinia prevalence, particularly basal Sclerotinia (ground level infection) has increased significantly in Western Australia in the last five years. Since 2020, commercial crop surveys have found basal Sclerotinia more common in lupins than in canola, and it is difficult to manage.
• From 2021–2025 extensive research was conducted in the laboratory, glasshouse and field trials by research partners Department of Primary Industries and Regional Development (DPIRD), Centre for Crop Disease Management (CCDM), Mingenew Irwin Group (MIG) and lupin growers. Key new findings applicable to lupin growers are:
• Sclerotinia infects narrow-leaf lupin via two pathways: canopy and basal. Basal infection is more damaging, causing around 60% yield loss on infected plants, while canopy infection can cause up to 25% yield loss, mainly by infecting the main spike pods. On a paddock scale, canopy infection usually causes around 10% yield loss, increasing to 25% in a growing season with a wet spring and/or high disease pressure. A model from field data has been developed which allows for yield loss estimation based on disease incidence.
• Sclerotia contamination of harvested grain varies widely, but field research has found it is more common in trials with higher incidence of canopy infection. No consistently effective management strategies to reduce sclerotia grain contamination have been identified.
• An integrated disease management strategy for Sclerotinia canopy infection is being developed using data from 2021–2024 field trials. The approach includes agronomic, cultural, and chemical control options such as risk assessment (paddock, crop and season factors), delayed sowing, wider row spacing, lower seed rates, and applying a registered foliar fungicide from full flower to early pod emergence on the main spike.
• Employing a disease management strategy is only likely to be necessary and profitable in high-risk scenarios outlined in the Lupin Sclerotinia disease risk assessment guide. Research shows management is more economically viable in the medium-high rainfall zones of the Geraldton port zone, followed by the Kwinana North port zone. In contrast, the Albany port zone had limited disease incidence from 2021–2024, resulting in few significant responses to management.
• Effective options for reducing basal Sclerotinia infection in lupins are currently limited, as foliar fungicide applied during crop flowering is often ineffective. Ongoing research aims to identify the drivers for basal infection and potential management strategies.
• Gather annual data on the distribution and impact of Sclerotinia (canopy and basal) in commercial lupin crops in Western Australia. The unique WA environment requires that local research be undertaken, as it differs from other cropping regions in Australia.
• Expand our understanding of the epidemiology and the infection process of Sclerotinia in lupin. Identify the growing seasons and paddock scenarios where Sclerotinia is likely to be problematic and determine when preventative actions are necessary and profitable.
• Improve understanding of how cultural practices, (e.g. crop rotation, row spacing, plant density and sowing time) influence disease development and determine the effectiveness and optimal timing of fungicides for managing both canopy and basal Sclerotinia infection.

Aims

Introduction

WA lupin crops are increasingly affected by Sclerotinia stem rot, caused by Sclerotinia sclerotiorum. This disease can significantly reduce yields in conducive growing seasons (regular rainfall, temperatures 16–25°C). The inoculum (sclerotia) is widespread across the WA grainbelt, and due to the long-term survival of sclerotia, paddocks sown in the past six years to canola or lupins should be assumed to be at risk of infection. Managing the disease is challenging due to the lack of resistant lupin varieties, its sporadic nature, the need to apply foliar fungicide before symptoms appear and challenges in fungicide application reaching the soil level to manage basal infection.

Method

The 2021-2024 research, conducted by DPIRD, CCDM and MIG through a GRDC co-investment, focussed on Sclerotinia sclerotiorum in narrow-leaf lupin (NLL; Lupinus angustifolius). DPIRD provided additional funding in the first two years to include albus lupin (Lupinus albus) in the field research experiments alongside L. angustifolius.

Field research 2021–2024

Small plot replicated field trials were conducted annually by DPIRD in the Geraldton, Kwinana North and Albany port zones with 35 trials in total established over the four growing seasons (GPZ: 25, KPZ: three and APZ: seven trials). These trials were either sown using a small-plot seeder or set up opportunistically in grower’s crops and the majority were sown with a common lupin variety (such as Jurien and Barlock (NLL) or Amira (albus lupin)). Field trials focussed on a range of treatments across different sites, including time of sowing, lupin variety or species, foliar fungicide timing, foliar fungicide active ingredient, row spacing, seeding rate, and crop rotation sequencing. Weather monitoring equipment was used to measure climatic conditions including relative humidity and temperature under the crop canopy and onsite rainfall. Foliar fungicides were applied in 100L/ha water volume with either a ute-mounted spray rig or a hand boom 0.5m above the crop canopy. Sclerotinia and other foliar diseases were monitored throughout the growing season, with disease incidence, severity and location on plants assessed. Plants were sampled from each treatment prior to plant maturity to determine yield components, such as pod counts. Yield and grain quality (including sclerotia contamination) were determined at most sites.

MIG growers conducted eight large paddock scale trials using growers’ machinery investigating the impact of narrow-leaf lupin varieties, seed rates and foliar fungicide treatments on Sclerotinia disease. MIG staff used the same protocols described above to monitor weather conditions, assess disease, and collect plants for yield and grain quality analysis. Yield map data were obtained where available. Several growers from outside the MIG region also conducted paddock scale trials (GPZ: six, KPZ: three trials), with DPIRD staff monitoring foliar diseases in them.

Annual commercial crop surveys were conducted by DPIRD in conjunction with the DPIRD disease surveillance project to record distribution and incidence of Sclerotinia sclerotiorum in WA lupin crops and identify other Sclerotinia species. In 2024, a yield loss assessment survey was conducted assessing loss of grain yield caused by canopy and basal infection in comparison to healthy plants.

Laboratory, growth room and hoop house research 2021–2025

From 2021–2024, CCDM developed robust methods for inoculating lupin plants to induce reliable canopy and basal Sclerotinia infection and conducted several pot experiments investigating the epidemiology of Sclerotinia in lupins at Curtin University, Perth. They determined the susceptibility of common NLL varieties (Jurien and Barlock) and albus lupin Amira to a diverse set of local WA Sclerotinia isolates, investigated the impact of canopy and basal infection at different lupin development stages (pre-flowering, flowering, podding), explored the effect of conditioning temperature, soil water content, soil type and isolate on myceliogenic germination of sclerotia, and used confocal microscopy to gain better insights into early infection on lupin tissues.

Pot experiments were conducted in growth rooms at DPIRD Northam from 2023–2025, inoculating soil with sclerotia to explore the impact of basal Sclerotinia on lupin root and shoot growth and to determine if the disease can be reduced by seed treatment or foliar fungicides.

DPIRD conducted laboratory experiments to determine if direct application of foliar fungicides to sclerotia and apothecia (actively germinating sclerotia) could reduce carpogenic and myceliogenic germination in Geraldton from 2022–2023. Studies are planned in early 2025 to investigate the influence of temperature on leaf lesion development. In 2023–2024 CCDM tested a range of commonly used foliar fungicides in vitro to determine if application would inhibit actively growing Sclerotinia mycelium and reduce viability of any sclerotia produced.

Results and discussion

Sclerotinia sclerotiorum is the dominant Sclerotinia species affecting WA lupin crops, with DPIRD annual commercial crop surveys from 2021–2024 finding the pathogen widely distributed across the WA grainbelt, with few cases of S. minor observed. Surveys found a higher prevalence of crop infection within the Geraldton and Kwinana North port zones, especially in wet seasons, compared to the Albany port zone. Sclerotinia infection occurred via two pathways: canopy and ground level infection (basal). CCDM screening of lupin varieties using local WA Sclerotinia isolates revealed disease outcome was highly variable, with several isolates more aggressive than others, leading to higher yield loss or production of greater sclerotia numbers. However, no geographical pattern was found for aggressive isolates, and lupin variety responses varied significantly, although all varieties tested were susceptible. Genetic resistance is not yet available; all lupin varieties currently available in WA are susceptible to Sclerotinia infection, as observed in pot experiments, field trials, and an NVT trial (Mingenew, 2024).

Risk factors for Sclerotinia infection

To identify which lupin crops need managing for Sclerotinia, it is crucial to understand the risk factors. Field trials and monitoring sites have confirmed that Sclerotinia risk is higher in lupin crops grown in paddocks with a history of Sclerotinia disease, high plant density, loamy soil type, early canopy closure and good yield potential, especially in seasons with ongoing moisture during winter and spring. More information is available in the Lupin sclerotinia disease risk assessment guide.

In the medium/high rainfall regions of Geraldton and Kwinana North port zones, Sclerotinia infection in lupins is more likely to occur early in the growing season and reach high incidence and severity due to close rotation with previously infected canola, and favourable weather conditions (milder winter temperatures, i.e. more days >16°C). Consequently, the greatest yield impact occurs in these port zones. Research from 2021–2024 found that for cooler southern regions, Sclerotinia incidence within crops was low and occurred later in the season, resulting in minor or negligible yield losses.

Canopy infection process and yield impact

In the field, Sclerotinia canopy infection can develop rapidly under favourable warm and wet conditions (relative humidity >80% and temperature 20–25°C), with Sclerotinia disease producing visible symptoms in lupins within seven days. In laboratory experiments, CCDM determined, by using confocal microscopy, that ascospore germination can occur within 24 hours under optimal conditions, with visible symptoms observed within 2–5 days. Both glasshouse and laboratory experiments revealed lupin pods developed necrosis before leaves, usually commencing at the pod base where senescing petals are located. This correlates with DPIRD field observations where the main spike pods are the most commonly infected plant part (rather than stems, as occurs in canola), causing significant yield loss in lupin. Infected lupin petals often remain in situ, directly infecting emerging pods, however infected petals can also drop onto leaves, which then wrap around stems and pods, causing further infection. In 2024, commercial crops in KPZ (North) and GPZ showed an average dry seed weight loss of 26% in plants infected with canopy Sclerotinia. A model has been developed from field trials that allows yield loss estimation from disease incidence. Grain quality can be affected by sclerotia contaminating the grain at harvest necessitating grading to meet delivery standards. Research has found the source is often sclerotia formed in and outside pods and branches.

Basal infection process and yield impact

CCDM laboratory research found that myceliogenic germination of sclerotia can occur on relatively dry soil, (e.g. 40% water holding capacity), but nearly saturated soil is needed for it to persist, expand and cause basal Sclerotinia in lupins. Basal Sclerotinia is usually first identified by wilting plants and fungal mycelium at the plant base, typically seen during crop flowering when leaf drop is underway (about three months after emergence in northern port zones). It can cause early maturation/death of plants or reduce pod formation and grain fill. The disease often spreads to nearby plants, leading to patchy infection areas. Crops that lodge are more susceptible to infection spread. In 2024, Kwinana North and Geraldton crops showed an average 57% dry seed weight loss in infected plants.

Basal Sclerotinia in lupin may be caused by one of two infection routes – direct myceliogenic germination of sclerotia in the soil or canopy infection spreading to the ground (through dropping infected plant parts). CCDM pot experiments found fallen petals and pods can initiate stem base infection, also observed by DPIRD in the field along with fallen infected leaves.

Basal infection can significantly reduce root and shoot growth in lupins. DPIRD Northam pot experiments showed basal infection (from sclerotia germination) significantly reduced fresh shoot and root weight, dry root weight, total root length, root surface area, and average root diameter.

Agronomic/cultural management strategies

Non-chemical strategies include crop rotation (reducing frequency of broad leaf crops in high-risk paddocks), using clean seed (grading out sclerotia), delaying time of sowing, and reducing crop density through wider row spacing and/or lower seed rate. Three out of four time of sowing trials conducted annually near Geraldton from 2021–2024 found the earlier sown lupins (April/May) developed infection earlier and had significantly higher incidence of canopy sclerotinia and yield impact than the later sown (May/June) lupins. In three out of five density trials conducted in the Geraldton port zone (GPZ) from 2022–2024, a high seed rate significantly increased canopy infection. One trial also showed higher basal infection at high seed rates (160 kg/ha ~ 60 plants/m²) compared to medium (80 kg/ha ~ 40 plants/m²) and low (40 kg/ha ~ 20 plants/m²) seed rates. Analysis of relative humidity under the crop canopy found lowering the seed rate allowed for better airflow (interrupting prolonged periods of high humidity) compared to higher seed rates. In two out of the five trials the highest seed rate (125–160 kg/ha) had significantly more sclerotia contamination in the grain than the lower seed rates. These findings suggest that using the standard seed rate of 100 kg/ha, or even reducing it, could be beneficial in paddock areas with high Sclerotinia risk. Although further research is needed to assess the economic and agronomic impacts, five out of seven density trials showed no yield penalty from significantly reducing the seeding rate, (e.g. to 60 kg/ha ~ 30 plants/m²). In fact, in one GPZ 2024 trial (decile 9 winter), the lowest seed rate outperformed higher seed rates. This trial, which is the only one to date providing valuable results on row spacing and seed rate, found that low seed rate combined with wide row spacing significantly reduced canopy infection compared to denser and narrower plots. Additionally, wide row spacing improved the effectiveness of fungicide in reducing canopy infection. Further research is needed to confirm the broader applicability of these findings.

Chemical management strategies

DPIRD field research found that application of a foliar fungicide at late flower/early pod emergence on the main spike was consistently the best timing to reduce canopy Sclerotinia infection and yield loss. Fungicide application in lupin should focus on protecting the emerging main spike pods (rather than the main stem as in canola), which is a vulnerable stage in lupin development.

While fungicide can be effective for reducing canopy infection, it does not always result in a yield response or a positive economic return. In all the field trials conducted from 2021–2024 by DPIRD, MIG and lupin growers, yield response in lupin was highly variable. In the 24 trials conducted in years conducive to disease (2021, 2022, and 2024), where a single foliar fungicide was applied and Sclerotinia was the dominant disease, 42% (10 trials) showed a statistically significant yield gain from the fungicide application during crop flowering/early pod emergence (Table 1). Of those 10 trials, nine were in the GPZ and one in the Kwinana North PZ. The average yield gain was 10% (0.3 t/ha), resulting in 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, with a higher chance of significant disease levels and yield gain from fungicide application in the GPZ followed by the high rainfall KPZ (North).

Table 1. Field trials conducted from 2021–2024 where Sclerotinia was the dominant disease present and application of a foliar fungicide provided a significant yield response. All trials to meet these criteria were on narrow-leaf lupin (SSP= sown small plot, GS = grower paddock, O = opportunistic small plot in grower crop).

Ciara Beard
DPIRD Geraldton
08 9956 8504
0438 468 484
ciara.beard@dpird.wa.gov.au

Dr Pippa Michael
CCDM, Curtin University
08 9266 2740
p.michael@curtin.edu.au