Agriculture: Alfalfa Pest Management Guidelines

Sclerotinia Stem and Crown Rot (White Mold)

  • Sclerotinia stem and crown rot (white mold): Sclerotinia sclerotiorum, Sclerotinia trifoliorum
  • Symptoms and Signs

    There are two species of Sclerotinia that cause stem and crown rot, both causing the same symptoms and requiring similar environmental conditions for infection. Sclerotinia sclerotiorum has a wider host range than S. trifoliorum, which mostly infects legumes. When the disease is active it is easily identified by white, cottony, mycelial growth on crowns or stems. In seedling fields infected plants wilt and die, often causing stand loss. For established fields, infected stems wilt and die. The disease can grow into crowns, but plants usually recover.

    The first obvious symptom of disease is wilting stems. If conditions are humid or moist, white mycelium can be found growing on the stems and sometimes on the soil adjacent to infected plants. Diagnosis can be confirmed by the presence of black, hard resistant structures (called sclerotia) that look like peppercorns. They can be round or irregular in shape and, when broken open, have a white interior. Sclerotia are found at the base of stems, on soil near the crown, or inside infected stems. Dead stems are hollow and easily flattened between the thumb and fingers, making it easy to feel sclerotia, if present, inside. Sclerotia found in stems are elongated in shape.

    Comments on the Disease

    Sclerotinia stem and crown rot is a cool-season disease. In wet or foggy winters, this disease can be serious on stands planted in September and October, especially when rapidly growing plants form a dense canopy in which high humidity is favorable for disease. Weeds, such as chickweed, further encourage disease by prolonging moist conditions in the canopy.

    All the stems of a plant may be infected and die, which makes the plant appear to be dead. But crowns may still be alive and healthy regrowth can appear later in spring, especially in established plants. If plants are young, weakened by stress or other factors, or if favorable conditions for disease exist long enough, entire plants may be killed.


    The best strategy for established fields is to remove as much foliage before winter as possible by mowing or grazing. When removing an alfalfa stand, deep plowing will prevent germination of most sclerotia in following years; however, neighboring fields of alfalfa or weed hosts (e.g., pineappleweed, sowthistle, groundsel, mayweed, mustards, radish, and legumes) can be the source of new infections. Good weed control reduces potential hosts. It also opens the canopy, allowing air movement and sunshine at the base of plants, thereby reducing humidity and moisture required by the fungus to start and maintain infections. In dry winters, this disease is not a problem. There is no effective genetic-based resistance incorporated into commercial varieties at this time.

    Early February plantings usually escape disease, because environmental conditions that favor disease do not usually last for extended time periods. Growers who prefer to plant in September and October face potential damage from this disease during the first winter. The disease may thin stands and, on rare occasions, replanting may be necessary.

    Research has not shown conclusively that using herbicides to burn back seedling growth is effective in reducing disease. The fungicide premix, pyraclostrobin/boscalid (Pristine), can reduce disease severity and increase yield in the first cutting, but timing of application is challenging. Apply just before or after infection. If fog develops after substantial rain, ground application may be difficult. Application in advance of rain and fog may not be useful if the forecast was incorrect and if dry windy conditions, which do not favor disease development, occur following a storm.

    The mixture of two active ingredients with different modes of action (pyraclostrobin and boscalid) is more expensive but provides better disease control and should slow the development of resistant Sclerotinia strains than using a strobilurin (pyraclostrobin or azoxystrobin) by itself.

    Common name Amount per acre REI‡ PHI‡
    (Example trade name) (hours) (days)
    Not all registered pesticides are listed. The following are ranked with the pesticides having the greatest IPM value listed first—the most effective and least likely to cause resistance are at the top of the table. When choosing a pesticide, consider information relating to the pesticide's properties and application timing, honey bees, and environmental impact. Always read the label of the product being used.
      (Pristine) 14–18 oz 12 14
      MODE-OF-ACTION GROUP NAME (NUMBER1): Quinone outside inhibitor (11) and carboxamide (7)
      (Headline) 6–9 fl oz 12 14
      MODE-OF-ACTION GROUP NAME (NUMBER1): Quinone outside inhibitor (11)
      (Quadris) 6–15.5 fl oz 4 14
      MODE-OF-ACTION GROUP NAME (NUMBER1): Quinone outside inhibitor (11)
    Restricted entry interval (REI) is the number of hours (unless otherwise noted) from treatment until the treated area can be safely entered without protective clothing. Preharvest interval (PHI) is the number of days from treatment to harvest. In some cases the REI exceeds the PHI. The longer of two intervals is the minimum time that must elapse before harvest.
    1 Group numbers are assigned by the Fungicide Resistance Action Committee (FRAC) according to different modes of actions. Fungicides with a different group number are suitable to alternate in a resistance management program. In California, make no more than one application of fungicides with mode-of-action group numbers 1, 4, 9, 11, or 17 before rotating to a fungicide with a different mode-of-action group number; for fungicides with other group numbers, make no more than two consecutive applications before rotating to fungicide with a different mode-of-action group number.
    Text Updated: 03/17
    Treatment Table Updated: 03/17