Sclerotinia stem rot in canola: spray timing at 20–50% flower

Symptoms, timing and look-alikes

Nothing you see in the crop at spray time is useful; infection has not happened yet. The Canola Council notes that plant infections rarely develop before mid-flowering. Lesions show up after petal fall, first as soft, water-soaked, greyish-white patches at leaf axils and on the main stem where petals lodged. They expand, bleach to white, and the stem becomes papery and shreds. Split a stem and you find hard black sclerotia, the resting bodies that return to the soil at harvest. Infected plants ripen early and lodge, usually visible from mid-July into August as bleached plants scattered or in patches through the greener crop.

Look-alikes. Blackleg also bleaches and kills stems early, but its canker sits at the soil line with black pycnidia on the lesion and a dark wedge in the crown cross-section, and there are no sclerotia inside. Clubroot patches ripen early with galled roots. Hail bruises and sun-scald on stems are superficial and do not shred. If you find sclerotia inside the pith, it is sclerotinia.

How the infection works

Sclerotia near the soil surface need at least 10 days of moist soil at moderate temperature (15–25 °C / 59–77 °F) to germinate and push up apothecia, small tan cups 5 to 15 mm (0.2 to 0.6 in) across. Apothecia release ascospores that land on the crop, but ascospores cannot infect green leaves or stems directly. They need a food source, and dead petals stuck to leaves and stems supply it. The infected petal then grows the fungus into the stem. Leaves and stems must stay wet for about two to three days for infection to succeed; lesion development is favoured by humidity and 20–25 °C (68–77 °F), and dry, warm weather shuts it down. Ascospores are short-lived (survival of up to 50 per cent after two days and about 1 per cent after three days in field exposure), so the disease tracks weather closely during bloom.

Staging bloom: the main-stem count

Percentage bloom refers to the main stem, not to how yellow the field looks. The Canola Council method: pull plants at a few spots in the field, strip off the secondary branches, and count the flowers on the main stem, including aborted flowers and the youngest developing pods.

Average 10 random plants per site. For thin stands of around 50 plants/m² (5 plants/ft²) or fewer, add a couple of flowers to each count, because thinner stands branch more and the main stem carries a smaller share of the bloom. A crop moves from first flower to 20 per cent in four or five days, so staging is a twice-a-week job once the first yellow shows.

The risk checklist

Score each field shortly after first flower, when about 75 per cent of plants have at least three open flowers (typically the last week of June or first week of July), and keep updating it through full bloom. The factors the Canola Council lists, in order of importance:

1. Rainfall and soil moisture. Regular rain or high humidity from two weeks before flowering and through flowering. This is the single biggest driver.
2. Weather forecast. Continued showers through petal drop extend the infection window.
3. Canopy density and yield potential. A thick, lodging-prone canopy holds humidity; a crop under about 1.7 t/ha (30 bu/ac) rarely justifies the cost unless conditions are ideal for infection.
4. Cultivar. Some hybrids carry partial sclerotinia tolerance; it lowers, but does not remove, risk.
5. Apothecia present. Look for the cups under the canopy in a field with a history after a wet fortnight.
6. Field history. Sclerotinia in the previous host crop (canola, pulses, sunflower, mustard) and years since that crop. Manitoba Agriculture puts sclerotia survival at up to four years.

The Canola Council's printed checklist card assigns points to each answer. It was developed from a Swedish model where a total of 40 points or more meant a spray was likely to pay; a 35-point cut-off caught nearly 90 per cent of fields that needed spraying but also included over 20 per cent that did not. The Council notes the threshold may shift under Canadian conditions and with fungicide cost and canola price, so treat the score as a structured argument rather than a verdict.

Petal tests. A DNA (qPCR) petal test returns results in one to two days; the older agar plate test takes about a week. Both use early flowers and tell you whether ascospores are landing on petals right now. The Council recommends using them alongside the checklist, not instead of it.

One application or two

Early main-stem infection costs the most yield, so the first pass earns its keep at 20 to 30 per cent bloom. If conditions are borderline at 20 per cent and rain arrives later, a single later application inside the label window can be the better call. Two passes make sense only when the product is registered for a split application, bloom is prolonged by cool weather or uneven staging, and the wet pattern continues. Registered intervals in Canada run from 7 to 14 days depending on product, with some labels requiring the second pass at 50 per cent bloom or a different mode of action for the follow-up. Protection from a single contact application lasts roughly two weeks when coverage is good, which is why water volume matters in a dense canopy.

Fungicide groups registered in Canada

As of October 2026, actives with sclerotinia claims on canola in Canada include, by FRAC group:

• Group 3 (DMI): prothioconazole, metconazole
• Group 7 (SDHI): boscalid, fluxapyroxad, pydiflumetofen, fluopyram
• Group 11 (QoI): azoxystrobin, picoxystrobin, fluoxastrobin, pyraclostrobin
• Premixes combining 3+7, 3+11, 7+11 or 7+12 (fludioxonil)
• Biologicals: Bacillus subtilis strain QST 713 (Group 44 on Canadian labels), applied in bloom; Coniothyrium minitans, a soil-applied sclerotia parasite used pre-plant or post-harvest

Bloom windows, water volumes, intervals and pre-harvest intervals differ by product and are on the label registered in your province. Products registered by the US EPA are not automatically registered in Canada; confirm the PCP number in Health Canada's PMRA label search or your provincial crop protection guide before buying.

When a spray pays and when it does not

The Canola Council rule of thumb is that per cent yield loss equals roughly half the per cent of plants infected (Manitoba Agriculture puts the multiplier at 0.4 to 0.5). A field heading for 40 per cent incidence is losing about 20 per cent of yield. Multiply that by expected yield and price, subtract the application cost, and the decision is usually obvious. Where it is not obvious, the weather decides: with rain in the two weeks before bloom and more in the forecast, the odds favour spraying; after a dry June with a thin canopy and a dry week ahead, they do not, whatever the field's history. Rotation helps less than it does for other diseases because sclerotia last up to four years and the host range covers most Prairie broadleaf crops, so the bloom-stage decision remains the main lever.