Stem CankerStem Canker. This 8-page, full color checkoff-funded publication is a comprehensive guide to recognizing and managing stem canker of soybean.


Stem canker is a disease of soybean in the United States and Canada where infections occur primarily on the lower portion of the stem. Multiple fungi in the genus Diaporthe cause the disease. However, identifying and managing stem canker is similar regardless of which fungus is involved.

There are similarities between symptoms of stem canker and other late season diseases, such as white mold or Phytophthora stem rot. Field symptoms of stem canker also look like early crop maturity. Because of these similarities, stem canker can be easily misdiagnosed. Growers and scouts should become familiar with and be able to distinguish among these late season diseases and conditions.

View Soybean Stem Canker: Re-emerging? webcast on the Plant Management Network website.

  • Scouting

    Scouting Stem Diseases


    Although infection probably only occurs in the early vegetative stages of soybean development, infections are generally symptomless until plants reach the reproductive stages of flowering and pod development. Some researchers report small reddish lesions on cotyledons. Early infection may spread into the stem, causing seedlings to wither and die. Seedlings may also die before emergence.


    Fields with a notable incidence of stem canker may be detected at any time from flowering to well into pod set and development. This usually is sometime from late July onward. In South Dakota, stem canker fields are typically reported in mid- to late August. At this time canker expansion and plant death may be rapid.

    Fields should be checked every two weeks from beginning pod fill to harvest maturity for the presence of stem canker. Stem canker may appear at low levels ( ‹ 1% incidence) without being noticed; however, when incidence is higher, symptomatic plants are easily noticed.

    Symptoms Plants with stem canker are often first noticed in field areas where the crop stand is thin. An infected plant will have one brown, slightly sunken lesion at the base of a branch or a leaf petiole on one side of the stem. The lesion expands along the stem and sometimes severely girdles it. Branches on the upper part of the plant can be killed, and the dead plants are most visible after the R3 stage.

    Scout for stem canker in the late season by looking for plants on which blacked leaves remain. These plants stand out against the background of healthy plants that have matured and undergone leaf drop. Inspect these “black leaf” plants for lesions and fruiting bodies (stroma) of the fungus at the lower nodes.


    From a distance, fields with stem canker may be mistaken for other diseases such as white mold or Phytophthora stem and root rot. For example, lesions can be found at the soil line, making it possible to confuse this disease with Phytophthora stem and root rot. In this case, pull out infected plants to examine the roots. The stem canker pathogen does not cause root rot, while Phytophthora does. Individual plants must be examined closely in order to confirm stem canker.

    For a complete discussion and comparison of symptoms of important late-season soybean diseases (stem canker, brown stem rot (BSR), Phytophthora stem and root rot (PRR), white mold, and Sudden death syndrome) please see Stem Canker, CPN 1006, 2015.

    If you are unsure about the diagnosis, seek assistance from an Extension educator, agronomist, or your state university Plant Diagnostic Clinic.

  • Symptoms

    Soybean stem canker showing late symptom expression of withered leaves that remain attached and green tissue both above and below the infected region. Photo: University of WisconsinClick on image to view a larger version.

    Early symptoms of stem canker include slightly sunken, reddish-brown lesions usually at the base of lower leaf or branch nodes. They are usually seen during reproductive growth, long after infections have occurred during early vegetative growth.

    Eventually the expanding canker may girdle the main stem, causing the plant to wilt and die. A diagnostic symptom of stem canker is green stem tissue present both above and below individual stem cankers. Brown discoloration may also develop inside the stem.

    Toxins may be transported to foliar tissue, causing an intervienal necrosis very similar to foliar symptoms of Brown stem rot or Sudden death syndrome.

    Lesions may occur at the soil line, making it possible to confuse this disease with Phytophthora stem and root rot. Stem canker, however, does not cause root rot, and the lesions lengthen down the stem. Lesions caused by the Phytophthora fungus begin on the roots and elongate up the stem.

    Disease Cycle

    Infection by the stem canker pathogen takes place early in the season on plants in the early vegetative growth stages. Rain-splashed ascospores and possibly conidia from the soil act as the primary inoculum. Warm temperatures during wet weather is optimum for disease development.

    Infection appears to be highly dependent on the timing of rainfall early in the season to provide a rain splash mechanism for infection. Researchers in South Dakota have observed that even when high levels of the pathogen occur in surface residue in no-till fields, infection did not occur in the absence of rainfall. In some cases, stems at the soil line may be infected directly from the fungus in the soil.

    The fungus survives as mycelium (vegetative tissue, called stroma) and as clusters of long-necked, black fruiting bodies (perithecia) on infected residue on or in the soil for many years. This may explain why fields that have not been planted to soybeans for years can still develop a high level of stem canker when soybeans are re-introduced to the rotation.

    The stem-canker fungus can also survive in infected seed. Levels of seed infection are thought to range from 10 to 20%, and may be an important source of long-range dissemination of this fungus.

  • Agronomic impact

    Soybean stem canker showing late symptom expression

    Yield loss from stem canker can approach 50 percent on susceptible cultivars under favorable conditions. Stem canker can cause premature death of soybeans in large areas of the field. These plants often have fewer and smaller seeds.

    The impact on yield is greatest when plants are infected early in the vegetative stages and weather is conducive for disease development. Infections that occur during reproductive stages often affect yield less.

    Soybeans with partial resistance to stem canker must be infected very early in the season for extensive yield loss to occur.

  • Risk Assessment

    Factors that favor the development of stem canker are

    • Field history: fields that have experienced stem canker are at high risk for outbreaks when planted again to soybean because of the pathogen's ability to survive for long periods in soil and residue. You can reduce disease development by planting fields with a history of stem canker last.
    • Tillage: infected soybean residue left in no-till or conservation tillage fields supports the survival of the stem canker fungus.
    • Fields high in soil organic matter or with high fertility are at increased risk for disease. Maintain adequate fertility to reduce disease impact.
    • Susceptible soybean variety planted
  • Management

    Stem Canker

    The best way to manage stem canker is to plant resistant soybean varieties, although resistance may not be available for early season varieties. Consult your seed dealer for current information about varieties with stem canker resistance.

    Rotating crops to a nonhost is recommended to reduce the amount of inoculum available to infect the next soybean crop. Rotate soybeans with a nonhost such as corn, wheat, and sorghum for at least two years after a severe disease infestation. If stem canker is severe, avoid rotating the field with alfalfa, which is also a host.

    • Plant high-quality, certified seed that is disease-free and has a high germination rate
    • There is not yet sufficient data regarding the efficacy of foliar fungicides for the management of stem canker (see NCERA-137 Fungicide Efficacy for Control of Soybean Foliar Diseases 2017) However, seed treatments may be effective. See Fungicide Efficacy for Control of Soybean Seedling Diseases 2017.
    • Plant in a warm, fertile, well-prepared seedbed to promote vigorous seedling growth
    • Maintain good soil fertility based on soil tests.
    • Harvest as soon as the crop is mature. When harvest is delayed under wet conditions, seeds may be infected throughout the plant
    • Bury infected crop residue after harvest, where soil erosion is not a problem. Do not use seeds from an infected crop

    Source: Stem Canker (Disease Management Series CPN 1006)

  • Resources

  • Photo Gallery

    soybean aphid

    Stem Canker

    Symptoms of stem canker on a soybean stem

    Without closer examination, stem canker might be easily misdiagnosed as white mold or other disease based on general field appearance.

    Symptoms of stem canker on soybean plants

    Close-up of stroma of Diaporthe on a soybean stem. Stroma are compact masses of fungal hyphae which the fungus forms as a means of survival. Perithecia will arise from stroma given appropriate levels of moisture.

    Perithecia (fruiting bodies) on a naturally-infected soybean stem incubated in a moist chamber.

    Stem Canker