Lupin Phomopsis and Sclerotinia

  • Geraldton port zone
  • Kwinana port zone

Pod Phomopsis and sclerotinia have been observed in many lupin crops in the Geraldton port zone and parts of the Kwinana port zone this season after ample winter and October rainfall. These diseases pose risks that need to be carefully considered going forward.


Phomopsis stem and pod blight is caused by the fungus Diaporthe toxica which can produce a toxin dangerous for livestock grazing on infected lupin stubble.

Phomopsis on lupin pod that has caused seed infection.
Phomopsis on lupin pod that has caused seed infection. Photo courtesy of: Ciara Beard (DPIRD).

Pod infection can appear as a dark, sometimes wrinkly, lesion on the surface of the pod, affecting part or all of the pod. This is distinctively different to saprophytic blackening which can occur in crops during wet weather prior to harvest (usually only the upper side of the pods exposed to the weather is dark). Phomopsis pod lesions can lead to fungal growth inside the pod and seed infection, causing shrivelled or discoloured grain ranging from golden to dark purple-brown colour. Cotyledons inside infected seeds can remain green rather than yellow. Pod and seed infection are more likely when there is rain during the period of seed and pod maturation.

Phomopsis black fruiting bodies visible on a lupin stem.
Phomopsis black fruiting bodies visible on a lupin stem. Photo courtesy of: Geoff Thomas (DPIRD).

Phomopsis stem lesions are not usually visible on green plants, the fungus will infect green plants but remains latent as microscopic structures until senescence of the plant tissue. Rain and moisture on senescing or dry lupin stems allow the fungus to grow saprophytically producing characteristic black fruiting bodies on affected stubble. Chemical desiccation or plants dying quickly in previously waterlogged areas can lead to rapid expression of stem symptoms as plants senesce.

Phomopsis stem and pod blight occasionally causes yield losses, however the major impact of infection is the production of a toxin by the fungus as it grows in mature lupin stems or in seed. The toxin, further promoted by summer rains, can cause sickness or death (lupinosis) in livestock if grazing of infected stubble or feeding of infected seed is poorly managed.

For more information contact your local DPIRD veterinary officer or refer to DPIRD’s Lupinosis in sheep page.

The fungus is present in all lupin growing regions and every year virtually all lupin crops in WA will be infected to some degree. Most modern narrow-leafed varieties are resistant but not immune to the fungus limiting its impact, however varieties such as Jenabillup, Quilinock and Coyote are more susceptible. Some differences between varieties is evident in expression of pod infection.

There are no fungicides registered for control of Phomopsis.

In most years occasional infected seed is present in most lupin samples, however this season some affected crops may have higher than usual presence of infected seed.

For more information on Phomopsis refer to DPIRD’s Diagnosing Phomopsis stem and pod blight in narrow leafed lupins page.


Sclerotia inside an albus lupin pod. This can result in grain contamination.
Sclerotia inside an albus lupin pod. This can result in grain contamination. Photo courtesy of: Anne Smith (DPIRD).

High incidence of the fungal pathogen Sclerotinia sclerotiorum in lupin crops this season has produced sclerotia (the black fruiting bodies that carry the disease over between seasons) in stems, pods and/or on roots of infected plants. These will spill into paddocks at harvest causing sclerotinia risk for future broadleaf crops including canola and other pulses. The same pathogen affects lupins, canola and other pulses.

Reports are coming in from the Geraldton area of growers who have had lupin grain deliveries rejected due to sclerote contamination.

Sclerotia are able to persist in the paddock and germinate causing disease risk for at least five years or more. This was demonstrated in DPIRD research this year, with sclerotia that were formed in the 2016 season, and have been exposed to the weather since then, germinating this year (after having germinated in previous years as well). 

There is no known toxicity risk to livestock of being grazed on lupins infected with sclerotia. However, keep in mind that sclerotia survive the digestion process so feeding them to livestock can potentially spread disease risk to clean paddocks.

Strategies to reduce sclerotinia risk:

  • Sow clean seed (that does not contain sclerotia)
  • Rotate with non-host crops (eg cereals) and avoid sowing close to last year’s infected crop
  • Sclerotinia infection appears to be most severe in crops (or parts of crops) with greatest plant density. In paddocks with identified historical risk aim to maintain lupin crop density at the recommended 40-45 plants / m2
  • If sowing a broadleaf crop into a paddock that has had sclerotinia infection within the last five years, your crop will be at risk. Budget for a fungicide application in canola crops and use the SclerotiniaCM decision support tool during crop flowering to determine if its needed. The value of fungicide application in lupins is still being determined, but several products are now registered for this use.

For a list of fungicides registered in canola and pulse crops refer to DPIRD’s Registered foliar fungicides for canola in Western Australia and Registered foliar fungicides for lupin and other pulse crops in Western Australia pages. 

For more information refer to DPIRD’s Diagnosing sclerotinia stem rot in narrow-leafed lupins and field peas page.


For more information on lupin diseases contact Plant Pathologists Ciara Beard, Geraldton on +61 (0)8 9956 8504 or Geoff Thomas, South Perth on +61 (0)8 9368 3262.


Article authors: Ciara Beard (DPIRD Geraldton) and Geoff Thomas (DPIRD South Perth).