Agriculture: Onion and Garlic Pest Management Guidelines

Fusarium Basal Rot

  • Fusarium oxysporum, including F. oxysporum f. sp. cepae, Fusarium proliferatum
  • Symptoms and Signs

    Fusarium basal rot (also known as FBR) is a fungal disease affecting onion and garlic, as well as other Allium crops such as leek. In field situations, Fusarium basal rot can cause damping-off of young plants, as well as foliar chlorosis, stunting, death of mature plants, and bulb rot. In garlic and onion, rot typically initiates in the basal plate (base of the bulb), then spreads into the bulb. In some cases, rot can start on the side of the bulb, potentially via wounds, or on the neck, necrotizing the bulb from the top down. When cut vertically, an infected bulb will show brown discoloration of the stem plate tissue. Later, the stem plate tissue becomes pitted and shows a dry rot. The stem plate and dry outer scales crack open under dry conditions. Bulb mites and maggots are commonly observed in rotten bulbs.

    Bulb rot prevents water and nutrients from reaching the foliage, resulting in yellowing of the foliage and leaf dieback from the tips at early or intermediate stages of crop development. Affected roots can become dark brown to dark pink, and a white fungal growth is sometimes evident at the base of infected bulbs.

    When bulbs are held under storage, Fusarium basal rot can cause rot of fresh market bulbs, mother bulbs used for seed production, and seed cloves.

    Fusarium basal rot can be mistaken for white rot; white rot, however, can be distinguished by the spherical, black bodies (sclerotia) produced by the white rot fungus.

    Bulbs rotted by Fusarium basal rot can also become secondarily colonized by bacteria, leading to a misdiagnosis of bacterial rot. To distinguish rots caused by Fusarium from those caused by bacterial pathogens, send samples of the plant at early stages of rot development to a diagnostic laboratory.

    Comments on the Disease

    Fusarium basal rot is a disease complex caused primarily by the fungi Fusarium oxysporum and F. proliferatum. Although other Fusarium species have also been documented as pathogens in California and other regions, they are rare.

    Post-harvest losses often have the largest economic impact in both onion and garlic production.

    Infection can occur through wounds or in the vicinity of old root scars at the base of the bulb.

    This disease progresses most rapidly in warmer soil temperatures, ranging from 77° to 82°F, but can occur when soil temperatures range from 59° to 90°F.

    Co-occurrence of stem and bulb nematode (Ditylenchus dipsaci) and Fusarium basal rot may result in greater yield reductions and rot incidence.

    Onion-Specific Comments

    Fusarium oxysporum f. sp. cepae (also known as FOC) is the primary pathogen of onions. Although Fusarium proliferatum has also been documented causing onion bulb rot, it is thus far uncommon as a bulb rot pathogen in California.

    Onion seed itself is not thought to become infected, but the mother bulbs used in seed production can harbor Fusarium basal rot, resulting in high levels of rot in seed-crop fields.

    Garlic-Specific Comments

    Fusarium proliferatum is the most virulent and common Fusarium pathogen of garlic in California.

    Fusarium oxysporum is also common and can cause severe symptoms in some cases. While F. oxysporum f. sp. cepae has been documented to cause garlic disease, most F. oxysporum garlic pathogens in California are not F. oxysporum f. sp. cepae; work is ongoing to identify these strains in order to develop effective crop rotations and diagnostic tools.

    Both pathogens have been documented to colonize garlic asymptomatically starting within 2 months of planting.


    Because the fungus can survive indefinitely in soil, preventing its introduction into new fields is one of the most effective strategies for management.

    In cases where it is critical to prevent field contamination, such as in the production of foundation seed and mother bulbs, sanitize field equipment before entering the field to prevent introducing pathogens. Effective sanitation includes both physically removing soil and debris with air or by pressure-washing, together with the use of a sanitizer. Sanitizers with low corrosivity that are effective against Fusarium species include quaternary ammonium compounds.

    To avoid favorable conditions for infection, store bulbs at temperatures below 39°F and at low relative humidity.

    Onion-Specific Management

    Long-day onions have partial resistance to F. oxysporum f. sp. cepae, although resistance gene efficacy is reduced under warm temperatures. There are no short-day cultivars resistant to F. oxysporum f. sp. cepae.

    In seed production, have mother bulbs tested for the presence of Fusarium basal rot before planting. Avoid planting mother bulb lots with high rot levels.

    Garlic-Specific Management

    There are no established methods to eradicate Fusarium pathogens from garlic seed cloves. Managing seed clove infection is critical for mitigating Fusarium basal rot losses in both fresh market and processing garlic production since seedborne infections can be a significant driver of pathogen spread and primary infection into other fields. Even asymptomatic seed can be infected.

    Use garlic seed that was tested for Fusarium basal rot pathogens. Avoid planting seed fields or production fields with seed lots that are heavily rotten, as Fusarium pathogens are likely present.

    Clean garlic seed is produced in standardized clean-seed programs that test for Fusarium basal rot pathogens in foundation garlic and that are grown in pathogen-free fields.

    Text Updated: 02/24