Understanding and managing sclerotinia stem rot in lupins

Page last updated: Friday, 24 June 2022 - 9:24am

With lupins being susceptible and grown in close rotation to canola, particularly in the northern WA wheatbelt, lupin growers are facing increasing pressure from sclerotinia stem rot (caused by Sclerotinia sclerotiorum). This page covers the results of current research investigating the epidemiology of the disease and how it develops and causes yield and quality impacts in lupin crops. Management strategies are in the early stages of being developed, but risk minimisation is discussed along with understanding of how cultural practices and fungicide application may reduce disease impact.

Symptoms in lupin

Sclerotinia stem rot (Sclerotinia sclerotiorum) is a fungal disease which infects most broad leaf crop and pasture species but not cereals. Canopy infection in lupin can occur on the stem and branches but the main yield limiting infection has been found to be infection immediately underneath or on the main spike including pods and lateral branch pods. Infected plant parts are often covered by white fungal growth and black sclerotia may be visible outside and inside branches and pods. Pods may be aborted or shrivelled on infected plants. Sclerotinia infection can also occur at ground level (basal infection) which causes plants to appear wilted and the whole plant may die and appear bleached. When pulled up out of the ground the plants display recognizable white fungal growth on the stem at ground level and sometimes on the roots. Harvested grain may be contaminated by sclerotia when disease levels are high. Sclerotinia survives as sclerotia (hard, dark resting bodies of the pathogen) in the soil for many years and can germinate to spread further disease (Figure 1). More information on diagnosis is available from Diagnosing sclerotinia stem rot in lupins and field peas

Sclerotinia infection on narrow leaf lupin podsSclerotinia infection on narrow leaf lupin showing dying branches and infected pods that wont fillBasal sclerotinia infection on narrow leaf lupin showing white fungal growth and sclerotia on outside of stem at ground levelWilted albus lupin plants with basal (ground level) sclerotinia infection

Distribution and severity of sclerotinia in lupin in WA

Historically sclerotinia in lupin was an issue in the Geraldton port zone only but, with more canola being grown across the WA wheatbelt, the disease is now found in many areas and appears to be becoming a more regular issue. Regional disease surveillance has found sclerotinia in lupin is generally a problem in wetter growing seasons in areas where lupins are grown in close rotation with canola that has had sclerotinia.

2021 surveillance conducted by DPIRD

In 2021, incidence of lupin sclerotinia infection was extremely high in the Geraldton port zone (GPZ) where Department of Primary Industries and Regional Development (DPIRD) found canopy infection in 95% of commercial lupin paddocks surveyed and basal (ground level) sclerotinia was found in 90% of paddocks surveyed. Severity was high in some lupin crops with pod infection common, closely associated with pod abortion, which is likely to have reduced yield. There were reports of several growers in the GPZ having to grade sclerotia out of their grain in order to meet CBH delivery standards in 2021.

Agronomists reported significant levels of basal infection were common in lupin crops around Moora, York/Avon Valley, Wongan Hills areas, and out to Merredin. DPIRD observed lupin sclerotinia at Badgingarra, Bolgart, Walebing, Buntine and Konnongorring in the Kwinana north port zone.

In the Albany port zone 70% of lupin crops surveyed by DPIRD had sclerotinia canopy infection but infection was late in the season and at low incidence and severity within paddocks with negligible basal infection evident. Lupin sclerotinia infection was found to be at low incidence in surveillance conducted in the Esperance port zone.

The 2021 growing season was characterized by an early start, dense crops and above average rainfall in most parts of WA where lupins are grown. In a season where moisture and humidity were not lacking for the most part in all port zones, it was evident that temperature appears to be an important driver for the sclerotinia infection process and if conditions are too cold (<16°C) in winter, which is what occurred in the Albany port zone, infection will be delayed. As a result, there was no recorded yield impact or fungicide response in field trials conducted in the Albany port zone.

Previous years

Lupin sclerotinia was present in the Geraldton port zone in some crops in 2020 (canopy infection found in 50% of paddocks surveyed and basal infection in 30% of paddocks surveyed) and there were also reports from Kojonup, Brookton and Esperance that year. Geraldton port zone had more of a widespread issue with the disease in 2016 and 2018 but it was not reported from other port zones. There was one report from the North Stirlings area of the Albany port zone in 2015.

Canopy and environmental conditions leading to crop infection

Collaborative research by DPIRD, Mingenew Irwin Group (MIG) and Centre for Crop and Disease Management (CCDM) is currently being conducted as part of a four-year GRDC funded project Sclerotinia management for narrow leaf lupin crops in Western Australian farming systems (DAW2104-002RTX). DPIRD funding is allowing for the inclusion of albus lupin research. The first year of the research project has begun to define the growing season weather conditions and the crop/paddock characteristics that pose a high risk of sclerotinia infection to lupin. Research to date has found that sclerotinia risk is usually higher in lupin crops grown in paddocks that have:

  • a previous history of the disease (eg within the last 5 years)
  • high plant density, and bulky crop
  • loamy/clay-loam soil type (allows humidity levels to build up from ongoing soil moisture)
  • early canopy closure
  • good yield potential.

In a sown 2021 Geraldton trial, sclerotinia canopy infection was found to be significantly higher when lupins (narrowleaf or albus) were sown early (mid-April) compared to later (early May) but further research in other seasons is required to determine if this is a common trend.

Lupin sclerotinia development is highly dependent on seasonal weather conditions, maybe even more than canola sclerotinia, and only develops in years where there is sufficient rainfall across the growing season. Favourable rainfall, humidity and temperature conditions are required at all stages of the sclerotinia lifecycle (Figure 1) for it to initiate, persist and spread. Infection can develop extremely rapidly within weeks under favorable weather conditions and can be difficult to manage with foliar fungicides when high disease pressure present.

Lifecycle diagram showing how sclerotinia infection occurs in lupin
Figure 1. The lifecycle of sclerotinia sclerotiorum infection in lupin showing canopy infection (carpogenic germination of sclerotia causing aerial infection of petals) and basal infection (caused by myceliogenic germination of sclerotia and direct infection of plant stems at ground level).

Close to average autumn and early winter rainfall is necessary for: a) good emergence and establishment of dense lupin crops which favours high humidity levels under the canopy to suit sclerotinia and b) sclerotia to germinate and form apothecia which spread ascospores initiating the disease cycle. Continuing regular rainfall and high relative humidity during winter and spring is needed to: a) favour presence of apothecia persisting under the crop canopy to coincide with crop flowering in order for ascospores to infect petals and b) opportunity for petals to infect canopy of dense lupin crops of good yield potential where c) stem/branch/pod infection occurs and spreads to yield limiting levels especially favored by a wet/humid end to the season. So, years of below average rainfall or where dry periods occur during crucial parts of the disease cycle (such as autumn and spring) will limit or prevent development and spread of sclerotinia in lupin. Wet growing seasons like 2021 that produce high lupin yields are also the years where sclerotinia disease levels are likely to be significant.

Distinct differences in the sclerotinia disease cycle and disease levels in lupin in the Geraldton port zone versus the Albany port zone (APZ) were observed by DPIRD in 2021. These differences help to illustrate the impact that seasonal weather conditions have on disease development.  In the Albany port zone, sclerote germination in DPIRD sclerote depots was not observed until late in winter (early August) and continued until October. Winter temperatures were too cool at the Albany port zone trial sites (<16°C), delaying initiation of crop infection to September/October by which time the crops were finishing up flowering. In the APZ, sclerotinia did not develop to yield limiting levels. In the Geraldton port zone, lupin crops were emerging in April, after Cyclone Seroja brought significant rain and apothecia were observed from late June to late August. Both canopy infection and basal infection were observed with mild winter temperatures greater than 16°C in most areas creating a large window for crop infection to occur while crops were still flowering. Many sites developed symptoms from July. Crops were dense and high yielding and sclerotinia caused significant yield impact (on average at least 6% yield loss) in the GPZ.

The economic/disease impact from lupin sclerotinia

Field research conducted by DPIRD and growers since 2016 has observed that the main yield impact of canopy sclerotinia in lupin is infection on the main spike and lateral pods. This differs from canola where the impact of the disease is predominantly from infection on the main stem. To date, the yield loss caused by sclerotinia canopy infection in lupin has been found to be variable, ranging from 0-23% in field trials across a range of different growing seasons. Future research will try to quantify the losses caused by basal (ground level) infection.

Damaging disease levels of sclerotinia in lupin are hard to predict, making decisions on value of management in each cropping situation challenging. Crop risk criteria have been described above to assist with decision making.  

Sclerotia left behind in the soil after crop infection are an ongoing disease risk for future broad leaf crops sown in that paddock. Grading sclerotia out of harvested grain in order to meet delivery standards or for using as a seed source is an added headache and cost that can result from the disease.

Disease management

DPIRD are evaluating a range of potential management options including cultural, agronomic, and chemical for the development of an IDM package for WA lupin growers. The following recommendations are based on research/observations to date but research is continuing:

Crop rotation

  • Incorporate non-hosts or lower-risk crops into the crop rotation e.g. cereals.
  • Separate last year’s infected canola/lupin stubble and new seasons’ crops by preferably 500m.

Clean seed

  • Always sow seed free of sclerotia, grade retained seed if necessary.

Crop management

  • Earlier sown crops may be prone to developing more severe infection but this is dependent on the weather conditions, particularly rainfall, each growing season.
  • Reduced seeding rates may increase air-flow through the canopy.

Foliar fungicide strategies

  • Foliar fungicides registered in lupin may be helpful for reducing sclerotinia canopy infection. Foliar fungicides reduce canopy disease but may not necessarily give a yield benefit. Foliar fungicide application, targeted at canopy infection, generally does not provide any reduction in ground level (basal) sclerotinia infection.  
  • Foliar fungicides should be timed to protect from damage to main stem pods and branch pods.
  • A range of products are now registered in lupin including Veritas® Opti, Amistar® Xtra and Miravis® Star and can reduce sclerotinia canopy infection. For more information, view the Registered foliar fungicides for lupin and other pulse crops in Western Australia webpage.

If a lupin crop meets the high risk criteria (described in the disease risk matrix) AND there is an outlook for ongoing moist and humid weather conditions with temperatures 16 - 25°C fungicide application may be profitable.

In field research trials conducted by DPIRD, MIG and growers from 2016-2021, several foliar fungicides  significantly reduced sclerotinia infection and severity in the upper canopy when applied during flowering or at early pod emergence on the main spike. Application at this time was observed to predominantly reduce infection on the main spike and lateral pods but did not significantly reduce basal (ground level) infection. In these trials, yield responses of 4-6% from a single foliar fungicide application were common but it should be noted that a yield response is not guaranteed. Larger yield responses (up to 25%) from foliar fungicide application have been achieved in some cases when applied at optimal time, other diseases were present, and the season finished with a wet spring. Yield and/or quality response to foliar fungicide application for sclerotinia are more likely if other diseases such as phomopsis or anthracnose are present as they are also managed by the same active ingredients, particularly with late season timings. In the Geraldton port zone in 2021, yield responses of 4-23%+ were recorded from a single foliar fungicide application in four out of seven trials conducted. Sclerote contamination in grain was significantly reduced by foliar fungicide application in two out of the seven trials.

Research has found that sclerotinia can develop extremely rapidly within lupin crops if favourable weather conditions and moisture continue. Profitable response to foliar fungicide application is more likely if applied prior to widespread infection developing (vulnerable crop growth stage coinciding with favourable weather events).

Recommendations from research conducted so far:

  • Aim to apply foliar fungicides from full to late flowering/early pod emergence on the main spike. This timing aims to protect main stem pods and penetrate the canopy which gets bulky and hard to penetrate at later growth stages.
  • Use high water rates (at least 100L/ha) to achieve good coverage and penetration into the canopy
  • Where possible, apply fungicide before a rainfall event as fungicides are most effective before significant infection is present.
  • In a favourable season, if an application hasn’t been done prophylactically, foliar fungicide should be applied as soon as possible after disease symptoms are observed in the canopy as the infection can develop rapidly if weather conditions continue to be conducive.

There are no in-furrow or seed dressing fungicides registered, or thought to be effective, for sclerotinia in lupin.

Research being conducted 

Research is currently being conducted as part of a four-year GRDC funded project Sclerotinia management for narrow leaf lupin crops in Western Australian farming systems (DAW2104-002RTX). DPIRD funding is allowing for the inclusion of albus lupin research. DPIRD and Mingenew Irwin Group (MIG) with lupin growers are conducting field research in the Geraldton port zone and Albany port zone, and Centre for Crop and Disease Management (CCDM) are conducting lab and glasshouse studies.

Both canopy infection and basal (ground level) stem infection are being investigated. Factors influencing disease development being investigated include: time of sowing, fungicide timing and fungicide active ingredients, crop rotation, position in the landscape, lupin species, soil type, weather conditions and geographical location.

The project is also utilising the skills and networks of agronomists, MIG and growers to establish on-farm research activities and extend project results to the growers impacted by lupin SSR.

Research goals (2021-2024):

  • Gather data on the distribution and economic/disease impact from SSR in commercial lupin crops
  • Understanding the epidemiology and the infection process of sclerotinia in lupin (canopy and basal infection): the conditions leading to infection, effect of temperature, sites of infection on the plant, effect of plant stage on susceptibility to infection, conditions favouring sclerotia germination, sclerote development and latent periods. Studies are being conducted in the field and in controlled environment activities to generate information on the epidemiology of SSR in lupins and how the disease cycle could potentially be interrupted.
  • Evaluating a range of potential disease management options (eg cultural, agronomic and chemical). Research is investigating how on-farm practices influence disease development - modifying some such as crop rotation, increased row spacing, lower plant densities and altered sowing time may provide some disease control and/or reduce fungicide usage. Ultimately by project end (2025) the aim is to develop practical and cost-effective integrated disease management packages for WA lupin growers and advisers.
  • Investigate the effectiveness and optimum timing of fungicides for managing sclerotinia in the canopy and at ground level (basal).

Acknowledgements and disclaimer

The information presented here includes results of three GRDC cofunded projects - Sclerotinia management for narrow leaf lupin crops in Western Australian farming systems (DAW2104-002RTX, a collaboration of DPIRD, MIG and CCDM), Disease epidemiology, modelling and delivery of management decision support tools (DAW2112-002RTX), and Integrated disease management in western region grain crops (DAW1907-001RTX).

Mention of trade names does not imply endorsement or preference of any company’s product by Department of Primary Industries and Regional Development. Any omission of a trade name is unintentional. Recommendations are current at the time of publication.

Contact information

+61 (0)8 9956 8504
Geoff Thomas