Identification of Diseases and Disorders of Onions

Factsheet - ISSN 1198-712X   -   Copyright Queen's Printer for Ontario
Agdex#: 258635
Publication Date: 12/95
Order#: 95-063
Last Reviewed: 12/95
History: Replaces Factsheet No. 81-003, "Field Diseases of Onions."
Written by: J. Chaput - Vegetable IPM Specialist/OMAFRA

Table of Contents 

  1. Introduction
  2. Seed and Seedling Diseases and Disorders
  3. Foliage Diseases
  4. Root and Bulb Diseases
  5. Useful References
  6. Related Links


A variety of diseases and disorders affect onions and related crops in Ontario. Most of the diseases are caused by fungi or bacteria whereas disorders may be caused by adverse weather, air pollutants, soil conditions, nutritional imbalances and pest control products. Sometimes several diseases and/or disorders can be present at the same time.

Accurate disease diagnosis is an important part of an Integrated Pest Management (IPM) program and this factsheet is intended to assist with identification of onion diseases and disorders that occur in the field and sometimes in storage. This Factsheet should be used in conjunction with the publication, Integrated Pest Management for Onions, Carrots, Celery and Lettuce in Ontario , which outlines monitoring and management guidelines.

It is important that onion diseases be recognized early in their development so that effective management strategies can be implemented. Careful and regular monitoring of the crop can provide this timely information. Knowledge of the field and cropping history can also provide valuable clues to the potential for diseases or disorders, because some diseases recur annually whereas others are more incidental and unpredictable. A soil test for pH, salt levels and nutrient availability is also a valuable tool.

Seed and Seedling Diseases and Disorders


Cold, wet soils often encourage the development of damping-off symptoms very early in the seedlings' growth. Seedlings may fall over and die as a result of breakdown of plant tissues at the soil line. Sometimes damping-off occurs before the seedling even emerges. The disease is usually caused by Pythium, Rhizoctonia or Fusarium fungi, either alone or in combination. Damping-off can occur in the field, or in the greenhouse if conditions are too wet. In most cases, damping-off is not a serious problem in Ontario onions.

Onion Smut

Onion smut is caused by the soil-borne fungus Urocystis cepulae and infects the flag leaf (cotyledon) as it grows through the soil. Often the seedling survives this initial infection and the characteristic black streaks and blisters appear in the leaves and small bulbs later in the growing season as the fungus moves from the infected flag leaf to younger leaves (Figure 1). Some seedlings will be killed by the disease in most years. A cool, wet spring increases the incidence of smut infection because the onion seedlings grow slowly and the flag leaf is in the soil for a longer period. Similarly, planting onion seeds too deep will also make them more likely to be infected. Smut spores survive in the soil for many years, and even long crop rotations may not reduce disease incidence. Seed treatments can reduce losses to the disease and growing onions from transplants avoids the disease. The disease is spread when contaminated soil or set onions are transferred to smut-free areas.

Onion smut.

Figure 1. Onion smut.

Botrytis leaf blight lesion.

Figure 2.Botrytis leaf blight lesion.

Seedling Disorders

Seedlings can be affected by a number of common disorders including tip dieback, stunting, poor growth, uneven emergence and physical injury.

A number of factors may cause such symptoms both in greenhouse transplants and in the field. The most common causes include adverse soil conditions (too hot, too dry or too wet); unfavorable pH levels; unfavorable salt concentrations; nutrient imbalances; herbicide or insecticide injury (phytotoxicity); wind, rain or hail injury.

In order to diagnose such disorders, accurate records of such factors should be kept and careful investigation of potential problems must occur. With the exception of weather factors, most of these conditions can be monitored and managed to reduce adverse effects.

Foliage Diseases

Botrytis Leaf Blight

Botrytis leaf blight is a very common disease that is caused by the fungus Botrytis squamosa, which overwinters as sclerotia in soil, on onion debris and on bulbs in cull piles.

Description: The first symptoms of leaf blight are greyish-white, oval-shaped spots, about 1 to 3 mm in length that appear on the leaves. These spots are often surrounded by a distinctive silvery-white "halo" with uneven margins (Figure 2). The centres of many spots become sunken and straw-colored and when numerous, the leaf tips begin to dieback, eventually affecting the entire leaf.

Monitoring and Management:This fungus disease usually develops after mid-June when temperatures and leaf wetness are favorable for infection. In some areas of Ontario a forecasting system known as BOTCAST is available to help growers predict the activity of the disease. Warm, (16-28 °C) wet weather is most favorable for disease development. Regular field scouting is still the best method to assess disease levels (see the publication IPM for Onions, Carrots, Celery and Lettuce in Ontario for monitoring guidelines). Once the level of Botrytis is determined, appropriate control measures can be implemented. Plant spacings that permit better air movement and irrigation schedules that do not extend leaf wetness periods may be helpful. To reduce the incidence and severity of Botrytis, remove cull piles and cull onions from field areas, rogue out volunteer onions and rotate crops.

Downy Mildew

Downy mildew of onions is caused by the air-borne fungus Peronospora destructor. This disease is not as common as Botrytis leaf blight, but when conditions are favorable for downy mildew, it can destroy an onion crop very quickly.

Description: The first sign of downy mildew is a purple-grey, velvety growth on otherwise green leaves (most easily seen in the early morning) (Figure 3). The disease often starts in patches and is favored by cool, (less than 22°C) humid weather. Diseased leaves quickly turn pale-green, then yellow, and collapse and die. The pale-green and yellow phase is characterized by oval-shaped lesions that often become infected with other diseases such as purple blotch or bacterial infections. Several cycles of sporulation and infection can occur and three or four of these cycles can destroy an onion crop over a period of 30 to 45 days.

Monitoring and Management: Refer to Botrytis leaf blight section and IPM for Onions, Carrots, Celery and Lettuce in Ontario for current monitoring and management guidelines.

Downy mildew.

Figure 3. Downy mildew.

Purple blotch.

Figure 4. Purple blotch.

Purple Blotch

Purple blotch, which is caused by the fungus Alternaria porri, is a disease that often appears on leaves that have already been damaged by other diseases or environmental factors.

Description: Warm, (18-30 °C) wet periods favor the development of purple blotch. Small brown spots with purplish centres are characteristic of this disease. Under favorable conditions, the spots form into oval lesions that have a purplish tint with concentric rings (Figure 4). Older leaves tend to be more susceptible to the disease.

Monitoring and Management: Refer to IPM for Onion, Carrots, Celery and Lettuce in Ontario for current monitoring and management guidelines.

Root and Bulb Diseases

Some of the diseases that affect the roots and bulbs of onions may start on the foliage and spread downwards and others may carry over into storage. This section will highlight diseases seen primarily on the roots and bulbs.

Bacterial Diseases

Description: Several bacteria (Pseudomonas and Erwinia spp.) cause a range of symptoms known as slippery skin, sour skin and soft rot. These diseases may start in the field on the leaves and sometimes may not be detected until the bulbs have been in storage for some time, depending on when infection occurred. In general, these bacterial diseases occur during wet periods and are favored by warm temperatures and damaged tissues. Initial foliar symptoms are characterized by severe breakdown of one or more leaves.

Onions with slippery skin often appear normal on the surface, but when they are squeezed the inner rotted portions slide out through the neck (Figure 5). Sour skin first appears as tan or brown partially rotted leaves on the growing plant. A soft rot develops near the neck and these leaves can be easily pulled off the onion. Sour skin is not as watery as slippery skin and the diseased scales separate from healthy ones (Figure 6). Soft rot symptoms can range from a spongy, water-soaked scale to complete bulb breakdown (Figure 7). Splashed soil is the main source of infection.

Monitoring and Management: Refer to IPM for Onion, Carrots, Celery and Lettuce in Ontario for current guidelines.

Slippery skin.

Figure 5. Slippery skin.

Sour skin.

Figure 6. Sour skin.

Soft rot.

Figure 7. Soft rot.

Pink Root

Pink root is caused by the soil-borne fungus Phoma terrestris and is present in many soils; however, losses to the disease are sporadic.

Description: Usually the main effect of this disease is reduced bulb size. The disease is easily recognized because the roots turn pink or maroon when infected. In severe cases the roots may die and the plants become weakened or stunted, especially in drier areas of the field (Figure 8). Unless the crop is suffering from heat or drought stress, yield losses are not likely to occur in good soils.

Monitoring and Management: Refer to IPM for Onion, Carrots, Celery and Lettuce in Ontario for current guidelines.

Pink root (bottom: healthy; top: infected).

Figure 8. Pink root (bottom: healthy; top: infected).

White rot.

Figure 9. White rot.

White Rot

White rot, caused by the soil-borne fungus Sclerotium cepivorum, is a very destructive disease that begins in the field and can carry over into storage.

Description: The first above-ground symptoms are a yellowing and dieback of the leaf tips, followed by a collapse of the affected leaves; however, these symptoms alone could easily be confused with other types of damage (i.e., onion maggot). When the bulbs and roots are examined, a white, fluffy mold and soft rot will be observed. Masses of tiny black sclerotia can also be seen within this mold (Figure 9). These sclerotia remain in the soil for many years. Infected bulbs can rot in storage boxes and stain other bulbs. White rot typically develops in patches in the field and is less of a problem when soils are warm (higher than 24 °C) and dry.

Monitoring and Management: Refer to IPM for Onion, Carrots, Celery and Lettuce in Ontario for current guidelines.

Fusarium Basal Rot

Basal rot is caused by the soil-borne fungus Fusarium oxysporum f.sp. cepae and generally occurs when soil temperatures are very warm (optimum 29 °C). This means that in Ontario the disease is not prevalent every year in all areas. It is often observed on Spanish onions growing in southwestern Ontario.

Description: The early symptoms in the field are yellowing of leaves and tip dieback. As the disease progresses, the whole plant may collapse and, if the plant is pulled, it often comes out without any roots attached since they have decayed. The basal plate of the onion becomes pinkish-brown and secondary bacterial rots may develop in the affected area (Figure 10). If infection occurs late in the season, the symptoms may not show up until the onions are in storage.

Monitoring and Management: Refer to IPM for Onion, Carrots, Celery and Lettuce in Ontario for current guidelines.

Fusarium basal rot.

Figure 10. Fusarium basal rot.

Neck Rot

This common storage disease can be caused by various species of Botrytis fungi including B. aclada, B. byssoidea and B. squamosa.

Description: Neck rot symptoms usually appear in storage; however, some necks may become soft and rotten immediately before harvest. There is usually a separation between healthy and diseased scales within the onion. As the disease progresses, the tissue becomes greyish and a grey mold may also develop (Figure 11). Black sclerotia eventually appear in the affected tissue. The decay symptoms can easily be confused with bacterial decay and eventually the whole bulb will break down. Sometimes both types of diseases are present.

Monitoring and Management: See section on Botrytis leaf blight and also ensure that curing and storage conditions are ideal.

Neck rot.

Figure 11.Neck rot.

Herbicide injury.

Figure 12. Herbicide injury.


Herbicide Injury: Some herbicides can easily damage the leaves of onion crops if applied at incorrect rates or during unfavorable weather. Contact herbicides can burn spots on the leaves and the leaf tips may wither (Figure 12).

Ozone Injury: The injury begins as small flecks, which can form into whitish spots. These spots could be confused with Botrytis, however, they do not have a distinctive halo (Figure 13).

Sprout Inhibitor Injury: If applied too early, maleic hydrazide can result in spongy bulbs (Figure 14).

Wind, Hail, Pelting Rain Injury: These weather factors can cause serious injury to all stages of onion growth. Hail stones can shred a crop in a matter of minutes.

Pelting rain drops cause whitish spots along one side of the leaves (Figure 15). This injury makes the onions more susceptible to foliage diseases.

Ozone injury.

Figure 13. Ozone injury.

Sprout inhibitor injury.

Figure 14. Sprout inhibitor injury.

Pelting rain injury.

Figure 15.Pelting rain injury.

Tipburn: The tips of the oldest leaves first show signs of yellowing and sometimes the symptoms affect the entire leaf. These symptoms are easily mistaken for Botrytis leaf blight, herbicide injury or ozone damage. The cause is believed to be anything that puts stress on the plant and may include heat, drought or fertilizer imbalance.

Nutrient Deficiencies: Onions require a well-balanced nutrient regime and if certain nutrients are low, some symptoms will be seen. Pale leaves may indicate that N or P levels are inadequate. A lack of manganese will show up as yellowing between the leaf veins. Zinc deficiency results in stunted, twisted and yellow-striped foliage.

Useful References

  • Integrated Pest Management for Onions, Carrots, Celery and Lettuce in Ontario, OMAFRA Publication
  • Vegetable Production Recommendations, OMAFRA Publication 363
  • Diseases and Pests of Vegetable Crops in Canada, The Canadian Phytopathological and the Canadian Entomological Societies, 1994 

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