Pre-harvest disease scouting

Why scout now?

Canola plant diseases are usually easiest to see and diagnose just before harvest. Post-harvest disease surveying can be difficult as other fungi set in as plants start to decay, clouding the common disease symptoms.

Use a scouting toolkit (including clippers and trowel) and follow the scouting and identification tips below. Fungicide spraying is not appropriate at this time. Instead, pre-harvest disease assessment is useful to implement disease-management practices – extend rotations, choose cultivars with appropriate disease resistance, and update fungicide decision-making.

How to scout?

Scouting should include targeted and random assessment.

For targeted scouting, check plants (individual or in patches) showing discolouration or premature ripening. Look for symptoms on above-ground parts and on roots.

For a random assessment, use this basic protocol:

–Check 20 plants at five sites in a “W” pattern (100 plants total) in each field. Check each plant for symptoms of the diseases listed below.

The Prairie Crop and Disease Monitoring Network has specific monitoring protocols for blackleg and sclerotinia stem rot and will soon have verticillium stripe and clubroot. The above protocol is sufficient for general pre-harvest scouting.

Clubroot scouting requires digging to look for galls. Plants that appear healthy can still have clubroot galls – and these galls will produce spores that can be spread around the field and infect canola the next time around. At the random scouting locations along the W, pull up a few plants and look at roots near ground level for swollen round tissue – galls. For clubroot, also check high-risk areas such as old and new field entrances, high traffic areas, low spots, areas with low pH and natural water runs.

What diseases to look for?

Sclerotinia stem rot

Examine the lower to middle areas of the stem looking for large bleached or tan lesions. In some cases, white fungal growth may even appear on green stems. (You may find infection very low on the stem, often where infected leaves fell against stems at ground level.)

As the infected stem dries, it will appear bleached or brown – like a bone – and may start to crack open or shred. Infected stem tissue is often hollow and hard.

Black sclerotia bodies – similar in appearance to mouse droppings – may be found inside the infected stems.

Sclerotinia can be found higher up in the canopy on side branches and pods, but yield loss for these infection sites is usually minimal compared to lower stem infections. See the table at the bottom for a good comparison of stem diseases.

Yield loss from sclerotinia stem rot is approximately 50 per cent of the disease incidence. For example, if 10 per cent of stems are infected, yield loss will be about half that — or five per cent. Read more.

Sclerotinia stem rot in canola. Credit: Justine Cornelsen

Sclerotinia – Sclerotia bodies in a sclerotinia-infected canola stem — Sclerotia bodies in a sclerotinia-infected canola stem

Blackleg

Examine the bottom to middle areas of the stem for lesions. Black pepper-like specks (pycnidia) may appear within the lesions. When blackleg is severe enough to cause yield loss, the plant will have irregular, knotty, woody cankers at the base of the stem. This infection will eventually grow through the stem, cutting off nutrient flow.

To scout, use garden clippers to slice through the top of the root, about half an inch below the base of the stem. If more than half the area of the stem is blackened, blackleg has likely reduced the yield of that plant.

If blackleg levels are higher than expected even with a fungicide, check notes to see the timing of the fungicide. To be effective, a fungicide labelled for blackleg should be applied at the 2- to 4-leaf stage of the crop with appropriate rate and water volume.

To manage blackleg, lengthen the break between canola crops in that field and change to cultivar with a different source of resistance.

Biglobosa. In the weeks before harvest, blackleg can form lesions higher in the canola. Look for pycnidia in upper stem lesions as a sign of blackleg. These could be caused by the less virulent L. biglobosa blackleg pathogen, which rarely has enough time in Western Canada to cause major yield loss. L. maculans versus L.. biglobosa.

Fall scout for infected stem pieces

After harvest, agronomists and canola growers can scout fields planned for canola next year, collecting old canola stem pieces for a blackleg test. These spore-carrying stem pieces left over from the last time canola went on the field can last 2-3 years and provide a clue to the extent of viable blackleg spores in the field. Look for stem pieces with pseudothecia, which look like tiny dirt pieces that don’t easily rub off. In a “normal” field with previously low levels of blackleg, very few pseudothecia will be found. Tests can help choose the best blackleg R-genes for that field.

Clip canola stems around ground level to check for blackleg. Credit: Justine Cornelsen

Clubroot

Canola plants may be infected with clubroot – even if above-ground symptoms are not present. It is important to pull or dig up plants to examine the roots for clubroot galls. Specific scouting tips for clubroot.

Even small galls can produce enough spores to greatly increase the disease risk in future crops.

Cultivar resistance and crop rotation are keys to management. Click that same link for tips on patch management within a field.

Even with clubroot galls this large, the canola plants didn’t appear to show above ground symptoms when compared on their own. But against the rest of the field, they appeared “riper” and not as green. Photo credit: Dane Froese — Even with galls this large, canola plants didn’t have obvious aboveground symptoms.

Verticillium stripe

Verticillium stripe is easier to identify at or after harvest. In the weeks leading up to harvest, symptoms may only show stem bleaching on one side of the stem. This can confused with sclerotinia stem rot.

Cross section root clippings may show a greyish hue that can be mistaken for blackleg.

Once an infected plant is fully ripe, the stem peels to reveal tiny black microsclerotia which resemble ground pepper. These microsclerotia remain on the plant stem or fall to the soil.

See the table below for more tips on how to distinguish vertilicillium stripe from blackleg, sclerotinia stem rot and grey stem. How to identify verticillium stripe.

Verticillium stripe. Peeling shows the darkening underneath the epidermis and outer cortex of the stem. Credit: Justine Cornelsen — Verticillium stripe. Peeling shows the darkening underneath the epidermis and outer cortex of the stem.

Verticillium stripe in a canola field. Photo credit: Justine Cornelsen — Verticillium stripe

Verticillium stripe in canola. Credit: MAFRD — Verticillium stripe in canola. Credit: Manitoba Agriculture

Alternaria black spot

Alternaria black spot normally results in leaf lesions and then eventually blackish spots on stems and then pod tissues. It is very evident before plants start to turn colour and mature.

Alternaria is not usually an economic problem in B. napus canola when the crop is standing. Alternaria tends to be more damaging in juncea or rapa canola, although sulphur deficiencies in any canola can exacerbate black spot issues.

If alternaria shows up on napus canola, it will be later in the season when weather and time have removed the protective wax covering on the plant. UV radiation, cool/warm fluctuations and hail will break down this wax barrier.

Cool wet weather can also increase alternaria infection, and rain splash can spread the disease to other plants.

In cases of heavy alternaria infection (which is rare), early swathing may have an overall economic benefit to later swathing if alternaria has moved to pods. When infected areas make up 50 per cent or more of the crop, swathing early may be the best way to salvage the yield in those infected plants. The disease can keep spreading on green material, and swathing hastens dry-down of the crop. Read more.

Some fungicide labels indicate alternaria control in canola, but by the time a grower identifies alternaria infection severe enough to warrant fungicide, the spray decision is too late.

Aster yellows

Aster yellows is a phytoplasma infection that causes misshapen pods and flower buds. These pods produce little to no yield. However, most fields in most years have less than one per cent infection, which is not an economic level of loss.

Aster yellow infection can also result in normal looking pods that contain only a few misshapen seeds. Other symptoms include sprouting in the pod, and purplish plants and pods – although note that purpling can result from many potential causes. Read more.

Canola plant exhibiting aster yellows symptoms. Credit: Jon Whetter — Aster yellows. Credit: Jon Whetter

Grey stem

Grey stem, caused by Pseudocercosporella capsellae, can be found in most canola fields when the crop is ripening, but it usually develops too late in the growing season to affect crop yields significantly. Silvery to purplish patches develop on the stem. These can cover whole stems and continue to spread in stubble as plants decompose.

Grey stem can be confused with other diseases that cause stem lesions and stem discolouration, including blackleg, sclerotinia stem rot and verticillium stripe. For identification help, see the table at the bottom of this article.

Grey stem plant disease in canola — Grey stem

Grey stem plant disease on canola plants (right). Blackleg disease on canola plants (left). Source: Randy Kutcher — Grey stem on the right. Blackleg on the left. Source: Randy Kutcher

Foot rot and brown girdling root rot

Fusarium foot rot infects at ground level, producing tan brown lesions with concentric markings. Brown girdling root rot (BGRR) symptoms are rusty brown lesions on the canola tap root, which may girdle and pinch off the root if severe. These diseases can be much higher in tight canola rotations. Read more.

Brown girdling root rot at its most severe will completely pinch off roots. The plant lodges and dies.

Fusarium wilt

This can cause bleached stems with a slight pinkish tinge typical of fusarium fungus. Discolouration can occur up only one side of a stem, a typical sign of fusarium wilt. This disease has been virtually eliminated through genetic resistance.

Sooty moulds

Sooty moulds can grow on mature canola plants, often if wet conditions occur just before harvest. These moulds can great dusty conditions for harvest, but do not usually affect yield or quality.

Kelly Turkington, plant pathologist with Agriculture and Agri-Food Canada, provides the following description:

Sooty moulds are a group of saprophytic fungi that grow on normally mature or prematurely ripened plants. Superficial growth of the sooty mould fungi gives canola plants a dusty dark grey or black colour.

The main species are Alternaria (not the pathogenic ones) and Cladosporium. They typically occur if there are wet conditions post maturity that delay the timely harvesting of crops, or on prematurely ripened plant tissues killed by abiotic stresses (e.g. hail, flooding, drought, high temps) or biotic factors (root rots, insect damage, etc.) in moist conditions.

There are no effective management tools for sooty moulds.

Sooty mould on canola pods. Credit: Amanda Smith — Sooty mould

Powdery mildew

Powdery mildew can set in late in the season in humid canola canopies. Note that the pathogens associated with powdery mildew in cereals (Blumeria graminis), peas (Erysiphe baeumleri) and canola (Erysiphe polygoni) are different and do not cross infect across species and even forms within species.

It can coat stems and leaves. While not a usually a factor for canola yield and quality, heavy mildew can add to harvest headaches. Southern Alberta experienced some heavy powdery mildew in 2025. The coating seemed to keep canola stems green, even when canola seeds were ready to harvest. Green stems make for slow going with the combine, and herbicide specialists expect it will impede uptake and activity of pre-harvest desiccant. AAFC plant pathologist Kelly Turkington says “powdery mildew mycelium is hydrophobic, so it will repel water. Thus, there may be issues in terms of getting good retention and penetration into canola tissues of Reglone or other desiccants.” Farmers with this experience will often opt to swath.

The other issue is that powdery mildew creates a cloud of dust, covering the swather and combine. It means regular window washing and regular dust removal to reduce fire risk and allow for proper engine air intake.

Powdery mildew on canola stem. All stems are white with mildew. The photographer wiped off one stem to reveal the healthy green stem underneath. Southern Alberta 2025. Andre Lacoursiere photo

Comparison tables

Blackleg, clubroot and sclerotinia stem rot

wdt_ID	Comparisons	Blackleg	Clubroot	Sclerotinia stem rot
1	Susceptible host plants	Canola and other brassicas	Canola and other brassicas, including some common weeds.	Broadleaf crops, including canola, soybeans, sunflower, pulses.
2	Key distinguishing features	Lesions with specks of picnidia inside form on leaves. Infection spreads to the base of the stem, where it forms cankers. Clipping open stems will reveal blackened tissue inside. Moderate cases will cause yield loss, even if the plant doesn’t die. Severe	Galls form on roots. In serious cases, large tuberous galls will restrict flow of nutrients and water up and down the plant, killing the plant.	Lesions form on leaves and stems. Eventually the stems rot, then turn white and brittle. Plants die prematurely and seed set is greatly reduced. Black sclerotia form inside (and sometimes outside) damaged stems.
3	How it rests waiting for the next host crop	On pieces of infected canola stubble	As each gall breaks down, it releases billions of spores into the soil.	As sclerotia bodies in the soil
4	How it spreads	Pseudothecia and pycnidia on infected canola residue release spores that continue the infection cycle. Pycnidiospores from pycnidia travel only a few metres. Smaller ascospores, shot into the air by pseudothecia, can travel farther.	Spores move with the soil. When soil moves, clubroot moves. Soil moving through fields and from field to field on machinery is the most common vector for spread of the disease. Spores infect host roots, continuing the cycle.	Sclerotia produce apothecia that release spores. Spores can carry for kilometres on the wind, but most will come from within fields or from connecting fields. When release coincides with canola flowering and moist/humid conditions, infection can occur.
5	Benefit of crop rotation	2- or 3-year break between canola can almost eliminate risk because host stubble deteriorates.	2- or 3-year break between canola can reduce viable spores by 90%, but this can still be enough spores for widespread damage if spore counts start off high. (1,000,000 per gram of soil.)	Rotation benefit for sclerotinia is less than it is for blackleg and clubroot because many crops are susceptible, sclerotia are widespread and released spores carry to nearby fields. However, higher severity will be observed with shorter rotations of susc
6	Genetic resistance available	Yes	Yes	Improving tolerance in selected varieties
7	Genetic resistance groups identified	Yes	No, but coming soon?	No
8	How to use R varieties as part of a disease management program.	Always use R or MR varieties, and if blackleg is getting worse, switch to a different R-gene.	Use R varieties in areas where clubroot is found or suspected. This will help keep soil spore loads low and limit yield loss for the long term.	Sclerotinia-tolerant varieties can reduce disease in high-risk situations, but fungicide may still be required.
9	Effective fungicides available	Yes, for early-season infection	No	Yes, for application at flowering

Canola stem diseases – A comparison

wdt_ID	Plant Disease	Sclerotinia	Blackleg	Blackleg	Verticillium Stripe	Grey Stem	Fusarium Wilt
1	Species	Sclerotinia sclerotiorum	Leptosphaeria maculans	Leptosphaeria biglobosa	Verticillium longisporum	Pseudocercosporella capsellae	Fusarium oxysporum
2	Stem Symptoms and distinguishing features	Bleached white appearance. Infected stems tend to shred and shatter very easily. White mouldy growth. Black sclerotia bodies will form inside the stem.	Stem lesions with pycnidia (black spots) forming inside the lesion. Base of stem (crown) becomes woody. Cross section cut reveals blackening.	Shallow stem lesions with pycnidia	Shredding of the stem tissue. Tiny black microsclerotia form beneath the peeling outer layer.	Large purple to grey-speckled stem. Pod lesions are also possible.	Discolouration of the stems; yellow or reddish-brown streaks on stems.
3	Pod	Withered pods if branch below is infected. Sometimes white mould, lesions.	No symptoms	No symptoms	No symptoms	Grey speckled pods.	No symptoms.
4	Crown (base of stem) exterior		Cankering
5	Crown cross-section	Clean, dried down	Solid black sections, often pie shaped. Fully black in extreme cases.	Typically does not reach stem in time	Greyish hue across entire cut. Gets darker as microsclerotia build up. Can extend many inches up the stem.
6	When to scout	Prior to swath timing	Prior to swath timing, 60% SCC.	Prior to swath timing, 60% SCC	Easier to ID post-harvest	Prior to swath timing, 60% SCC.	Prior to swath timing, 60% SCC.
7	Yield Loss	Potential yield loss in a field can be determined by: % Potential Yield Loss = % Infection x 0.5	For every unit of increase in disease severity, a 17% loss in plant seed yield can be expected.	Comes in too late in the season to cause a significant impact	Does occur but no system to measure at this time.	Not known.	Varieties are resistant, rare to find.

While scouting look for…

Insect damage to pods. Debarked pods (indicating bertha armyworm or grasshopper feeding), larger holes in pods (which could be from diamondback, grasshopper or bertha armyworm feeding) and brown rotted seeds (which can result from lygus penetration of the pod).

Exit holes from cabbage seedpod weevil larvae. If more than 25 per cent have exit holes and the crop was not sprayed, it probably should have been.

Root maggots. Their tunnelling can reduce root function, with greenhouse studies showing a negative yield impact. Either way, severe root maggot may cause yield loss but limited options exist that might discourage the number of Delia species flies that produce the root maggot larvae. Large isolated plants tend to encourage more egg laying and larvae feeding than smaller more numerous stems.

Missing pods. Insects are just one reason. Heat is a common reason. Ten reasons for missing pods.

Seed colour change. Open up some pods and assess the degree of colour change. This can help with harvest timing.