The trials at the Ian M. Morrison Research Station in Carman, Man., come at a critical time. BLS isn’t new to Canada, but infections are being reported with increasing regularity across the Prairies.

“Bacterial leaf streak has been detected in Canada since the 1920s but we are seeing the re-emergence of it. And it’s worsening rapidly,” said Dr. Shaheen Bibi, a plant pathologist and postdoctoral fellow at the University of Manitoba in Dr. Dilantha Fernando’s lab. Fernando and his BLS team lead the Carman trials.

Identification can be tricky

BLS often goes unreported because it mimics other cereal leaf diseases. Farmers may mistake it for tan spot or, in later stages, confuse necrotic lesions with natural senescence. Accurate diagnosis often requires lab expertise or a trained eye. That diagnostic challenge makes scouting all the more important during the growing season.

The disease is caused by Xanthomonas translucens, a bacterium with two pathovars of concern in Prairie cereals: pv. undulosa, which infects both wheat and barley, and pv. translucens, which primarily infects barley.

On leaves, the disease shows up as long, translucent streaks — hence the name translucens — that begin as small water-soaked lesions. Under wet conditions, lesions may exude a milky or yellow ooze — a key diagnostic feature that separates BLS from fungal leaf spots such as tan spot. As lesions mature, leaves lose photosynthetic area, and the flag leaf in particular, the part of the plant that contributes the most to grain fill, can be severely damaged.

Severe infections destroy photosynthetic tissue, and anecdotal reports suggest yield reductions of up to 50 per cent. The potential for loss is especially high because damage peaks at the flag-leaf stage.

But yield isn’t the only economic concern. The same bacterium can also infect heads, causing a symptom known as black chaff, which can reduce marketability by downgrading grain due to discoloration. Infected seed may also carry the pathogen, creating problems for seed use and resale.

Black chaff appears as dark streaks or bands across glumes and awns, sometimes alternating with healthy green tissue in awned varieties. In severe cases, glumes may turn completely black, and exudates can give heads a water-soaked appearance.

Conditions matter

BLS thrives during warm days, cool nights and in moist environments. Wetter years tend to bring more problems than drier ones, and areas that are naturally arid are less prone to outbreaks.

“Last year at Carman, we saw more of it because it was so moist,” said Bibi. “This year, not so much.”

Moisture also drives how the disease moves within fields. Rain splash, wind-driven rain, irrigation and even mechanical activities can help spread bacteria from plant to plant. On the Prairies, irrigation is a particular concern, especially in southern Alberta, where irrigated acres are more common. That’s one reason Fernando’s BLS team uses sprinkler irrigation on their Carman plots: to create the humid canopy conditions that allow the disease to develop.

The bacterium is primarily seed-borne but can also survive in crop residue, volunteers and perennial grasses. Because it is bacterial, standard fungicides, whether seed treatments or foliar sprays, are ineffective.

Management today

With no resistant varieties thus far in Canada, and no chemical options, growers are left with cultural practices and careful scouting to reduce risk. To help farmers manage the threat, a group of Prairie cereal organizations, including SaskWheat, SaskBarley, Alberta Wheat, Alberta Barley and the Manitoba Crop Alliance, released a joint fact sheet in 2023 outlining key practices and scouting strategies to reduce inoculum levels and slow the spread of BLS.

Start with clean seed. Infected seed is the main source of inoculum. If BLS is suspected in a field, especially when black chaff is visible, harvested grain should not be used for seed. Certified seed is not routinely screened for Xanthomonas translucens in Canada, so growers are encouraged to ask about testing or send samples to independent labs.

Stretch the rotation. Extending the break between cereal crops to more than two years helps reduce inoculum in residue. Volunteers and grassy weeds should be controlled to cut down on secondary hosts.

Scout carefully. Begin at herbicide timing and continue through senescence, with extra passes after storms that might wound plants. The best time to distinguish BLS is at the flag-leaf stage, when translucent streaks are most visible. Avoid walking fields in wet conditions, since the disease can spread on boots and clothing.

Manage irrigation. In irrigated areas, water management can reduce risk. Practices such as irrigating in the evening when the canopy is already wet with dew, letting the canopy dry between sets, and avoiding unnecessary irrigation can shorten the hours of leaf wetness that favour bacterial spread.

Assume susceptibility. No Prairie varieties are currently rated for resistance to BLS. Some U.S. wheats (Glenn, Faller, Prosper, Bolles) and barleys (AAC Connect, AAC Synergy) have shown partial resistance, but local screening is still underway. For now, farmers should plan as though their chosen variety is susceptible.

Research directions

Fernando’s BLS team is running controlled trials in Carman with inoculated seed and irrigation to create conditions for infection. The aim is to better understand how much seed infestation translates into seedling infection, how moisture drives spread, and whether genetic resistance is possible.

Fernando’s lab is tackling several angles at once. One project is characterizing Canadian isolates of the bacterium — collecting strains from different provinces to see how diverse they are and how that diversity affects disease severity. Another is mapping quantitative trait loci (QTLs), regions of DNA linked to traits such as disease resistance that breeders might eventually use. The team is also testing biocontrols that have shown promise in the greenhouse.

Most notably, they’re looking at cereal genes already known to confer disease resistance. The Manitoba team is focusing on two in particular — Lr34 and Lr67 — named for the leaf rust (Lr) resistance they provide. Both are broad-spectrum, meaning they protect against more than one disease. Lr67, for example, has shown some resistance to fusarium head blight and is most effective in mature plants.

Early trial results suggest Lr67 lines may show more resistance than Lr34. It’s too early to call, but the work could point to varieties with at least partial protection against bacterial leaf streak.

For now, clean seed, long rotations, careful scouting and mindful irrigation remain the most practical defences against a disease that is re-establishing itself across the Prairies. But resistance research offers a hint that the playbook could expand in the years to come.

“What we want to see is whether there are any lines showing resistance to BLS that could be used in breeding programs in the future,” said Bibi.

Article updated Nov. 6, 2025 to replace photo at top.

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That’s the message from Dan Undersander, forage agronomist and professor emeritus at the University of Wisconsin. He spoke during a three-day intensive forage workshop hosted by the Canadian Forage and Grassland Association at the University of Manitoba in March.

While many growers are aware of winterkill and stand thinning, they might not realize just how many diseases are chipping away at their yields — or when those issues can start.

“If you don’t know what you’re looking for, you won’t see it,” Undersander says. “And you’ll think that everything is just fine when it isn’t.”

Black stem

Black stem is caused by the fungus phoma medicaginis and is one of the most common alfalfa diseases across Canada’s Prairies. It tends to show up in cool, wet conditions and often appears early in the season.

According to the Manitoba Agriculture website, the disease can be identified in early spring by numerous dark spots on the lower leaves, petioles, and stems. These may expand into large black areas. Infected leaves often turn yellow and fall prematurely, and lesions that girdle the stem can cause wilting above the damage.

“If it causes complete girdling of the stem, then the stems will die,” Undersander says. “If you have enough of that, then your plant will die.”

Early cutting can help reduce losses, as can rotating with non-legumes for a few years before reseeding alfalfa.

Crown rot, root rots

A wide range of fungi — including fusarium, rhizoctonia, and phoma — cause crown and root rot, especially in older stands or those affected by winter injury. Symptoms include stunted growth, yellowing, and poor vigour.

“If crown rot is less than 50 per cent of the crown’s diameter, it’s probably worth keeping the stand,” Undersander says. “But if it exceeds 50 per cent, you should think about turning it over, because there’s a good chance it won’t survive.”

Winter crown rot, also known as snow mould, is another threat to alfalfa and other legumes. It’s caused by several soil-borne fungi that are most active during late fall and early spring when plants are dormant and soil temperatures are near freezing. Once the soil warms above 0 C, these fungi become inactive, and alfalfa is no longer at risk for this disease.

Aphanomyces

Aphanomyces is another type of root rot, caused by the oomycete aphanomyces euteiches, and has become a significant disease in alfalfa production, particularly in wet or poorly drained soils.

“If the seedlings are coming up and the cotyledon dies, but the seedling stays erect — that’s probably aphanomyces,” Undersander says.

It often appears on slopes rather than in low-lying areas, and its biggest effect is on root development. Undersander explained that aphanomyces causes root pruning, which weakens the alfalfa’s root system. As a result, the plants become less competitive, creating opportunities for weeds to invade the field.

Verticillium wilt

This cold-weather vascular disease was introduced from Europe and has been causing problems in British Columbia since the 1970s. It was first detected on the Prairies in 1998, in Manitoba, but has since spread to Saskatchewan and Alberta.

Undersander says it can be identified by what he calls a “thumbprint” on the leaf — irregular, pale or yellowish patches that appear on the leaves, which can resemble the shape or impression of a thumb.

“This is a disease that causes dead leaves on a green stem,” he says. “It causes problems because it’s attacking the vascular system.”

Symptoms are worst in spring and fall. Infected stands may die out in a few years, especially under irrigation. Rotating with cereals or grasses — and avoiding potatoes, sunflowers and sweet clover — is recommended.

Common leaf spot

Caused by the fungus pseudopeziza trifolii, this disease shows up as tiny black or brown circular spots on leaflets, with a lighter brown raised disc in the centre. As the infection spreads, leaves will yellow and drop early, reducing yield potential. It thrives in moist weather and overwinters in crop residue.

Manitoba Agriculture recommends cutting before leaves begin to fall, and using resistant varieties such as Rambler.

Downy mildew

This foliar disease shows up as pale blotches on the top of leaves and a violet, downy growth underneath. Plants may appear bunched or twisted at the top. It’s most active in spring and fall under wet, humid conditions but usually doesn’t cause serious damage.

Undersander points out that downy mildew can be a concern in both spring and fall. “Depending on the time of year, different organisms can be a problem,” he says.

According to Manitoba Agriculture, resistant cultivars such as Algonquin can be used for control, and rotating with cereals or grasses can help reduce infection.

Phytophthora

Phytophthora root rot is especially problematic in poorly drained areas and spreads through standing water in warm weather.

Even if phytophthora doesn’t kill the plant right away, Undersander says, it can severely damage the root. The plant may appear healthy for a while, but when dry conditions hit, it often can’t access enough moisture and will die as a result. He advises digging about six inches to check root health.

“You might keep the alfalfa for the current season,” he says, “but if the root is rotted off, you should plan on turning it over.”

Anthracnose

Though it’s often associated with lentils and dry beans, anthracnose can also be a yield thief in alfalfa — and it frequently goes unnoticed, Undersander says. The disease is identifiable by diamond-shaped lesions on the stem and sudden dieback at the top of the plant.

“There has been good resistance to it,” he says. “And we should think about taking advantage of that, because it will cause as much as a 20 or 30 per cent yield loss if you’re not paying attention.”

Timing matters

The appearance and impact of alfalfa diseases often depend on both the age of the stand and the time of year. Diseases such as phytophthora, pythium and black stem typically show up in new seedings, while bacterial wilt, fusarium wilt, crown rot and verticillium wilt are more common in older stands.

“You wouldn’t expect to see them in the first year or two, but you would maybe see them in the third or fourth year,” Undersander says.

Seasonal conditions also influence disease expression. Some pathogens thrive in cool, wet weather: downy mildew and verticillium wilt, for example, are often seen in spring and fall. Others, such as spring black stem and pythium, emerge early in the season, while summer black stem appears later.

Understanding when a disease is likely to appear can help with diagnosis and inform decisions about cutting, rotation and stand management.

Management tips

Undersander offers several general tips for alfalfa growers aiming to manage disease risk.

He recommends starting with good-quality seed and avoiding planting alfalfa after another legume. Where possible, he says, farmers should stick to planting in well-drained fields to help prevent root rot diseases and avoid wet spots that can foster pathogen growth. Maintaining good pH and nutrient levels is important, he adds, because vigorous plants are more disease-resistant. He suggests controlling insects, since they also introduce pathogens to a crop.

READ MORE: Alfalfa aptitude: five things to consider when selecting varieties

Farmers should also mow new seedlings before old stands, and try to mow clean fields before infected ones, to reduce disease spread.

“Wait till the dew is off before mowing,” Undersander advises. “I don’t recommend expecting all the dew to be gone, but at least a high portion of it.”

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Almost all pulse leaf diseases are triggered by rain and moisture in the canopy, said Dr. Sabine Banniza, plant pathologist with the Crop Development Centre. “Many need the rain in order to spread.”

So which diseases should farmers be guarding against in their lentils? Banniza outlined the top leaf diseases she sees in Saskatchewan during a Saskatchewan Pulse Growers webinar.

Anthracnose

“The number one lentil disease we have in the province these days is anthracnose,” said Banniza.

Anthracnose causes beige or brown lesions. Those lesions are not very conspicuous, Banniza said, and so farmers and agronomists would have to look closely to see them. Once the disease is established, farmers will likely see leaf drop.

Those stem lesions can also girdle the stem, killing the plant above the girdle, she said. “And when this happens, you all of a sudden start seeing these dead patches in your lentil crop.”

There is anthracnose resistance in lentils, but that resistance covers Race One, the less aggressive strain. Race Zero is more aggressive and more common, and there is currently no resistance to it in cultivated lentil varieties.

Ascochyta blight

Ascochyta blight used to be the top lentil disease in Saskatchewan. But the last serious outbreak was in 2005, said Banniza. That drop is a success story of lentil breeding program, she said.

“We’ve bred quite good resistance into almost all the lentil cultivars that are available now,” said Banniza. As a result, the ascochyta blight population “has just imploded and hasn’t really been able to come back.”

Stemphylium blight

Stemphylium blight starts out as light beige lesions that coalesce. The whole leaf eventually turns brown. Farmers will also see leaf drop.

Spores are airborne, making it difficult to do field research on the pathogen, Banniza said. But the research they’ve done indicates that early to mid-flower infections may cause yield loss, seed stain, and seed infection.

However, stemphylium blight often rolls in late in the season. Those late infections probably don’t cause much damage, Banniza said. “And if it’s really late, it may actually work like a natural desiccant because it defoliates the leaves.”

White and grey mould

Sclerotinia white mould and botrytis grey mould are two different organisms. But they are “like sister and brother,” said Banniza. “They often show up together because they both thrive in the same conditions.”

These diseases are very recognizable because they grow on the outside of the plants, said Banniza. Cottony white mould on stems, leaves, flowers, and pods is sclerotinia, while fuzzy grey growth indicates botrytis.

Both diseases show up late in the season when canopies are dense and moist. Tall, lush lentil crops are more likely to suffer an infection. Lentils tend to lodge in those conditions, creating an even denser mat of biomass that doesn’t dry.

“And that’s when these two diseases really get going,” said Banniza.

Managing leaf diseases

Banniza recommends a four-year rotation to control leaf disease. Tightening the rotation raises the risk of building disease inoculum in the fields.

“And if you run into a year when conditions are conducive, you’ll see an earlier outbreak and a much more severe outbreak which is more difficult to control,” said Banniza.

However, that longer rotation is unlikely to reduce stemphylium blight because the spores are airborne, she added.

Farmers should also choose resistant cultivars when they can, she said.

Scouting is very important, said Banniza. The eight- to 10-node stage is the best time to apply fungicide, so scouting needs to be done before then.

Banniza said the management strategy is the same for several of the leaf diseases.

“So if you see lesions early on in your crop, and conditions are conducive to infection, it doesn’t matter whether it’s an anthracnose lesion or an ascochyta blight lesion or a stemphylium blight lesion.”

However, it’s a “different story” for sclerotinia white mould and botrytis grey mould, she said. Because those diseases develop in thick lentil stands, usually after canopy closure, fungicides don’t penetrate the canopy.

If a farmer is lucky, the fungicide will reach the top third of the canopy in those cases, Banniza said, but the disease is usually at the bottom. “So for these two diseases unfortunately fungicide is not a very good option.”

In fact, there are no great control options for sclerotinia white and botrytis grey moulds, she said.

“The best option is to manage your canopy. But that’s obviously very tricky because when you seed it, you don’t know what the growing season will look like,” said Banniza.

“If you knew it was going to be a wet year, you would probably try to seed at a slightly lower rate just to make sure the canopy is a little bit more open.”

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That’s certainly been the case in Saskatchewan, where farmers in most regions are actively scouting for, or in some cases spraying for, crop diseases, according to the provincial crop report.

So which leaf diseases should pulse growers watch for? And what are the management options? Dr. Sabine Banniza, plant pathologist with the University of Saskatchewan, reviewed the major pulse diseases in a recent Saskatchewan Pulse Growers webinar.

Anthracnose — Anthracnose is the number one disease for lentil growers in Saskatchewan these days, Banniza said. Lentil growers should look closely for brown or beige lesions. Once the disease is more established, farmers are likely to see leaf drop. Lesions can eventually girdle the plant, killing it, she added.

Resistant lentil varieties are available; however, she said, they are only resistant to race one. Race zero, the more aggressive and common anthracnose strain, can overcome those resistant varieties. Lentil breeders hope to have race zero resistance “in a short period of time,” she said.

Ascochyta blight — “Of all the pulse crops, I would say ascochyta blight in chickpeas is the most aggressive. It spreads very, very fast and you really have to be on top of managing that disease,” said Banniza.

The disease can also infect faba beans and lentils. Mycosphaerella blight, an ascochyta disease, hits peas, too. Although each crop species is susceptible to a different ascochyta species, they look similar, said Banniza. Farmers should watch for lesions with a darker border and spots in the centre.

In faba beans and chickpeas, the disease can look similar to herbicide damage, so farmers should think about field history and recent weather when trying to diagnose the problem.

Stemphylium blight — In lentils, stemphylium blight starts out as light beige lesions. Those lesions eventually merge, turning the entire leaf brown. Leaf drop also occurs.

Conducting field research on this disease is difficult because spores are airborne. But Banniza said their research shows early to mid-flower infections may cause yield loss, seed stain, and seed infection in lentils.

Often stemphylium blight shows up late in the season. Late infections probably don’t do much damage, Banniza said. In fact, very late infections may work as a natural desiccant, defoliating lentil leaves, she added.

Sclerotinia and botrytis — Sclerotinia white mould and botrytis grey mould are relatively easy to diagnose. As their names suggest, they cause a “cottony white” or “fuzzy grey” mould on the plants stems, leaves, flowers, and pods, Banniza said.

Very wet conditions favour these moulds. Lentil growers with very thick, lush stands are more likely to see these diseases late in the season, especially if the crop lodges. Faba beans and chickpeas can also be infected by sclerotinia white mould.

Chocolate spot — Faba beans are susceptible to a specific species of botrytis grey mould, known as chocolate spot in this crop. Banniza said the disease can be “very devastating” if conditions are wet.

Chocolate spot can develop very quickly, causing defoliation and even lodging. Initial symptoms are tiny reddish lesions. Those lesions enlarge, coalesce, and turn the entire leaf brownish-black.

Banniza cautioned the disease can be confused with herbicide damage. Farmers need to think about weather patterns when diagnosing the problem, as it’s a rain-driven disease. They can also send tissue samples to a lab, she added.

Tips for managing disease

A four-year rotation is an effective way to reduce most of the leaf diseases, as it reduces the inoculum in the fields, Banniza said. However, airborne diseases such as stemphylium blight can’t be managed through rotation, she added.

Scouting is also crucial. Foliar diseases tend to start at the bottom of the plant, Banniza said, so it’s not good enough to glance across the field. Banniza also recommended paying more attention to high-risk fields — for example, wet fields, as well as fields with dense canopies or lodging crops.

Because ascochyta blight is so aggressive in chickpeas, Banniza recommended a preventive fungicide application very early in the season. Whether or not chickpea growers will need to spray again will depend on weather and disease symptoms. Banniza suggested reviewing the SaskPulse fungicide application checklist.

Lentil growers can manage many of the leaf diseases the same way, Banniza said.

“If you see lesions early on in your (lentil) crop, and conditions are conducive to infection, it doesn’t matter whether it’s an anthracnose lesion or an ascochyta blight lesion or a stemphylium blight lesion. You will follow the same disease management categories.”

Lentil growers should be scouting early, and if a fungicide application is warranted, spraying at the eight- to 10-node stage, she said. Sask Pulse has a fungicide application checklist available online.

If lentil growers see more wet weather, they should consider a second fungicide application in three weeks, says Banniza. The application efficacy from the first application will decline in two or three weeks. New growth will also be unprotected, she says.

Fungicide efficacy for mycosphaerella blight in peas is variable, according to several field trials done by various research groups, Banniza said. “You can’t predict, it appears, whether a fungicide application really translates into a yield gain.”

For pea growers facing a mycosphaerella blight infection, spraying may be more of an economic decision, she said.

Banniza doesn’t recommend fungicide applications for sclerotinia white and botrytis grey mould in lentils, either. Because the diseases infect thick lentil stands late in the season, the fungicide is unlikely to penetrate enough of the crop canopy to make a difference, she explained.

“The best option is to manage your (lentil) canopy. But that’s obviously very tricky because when you seed it, you don’t know what the growing season will look like,” said Banniza.

As for faba beans, fungicide application is “an important tool,” Banniza said. If farmers see disease symptoms during flowering in the lower canopy and weather conditions favour disease, application is warranted, she says. The most yield potential is in the middle of the faba bean plant, so farmers should try to protect that area, she said.

A free version of the Crop Protection Book is available through Alberta Agriculture’s website.

— Lisa Guenther is a field editor for Grainews and Country Guide at Livelong, Sask. Follow her at @LtoG on Twitter.

CORRECTION, Aug. 2 2016: A previous version of this article incorrectly stated ascochyta blight looks similar to herbicide damage in chickpeas as well as faba beans.

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Fungicide spraying has occurred to control diseases such as fusarium head blight and leaf diseases, but farmers are running into some problems with applications, according to Bruce Burnett, crop specialist with CWB in Winnipeg.

“In Manitoba especially, some of the rainfall here has been fairly persistent. Farmers have had to either spray multiple times, or have had difficulty getting the spray on right at the correct time,” he said.

The story is a bit better in eastern Saskatchewan and western Manitoba, where the crop is in reasonable shape. Conditions aren’t looking so great further west due to persistent dryness this spring and early summer.

“It’ll be lowering yields out in the western areas,” Burnett said. “We’re especially concerned about the heat that we’re expected to get over the next week or so because most of the winter cereal crops should be flowering or in that general stage at that point in time.”

When crops are flowering, cooler temperatures are more favourable, as hot and dry conditions could harm the crop’s progress.

Yields may not be the best, and harvested area will likely be down from earlier expectations due to unfavourable weather, according to Burnett.

But Western Canada’s winter wheat crops have been developing at a faster than normal pace this year, mainly due to a warmer than average spring.

“The harvest should be a little earlier than normal. Basically the winter wheat crops are mostly headed now, so you’d be looking at a harvest around the end of July for most of the crops in the southern growing areas,” Burnett added.

The winter wheat harvest normally begins within the first two weeks of August, thus on track to start about a week early this year.

— Terryn Shiells writes for Commodity News Service Canada, a Winnipeg company specializing in grain and commodity market reporting.

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