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Alliums, Post Harvest and Storage Diseases

Fusarium Basal Rot (Fusarium oxysporum f. sp. cepae)

For more detailed information on this disease, please see our main Alliums, Fusarium Basal Rot article.

Fusarium basal rot is caused by Fusarium oxysporum f. sp. cepae. This disease can affect onion, garlic, and other Allium spp. The fungus lives a long time in soil. Infection often is associated with mechanical or insect injury. Foliar symptoms appear as a unilateral or general wilt and a yellow to tan dieback of leaf tips during mid to late season. Foliage death may occur over several weeks. In onions, red-brown rot appears where roots are attached to the basal plate. Rot and discoloration usually affect all of the base and up into the bulb scales; affected tissue appears brown and watery when bulbs are cut open. Sometimes, a white moldy growth develops on the stem plate or between affected scales. Bulbs may appear normal at harvest, but rot may progress in storage.

In storage, garlic bulbs appear spongy or sunken. Infected bulbs are softened, brown and watery when cut open. There may be a white, light pink or reddish fungal growth (mycelium) covering the cloves, or in the rot cavities. Deep cracks form in the cloves, followed by break down of the tissue, which will eventually dry down to a portion of its original size, the cloves becoming crinkled and small.

Cultural control:

  • Use 4-year or longer crop rotations.
  • Plant resistant varieties. In a Malheur County, OR test, these cultivars had less basal rot: ‘Golden Cascade’, ‘Cima’, ‘Oro Grande’, ‘Valient’, and ‘Cashe’. Your mileage may vary in the Northeast. Other onion cultivars described as tolerant are ‘Bronze Reserve’, ‘North Star’, ‘Sassy Brassy’, and ‘Sentinel’.
  • Protect plants from insect, fertilizer, or other injury.
  • Storing bulbs at 39oF minimizes postharvest losses.

Botrytis Neck Rot (Botrytis allii)

For more detailed information on this disease, please see our main Alliums, Botrytis Neck Rot article.

Botrytis neck rot is caused by Botrytis allii, a fungus that overwinters on plant debris in soil, on infected bulbs, and as sclerotia in soil. The pathogen can also be seed-borne. Botryitis neck rot is caused by a different pathogen from Botrytis leaf spot. Botryitis neck rot is seen primarily in storage. Most common causes of severe losses are excessive nitrogen, which delays crop maturity; irrigation and/or rain late in the season; inadequate or improper curing; and improper storage. Infection is through neck tissue or wounds in bulbs. Some bulb infections may arise from symptomless leaf infections, but often the fungus directly enters the neck via airborne spores when onions are topped before soft, susceptible top tissues dry properly.

Symptoms: In onion, the disease is more apparent after harvest, while bulbs are in storage. At first, soft neck tissue looks water soaked, and a yellow discoloration moves down the neck into the scales. Bulbs break down to a soft mass. A gray mold develops between the onion scales, later producing small to large black bodies (sclerotia) which develop as a solid layer around the neck.

In garlic, the disease usually appears first on necks near the soil line at any time after spring greenup when weather conditions permit. The disease becomes worse when it starts early in the season. Extensive development of sclerotia is best seen on maturing bulbs just before and during harvest. The fungus moves rapidly into the succulent garlic bulb’s neck region, producing a water-soaked appearance. A gray mold develops on the surface of or between garlic scales, later producing black bodies (sclerotia) which develop around the neck. Before bulbing, plants may die or recover if weather permits. Bulbs infected late break down to a soft mass, and secondary infections by other organisms follow.

Cultural control: Bulb onions:

  • Allow tops to mature well (at least half of leaves brown), then lift or undercut the onions. In dry weather, cure onions on the ground 6 to  10 days.
  • Be sure onions are well dried and necks tight (i.e. the tissue does not slide when you roll your neck between your fingers) before topping. Bacterial diseases and Botrytis Neck rot can move through green tissue into bulbs. These diseases do not move in dry tissue.
  • Minimize bruising and mechanical injury in topping and storing.
  • Store in well-ventilated houses at 32°F or slightly higher. Use higher temperatures if humidity cannot be held below 75%. Practice a crop rotation of at least three years.

Cultural control: Garlic

  • Allow the tops to mature well, then lift or undercut the garlic. - If normal dry weather prevails, cure garlic on the ground for 6 to 10 days. Otherwise, cure in a well ventilated area at 70-80 °F.
  • When topping, minimize bruising and mechanical injury.
  • Store garlic in well-ventilated houses at temperatures of 32°F, or just slightly higher.
  • Avoid frequent and excessive irrigation. - Visual inspection of seed garlic with a hand lens may help. Examine the basil plate or bottom of garlic for gray mold.

Purple Blotch (Alternaria porri)

For more detailed information on this disease, please see our main Alliums, Purple Blotch article.

Purple blotch is caused by Alternaria porri, a fungus that overwinters on infected bulbs and debris in the field, and can be seedborne in onion. Another fungus, Stemphylium vesicarium, can also cause purple blotch in onions. These are most common as leaf diseases, but can affect bulbs in storage. Infection often follows injury caused either by other fungi, such as Botrytis, by thrips feeding injury or by sand or dust during windstorms. Older leaves are more susceptible, and plants approaching maturity are more susceptible than young plants. Spores require rain or persistent dew to cause infection. Optimum temperatures are 77 to 81°F. Almost no infection occurs below 55°F. ‘Sweet Spanish’ onions are very susceptible.

Symptoms: A small, water-soaked lesion develops on leaves and soon develops a white center. Zones may appear as the spot enlarges and the lesion turns brown to purplish. Red or purple margins often encircle the purplish centers and are surrounded by yellowish tissue. In moist weather, the spot’s surface usually becomes covered with a brownish black, powdery fungus growth. Leaves with large spots turn yellow and are blown over by the wind. Bulbs may decay during and after harvest. Decay shows first as a watery rot around the neck and is particularly noticeable because of the yellowish to wine-red discoloration in the neck region. As the fungus moves through onion scales, the tissue turns yellow then a wine-red and dries to a papery texture.

Cultural control:

  • Practice long rotations with unrelated crops.
  • Reduce hours of leaf wetness with wider plant spacing and good weed control.
  • Destroy old onion cull piles and bury debris.
  • Avoid injuring bulbs during production.
  • Properly cure bulbs in the field; lift and allow onions to dry several days before topping.
  • Plant tolerant or resistant varieties. Avoid Sweet Spanish onion because they are extremely susceptible.

White Rot (Sclerotium cepivorum)

For more detailed information about this disease, please see the full Alliums, White Rot fact sheet.

White rot of garlic and onions is caused by a fungus, Sclerotium cepivorum, that produces hardy sclerotia which may live in soil for years. Only Allium spp. such as onion, leek, and shallot are attacked. Sclerotia can infect plants from 12 inches below the soil surface. One sclerotium can infect a group of 20 to 30 adjacent plants. Fungal activity is favored by cool soils and is restricted above 75°F. Once the disease is in a field, it is very difficult to grow Allium spp. successfully. Disease spreads with infected sets or transplants, grazing animals, and movement of infested soil.

Symptoms: Leaves decay at the base, turn yellow, wilt, and topple over. Older leaves collapse first. Roots rot,and the plant can be pulled up easily. Fluffy mycelium may be on remaining roots and bulb. Affected bulbs may become watery, and outer scales crack as they dry and shrink. Small sclerotia (0.02 inch, or about the size of a poppy seed) form in and on the surface of affected bulb parts, often around the neck. White rot can continue to decay infected bulbs in storage if humidity is not kept low.

Cultural Controls:

  • Plant only disease-free material in disease-free soil.
  • When working in infected fields avoid moving soil contaminated with sclerotia into new fields by washing equipment before it enters another field.
  • If practical, dig out all plants in infested spots in the field and the healthy plants growing next to diseased ones. Remove some soil with both diseased and healthy plants. Dispose of the material in a landfill or hot composting operation.

Blue Mold (Penicillium spp.)

Blue mold of onion and garlic may be caused by several Penicillium species. These fungi attack a wide range of fruits, vegetables, bulbs, and seeds; they are common in the soil growing on infected animal and plant debris. Symptoms of the disease start as pale blemishes, yellow lesions, and soft spots. A blue-green mold develops on lesions. When bulbs are cut open, one or more of the fleshy scales may be discolored and water-soaked. In advanced stages, bulbs may deteriorate into complete decay. In garlic, the pathogens survive in infected cloves. Invasion of onions is usually through wounds, sunscald, or freezing injury, although the fungi are able to infect uninjured bulbs. Blue Mold pathogens are often present in internal scales of onions with neck rot.

Penicillium decay of garlic caused by P. hirsutum is responsible for poor plant stand in the field and storage decay. Symptoms in the field include clove decay after planting and wilted, yellowed, or stunted seedlings. Infected plants are weak and stands are poor. 

Cultural control:

  • Control other diseases in the field to prevent avenues for infection.
  • Harvest bulbs with a minimum of bruising and wounding and dry promptly.
  • Store bulbs at 5° C (40° F) with low relative humidity.

Black Mold (Aspergillus niger)

Black mold, caused by Aspergillus niger, occurs in the field, during transit, and during storage. The fungus grows saprophytically on dead tissue and is a common inhabitant of the soil; spores are also common in the air. Bulb infection usually occurs through injured tissues in the neck or wounds on roots, basal stem plates, or outer scales. Uninjured bulbs are seldom infected. Seeds may be infected and the pathogen disseminated in infected seeds or transplants. Preemergence damping-off can occur if infected seed is planted. The disease is favored by warm temperatures or under warm storage conditions. Infected bulbs display a black discoloration at the neck or in bruised areas, lesions on outer scales, or black streaks beneath outer scales. As the disease develops, the entire bulb may appear black and shriveled as all scales are infected. Soft rot bacteria may invade and the bulbs exhibit a watery rot. Some bulbs will show no external symptoms, but when the bulb is cut open, central portions may be gray to black.

Smudge (Colletotrichum circinans)

Smudge, caused by the fungus Colletotrichum circinans, affects onions, leeks, and shallot, but not garlic. The pathogen is soil-borne, surviving in colonized onion debris and it can persist in soil for many years. The pathogen is spread by infested plant material and soil and is favored by warm, wet weather; it can complete its life cycle in a few days when conditions are favorable. Smudge appears on dried outer scales and lower portions of the bulb as dark green dots which turn black. The symptoms may be scattered but often appear in distinct circular, concentric rings. The fungus produces enzymes that break down cell walls and allow mycelium to proliferate throughout the bulb.

General Onion & Garlic Storage Disease Management

  • Control other diseases and insects in the field to prevent entry of storage rot organisms.
  • Avoid bruising and other mechanical injury when bulbs are being harvested or transported.
  • Treat bulbs with fungicide. This is only recommended in some cases.
  • Cure onions and garlic with hot, dry conditions. A healthy onion with a well cured neck is rarely infected with neck rot during storage.
  • Inspect garlic and onion before storing and discard all symptomatic bulbs.
  • Practice cultural methods that hasten curing. Undercut bulbs at harvest to sever all roots. Avoid N fertilization late in the season. Plant at proper spacing (For onions: 2-4 rows/bed, 9”-18” between rows, and 6-9 plants/foot or plants 3”-4” apart in the row. For garlic: 2-row beds 30" apart on center with 6"  spacing in and between rows; 3 or 4 rows per bed, with 6-8" between and within rows; single rows spaced 24-30" with 6" spacing in the row.)
  • Store bulbs under ideal conditions: 32-34°F with 70-75% relative humidity.


- adapted by A. Cavanagh & R. Hazzard, information & images from Oregon State Extension: Includes sections from "Storage Diseases of Onion and Garlic", written by M.B. Dicklow, UMass Extension.

Last Updated: 
January 2013

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