Brown Stem Rot

Internal browning, seen on the stem on the left, is diagnostic for brown stem rot. Photo: University of Wisconsin


Brown stem rot (BSR) is a major disease of soybean and is widely distributed in soybean fields throughout the North Central region. The increase in the incidence of BSR is thought to be a result of shorter rotations between soybean and corn, which encourages a build-up of the brown stem rot pathogen.

Brown stem rot is caused by the fungus Phialophora gregata. The fungus survives mainly on crop residue left on the soil surface. In the spring, spores are produced that infect soybean roots.

The pathogen eventually reaches and invades the vascular system of soybean plants, and impedes the movement of water and nutrients needed for growth. Internal browning of the stem (see photo) is diagnostic for brown stem rot.


  • Agronomic impact

    Brown Stem Rot

    Late season soybean field with symptoms of BSR. Photo: University of Wisconsin

    Yield losses to BSR of 10-30% are common. BSR may reduce both seed number and seed size. Severely diseased plants may wilt, defoliate prematurely and lodge more readily than non-infected plants.

    Yield loss is greatest in cultivars with a longer relative maturity and if foliar symptoms as well as stem symptoms are present.

  • Scouting

    Brown Stem Rot

    Cut stems longitudinally in several places at full pod stage to check for internal browning (left), compared to white healthy stem (right). Photo: Dean Malvick, University of Minnesota

    Recognizing brown stem rot isn't easy. Symptoms are usually not evident until late in the growing season, and are often confused with early crop maturity or the effect of dry soils.

    At the full pod stage, cut stems longitudinally in several places, and check for a chocolate-brown discoloration in the pith, especially at and between nodes near the soil line. Initially the discoloration may only be found at the nodes, but it becomes continuous through the stem as the plant ages and cool temperatures prevail.

    BSR often causes only internal stem browning and a general mild necrosis, wilting or premature maturation and defoliation of infected plants. Foliar symptoms (browning between the leaf veins) are seen only sporadically.

    Brown stem rot can be mistaken for sudden death syndrome or stem canker because these diseases cause similar leaf symptoms. However, root and stem symptoms differ among the three diseases.

    Table 1. Comparison of the signs and symptoms of brown stem rot, sudden death syndrome, stem canker.

    Plant Part BSR Stem Canker SDS
    Roots Healthy Healthy Root Rot
    Exterior Stem Healthy Dark, Reddish-Brown Sunken Canker Starting at Node Healthy
    Interior Stem Brown Pith (center) Slight Browning at Nodes to Completely Deteriorated Stems White, Healthy Pith
    Leaves No Symptoms or Yellowing Between Veins General Yellowing of Leaves Yellowing Between Veins Similar to BSR

    Adapted from: Agronomy Guide for Field Crops (Soybeans: Brown Stem Rot, Stem Canker and SDS) Ontario Ministry of Food and Agriculture.

  • Symptoms

    Brown Stem Rot

    Browning between the leaf veins is also a classic BSR symptom. However, it does not always occur in infected plants. Photo: University of Wisconsin

    Recogizing brown stem rot is a major problem. There are no symptoms of brown stem rot until after pod development begins. At that time, internal stem browning is evident in infected plants if the stems are split longitudinally. This is a diagnostic symptom of BSR.

    Wilting, premature defoliation and lodging may also occur. These symptoms are heightened when infected plants are subjected to drought stress.

    The internal browning and infection can be severe in the absence of foliar symptoms. However, yield loss is generally greatest when foliar symptoms develop, compared to when symptoms are only evident inside stems.

    The factors that control symptom development are under study , and probably include host resistance, temperatures, soil moisture and different pathotypes of P. gregata.

    Foliar symptoms
    Although BSR occurs commonly in the North Central states, the classic foliar symptoms of browning between the leaf veins are seen only sporadically. If foliar symptoms do appear, it is late in the growing season and are often confused with early crop maturity or the effect of dry soils.

    Foliar symptoms may fail to develop if seasonal precipitation is below normal. When rain or irrigation follows flowering, foliar symptoms tend to be more severe in infected plants. Above-normal air temperatures are reported to suppress development of foliar symptoms.

    Look-alike diseases
    BSR may be mistaken for sudden death syndrome (SDS) or stem canker because these diseases show similar leaf symptoms. However, SDS has symptoms on both leaves and roots. BSR and stem canker do not cause root rot. The brown discoloration of the pith is also diagnostic for BSR, but not for SDS.

    BSR Pathotypes
    Pathotypes of P. gregata appear to vary in their pathogenicity. Two types have been distinguished genetically and in the severity of diseases they cause. Pathotype "A" (defoliating pathotype) causes more severe internal stem symptoms and defoliation than the other pathotype, called Pathotype "B" or "nondefoliating".

  • Risk Assessment

    Brown stem rot will have a greater negative effect on yield if temperatures are cool (64-75°F) in early August, followed by hot, dry weather during late pod-fill. Other factors that favor disease are short rotations, susceptible varieties, overwintered stem tissue, and the presence of SCN.

    Seasonal Risk Factors for BSR Long-term risk factors for BSR
    • Continuous soybeans
    • Susceptible soybean variety
    • Variety with long maturity
    • Short rotations
    • Low soil pH (less than 6.8)
    • History of brown stem rot
    • Virulent pathotype present
    • SCN present
    • Rain or irrigation following flowering
    • Cool air temperatures (less than 27°C)
    • Reduced tillage
    • No-till
    • Slow residue decomposition
    • Spread of soil from field to field
  • Management

    Brown Stem Rot

    Use BSR-resistant varieties together with crop rotation and residue management. Photo: University of Wisconsin

    Brown stem rot can be effectively managed with crop rotation, selection of resistant varieties, and residue management.

    • Rotate crops
      A minimum of two years between soybean crops in fields with a history of brown stem rot will effectively reduce pathogen populations and the risk of BSR. Corn, small grains and forage legumes are all good rotation crop choices. Soybean is the only host for the brown stem rot pathogen.

    • Plant resistant soybean varieties and rotate among resistant varieties
      Soybean varieties with some resistance to BSR are commercially available. However, the genetic source of brown stem rot resistance is limited. It is not recommended that growers rely only on resistant varieties, but use a combination of management practices to reduce the incidence and severity of this disease. Rotate soybean varieties to preserve the effectiveness of resistance genes.

      Early-maturing varieties may escape the yield reducing effects of brown stem rot in comparison to cultivars with later maturity or planting later in the season.

    • Manage residues
      Because the brown stem rot fungus survives mainly on crop residue left on the soil surface, decomposition of the residue is believed to be an important factor in managing this pathogen.

      In no-till systems, longer crop rotations and shredding soybean straw with a combine-mounted shredder are effective practices to reduce pathogen populations.

  • Resources

  • Photo Gallery

    Stem browning (left) is diagnostic for BSR. Photo: University of Wisconsin

    Stem browning caused by Philaphora gregata. Photo: University of Wisconsin

    Stem browning. Photo: University of Wisconsin

    BSR leaf symptoms.Photo: University of Wisconsin

    Early leaf chlorosis.Photo: University of Wisconsin

    BSR variety trials at the University of Wisconsin. Photo: University of Wisconsin

    BSR leaf symptoms. Photo: University of Wisconsin

    Late-season foliar symptoms. Photo: University of Wisconsin

    Late-season foliar symptoms. Photo: University of Wisconsin

    Late-season foliar symptoms. Photo: University of Wisconsin

    BSR variety trials at the University of Wisconsin.Photo: University of Wisconsin