How to keep sclerotinia infection to less than five per cent

New research shows fungicide applied at or just after 20 per cent flowering is still the best way to stop sclerotinia stem rot from shredding canola profits

Apothecia germinate from sclerotia in the soil. They are tiny but can be in great numbers, releasing billions of spores that go everywhere. The ones that land on canola petals are the concern for sclerotinia stem rot and are the target for fungicide applications.

Like a detective piecing together the timeline of a crime, Dwayne Hegedus has played and replayed the sequence of events from when a sclerotinia-infested petal drops onto a canola leaf to the all-is-lost cleaving of the cuticle. The scientist with Agriculture and Agri-Food Canada in Saskatoon now knows, genetically, what arrows the pathogen shoots and what scorched-earth defences the plant lights up. He knows that the aggressor — a mastermind among plant pathogens — has already won if allowed to stick its hyphae into the plant.

Hegedus’s empirical evidence supports the time-tested tip: Preventative fungicide sprayed before the petals fall is the best defence against sclerotinia stem rot. Without that, a grower can do little but watch (or not watch) while infected stems wither.

The scene

Sclerotinia, like any other disease, requires all three points of the “disease triangle” to occur. Point one is a host. Canola is but one of many hosts for Sclerotinia sclerotiorum. It also infects sunflower, soybeans, pulses, potatoes and even weeds such as Canada thistle. Point two is the pathogen. With 20 million Prairie acres of canola, (plus the acres of other host crops) and with regular yearly incidence, we can assume the pathogen is everywhere. Point three is environment — mainly weather. With the host and pathogen ever-present, the amount of infection comes down to rainfall or even just canopy humidity. (If you get wet pants on a morning walk through a field, that field is at risk from sclerotinia infection.)

If conditions are moist from three weeks before and through flowering, the little mushroom-like apothecia will germinate from the sclerotia and release spores at the right time for infection. Those spores land on the petals, which fall into the canopy and onto leaves. The petals start to rot. The pathogen feeds on this rot and roars to life.

Sclerotinia spores use energy from the decomposing petal to infect leaves and stems. photo: CCC Apothecia

In this situation, there is one highly effective way to stop the disease — fungicide. If the crop canopy is thick, yield potential is high and the moisture continues, farmers will probably want to spray right around 20 per cent flowering — the point just before those spore-infested petals start to drop.

Growers who want a clear indicator that petals are indeed spore-infested have tools for that: Spornado from 20/20 Seed Labs or DNA-based petal-testing kits such as those offered by Quantum Genetix and Discovery Seed Labs.

Zoom out

With the right conditions, sclerotinia will work through its cycle and be as widespread and damaging as weather allows. It will be less damaging in drier areas and years. It will be worse in years that are moist to wet and in areas with a history of growing more acres of host crops.

“Each farmer assesses their risk situation, decides what they can tolerate for loss and acts accordingly,” says Clint Jurke, director of agronomy for the Canola Council of Canada. “As part of their decision-making, we’d like farmers to think more about the loss threshold. We want them to know the typical loss levels for their areas, and include fungicide in their planning if sclerotinia routinely has an incidence rate of five per cent.”

Based on disease surveys, sclerotinia can be found in almost every canola field during any particularly wet year. For example, the percentage of fields with at least some level of infection in 2016 was 93 per cent in Manitoba, 92 per cent in Saskatchewan and 81 per cent in Alberta. But in 2018, a drier year, this “prevalence” was 36 per cent in Manitoba, 57 per cent in Saskatchewan and 43 per cent in Alberta. (Last year was an odd year, with lower prevalence in Manitoba but much higher levels in Saskatchewan.)

“Incidence” is the percentage of plants infected in each field. Even in relatively dry 2018, the provincial average incidence rates were eight per cent in Manitoba and 5.3 per cent in Saskatchewan. Based on this, the average field with sclerotinia would have probably benefited from fungicide  — even in 2018.

“Yield loss is about half the incidence rate, so an incidence rate of five per cent means a 2.5 bu./ac. yield loss — which would be above the economic threshold for a fungicide application for many growers,” Jurke says.

Zoom in

Of course, every field will be different, which is why each farm should do its own assessment of risk. “Unless the yield potential of the crop is poor, even a below-average-yielding crop can benefit economically from a fungicide application if soil moisture is moist in the weeks before and during flowering,” Jurke says.

Apothecia germination and subsequent spore release can occur throughout the growing season as long as soils stay moist. If soil is dry for a long period, then is moistened and stays moist, it will take two to three weeks from the first moment of moistening for spore release to begin.

Spores that land on petals are of greatest concern. When infested petals fall into the canopy and land on leaves and stems, the infection stage begins. Once petals drop and start to decay, infection proceeds quickly with lesions visible in as little as 24 hours.

Hegedus’s research outlines the sequence of events in those 24 hours:

  • The fungus penetrates the cuticle — the waxy outer surface of the plant — within hours.
  • Once the cuticle is penetrated, the fungus grows within the plant tissue in a kind of stealth mode for a short but critical period that lasts six to 12 hours.
  • Interestingly, the standard plant defence of killing off its own cells to cut off the pathogen — referred to as “hypersensitive reaction” or “programmed cell death” — which works for other diseases including blackleg, is like fuel for sclerotinia. “The pathogen tricks the plant by exploiting its natural defence response, using that dead tissue to feed itself,” Hegedus says.
  • The fungus then rapidly colonizes the plant as hyphae begin to spread through the plant over the next 12 to 24 hours. The fungus produces generous amounts of acid, digestive enzymes and toxins during this phase.
  • After just one day, the first visual symptoms of plant tissue death (necrosis) appear.

If fungicide is present, it will kill the hyphae before they penetrate the cuticle. Even if fungicide applied after penetration could reach deep into the canopy, it’s still too late. “Fungicides do not have action inside the plant,” Hegedus says.

This information underlines the importance of early fungicide application when conditions are right for disease. “Best results from the fungicide tend to come from preventing the earliest infections because these will have the biggest impact on yield,” Jurke says.

Zoom forward

The other common disease management tool is genetic resistance within the plant. Varieties with improved tolerance to sclerotinia have been available for a few years. As written in the Canola Encyclopedia at, “These varieties have demonstrated a significant ability to reduce sclerotinia severity in the field and protect yield when the disease is present, although a fungicide application may be still be warranted depending on the conditions.” This is not full resistance like we get from a canola hybrid with an R-rating for blackleg. Could we get there for sclerotinia stem rot? It may be closer than ever.

Infected stems dry out and turn brittle. Little black sclerotia form inside these stems and eventually end up in the soil to continue the cycle. photo: CCC Apothecia

Research and plant breeding efforts continue to improve varietal resistance, and work is underway to incorporate new sources of resistance into canola lines.

Hegedus is part of an international collaboration of researchers from Australia, China, France and South Korea working on sclerotinia resistance. In an odd twist, genetic resistance for sclerotinia stem rot may actually come from turning off those genes responsible for the natural defence mechanism that promotes localized cell suicide. If the plant stops scorching itself, the disease has less fuel and infects more slowly.

“This was an unexpected and extremely exciting discovery,” Hegedus says.

The key for Hegedus and his AAFC colleagues and international collaborators will be to “turn off” the genes for highly specific response to sclerotinia stem rot, but “leave on” the genes that respond to blackleg and other diseases. That is part of the challenge, but to finally find “genuine and durable” genetic resistance to probably the most important disease — based on loss of yield and profits — of canola in Canada will be a major event.

Meanwhile, a preventative fungicide remains the key defence against this plant-killing yield robber. Fungicides are effective, and their economic threshold — when around five per cent of plants in a field are infected — occurs more often that most farmers probably realize. Which brings us back to the point of this article: Fungicides can greatly reduce sclerotinia infection, but they only work if they’re applied. And, in most cases, they need to be applied early to provide the greatest economic benefit.

Sclerotinia stem rot risk assessment

The sclerotinia stem rot chapter in the disease section at has more information on forecasting and risk assessment, including how to use petal tests effectively. As written in the Encyclopedia, “Ideal canola growing weather is also ideal for sclerotinia,” but the disease can also cause economic levels of damage when moisture conditions and yield potential are just barely average.

—Jay Whetter is communications manager with the Canola Council of Canada.

About the author


Jay Whetter is communications manager for the Canola Council of Canada.



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