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Spring Alfalfa Diseases

April 17, 2003

This article will provide basic information on three diseases of alfalfa that are often seen in the spring: Sclerotinia crown and stem rot, Aphanomyces root rot, and spring black stem and leaf spot. Additional information and photographs for these and other alfalfa diseases can also be found at the University of Illinois Field Crop Diseases Web site (

Sclerotinia crown and stem rot is an alfalfa disease that is most common in the southern half of Illinois. It is initiated primarily in the fall and continues to spread and infect into the spring. The damage is usually most readily seen in the spring and may be noticed as dying or rotting plants in large or small patches. This disease can destroy stands of alfalfa or thin out stands to result in low yields.

Sclerotinia crown and stem rot of alfalfa in the Midwest is thought to be caused primarily by the soilborne fungus Sclerotinia trifoliorum. A similar disease, white mold of soybean, is caused by a different pathogen (Sclerotinia sclerotiorum). Sclerotinia crown and stem rot of alfalfa causes soft rot of infected plant tissues. Young plants that are killed by this disease often degrade quickly and are seen as brown, dead tissue lying on the ground. On established plants, individual stems often wilt and die. These plants typically have infected internal crown tissue that is a brown-yellow color, and the infection may spread to kill the crown and all stems. A telltale sign of infection on infected tissue is sclerotia, which are small black to gray fungal structures that are round to elongated and about 1/8 to 1/4 inch in diameter and length.

Management of Sclerotinia crown and stem rot of alfalfa is based primarily on planting date, crop rotation, and resistant cultivars. Spring planting allows the plants to develop resistance prior to the time infection occurs in the late fall. This disease is typically most destructive in fall-seeded stands. If possible, new fields of alfalfa should be established where there is no history of severe Sclerotinia crown and stem rot of alfalfa or red clover. Alfalfa cultivars with resistance/tolerance to this disease have been developed that can be more productive than other cultivars under conditions of low to moderate disease pressure. If Sclerotinia crown and stem rot of alfalfa is seen in Illinois, please collect plants and contact Dean Malvick by phone at (217)265-5166 or e-mail at

Aphanomyces root rot is caused by the soilborne fungal-like pathogen Aphanomyces euteiches, which infects alfalfa roots in slowly drained soils and during extended periods of rain. This disease is typically most damaging to seedlings. It can dramatically reduce stands and reduce vigor and yield of plants that survive infection. We have found Aphanomyces euteiches to be very common in Illinois alfalfa fields, and race 2 appears to be more common than race 1 in our preliminary work.

Aphanomyces root rot can be difficult to diagnose in the field. Infected seedlings typically become stunted and yellow before they wilt and die. Cotyledons usually turn yellow first, and seedlings then often develop a purple tint. Older stands with significant disease pressure from Aphanomyces root rot may be stunted and significantly thinned. Two similar diseases, which are also favored by wet soil conditions, are caused by the pathogens Pythium and Phytophthora; but these pathogens tend to kill seedlings quickly before plants become severely chlorotic or discolored.

Management of Aphanomyces root rot is based primarily on resistant varieties and avoidance of slowly drained fields. Fungicides are not available for control of Aphanomyces root rot of alfalfa. The seed-treatment fungicides Apron XL, Allegiance-FL, and Apron-FL are not effective against Aphaomyces, but they do reduce seed rot and seedling damping-off caused by Pythium and Phytophthora.

The best approach to managing Aphanomyces root rot is through the use of resistant alfalfa varieties. Many varieties are resistant (R) or highly resistant (HR) to Aphanomyces root rot. They should be planted where slowly drained soils occur and where Aphanomyces may be a problem. However, most varieties with resistance to Aphanomyces are resistant only to race 1, and these can be killed by race 2 of Aphanomyces. Because we now know that race 2 appears to be common in many areas of Illinois, resistance to race 1 may not be effective in many Illinois fields. Several alfalfa varieties are available that are resistant to both races of Aphanomyces. If resistance to race 2 is not specified for an Aphanomyces-resistant alfalfa variety, then it is likely to be resistant only to race 1.

Spring black stem and leaf spot (caused by the fungus Phoma medicaginis) is a common disease at this time of the year (and in the fall). This foliar disease will be favored by the wet and cooler weather that is predicted in Illinois over much of the next week. This and other foliar diseases can develop quickly during favorable conditions. This disease often is most severe on the leaves, petioles, and stems near the soil and tends to progress upward in the plant. Small to large dark brown to black spots develop on the leaves, and lesions on the stems can become severe and girdle the stems. This disease can cause defoliation, which leads to reduced yield and forage quality.

Yield and quality losses caused by spring black stem and leaf spot can be reduced by cutting. Stands should be harvested as soon as possible if the disease becomes severe, and this may mean before the optimal harvest date based on growth stage of the alfalfa. Choose high-yielding alfalfa varieties adapted to your area. Alfalfa cultivars are not available with high levels of resistance to spring black stem; however, some new varieties are reported to be damaged less from this disease than older varieties. Good management and fertilization (especially K) practices may also help to reduce losses from foliar diseases.

If you wish to have alfalfa diagnosed for these or other diseases, samples can sent to the University of Illinois Plant Clinic in Urbana (217-333-0519; Malvick

Author: Dean Malvick

The Pest Management and Crop Development Bulletin
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