Disease outlook 2025: Must-have updates, best advice and what’s coming next

By Treena Hein

Farm Forum talks with three experts about what to expect in terms of disease pressure in 2025, disease trends, plus top disease management reminders and tips to achieve optimal control. Let’s jump right in.

Canola: Blackleg is back

Chris Manchur, Agronomy Specialist, Canola Council of Canada (CCC)

Current state of play

Manchur says blackleg has revved up over the past two years in both incidence and severity with yield losses ranging from minor to over 50 per cent. Sclerotinia was also exacerbated in 2024 with frequent rain leading up to and during flowering with yield losses in crops that were left unsprayed.

Verticillium stripe is the other major pathogen making an impact. Commonly found in Manitoba, verticillium stripe has also been documented in Saskatchewan and Alberta. “This has been the culprit in fields where farmers are wondering why they did not achieve yields they expected during harvest,” says Manchur, adding this is down to verticillium stripe’s late season impact. He says that in some cases, yield losses were up to 20 bushels per acre.

Scouting in 2025

In the early season (cotyledon to 2-leaf), rainy periods with warm weather can facilitate blackleg infection of young plants. Manchur says to scout for old canola stubble with a pinkish ooze containing infectious pycnidiospores. If present, a foliar fungicide may be required around the 2-leaf stage. 

Start scouting for sclerotinia at early flower. Manchur advises watching soil moisture and for persistent humidity after rain. “The decision to apply fungicide happens before you see any symptoms,” he says. “If you see small cup-shaped mushrooms the size of a dime (apothecia) on the soil, you likely have spores infecting your canola.” 

During late season from 60 per cent seed colour change to maturity, survey your canola for blackleg (basal cankers at the stem base) and verticillium stripe (striping of the stem). Check for both diseases by cutting the crown, where root meets shoot, of a handful of plants at multiple field locations. “Testing results shows that these two diseases can often occur in the same plant, so be aware of how they look together and separately,” says Manchur.

Best advice

Disease control planning for 2026 begins at 2025 harvest, he says, so carefully plan your cultivar, seed treatment and crop rotation decisions this year, keeping in mind that rotation is the main tool for verticillium control.

For blackleg, Manchur advises maintaining a two-year break from canola if possible. Submit diseased stubble for DNA testing and select cultivars with R genes that match the blackleg races found in your field. If blackleg concerns continue, consider additional seed treatment or early-season (cotyledon to 2-leaf stage) fungicide application.

For sclerotinia, the CCC has developed an online risk assessment tool. Manchur advises that farmers in a high-risk situation should consider a dual fungicide application or a multiple mode-of-action product.

Cereals: mild winters, more disease?

Kelly Turkington, Plant Pathologist, Agriculture & Agri-Food Canada (AAFC)

Current state of play

Rusts, especially on the Prairies, typically infect Canadian crops via wind-borne spores from the U.S. where they overwinter on winter wheat. However, transmission of stripe rust can occur locally when spring wheat is infected from June to August and those spores are blown into winter wheat fields. “If winter conditions are milder and you have good snow cover, this pathogen can overwinter and resume development the following spring,” says Turkington, adding that volunteer spring wheat and regrowth provide the “green bridge” needed for stripe rust to move from spring to winter wheat crops. 

The yield impact of leaf spot complex (tan spot and the septoria complex) and fusarium head blight (FHB) is largely related to weather in June and July, crop variety and the extent of infection in the U.S. (and wind movement to Canada).

Turkington’s main concern is that, with milder winters, we may see higher potential for viral infections to overwinter — diseases such as barley yellow dwarf virus, mycoplasma-related disease (aster yellows), or even issues like powdery mildew in wheat.

Scouting in 2025

Turkington advises scouting regularly throughout the growing season, but especially from June to mid-July. “The nice thing about cereal leaf diseases is that one can follow their development from tillering to upper canopy leaf emergence to head emergence and then decide if a fungicide is needed and the timing,” he says, adding that farmers should check the Prairie Crop Disease Monitoring Network forecasts from mid-May to early July.

For those grappling with FHB, the University of Manitoba has developed the Fusarium Head Blight Risk Mapping Tool, an online resource to help assess potential FHB damage and plan accordingly.

Best advice

Get a fungal screen test on harvested seed you intend to plant and, in-season, monitor continually. “Knowing the disease issues at play, you can use the provincial variety guides for seed treatment and in-crop fungicide options,” says Turkington.

Scout carefully, too. He reminds farmers that foliar fertilizer, herbicide or abiotic/biotic issues can sometimes produce symptoms that are mistaken for fungal leaf spots. “Finally, fungicide application does not mean a completely disease-free crop, so make sure to leave unsprayed areas to assess fungicide performance.”

Corn and soybean

Albert Tenuta, Plant Pathologist, Ontario Ministry of Agriculture, Food & Agribusiness (OMAFA)

Current state of play

Corn: In 2024, environmental conditions favoured tar spot and, for the first time, the disease spread into Eastern Ontario and Quebec. Tenuta says spores are easily dispersed in storms and on wind currents, and the disease thrives in moderate temperatures and high relative humidity (greater than 75 per cent), along with prolonged periods of leaf wetness and cool nights. Resistant hybrids will come, eventually.

And, as always, Northern corn leaf blight (NCLB) and Gibberella ear rot (GER) are threats to watch out for.

Soybean: White mould (sclerotinia) is the main concern and continues to be a problem in all soybean-growing regions, particularly when conditions are warm and humid during canopy closure.

Scouting in 2025

Corn: For areas with a history of tar spot, Tenuta says to start scouting for disease development in early July through to the end of the season. In southern Ontario, monitor storm fronts and check for tar spot development after a system moves through. In eastern Ontario and Quebec, watch for alerts from southern Ontario and the U.S. and don’t forget to assess overwintering potential.

Soybean: Start scouting for white mould before mid-season. Apply fungicide at the R2 to R3 stage with flowers present and Tenuta says to use larger-sized droplets that have the velocity to penetrate the canopy and decrease drift.

Best advice

Corn: For tar spot, have a detailed disease plan ready – start by knowing what to look for when scouting, especially the early signs of infection. “Be aware of, but do not fear tar spot,” says Tenuta. “OMAFA and the University of Guelph, as well as our collaborations with U.S. colleagues have shown it can be managed effectively. But you need to be vigilant and prepared to respond in-season with a fungicide.”

Tenuta says fungicide application at the RI silking stage is the most consistent bet for tar spot (also for NCLB and GER). “A second fungicide application at R3 stage or later has not provided a consistent ROI,” he says. “But in some situations – where there’s heavy pressure, very susceptible hybrids and prolonged favourable weather conditions – it can be beneficial.”

For NCLB and GER, management begins with planting resistant or tolerant hybrids, so check with your seed dealer as well as Ontario Corn performance trials at GoCrops.ca for the DON hybrid report.

Soybean: The sclerotia (fruiting bodies) will naturally die if left on the soil surface, so do not till after harvest. Indeed, no-till fields tend to have less of this disease because more of the sclerotia die off during spring and early summer. But, because sclerotia can survive in soil for years, use rotations to put as many years as possible between soybeans, edible beans and canola, which are all susceptible to sclerotinia.

Resources

Canola

CCC Blackleg loss calculator: https://www.canolacouncil.org/calculator/blackleg-loss

CCC Sclerotinia economic threshold calculator: https://www.canolacouncil.org/sclerotinia-calc/economic-calculator

CCC Blackleg vs Verticillium wilt identification tech sheet: https://www.canolacouncil.org/download/130/agronomy-guides/28744/verticillium-stripe-blackleg-resource-v5

Cereals

Prairie Crop Disease Monitoring Network: https://prairiecropdisease.com/

U of M FHB Risk Mapping Tool: https://prairiefhb.ca/