An Overview of Stem Canker

***Updated in 2025, this version replaces the previous Overview of Stem Canker publication.***

Introduction

Stem canker is a significant disease of soybean in the United States and Canada, where infection typically occurs on the lower portion of the stem. The disease is caused by two species of Diaporthe fungi: D. aspalathi and D. caulivora. Although the pathogens are now recognized as causing a similar disease, it’s important to note that they were previously categorized under distinct names: southern stem canker and northern stem canker, based on the geographic regions in which the diseases were commonly observed. D. aspalathi was primarily recovered from symptomatic plants in the southern United States, while D. caulivora was recovered from symptomatic plants in northern states. Both species have now been confirmed across broader geographies and overlap in some regions, meaning the former classifications of northern and southern stem canker are no longer accurate.

Symptoms and Signs

The first symptoms of stem canker are often dead plants with dried leaves still attached to petioles late in the season. Diseased plants usually occur in patches within fields (Figure 1). Initial symptoms typically appear on the lower third of the stem shortly after flowering (growth stage R1).

Stem canker lesions start as small, reddish-brown spots at the base of a branch or leaf petiole and then expand to form slightly sunken cankers that are reddish-brown with reddish margins (Figures 2-3). Cankers may remain on one side of the stem and can extend over several nodes or girdle the stem, killing the plant (Figure 4). In some cases, top dieback occurs, with a dark brown canker forming on the upper four to six internodes, which kills only the top of the plant (Figure 5). The canker may no longer be visible on dead plants.

Interveinal foliar chlorosis and necrosis may occur, but it is difficult to distinguish foliar symptoms from several other soybean diseases that cause similar symptoms (see Diseases with Similar Symptoms).

Disease Cycle

The fungi that cause stem canker survive in residue or in the soil for several years. Seed can be infested, but fungal spores from infested residue are usually the primary source of the fungus to initiate infection each season. Several weed species also serve as hosts, including black nightshade, curly dock, and others. However, many weed hosts serve as a reservoir for these fungi and do not express symptoms of stem canker.

The causal fungi produce spores during rainy weather, which then splash onto plant stem tissue (Figure 6). Infection occurs during the early vegetative stages of soybean growth, although cankers are not visible until the plant enters reproductive stages. Secondary spore production on infected plant tissue can occur, but later infections will not have as great an impact on disease development.

Infection can occur over a wide range of temperatures, but the fungus requires extended moist periods to infect. Disease can develop to epidemic levels when rainy weather persists during the reproductive stages of soybean growth.

Yield Loss and Impact

Yield loss from stem canker can approach 50 percent or greater on susceptible cultivars under favorable conditions. Stem canker can cause premature death of soybean in large areas of the field (Figure 7). These plants often have fewer and smaller seeds. The greatest impact on yield occurs when plants are infected early during the vegetative stages, and favorable weather conditions persist until later reproductive growth stages, allowing for continued disease development.

Disease Diagnosis

Several soybean diseases can cause similar symptoms, which can make stem canker diagnosis difficult (see Diseases with Similar Symptoms). Cankers may be isolated between nodes, or extend from a node to the soil line (Figure 8). Plants infected by the fungi that cause stem canker typically do not have interior taproot discoloration. You may need a laboratory diagnosis to distinguish stem canker from other diseases.

Diseases with Similar Symptoms

Brown stem rot (BSR; Cadophora gregata)

The foliar symptoms of brown stem rot (BSR) include yellowing and necrosis between veins. The stem symptoms include brown, discolored pith tissue, especially near the nodes of soybean stems (Figure 9).

How to distinguish BSR from stem canker: Stem canker’s foliar symptoms are similar to those of BSR, so the key difference is visible on the stem. Plants infected with the BSR fungus have no external stem lesions, and when the stem is split longitudinally, the pith is discolored brown.

Fusarium wilt (Fusarium oxysporum)

Fusarium wilt affected leaves turn yellow, die, and remain attached to the stem (Figure 10). Plants affected by Fusarium wilt have brown vascular tissue in the roots and stems, which cause plants to eventually wilt and possibly die (Figure 11).

How to distinguish Fusarium wilt from stem canker: Plants with Fusarium wilt do not show external decay or stem lesions above the soil line, and the vascular tissue in the roots and stems is discolored brown.

Neocosmospora root and stem rot (Neocosmospora vasinfecta)

Neocosmospora root and stem rot is primarily observed in Arkansas and Mississippi. Affected plants have interveinal chlorosis on leaves, small red fungal structures at the crown of the plant, and a discolored pith (Figure 12).

How to distinguish Neocosmospora root and stem rot from stem canker: Small red fungal structures at the crown are not observed with stem canker.

Southern blight (Agroathelia rolfsii)

In general, southern blight is observed across soybean production areas in the southeastern U.S. Affected plants generally have light interveinal chlorosis at advanced reproductive growth stages, generally between R5.5 and R6.

How to distinguish southern blight from stem canker: Distinctive white fungal growth that starts at the crown and extends upwards is generally observed on plants affected by southern blight (Figure 13). Sclerotia, which tend to begin white and turn dark brown with age, occur at the soil line around affected plants or on plants in the field if conducive environmental conditions persist. Plants killed by the fungus causing southern blight can also retain their leaves and are generally present in clumps in the field. Plants exhibiting southern blight symptoms do not have cankers on the stem.

Phytophthora root and stem rot (PRR; Phytophthora sojae; P. sansomeana)

Phytophthora root and stem rot (PRR) generally occurs in wet, waterlogged, compacted soils. Symptoms of this disease often appear during or shortly after waterlogged soil conditions.

How to distinguish PRR from stem canker: The stems of Phytophthora-infected plants have a characteristic dark brown lesion on the outer stem tissue that starts on the tap root beneath the soil surface and extends up the stem (Figure 14). Extensive root rot is also observed. No root rot is observed with stem canker.

Pod and stem blight (Diaporthe species)

Pod and stem blight is a disease also caused by Diaporthe fungi, but it is distinct from stem canker (Figure 15). It affects mature plants and seeds.

How to distinguish pod and stem blight from stem canker: Lesions from pod and stem blight tend to be more elongated, shallow, and typically tan colored with dark margins in comparison to stem canker lesions.

Red crown rot (Calonectria ilicicola)

The lower stem and roots of plants affected by red crown rot may be discolored , while interveinal chlorosis and necrosis are observed on the leaves (Figure 16). Leaves generally remain attached to the petioles.

How to distinguish red crown rot from stem canker: The red crown rot fungus may produce small reddish-orange fungal structures on the lower stem and roots at the end of the season. These fungal structures are not present in plants affected by stem canker.

Southern root-knot nematode (Meloidogyne incognita)

Plants infected by the southern root-knot nematode may appear stunted, with discolored leaves.

How to distinguish southern root-knot nematode from stem canker: The southern root-knot nematode causes rounded galls on infected roots (Figure 17). Plants affected by stem canker will not have galls on roots.

Sudden death syndrome (SDS; Fusarium virguliforme)

SDS symptoms are expressed as yellowing and necrosis between the veins of leaflets during the mid- to late reproductive stages. The veins of symptomatic leaves generally remain green.

How to distinguish SDS from stem canker: SDS-affected plants do not have external lesions like stem canker-affected plants do. As the foliar symptoms of SDS progress, the leaflets eventually curl or shrivel and drop off with only the petiole remaining (Figure 18), instead of remaining attached and dead as they do with stem canker.

Tobacco streak virus (TSV)

Tobacco streak virus (TSV) causes bud blight, leaf and flower bud proliferation (Figure 19), green stem disorder, and sometimes a lesion or blotch near the nodes (for example, red node). The internal stem tissue of infected plants also can be brown near the nodes.

How to distinguish TSV from stem canker: Stem canker does not cause bud proliferation. TSV lesions near the node are much smaller than stem canker lesions.

White mold (Sclerotinia stem rot; Sclerotinia sclerotiorum)

White mold (Sclerotinia stem rot) is typically more of a problem in northern climates in years when conditions are rainy and cool during flowering. Lesions develop on the nodes and expand up the stems. Infected leaves often die and remain attached to the stem.

How to distinguish white mold from stem canker: Sclerotinia-infected plants can be identified by the presence of white fungal growth on the outside of the stems (Figure 20). In addition, the white mold fungus produces sclerotia that are hard and black.

Management

The best way to manage stem canker is to plant resistant soybean varieties. Consult your seed dealer to obtain current information about varieties with stem canker resistance. While many sources, including older literature, still refer to the disease as "southern" or "northern" stem canker, this nomenclature is no longer entirely accurate in light of the broader distribution of the two pathogens. It is still important, however, to differentiate between the two species because host resistance genes can vary depending on the specific pathogen.

Rotating crops to a nonhost may reduce the amount of inoculum available to infect the next soybean crop. Soybean rotations to nonhosts such as wheat and sorghum are recommended for at least two years after severe disease in a field (Figure 21).

Most foliar fungicide labels do not include stem canker as a target disease. University field research trials evaluating foliar fungicides for stem canker management have not shown consistent efficacy with fungicides, especially with susceptible cultivars.

Fields under minimum or no-till production are at greater risk for stem canker development because they have more crop residue. Incorporating infested crop residue into the soil will reduce the survival rate of the fungus and the amount of fungus available to infect the next soybean crop. Maintain adequate fertility to reduce disease impact.

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Acknowledgments

Authors

Kiersten Wise, University of Kentucky; Carl Bradley, University of Kentucky; Martin Chilvers, Michigan State University; LeAnn Lux, North Carolina State University; Dylan Mangel, University of Nebraska-Lincoln; Febina Mathew, North Dakota State University; Daren Mueller, Iowa State University; Madalyn Shires, South Dakota State University; Damon Smith, University of Wisconsin-Madison; and  Albert Tenuta, Ontario Ministry of Agriculture, Food and Agribusiness

Reviewers

Tom Allen, Mississippi State University; Alyssa Betts, University of Delaware; Mandy Bish, University of Missouri; Maira Duffeck, Oklahoma State University; Travis Faske, University of Arkansas; Horacio Lopez-Nicora, The Ohio State University; Dean Malvick, University of Minnesota; Boyd Padgett, LSU AgCenter; Alison Robertson, Iowa State University; Adam Sisson, Iowa State University; Darcy Telenko, Purdue University; and Richard Wade Webster, North Dakota 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.