Diseases of Field Crops: Cereal Diseases


| Corn | Soybeans | Forages | Cereals | Dry Edible Beans |
| Spring and Winter Canola | Other Crops | Soil Management |
| Soil Fertility and Nutrient Use | Field Scouting |
| On-Farm Stored Grain Management | Weed Control |
| Insects and Pests of Field Crops | Diseases of Field Crops | Appendices |

Pub 811: Agronomy Guide >Diseases of Field Crops> Cereal Diseases

Order OMAF Publication 811: Agronomy Guide for Field Crops


Seedling Diseases

Seed Rot, Seedling Blight, Root Rot

Incidence and Management Strategies: See General Seed Rots and Seedling Blights.

Disease Cycle: Organisms that colonize seed and soil are responsible for early-season seed rots and seedling blights, as well as the smut (bunt) diseases of the grain (See Plate 144). Apply a fungicide seed treatment to all wheat seed to control soil-borne and seed-borne diseases, such as seed rots and seedling blights, seed-borne septoria, seed-borne fusarium seedling blight, seed-borne dwarf bunt, common bunt and loose smut. The best protection against seedling blights, smut and the bunts can be achieved through the use of a seed treatment that contains a combination of fungicides, since no one fungicide is effective against all these diseases. Good seed coverage is essential to maximize performance of seed treatment. Significant yield losses continue to occur from these diseases in fields where fungicide seed treatments have not been used.

Plate 144. Seedling blights are caused by several organisms. Many seedlings fail to emerge, or emerge looking yellow with brown or red-brown rot on the lower stem.

Photo showing how seedling blights are caused by several organisms. Many seedlings fail to emerge, or emerge looking yellow with brown or red-brown rot on the lower stem.

Fusarium Seedling Blight
Fusarium Crown Rot
(F. culmorum, F. graminearum and F. avenaceum)

Incidence: Fusarium seedling blight can be carried on seed or in crop debris. Poor stand establishment, non-uniform emergence, "gaps" or missing plants are primary symptoms of seed or seedling infection (from planting to several weeks after emergence).

Appearance: Seed rots or seedlings are killed before emergence. Seedlings that do emerge are stunted and yellow, with the crown, roots or lower stem having a brown to red-brown rot. Brown or reddish streaks may occur on the stem. Lesions are variable in shape and size and do not have distinct margins. The disease may occur on older plants as well, causing a reduction in the number or size of tillers that mature prematurely with white and shrivelled heads. Plant vigour is reduced in infected plants.

Disease Cycle: These fungi infect many cereals, grasses and other plants, including corn. They survive in seed, in crop residue and in soil. In winter cereals they grow from these sources into the crown, roots or leaf sheaths in the fall. At this stage, they can cause seed decay and seedling blight. In spring, the lesions continue to expand so that crown rot, stem rot and root rot develop. Moist soil in the fall favours infection of the plant, but dry soil and high levels of nitrogen fertilizer favour the progress of the disease in the spring. The fungi, especially F. graminearum, also infect heads and contaminate seed. The disease is likely to be more severe on wheat that follows wheat, barley or corn.

Management Strategies: Delay planting until conditions will result in a rapid and uniform emergence. Avoid planting after corn and maintain a balanced fertility program. Fungicide seed treatments are very effective against seed-borne and soil-borne organisms that cause this disease. Other options include the use of tolerant varieties and planting disease-free seed. Use wheat in at least a 3-year crop rotation since these organisms can survive in wheat residues. Avoid planting wheat after corn.

Pythium (Browning) Root Rot (Pythium spp.)

Incidence: Pythium root rot damage on wheat is common in Ontario and is one of the primary seedling diseases of small grains. There are several species of Pythium that attack small grains and, although Pythium is present in all soil types, losses are greatest in cold and wet clay soils. Pythium (like Phytophthora) is a "water mould" that thrives under wet, saturated conditions. Therefore, infection is very dependent on soil moisture and the clay content of the soil. The wetter the soil and the higher the clay content, the greater the potential for infection. Pythium produces mobile spores that migrate through the water film in the soil.

Appearance: Although infection occurs in the embryo 1 or 2 days after planting, seedlings are rarely killed. Infected plants appear stunted with small, pale-green to yellowish leaves. This is often incorrectly identified as a nutrient deficiency. These symptoms often go unnoticed until spring when non-infected plants begin to grow rapidly. Infected roots are light-brown with few or no root hairs. Infection begins at the root tips and disintegrates root hairs and the fine lateral roots, which are critical for nutrient uptake. Affected plants often occur in patches with a general unhealthy appearance. Severely infected plants may break at the soil line.

Disease Cycle: The fungi survive in the soil and crop residues. They produce spores that swim through moisture films on soil particles and invade the wheat roots. Some species are most damaging in warm soils, while others prefer cold soils. The disease is less severe when phosphate levels are adequate for good root growth.

Management Strategies: Minimize soil compaction and remove excess moisture through increased drainage. Seed treatments containing metalaxyl or metalaxyl-M can reduce infection. Delay planting until conditions will result in a rapid and uniform emergence.

Take-all (Gaeumannomyces graminis)

Incidence: Take-all is a fungal disease that can infect wheat, barley, rye, various grasses, and, to a lesser degree, oat.

Appearance: Take-all usually becomes noticeable at the heading stage when the heads, stems and leaves of badly affected plants become prematurely bleached (See Plate 145). The bleaching of tillers takes only 2 or 3 days. Affected plants occur in circular patches, one to several metres across, or as individuals or small clusters scattered across the field. Many plants appear moderately to severely stunted and bear few tillers. The bleached heads (whiteheads or deadheads) normally are sterile and usually appear 3-5 weeks before harvest. Whiteheads may also be caused by factors other than take-all. Dark-coloured moulds tend to grow on the whiteheads, especially in damp weather. The conspicuous bleaching is secondary to disease on the roots, crown and lower stem.

The roots of diseased plants are sparse, blackened and brittle. The dark-coloured rot often extends to the crown and basal stem. Removal of the lowest leaf sheath reveals a dark shiny layer of fungal material on the stem that is easily scraped off. Weakened stems lean or lodge in various directions as in eyespot. In many instances, the disease is confined to the roots, and no symptoms appear on the crowns, stems and heads. The wheat take-all fungus produces spores inside tiny black structures (perithecia) on the sheath of the lower leaf and on stubble residues at the soil surface.

Disease Cycle: The main source of the fungus is infested crop residues in the soil. The fungus survives best in the residues when the soil nitrogen content is high. Brown strands of the fungus grow from the residues, through the soil and over the surface of the roots, crowns and stems. The fungus spreads from plant to plant by means of "root bridges." Using a hand lens, it is often possible to see the brown strands on the roots while the roots remain whitish. The roots turn black after the fungus penetrates into them. Invaded crowns and stems develop a brownish, dry rot.

The severity of take-all generally increases as soil pH rises and fertility (especially nitrogen and phosphorus) decreases. Wet soil, especially in spring and early summer, is highly favourable to the disease. Soil compaction aggravates take-all. Cool weather (12°C-18°C) is more favourable than warm weather. The disease is more severe when wheat is sown early than when sown near the end of September or in October. When wheat is grown continually on the same land, take-all becomes increasingly severe during the first 3-5 years but subsequently declines. Take-all predisposes wheat to moisture stress, especially in June and July.

Management Strategies: Carefully manage soil fertility. Neutral to alkaline and infertile soils are most at risk. Do not apply lime before planting. Soils deficient in potassium and phosphorus cause plants to be more susceptible because of poor root development. Nitrate-nitrogen increases disease severity. Control grasses and avoid early planting. Use a 3-year crop rotation and avoid planting wheat after wheat.

Plate 145. Take-all is noticeable at heading. Head, stem and leaves all become bleached due to this root disease.

Photo showing how take-all is noticeable at heading. Head, stem and leaves all become bleached due to this root disease.

Leaf and Stem Diseases

Eyespot (strawbreaker) (Tapesia yallundae)
Rhizoctonia Sharp Eyespot (Rhizoctonia cerealis)

Incidence: The fungi that cause these diseases can have the ability to cause disease in many crops. These diseases become a problem in fields or regions that predominantly grow cereal crops under cool, moist conditions.

Appearance: Eyespot and sharp eyespot produce lesions on the lower sheaths and stems of most cereals (See Plate 146). Winter wheat is more susceptible than spring cereals. In the spring, both diseases produce elliptical, eye-shaped lesions on the lower internodes near the soil line. Lesions have a dark-brown border with a tan or straw-coloured centre.

Distinguishing between the two diseases is difficult. Rhizoctonia sharp eyespot lesions are more superficial and their margins are sharply defined. Plants infected with eyespot (strawbreaker) have a white fungal growth in the lower stem cavity. In severe cases, plants infected with these diseases may lodge, bend or break at the soil line from a weakening of the stem at the lesion areas. Other symptoms include reduced yields, whiteheads and death of tillers.

Disease Cycle: The eyespot fungus survives in the residue of infected plants for 3 or more years and is most severe under cool, wet conditions. The sharp eyespot fungus survives in the soil and on infected crop residues. Sharp eyespot is most severe in light, dry, acidic soils during cool springs. Dry conditions in the fall and spring favour development of sharp eyespot.

Management Strategies: Avoid planting cereals 2 years in a row, preferably leaving at least 2 years between cereal crops. Practices that bury stubble in the soil are effective in reducing eyespot severity. Eyespot can be severe when the stubble remains on the surface. Sharp eyespot can be severe when crops are planted early and deep. Fungicide seed treatments may reduce losses.

Plate 146. Eyespot produces elliptical, eye-shaped lesions on the lower internode near the soil line.

Photo showing eyespot produces elliptical, eye-shaped lesions on the lower internode near the soil line.

Snow Mould (Microdochium nivale, Typhula spp.)

Incidence: Although snow moulds do require specific environmental conditions, they occur most years to some degree. Severity increases in years when an early snow cover in the fall (mid-November) persists until late March or April.

Appearance: Snow mould symptoms appear soon after snow melt. Individual plants, groups of plants or large areas can be affected. The most obvious symptom is dead plants that are slimy, brown and rotted (See Plate 147). Early-planted wheat is usually affected, since lush "top-growth" promotes infection and aids in disease spread from plant to plant. Plants that have not been killed (i.e., have a healthy crown) may have one or many leaves that are totally or partly necrotic (i.e., have brown tips). Symptoms are most pronounced in areas of the field that had heavy snow cover, such as field borders, headlands and down slopes of hills. Typical winter injury on wheat due to other causes will most often occur in areas that had no snow or were covered in ice. Symptoms are pronounced in fields planted with poor-quality or untreated seed. Warm, dry weather in the spring will stop disease development and promote rapid plant growth. Plants with considerable damage often recover from the disease with little or no impact on yield.

Disease Cycle: The group of fungi that cause snow moulds are temperature tolerant and will grow under heavy snow cover. Snow deeper than 30 cm (12 in.) will insulate the soil, preventing it from freezing while maintaining a soil surface temperature at or just above 0°C. Under these conditions, photosynthesis is significantly reduced, and the developing wheat plant has no choice but to use its stored carbohydrates and proteins to survive. The result is a stressed plant that is more susceptible to diseases, especially snow moulds.

Management Strategies:
Although no winter wheat cultivar is resistant to the disease, cultivars do differ in tolerance. Seed treatments are very effective against snow moulds, but good seed coverage is essential. In years when snow mould causes substantial reductions in stands, replant to a spring grain or soybean crop. The disease does not affect spring-planted grain.

Plate 147. Snow mould appears when the snow melts after long periods of snow cover. Dead plants are slimy, brown and rotted.

Photo showing how snow mould appears when the snow melts after long periods of snow cover. Dead plants are slimy, brown and rotted.

Leaf Rust (Puccinia triticinia)
Stem Rust (Puccinia graminis)
Stripe Rust (Puccinia striiformis)

Incidence: There are various species of rust that cause disease on wheat and barley. The three rust diseases that affect wheat are leaf rust, stem rust and stripe rust (see Table 14-3, Comparison of Common Rusts That Occur on Small Grains in Ontario). Of these, leaf rust is the most common. It can be found in varying amounts each year and poses the biggest risk to small grain production. Although stem rust has been declining, it may be a serious problem when small grains are grown near the common barberry bush. A new stem rust threat to world wheat production has been developing in other parts of the world. Stripe rust has been increasing over the past few years but is very dependent on early-season environmental conditions. Most years, yield losses from these three rust diseases are low, since disease development often occurs after the winter wheat crop has begun to mature. The earlier rust infection occurs in the crop, the greater the impact on yield.


Table 14-3. Comparison of Common Rusts That Occur on Small Grains in Ontario

Leaf Rust
Stripe Rust
Stem Rust
Plant parts affected leaf leaf and head stem and leaf
Lesion (pustule) colour orange yellow dark red
Lesion shape single stripes single
Temperature range 15°C-27°C 12°C-21°C 18°C-30°C
Occurrence in Ontario yearly - varying amounts increasing - past 2 years trace

Appearance: Leaf rust affects the leaf blades and sheath, whereas stem rust can be found on leaves, sheaths, stem and heads. The disease begins as small, yellow-brown pustules that contain orange to orange brown spores (See Plate 148). In most cases, infection is found on the upper surfaces of the leaves and leaf sheath. In severe cases, leaves turn yellow and brown. In spring grains, late-planted fields are most likely to show the disease, whereas late-maturing winter wheat may be slightly more at risk.

Stem rust begins as dark reddish-brown spots on both sides of the leaves, stems and heads (See Plate 149). When developed, spots will rupture through the surface, releasing spores into the air. The surface of the tissue appears ragged and torn.

Disease Cycle: Common barberry is necessary for the stem rust fungus to complete its lifecycle. Leaf rust, on the other hand, rarely overwinters in the province but is blown into Ontario on southerly storm fronts from infected plants in the southern U.S. and Mexican wheat regions. In most years, leaf rust spores arrive late (after flowering), resulting in little economic impact. These diseases are most severe when warm temperatures (20°C-28°C in day, 16°C-22°C at night) and frequent dews occur when the crop is at the flag leaf-to-flowering stages (Zadok's 37-71).

Unlike leaf and stem rust, stripe rust does not require an alternate host to complete its life cycle. In addition to wheat, the host range of stripe rust includes many grasses such as rye, barley and many perennial grasses that can act as a reservoir. Stripe rust does not overwinter in Ontario and of the three rust diseases, stripe rust prefers cooler temperatures. Early spring conditions or a prolonged cool period (10°C and 15°C with increased leaf wetness) are ideal for stripe rust development.


Table 14-4. Comparison of BYDV, SBWMV and WSSMV

Major Symptoms
Additional Hosts
Barley yellow dwarf virus aphids general chlorosis, reddening, purpling, stunting barley, oat, corn, sorghum, millet, grasses
Soil-borne wheat mosaic virus soil-borne fungus
(Polymyxa graminis)
yellow-green mosaic, stunting, resetting rye, barley, grasses, sorghum
Wheat spindle streak mosaic virus soil-borne fungus
(Polymyxa graminis)
green-yellow mosaic, streaks, spindles rye, barley

Management Strategies: Removing the alternate host, common barberry, will reduce stem rust. Use tolerant varieties when possible. Since leaf rust usually appears on the upper two leaves first, it is important when scouting for rust to check the second leaf from the top prior to head emergence, and the flag leaf during head emergence, for signs of disease. Use foliar fungicide treatments when the flag leaf has 5-10 pustules or 1% of the flag leaf area is affected (during head emergence to the end of flowering) and the weather forecast predicts rainy, wet weather. Planting spring grains early allows plants to mature before inoculum levels become heavy. In oat, crown (leaf) rust is dependent on European buckthorn as the alternate host.

Plate 148. Leaf rust affects the leaf blades and sheath. Small, yellow-brown spots contain orange to orange-brown spores.

Photo showing  how leaf rust affects the leaf blades and sheath. Small, yellow-brown spots contain orange to orange-brown spores.

Plate 149. Stem rust can be found on the leaf sheath, stem and head.

Photo showing how stem rust can be found on the leaf sheath, stem and head.

Barley Yellow Dwarf Virus

Incidence: Barley yellow dwarf virus (BYDV) has been called the most widely distributed and most destructive virus disease of cereals. BYDV attacks a wide range of grass hosts, including wheat, oat and barley. Of these, oat is considered the most susceptible.

Appearance: The primary symptoms are stunting and yellowing, reddening or purpling of the leaf tips (See Plate 150). BYDV is often confused with other virus diseases, such as spindle streak mosaic virus and soil-borne mosaic virus, nutrient deficiency or environmental causes (see Table 14-4, Comparison of BYDV, SBWMV and WSSMV). Identifying viral pathogens is very difficult and requires accurate serological tests. It is best to send samples to a diagnostic lab with these capabilities.

Disease Cycle: BYDV is transmitted by aphids only. Several species of aphids have been identified as vectors for BYDV, including the greenbug, the corn leaf aphid, the English grain aphid and the bird cherry-oat aphid. Damage occurs as a result of aphid feeding, since aphids feed directly on plant sap and therefore reduce the nutrients available for plant growth. The contact with the plant sap makes aphids ideal vectors for BYDV. It is usually found in patches 1-2 m (6.5 ft) in diameter but can occur uniformly throughout the field if aphid populations are also uniform throughout the field. Yield losses are very dependent on the crop stage when infected. Generally, losses are greater when infection occurs on young seedlings in the fall (>30%), rather than in the spring.

Management Strategies: Few control options are available. In winter cereals, the best strategy is to avoid early planting. Early planting allows the aphids more time to infect the plants in the fall. Recommended or optimum planting dates for winter wheat take into consideration BYDV and Hessian fly and promote a vigorous plant to maximize winter hardiness. See Figure 4-4, Optimum Date to Seed Winter Wheat Across Ontario. Planting earlier during mild or late autumns allows the aphids to survive longer than usual. Early seeding is an advantage in spring grains. Chemical sprays to control the aphid vectors are not practical or economical, since scouting or detecting the aphids is very difficult. By the time populations reach detectable levels, virus transmission has most likely already occurred. Preventative sprays would not be economic, as BYDV is unpredictable.

Plate 150. Barley yellow dwarf virus (BYDV) is transmitted by aphids. Symptoms are stunting and yellowing with reddening or purpling of leaf tips.

Photo showing how barley yellow dwarf virus (BYDV) is transmitted by aphids. Symptoms are stunting and yellowing with reddening or purpling of leaf tips.

Soil-borne Wheat Mosaic Virus
Wheat Spindle Streak Mosaic Virus

Incidence: Soil-borne wheat mosaic virus (SBWMV) and wheat spindle streak mosaic virus (WSSMV) are often easily confused with each other since the disease symptoms, life cycle and field pattern are similar. In certain cases, both viruses may be present in the same field.

Appearance: Typical symptoms of SBWMV on wheat leaves is a mosaic of green islands or blotches on a yellow background. Typical leaf symptoms of wheat spindle streak are yellow-to-light green streaks that are parallel to the leaf veins. The streaks are often tapered, which gives the lesions a spindle shape, hence the name. This is in contrast to soil-borne mosaic virus lesions, which are blotches. WSSMV can also cause stunting and reduced tillering in infected plants.

Disease Cycle: It is not uncommon to find that many plants are infected with both viruses since they share a common vector. The common link is a soil-borne fungus called Polymyxa graminis. The fungus produces zoospores (swimming spores) that invade root hairs and epidermal cells of young plants during periods of high soil moisture or in low, wet areas of the field. The virus is carried into the plant by the zoospores. The fungus can remain in the soil for at least 8 years. It is not as important to determine which of the two viruses is present as it is to determine that the symptoms are not due to other causes (fungal, bacterial, etc.). Fields at risk are those that have had several crops of winter wheat in the past 8-10 years. Yield losses range from less than 5% to 40%, but generally losses are low. Symptoms usually appear early in the spring when growth resumes. The optimum temperature for symptom development is 5°C-15°C.

Management Strategies: Since the fungal vector for both viruses can survive for many years in the soil, crop rotation as a management option has had limited success. Fields that have been fertilized with liberal amounts of poultry and livestock manures appear to have a reduced wheat spindle streak mosaic virus build-up.

Powdery Mildew (Blumeria graminis f. sp. tritici)

Incidence: Powdery mildew is a common plant disease that can cause damage when present in wheat and barley fields. Wheat cultivars will vary in their susceptibility to the disease. The yield impact of powdery mildew infections is hard to predict. The disease robs the plant of nutrients and reduces the photosynthetic ability of the leaf. Yield losses are generally minimal from early infections unless the weather remains cool and humid. Mildew infections that attack the flag leaf and the second leaf are more serious. The health of the top two leaves determines the kernel size, test weight and yield. Losses due to powdery mildew have been stated anywhere from 2%-30% of total yield. Very rarely in Ontario have losses been greater than 10%-15%.

Appearance: The characteristic symptom of the disease is the production of a fluffy-white to grey fungal growth that often begins on the lower leaves (See Plate 151). Infection can move rapidly up the plant on leaves, sheaths, stems and heads under favourable conditions. Leaves develop elongated yellow streaks or areas that may turn brown and die prematurely. Severely diseased plants may lodge or result in poor grain fill. Older, light-grey areas of fungal growth often have small black spots. The white to light-grey fungal growth is most noticeable in the early morning while the plants are still wet. The infection is superficial, and the fungal growth can be easily removed with a finger or a knife.

Disease Cycle: The fungus survives on crop residues, such as straw or stubble, fall-planted winter wheat seedlings, volunteer cereals and wheat. Spores that are released are primarily spread by the wind. The spores require nearly 100% relative humidity and temperatures between 15°C and 21°C. A dense stand and vigorously growing crop can lead to poor leaf-drying conditions, which are favourable conditions for powdery mildew. The disease is very susceptible to weather conditions that promote drying of the crop environment such as hot, dry, sunny weather. Powdery mildew also thrives in fields where high rates of nitrogen have been used. Nitrogen not only increases tiller formation, causing dense stands, but also increases the susceptibility of the crop. Watch for mildew in fields that have had more than 78 kg N/ha (70 lb N/acre). Powdery mildew growth stops when temperatures are above 25°C.

Management Strategies: In most cases, powdery mildew has little impact on rye or oat since these crops are very resistant to the disease. In areas prone to severe mildew, use resistant (tolerant) winter wheat varieties. Removal of crop residue through tillage in conjunction with a crop rotation that limits wheat or other susceptible cereals from being planted in the field for a minimum of 2 years may lower disease risk. Foliar fungicide applications are necessary when disease levels will result in yield losses. Thresholds for fungicide applications differ depending on the age of the crop. Early-season powdery mildew control is warranted when 5%-10% of the lower leaves are infected, which may limit later infection. Later in the season, powdery mildew symptoms on the flag leaf (1% of leaf) and the second leaf (3%-5% of the leaf) require immediate attention, especially if prolonged wet, humid weather is forecast.

Plate 151. Powdery mildew produces a white-to-grey fungal growth on the lower leaves and moves up the plant.

Photo showing how powdery mildew produces a white-to-grey fungal growth on the lower leaves and moves up the plant.

Head and Grain Diseases

Septoria Leaf Spot (Septoria tritici)
Stagonospora Leaf and Glume Blotch (Stagonospora nodorum)

Incidence: Septoria leaf spot and stagnospora (septoria) glume blotch are two diseases that are caused by different species of Septoria. Both diseases are of economic importance. They attack most small grains and many grasses, but wheat is the only important commercial host.

Appearance: Septoria leaf spot attacks only leaves, whereas stagonospora glume blotch appears on the leaves and glumes. Initial infections from septoria leaf spot appear as small, light green-to-yellow spots between the veins of the lower leaves (See Plate 152). These spots elongate to form irregular reddish-brown lesions. Embedded in these lesions are small, dark-brown to black fungal bodies (pycnidia) that can be seen easily with the use of a hand lens.

Stagonospora glume blotch develops after the heads emerge and is favoured in warm, humid conditions. Small, oval, irregular, grey-to-brown spots appear on the leaves and purplish-brown areas on the glumes (See Plate 153). The affected areas are also speckled with small black pycnidia. The presence of pycnidia is an important diagnostic feature that aids in distinguishing septoria leaf spot and stagonospora glume blotch from other leaf spot diseases.

Disease Cycle: Septoria fungi survive on seed, straw, stubble or volunteer wheat and are favoured by wet or humid conditions, and moderate temperatures. Along with powdery mildew, leaf diseases caused by Septoria are often the first that occur in the spring since they thrive under cool, humid, wet conditions. Although both fungi are limited by hot weather, Stagonospora can tolerate somewhat higher temperatures than Septoria. Prolonged wet periods in May and early June result in increased disease incidence. The leaf phases of both diseases characteristically move from infected lower leaves upward (secondary disease cycles). The glume stage of stagonospora glume blotch, on the other hand, does not move vertically within the canopy but quickly across the field, infecting only the heads.

Management Strategies: Rotation with crops other than cereals, plowing down cereal residues and removing volunteer wheat will reduce the survivability of these fungi. Unfortunately, in most years, spore levels are sufficient to cause disease under favourable environmental conditions. Balanced fertility programs are important since high rates of fertilizer and early planting may result in dense foliage going into the winter, thus increasing disease levels. Septoria leaf spot may develop under snow cover in winter wheat. Use good-quality seed that has been treated with a fungicide seed treatment to prevent seed-borne infection. Current varieties have limited tolerance. Foliar fungicides provide effective control of septoria leaf spot and stagonospora glume blotch. Application thresholds vary, depending on wheat-growth stage. Applications are justified when one to two lesions (1% of the leaf area) are found on the leaf below the flag leaf up to the boot stage, or when one to two lesions (1% of the leaf area) are found on the flag leaf at head emergence (flowering).

Plate 152. Septoria leaf spot appears as small, light green-to-yellow spots that elongate to form reddish-brown lesions.

Photo showing septoria leaf spot appears as small, light green-to-yellow spots that elongate to form reddish-brown lesions.

Plate 153. Septoria glume blotch appears as small, oval, grey-to-brown spots on the leaves and purplish-brown areas on the glumes.

Photo showing how septoria glume blotch appears as small, oval, grey-to-brown spots on the leaves and purplish-brown areas on the glumes.

Tan Spot (Pyrenophora tritici-repentis)

Incidence: Tan spot has been increasing in the province as a result of reduced tillage. Economic losses from tan spot have not been significant. However, the disease is often confused with septoria leaf spot, and misdiagnosis could result in unnecessary applications of foliar fungicides. Barley and oat are much more tolerant to tan spot than wheat.

Appearance: Tan spot begins on the lower leaves as small, tan-brown flecks that enlarge into oval- or lens-shaped tan lesions, 5-15 mm (1/5-3/5 in.), with a small, dark brown centre. A bright yellow zone or halo surrounds the tan lesion. The lesion is best viewed when the leaf is held to the sun.

Disease Cycle: The fungus survives on wheat residues. Disease development is favoured when prolonged, cool, cloudy, humid weather occurs early in the growing season. Spores are spread by the wind.

Management Strategies: Most wheat varieties are susceptible to tan spot. Include non-host crops such as other cereals, corn, soybeans and alfalfa in the rotation.

Loose Smut (Ustilago tritici)

Incidence: Loose smut has traditionally been one of the most destructive diseases of wheat and barley in Ontario. The use of fungicidal seed treatments manages the disease very effectively. Planting untreated, infected wheat seed can result in yield losses of 10%-30%.

Appearance: Kernels are replaced by dry, black masses of spores, visible soon after heads emerge (See Plate 154). Over time, all that remains is the naked spike. Infected plants appear normal until heading time.

Disease Cycle: The fungus that causes the disease survives in infected wheat seed and subsequently infects the developing plant. The fungus grows throughout the plant, eventually infecting the head and replacing the grain. Spores are spread by wind and infect adjacent plants. Infected seed appears normal and cannot be separated out. Wheat and barley are the main hosts, whereas oat and rye are quite tolerant.

Management Strategies: Plant pedigree seed that has been treated with seed protectant that contains a systemic fungicide.

Plate 154. Loose smut causes the kernels to be replaced by dry, black masses of spores, visible soon after the head emerges.

Photo showing how loose smut causes the kernels to be replaced by dry, black masses of spores, visible soon after the head emerges.

Fusarium Head Blight (Scab)
(Fusarium graminearum)

Incidence: Fusarium head blight (FHB), or scab, is one of the most important diseases of small grains in Ontario. In recent years, severe outbreaks have occurred when the weather is warm and wet at the flowering to soft-dough stages. Besides the potential for significant yield losses, mycotoxins that are harmful to livestock can be produced.

Appearance: Symptoms of scab become noticeable soon after flowering. Diseased spikelets (glumes and florets) appear to have ripened prematurely (bleached) in contrast to healthy, green heads. The fungus may attack all or only part of the head. Bleaching of the heads or head blight appears 3-5 days after infection. The entire head may be killed when the neck (the stem immediately below the head) is infected (See Plate 155). During warm, humid weather, the fungus produces a salmon-orange to pink ring of spores at the base of the spikelet or in the crease of the kernel. If conditions continue, the infection may spread to adjacent kernels. Infected kernels are usually shrunken, wrinkled and light in weight. These kernels have a rough, scabby appearance and range in colour from light-brown to pink to greyish-white. The amount of scab on the seed depends on the time of infection and the weather conditions at the time of infection.

The planting of infected seed can result in the development of the seedling blight phase of the disease, which is separate from scab. Infected kernels may not germinate and can result in poor stands. Infected plants that emerge may lack vigour and will often die before they become established. Infected seedlings can appear light to reddish-brown and may be covered with a white or pink mould. As the plants mature, they are usually smaller with few tillers and small heads. If the root or crown is cut, a light-to-reddish-brown root rot can be observed.

Disease Cycle: Although several species of Fusarium can cause scab, the principal pathogen is Fusarium graminearum, which can infect corn, wheat, barley, oat and rye. All species overwinter in infected kernels, chaff, stubble or straw/stalk residues left on the soil surface. They survive between crops as asexual spores, fungal strands and within dark purplish-black fruiting bodies, which the sexual spores are borne in. The fungi will continue to grow and produce spores from harvest until the crop residues have decomposed in the soil.

Both types of spores can be carried from infected residues of the previous crop by wind or rain splash onto the wheat head. The conidia are produced during warm, moist weather on corn and small grain residues, while the ascospores are released during wet and dry cycles. By doing so, the fungus is able to spread spores into the air for a longer period of time. Spores that land on the head require rainfall or heavy dew to germinate and invade flower parts (anthers, glumes and other portions of the head). The potential for disease increases substantially when these spores land during an extended warm period at 22°C-27°C temperatures with wet, humid weather. The longer it stays wet during flowering, the greater the chance of infection and therefore increased disease severity. If warm, moist weather continues, the salmon-pink spore masses produced on the spikelets will be air-borne and can act as another source of infection.

Management Strategies: Avoid planting wheat following wheat or corn. When residues of either of these crops are left on the surface and wheat is subsequently planted, the chances of FHB infections are greatly increased. Clean plowing of infected residues reduces the risk of infection from spores originating from within the field. However, FHB may still develop from spores blown in from surrounding fields under weather conditions favourable to disease development. As many of the infected kernels are small, shrunken and lighter than sound kernels, it is possible to blow a large proportion of these kernels out the back of the combine by increasing the air blast above normal ranges. This may cause some additional loss of good kernels (up to 0.13 t/ha or 3 bu/acre). Proper storage and drying will limit further FHB development after harvest. The availability of tolerant varieties is increasing and they can reduce infection potential.

Research done at the University of Guelph - Ridgetown Campus on FHB management has led to a mycotoxin prediction model (DONcast). See Caution. The model was developed over many years and is quite innovative since it relates DON accumulation in the wheat grain to the environmental conditions surrounding heading and how it relates to inoculum production, wheat head infection and subsequent fungal growth within the head. See the Weather INnovations Incorporated website at www.weatherinnovations.com/ for more details.

Plate 155. Fusarium head blight bleaches all or part of the head. Typically, the stem remains green.

Photo showing fusarium head blight bleaches all or part of the head. Typically, the stem remains green.

Dwarf Bunt (Tilletia controversa)
Common Bunt (Tilletia tritici)

Incidence: Common bunt (stinking or covered smut) occurs anywhere in Ontario where both spring and winter wheat is grown. Dwarf bunt on the other hand, primarily occurs in the counties bordering Georgian Bay and Lake Huron, where snow cover is deep and persistent in late winter and early spring. In severe years, some fields have had over 50% bunt infected plants.

Appearance: In Ontario, there are three fungal species that can cause bunt in winter wheat. The first two are Tilletia tritici and Tilletia laevis, which cause common bunt or covered smut. The third is Tilletia controversa, which causes dwarf bunt in winter wheat. The main symptom of all three of these pathogens is the production of "bunt balls," which replace healthy kernels. These bunt balls contain masses of black powdery fungal spores called teliospores. When infected grain is harvested or crushed, these bunt balls rupture easily, releasing their spore contents, resulting in contamination of the grain. Besides the bunt balls, one of the most obvious signs of these diseases is the pungent, fishy odour of the spores. The odour is important, since the disease has quarantine significance. Many importing countries have zero tolerance for bunt-contaminated wheat shipments. Often the spore cloud and the distinctive odour are the first signs that a crop may have the disease.

Common bunt and dwarf bunt are difficult to distinguish between and often require microscopic examination. One difference is that the bunt balls of common bunt are similar in shape and size to the kernels they have replaced. For dwarf bunt, the bunt balls are smaller and tend to be rounder. Plants infected with dwarf bunt are dramatically shorter (half as tall as healthy plants). Plants infected with common bunt suffer only a slight reduction in height. A fourth bunt fungus causes Karnal bunt or partial bunt. Fortunately, this disease does not occur in Ontario.

Disease Cycle: Dwarf bunt and common bunt can infect winter wheat plants either through the seed (seed-borne) or from the soil (soil-borne). Although common bunt can be soil-borne, the fungus appears to be primarily a seed-borne disease and can be effectively controlled with currently registered seed treatments. Dwarf bunt is harder to control, since spores of the fungus can survive for 10 years or more in the soil.

Management Strategies: Plant seed that is free of bunt spores. Do not keep seed if bunt was present in the field. Some registered seed treatments are more effective than others.

Management Tips:
  • Cut high with the combine.
    Wheat infected with dwarf bunt will be substantially shorter than healthy plants. Raising the header will reduce the amount of bunt balls harvested.
  • Harvest below 15% moisture.
    Bunt balls and spores that are dry tend to be sent out of the combine easier. The wetter the grain, the more likely bunt spores will adhere to it. Removing wet spore balls through the combine is very difficult since they are very heavy.
  • Set combine wind-blast at maximum.
    Turning the wind-blast settings up will remove a large portion of the bunt balls. Minimal good grain will be lost at maximum wind.
  • Harvest fence rows and bush areas separately.
    Infection is most severe where snow was the deepest and stayed the longest. Harvesting those areas separately from the rest of the field should minimize the number of bunt balls in the sample.


  • Clean grain before storage.
    It is important to remove as many bunt balls as possible from the sample before storage. Bunt balls will rupture during grain handling or removal from the bin. Bunt balls are similar in size to wild buckwheat seed. Therefore, screens that remove wild buckwheat should remove many of the bunt balls in the sample.


  • Put grain into the bin with full aeration.
    It will take an extended period of aeration to remove the odour from the sample.

Ergot (Claviceps purpurea)

Incidence: Ergot occurs from time to time on barley, wheat and triticale. Although yield loss in most cases is insignificant, the impact of the disease on grain quality and marketability can be significant, since ergot bodies are toxic to livestock and humans. Exercise caution in feeding grain containing the black ergot bodies to livestock, especially swine. Outbreaks in Ontario are infrequent and sporadic, but ergot can be severe in some fields that have been damaged by frost, herbicide, etc., that resulted in sterile heads. Sterile florets tend to remain open and thus more prone to infection.

Appearance: The first sign of this fungal disease is often the brown to purplish-black sclerotia ("ergot bodies") protruding from the spikelets of the head. These ergot bodies replace the kernels and can be up to 1 cm (1/2 in.) in length.

Disease Cycle: The fungus survives the winter as sclerotia in the soil and on seed. From here, spores are released that infect the florets and with the aid of insects are transferred to other spikes. Rainy, wet and cool weather that prolongs flowering increases the likelihood of infection. Ergot "sclerotia" are well adapted and can survive for many years in the soil.

Management Strategies: Use clean seed and do not plant seed containing ergots. Allow a minimum of 1 year between other susceptible crops (rye, wheat, barley, triticale).

Barley Diseases

Seedling Blight, Common Root Rot, Spot Blotch (Cochliobolus sativus)

Incidence: Spot blotch (See Plate 156), seedling blight and common root rot are often serious and widespread, and are caused by the same fungus. The fungus overwinters in seed, barley debris and soil. Treat all barley seed with fungicide. To reduce the severity of spot blotch, avoid growing barley after barley, wheat or grasses. Early planting helps avoid serious disease in July. Disease is less severe on barley grown in combination with oat.

Plate 156. Spot blotch in barley causes brown spots on the leaf and can cause seedling blight with rot appearing on the lower stem.

Photo showing how spot blotch in barley causes brown spots on the leaf and can cause seedling blight with rot appearing on the lower stem.

Net Blotch (Pyrenophora teres)
Scald (Rhynchosporium secalis)

Net blotch (See Plate 157) and scald occur especially in cool, humid seasons. Two-rowed cultivars are usually more susceptible to net blotch and scald than are six-rowed cultivars. To help prevent the build-up of these diseases, avoid growing barley after barley, plow down stubble and straw as completely as possible, and treat seed with fungicide.

Plate 157. Net blotch starts as light green or brown spots, enlarging, with lines appearing to give a "net" appearance.

Photo showing net blotch starts as light green or brown spots, enlarging, with lines appearing to give a "net" appearance.

Fusarium Head Blight

See Fusarium Head Blight (Scab).

Oat Diseases

Septoria Leaf Blotch
Septoria Black Stem (Phaeosphaeria avenaria)

Septoria leaf blotch in oat can cause severe damage in all recommended varieties. The disease is recognized by the appearance of mottled, light and dark-brown, elongated blotches on the leaf blade, extending to the leaf sheath and culm. Advanced stages on the culm turn black, and the weakened culm breaks over easily, resulting in damage due to lodging. Avoid planting oat after oat or mixed grains.

Oat Leaf Rust
Crown Rust (Puccinia coronata var. avenae)

Crown rust, also called leaf rust, is specific to oat and some wild grasses such as fescue and ryegrass. Oat leaf rust is often serious, and substantial losses can occur, especially in Central and Eastern Ontario.

Appearance: The most distinctive symptoms of the disease is the production of orange pustules (volcanoes) on the oat leaves and sheathes. These pustules can produce thousands of orange-yellow coloured spores that can spread to other fields or infect adjacent plants.

Disease Cycle: The pathogen is not seed- or soil-borne. European buckthorn is the primary local source of spores while another source of spores is blown in from the southern U.S. There are different races of the fungus and they change over time, which can affect a variety's performance over time. Crown rust is most problematic when the disease develops early and the conditions are mild to warm (20°C-25°C) during the day and mild at nights (15°C-20°C) with adequate moisture (rains, frequent dews).

Management Strategies:

  • Use a tolerant variety. Varieties differ in their susceptibility to the disease, and, since new rust races develop, this can reduce a variety's tolerance levels. See the Ontario Performance Trials for Spring Cereal Crops.
  • Plant as early as possible in the spring, which may allow the plants to escape the disease from late-season infection.
  • Apply foliar fungicides in a timely manner and close to flag leaf emergence in order to protect the flag leaf.
  • Remove or destroy buckthorn.

  • Oat Cyst Nematode (Heterodera avenae)

    Damage by the oat cyst nematode is first noticed about 2 or 3 weeks after oat plants emerge. At that time heavily infected plants appear to suddenly stop growing, leaves turn pale and begin to die back from the tips downward. These plants fail to tiller, resulting in a thin stand of stunted plants that produce little grain. Below ground, the root systems are severely stunted and usually discoloured, from a pale-yellow in early growth to a yellow-brown in mature plants, as compared to the clear-white in healthy plants.

    To confirm suspected oat cyst nematode damage, send a sample of several plants with adhering soil to the Pest Diagnostic Clinic. See Appendix I, Diagnostic Services for details.

    If oat cyst nematodes have caused damage, do not plant spring grains the following year. Use legume or row crops in the rotation. Corn can be used if the nematode population is low but will suffer damage if the soil is heavily infested. The nematode invades corn roots but does not reproduce in them. Therefore, consecutive cropping to corn effectively reduces the population of oat cyst nematodes.

For more information:
Toll Free: 1-877-424-1300
E-mail: ag.info.omafra@ontario.ca
Author: OMAFRA Staff
Creation Date: 13 May 2009
Last Reviewed: 13 May 2009