Scouting for Soybean Stem Diseases

***Updated in 2025, this version replaces the previous 2016 Scouting for Soybean Stem Disease publication.***

Effective management of soybean stem diseases starts with proper identification. Symptoms typically appear in the mid to late reproductive stages of soybean.

Figure 1. Symptom key for stem diseases without external stem symptoms or signs.

Figure 2. Symptom key for stem diseases with external stem symptoms or signs.

Anthracnose stem blight (fungus: Colletotrichum truncatum)

Stems and petioles with red to brown irregular shaped blotches in early soybean reproductive growth stages and black fungal bodies near soybean maturity. Leaf symptoms include reddish veins and rolling. Infected petioles cause leaves to twist down into a shepherd’s crook and can result in early defoliation.

Brown stem rot (fungus: Cadophora gregata)

Stems will have reddish-brown discoloration in the pith (center of stem), which may only be found at nodes. Although it appears healthy in most cases, the stem exterior of severely infected plants may look olive green and shiny. Leaf symptoms include interveinal chlorosis and necrosis of youngest leaves, but leaf symptoms may not occur on all plants. Root rot is typically not evident in plants with brown stem rot, unlike roots with sudden death syndrome.

Charcoal rot (fungus: Macrophomina phaseolina)

The lower stem and taproot appear light gray or silver and small, dark fungal structures called microsclerotia can be present. The interior of stems and taproot will be discolored with microsclerotia. Leaves yellow and die but remain attached to the plant.

Fusarium wilt (fungus: Fusarium spp.)

The inside of the stem and roots will have brown vascular tissue. Upper leaves wilt and lower canopy leaves drop early. Roots are stunted with purplish-brown to black discoloration. If plant roots are incubated, there will be no purple/blue spore masses, unlike roots with sudden death syndrome.

Neocosmospora root and stem rot (fungus: Neocosmospora vasinfecta)

Primarily observed in Arkansas and Mississippi, this disease is not widespread in most soybean-producing areas. However, Neocosmospora root and stem rot symptoms include interveinal chlorosis on leaves, small pinpoint red fungal structures at the crown of the plant, and general discoloration of the pith, which can resemble other stem diseases, particularly red crown rot. Interveinal chlorosis will progress over time, leading lower leaves to drop prematurely. Roots and pith can be discolored.

Phytophthora root and stem rot (oomycete: Phytophthora sojae and P. sansomeana)

Infection by P. sojae may be characterized by a dark brown lesion beginning at the taproot and extending up several nodes on the stem can be observed. This lesion surrounds the entire stem. Brown internal stem discoloration can be observed on plants at any stage. Roots are discolored and leaves yellow and wilt but remain attached to the plant. Infection by P. sansomeana often only results in seed or root rot, and not the characteristic stem lesion that can be induced by P. sojae.

Pod and stem blight (fungus: Diaporthe sojae and D. longicolla)

Black, raised specks (pycnidia) arranged in linear rows, often accompanied by reddish discoloration, are visible on mature soybean stems. Pycnidia can also be found on petioles and pods.

Sclerotinia stem rot (white mold; fungus: Sclerotinia sclerotiorum)

White, cottony mold can be seen on the lower stem and black, hard fungal structures called sclerotia may be present. These sclerotia can also be embedded inside the stem. Leaves wilt and turn grayish green between veins but remain attached to the plant.

Southern blight (fungus: Agroathelia rolfsii)

White fungal growth is present on the exterior of the stem. This growth can look like a fan extending up the stem of the plant from the soil line. In some cases leaves in the upper canopy can exhibit some interveinal chlorosis. Sclerotia can also form along the fungus growing on the stem when environmental conditions are favorable.

Sudden death syndrome (fungus: Fusarium virguliforme)

The stem interior shows brown or gray discoloration below the outer layer but pith is white (unlike brown stem rot). Leaves show interveinal chlorosis and necrosis and drop from the plant after they die. Root discoloration and rotting, along with internal browning of the taproot, can be observed.

Stem canker (fungus: Diaporthe caulivora and D. aspalathi)

A sunken canker, ranging from reddish-brown (D. caulivora) to dark brown (D. aspalathi), typically forms at a node and may extend across several nodes. These lesions often do not completely encircle the stem. Inside the stem, discoloration or browning is observed near the lesion. When infected by D. aspalathi, leaves may exhibit interveinal chlorosis and necrosis, but they often remain attached to the plant.

Red crown rot (fungus: Calonectria ilicicola)

Red discoloration of lower stem and roots can appear as early as the vegetative stages, with extensive root rotting by the end of the season. Interveinal chlorosis and necrosis may occur in leaves, along with premature death. Leaves generally will stay attached to the petioles. The pith of the lower stem of affected plants may have a gray appearance. The fungus may produce small (less than 1/16 inch (2mm) in diameter) reddish-orange spherical structures called perithecia that can occur toward the end of the season on the lower stem and roots.

Acknowledgements

Authors

Kiersten Wise, University of Kentucky; Tom Allen, Mississippi State University, Carl Bradley, University of Kentucky; Boris X. Camiletti, University of Illinois, Martin Chilvers, Michigan State University; Dylan Mangel, University of Nebraska-Lincoln; Febina Mathew, North Dakota State University; Daren Mueller, Iowa State University; Adam Sisson, Iowa State University; Damon Smith, University of Wisconsin-Madison; and Albert Tenuta, Ontario Ministry of Agriculture, Food and AgriBusiness.

Reviewers

Darcy Telenko,Purdue University; Dean Malvick, University of Minnesota; Richard Wade Webster, North Dakota State University; Gary Bergstrom, Cornell University; Travis Faske, University of Arkansas; Mandy Bish, University of Missouri; and Horacio Lopez-Nicora, The Ohio State University.

Sponsors

The authors thank The United Soybean Board, Grain Farmers of Ontario, and United States Department of Agriculture - National Institute of Food and Agriculture for their support.