An Overview of Sclerotinia Crown and Stem Rot in Alfalfa

Introduction 

Sclerotinia crown and stem rot of alfalfa is primarily caused by the soilborne fungus Sclerotinia trifoliorum, though it also can be caused by S. sclerotiorum. Commonly known as “white mold,” this disease can significantly impact alfalfa production when environmental conditions favor disease development. Accurate identification and effective management are essential to limit the disease’s impact. 

Symptoms and Signs

Sclerotinia crown and stem rot typically appears in the spring, causing small patches of plants to wilt and eventually collapse in the field. This disease leads to weak stems, resulting in a thin stand. White, fuzzy fungal growth (mycelium) can often be seen at the base of the alfalfa stems near the soil line (Figure 1). Fungal growth may spread to adjacent plants, creating patches of dead plants in the field (Figure 2). Weeds may establish in these patches causing further yield losses and management challenges. Affected stems will eventually turn brown or gray as the plants wilt and die (Figure 3). Crowns of affected plants may turn yellow before eventually browning. The fungus produces small, black, survival structures called sclerotia that may be present on the stems or crowns (Figure 4).

Disease Cycle 

The sclerotia produced by the fungus, S. trifoliorum, can remain dormant in the soil for many years. In most regions of the U.S. and Canada, this survival structure can be found in the soil or on infected plant parts. In the fall, when soil moisture increases and soil temperatures decrease, the sclerotia will germinate and produce structures known as apothecia (Figure 5). Apothecia are small, cup-shaped fungal structures that eject spores, which are carried by the wind to nearby alfalfa plants, causing new infections (Figure 6). Secondary infections occur as the fungal mycelium moves from plant to plant. Other forage legumes, such as clovers, can also be infected by S. trifoliorum, which can sustain the fungus in the field or be a source for inoculum. There is potential for alfalfa seed to be contaminated with sclerotia, which could disseminate the pathogen over long distances. This is one reason alfalfa farmers can experience outbreaks in areas where the disease has not previously been reported.

Conditions that Favor Disease Development 

The fungus that causes Sclerotinia crown and stem rot is most active at mild temperatures (50 to 68°F; 10 to 20°C) and requires continuous moisture for infection and growth. Prolonged snow cover can enhance damage from this disease by creating an insulating effect, which keeps temperatures within the favorable range for infection and maintains moisture, stimulating fungal growth. In contrast, dry years tend to reduce disease impact. Alfalfa fields seeded in the spring are less susceptible to infection because the stands can develop stronger crowns before the pathogen’s infectious period in the fall. In contrast, fields seeded in late summer or early fall are most susceptible to the disease, as young plants have smaller crowns during the infection period.

Weed hosts can increase disease pressure as sources of inoculum. Additionally, since this disease is caused by a fungus that produces airborne spores, small alfalfa fields surrounded by pastures or fields with alternative hosts may also be at risk.

Yield Losses and Impact 

Sclerotinia crown and stem rot is most damaging during the first production or harvest year. When conditions favor the disease after seeding a new stand, complete loss can occur. Reduced biomass and poor yield may be observed when stands are affected within the first year of planting. Less damage is typically observed in stands older than one year.

Diagnosis

Sclerotinia crown and stem rot is one of a few diseases that can be easily diagnosed in the field by trained personnel, though compounding factors may require samples to be submitted to a diagnostic laboratory. The presence of the white, fuzzy fungal growth in or on the base of the stem, along with hard, black sclerotia on or near affected plants, can indicate Sclerotinia crown and stem rot. In rare cases, if infection occurred in the fall, and winter conditions were favorable for disease, no living plants may be visible in affected areas in the spring when alfalfa breaks dormancy. Sclerotia may still be visible on these dead plants and near the soil line, aiding in diagnosis. Growers unfamiliar with this disease can mistake symptoms for winterkill. However, Sclerotinia crown and stem rot can be differentiated from winterkill by inspecting the base of wilted or dead alfalfa stems for the fuzzy white fungal growth and sclerotia. Plants affected by winterkill will not have these fungal structures. 

Disease Management 

Planting Strategies 

In areas where Sclerotinia crown and stem rot is problematic, a primary strategy for preventing disease development is to plant alfalfa in the spring or early summer. Fall-planted alfalfa should be seeded as early as possible to ensure seedlings are well-established and have reached adequate plant growth before environmental conditions become favorable for infection. It is also important to ensure that any alfalfa seed used is free of sclerotia, as using pathogen-free seed can help prevent the disease from spreading to new areas. In fields where the disease has already been reported, consider reducing the seeding rate per acre to decrease the humidity in the crop canopy.

Cutting Timing

Scouting fields for disease in the spring helps identify infected plants. Planning an early cutting of the affected fields can help reduce humidity and moisture in the canopy, creating less favorable conditions for disease development. 

Tillage

Tillage is not a reliable management option for this disease. While initial tillage can bury sclerotia, thereby reducing the potential inoculum for infecting subsequent plantings, repeated tillage can bring sclerotia back to the soil surface. Long-term conservation tillage can eventually deplete viable inoculum in the upper soil profile, potentially reducing overall disease severity. However, the exact duration of conservation tillage to effectively reduce disease severity can vary depending on soil type and local pathogen populations.

Crop Rotation

The primary fungus responsible for Sclerotinia crown and stem rot in alfalfa (S. trifoliorum) differs from the species that affect soybean, peanut, tobacco, canola, or vegetable crops. Therefore, field crops (e.g., corn, cotton, wheat, sorghum) and annual forage grasses (e.g., Sudangrass) can be used in crop rotation. However, farmers should keep in mind that the sclerotia of the fungus can survive in the soil for up to 5 to 6 years without a host plant. Once the pathogen is well established and the soil is highly infested with sclerotia, crop rotation may become less effective due to the long survival period of these fungal structures. 

Weed Management

The fungus that causes Sclerotinia crown and stem rot in alfalfa can remain on volunteer clovers and birdsfoot trefoil in a pasture indefinitely. Weeds, such as chickweed, contribute to disease by prolonging moist conditions in the canopy. Other weed hosts, including pineappleweed, sowthistle, groundsel, mayweed, mustards, radish, and legumes, can also be sources of new infections. Effective weed control reduces the potential survival of the fungi and helps reduce humidity in the crop canopy, thereby mitigating disease risk.

Disease Resistant Varieties

Alfalfa varieties differ in susceptibility to Sclerotinia crown and stem rot. If available, select partially resistant alfalfa varieties to help reduce the risk of disease.

Chemical Control

Foliar fungicides are available for managing Sclerotinia crown and stem rot in alfalfa, but their effectiveness is mostly unknown across major alfalfa production areas. 

Find Out More

Other publications in the Alfalfa Disease Management series are available at the Crop Protection Network.

Acknowledgements

Authors 

Kiersten Wise, University of Kentucky; Kelsey Andersen Onofre, Kansas State University; Adam Sisson, Iowa State University; Deborah Samac, USDA-ARS; Damon Smith, University of Wisconsin-Madison; and Maira Rodrigues Duffeck, Oklahoma State University.

Reviewers

Gary Bergstrom, Cornell University; Martin Chilvers, Michigan State University; Dean Malvick, University of Minnesota; Joshua Michel, Iowa State University; Darcy Telenko, Purdue University; Daren Mueller, Iowa State University; and Travis Faske, University of Arkansas

This publication was developed by the Crop Protection Network, a multi-state and international collaboration of university/provincial extension specialists and public/ private professionals that provides unbiased, research-based information to farmers and agricultural personnel.

This work is/was supported by the USDA National Institute of Food and Agriculture, Crop Protection and Pest Management Program through the North Central IPM Center (2022-70006-38001).