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Phytophthora Infection in Soybeans and Management Options


While soybean farmers face different soil types and growing conditions, many share the common challenge of controlling Phytophthora root and stem rot. Phytophthora sojae is a destructive soybean pathogen that can be a major cause of stand establishment problems.

Phytophthora root and stem rot not only damages seedlings, but it can also harm plants throughout the growing season until just before harvest. Phytophthora tends to present itself when there are wet and warm soil conditions early in the growing season. Seeds and seedlings can be infected and killed any time after the seed has absorbed moisture. Later in the season following periods of heavy rain, Phytophthora infects and kills soybeans by causing stem rot or chronic root rot.

Soils warmer than 60°F and flooded or saturated clay soils are optimal conditions for infection. Clay and compacted soils along with poorly drained areas also tend to trigger the disease. Phytophthora infection is most common in fields with poor drainage, but it also occurs in well-drained fields if the pathogen is present and the soils are saturated for 7 to 14 days due to heavy rain or irrigation. 

Stem and root rot phase

When Phytophthora strikes early in the season, it attacks and kills seedlings in the ground or soon after emergence. Infected stems typically appear bruised and are soft. Leaves often turn yellow and brown, and some plants may wilt and die. However, some plants can be infected early in the season and not show severe symptoms until later in the summer.

Look for Phytophthora infection following rainy periods later in the season. Tell-tale signs usually include brown lesions on roots, along with a dark chocolate-brown discoloration of the stem that frequently extends from below the soil line upward into lower parts of the plant. Soybeans diseased by Phytophthora tend to die in patches or in sections of rows. 

Phytophthora root rot phase is not as easily recognizable as its stem rot phase. Infected plants can be stunted and less vigorous, but this is hard to spot unless the infected plants are near a healthy comparison. Often you will see a general severe wilting of the plant, which can look gray-green from a distance. This is known as “Shepherd's Crook” since you are seeing the undersides of the leaves as they droop. The condition can be confused with herbicide injury since symptoms commonly run down a row for some distance rather than appearing in a circular area, which is how many diseases express themselves within a field. 

When scouting, you are most likely to find the disease in the following places:

  • Low and wet spots in a field
  • Fields with high clay content
  • Fields that have been in no-till for a few years
  • Weedy areas that may be the result of stand reduction earlier in the season


  • Stem canker: The symptoms of Phytophthora can look similar to stem canker. However, one way to distinguish between the two is to check whether the diseased plants have root rot. Stem canker does not cause root rot, only stem lesions. 
  • Flooding: Flooding injury can also be mistaken for Phytophthora. If damaged by flooding, the root’s outer area can easily be pulled off, leaving a “rattails” look.


During the growing season, management options are severely limited since measures must be taken during the planting season to protect against the disease. If Phytophthora is present in your field now, begin planning your management options for next season as the disease is likely to appear again. By looking ahead to planting, you can prevent Phytophthora from damaging more of your soybeans.

  1. Plant resistant varieties: In areas with a history of Phytophthora, plant resistant varieties that contain built-in tolerance. When Phytophthora-tolerant varieties are selected, plants are more likely to be stunted rather than killed, and yield damage will not be as severe. There are 2 types of genetic resistance. Single-gene resistance is very specific to particular races with the most common being Rps1a, Rps1c, Rps1k, Rps3a, Rps6 or a combination of these. Field tolerance levels will vary with all resistance genes.
  2. Use quality seed treatments: At planting, your local Golden Harvest Seed Advisor can determine specific seed treatments that fit your field’s needs. Higher usage of seed treatments can reduce Phytophthora early in the season, but they may offer little help against the stem and root rot phase of infection later in the season. 
  3. Improve soil drainage: This is one of the most important control measures since well-drained fields dramatically reduce the incidence of the disease. Increase drainage and avoid soil compaction to create a field environment that reduces the likelihood of saturated soils.
  4. Rotate crops: Crop rotation will not eliminate the disease since it can live in the soil for years. However, planting soybeans continuously will increase the inoculum levels in the soil and increase the disease pressure.

Contact your local Golden Harvest Seed Advisor with questions or for additional agronomic insights.

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