Gain knowledge on stem diseases of alfalfa

This second of three articles on alfalfa diseases gives a brief look at common stem diseases, which can cause loss of vigor and reduction in yield and quality.

Stem diseases in alfalfa typically cause loss of vigor and reduction in crop yield and quality. Disease pressure is increased by late, cold and wet spring seasons, and when the crop is kept moist by rainy weather or heavy dews. When nurse crops are present, alfalfa disease can be worse. Tall stubble after cutting and weeds growing around plants also contribute to disease pressure.


The fungus Collectotrichum trifolii causes this disease. Straw-colored lesions appear on plant stems and may girdle stems, causing shoots to yellow, wilt and form a “sheperd’s crook.” It is favored by warm, humid conditions and becomes more severe after first cut. High resistance has been bred into most new alfalfa varieties, but older varieties may be susceptible. Selection of a resistant variety, keeping harvest equipment clean from year to year, harvesting younger stands first, and rotating out of alfalfa for at least one year will help control anthracnose.

Rhizoctonia stem canker

Caused by the fungus Rhizoctonia solani, this disease causes elliptical to circular, somewhat sunken, tan to reddish or dark-brown lesions (cankers) on lower stems, as well as on the crown and taproot. When the disease becomes severe, stems may be girdled, causing leaves and shoots to yellow, wilt and die. Hot, humid weather and thick alfalfa stands are most vulnerable. If present, the disease can kill seedlings before or after emergence. The fungus can survive for years in the soil.

Sclerotinia crown and stem rot

The fungus Sclerotinia trifoliorum causes this disease in alfalfa. It is also the cause of similar “white mold” diseases in legumes, sunflowers, canola, most vegetables, many flowering bedding plants and stone fruits. The fungus survives in soil or in infected plant material as sclerotia, small, hard, black masses of fungal mycelium. The disease is enhanced by cool, wet weather and can infect plants at all growth stages. Symptoms in seedlings will show up as small, circular patches of dying or dead plants. On older plants, leaves and stems yellow, weaken and fall over. A cottony mass forms on the dead plant material, hence the name “white mold.” Dark brown or black sclerotia form in the fluffy growth. These will return to the soil and perpetuate the disease. Alfalfa crown can become infected, turning soft and grayish-green. Shoots from an infected crown will wilt and die.

Summer black stem and leaf spot

Also called Cercospora black stem, this disease is caused by the fungus Cercospora medicaginis. It is fairly common after first cutting in warm, moist weather. Small brown spots appear on leaves, enlarging to form larger lesions. Bad cases will cause early defoliation. Stem and petiole lesions are elongate, elliptical and reddish-brown, and may expand and girdle stems and petioles. The fungus overwinters in crop residue and may be seed-borne.

Spring black stem

Caused by the fungus Phoma medicaginis, this disease is similar to summer black stem, but is favored by cool, wet weather in spring and affects first cutting. Dark green, water-soaked lesions develop in the stems and petioles, turning brown to black with age. This fungus also overwinters in crop residue and may be seed borne.

See the first article of this series, “Be familiar with root rot diseases of alfalfa” for more information on certain root rot diseases and the third, "A closer look at leaf diseases of alfalfa," for more information on leaf diseases.


For more information, contact MSU Extension educator Jim Isleib at 906-387-2530

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