Soybean Diseases

Brown Stem Rot


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. BSR 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

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.


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.
  • It 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.
  • 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.

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.


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.

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


Information and photos on this information page has been provided by Crop Protection Network. For information about Brown Stem Rot, and other soybean diseases or pests, visit our resource page at: