Agronomy Alert: Seedling Diseases of Soybeans


This year has been full of challenges across the southern portion of Minnesota. We have been challenged with delayed plantings due to a late snowfall and excessive spring rains. It was a major push to put the crop in this season, and we are now seeing some issues across the state in our soybean fields due to the continued wet weather. While walking many soybean fields, I have seen more seedling diseases this year than in previous years. The most common diseases we are experiencing are pythium, phytophthora, and rhizoctonia.


Soybean seedling diseases are usually caused by fungal pathogens which can slow or kill soybean germination. A seed-applied fungicide will help suppress these diseases, but if the environment is favorable to these disease pathogens, the seed treatment will not guarantee complete control. We are most prone to seeing these diseases in soybeans when we are exposed to conditions favorable for diseases like cool or warm wet soils, especially in poorly drained or compacted soils. Once the disease is present in the field, it cannot be eliminated for the season. All you can do is manage the field in a way to minimize stress to the plant for the rest of the season. Examples of that would include foliar feeding, suppressing weeds, and adding a fungicide application.

Distinguishing the differences in seedling diseases:

Pythium Root Rot

  • Hypocotyl will appear rotted. Leaves of infected seedlings will turn brown before dying. Stems are soft and watery.
  • Common in wet, poorly drained, and compacted soils.
  • More common in cooler temperatures (50-60 degrees Fahrenheit).

Phytophthora Root and Stem Rot

  • Symptoms are very similar to Pythium infection.
  • Common in wet, poorly drained, and compacted soils.
  • More common in warm temperatures (80 degrees Fahrenheit).
  • Will also affect older plants throughout the year.

Rhizoctonia Root Rot

  • Localized reddish-brown lesions can be seen in the cortical layer of the main root or hypocotyl. Stems remain firm and dry.
  • Symptoms usually appear below the soil line.
  • Common in moist (but not standard) soil conditions.
  • Common in warm temperatures (80 degrees Fahrenheit).


Seedling diseases are very difficult to control once they have developed, so it is extremely important to use preventative control. This would include: using a fungicide seed treatment, avoiding planting when the soil conditions are less than ideal, and waiting to plant if a cool and rainy stretch of weather is on the horizon. Soybeans laying in wet soils for a week or more is the perfect storm for seedling diseases. Any factor that delays germination or emergence increases the chances of seedling diseases. Fungal diseases overwinter in residue, so tillage and crop rotation are both important in order to help suppress the seedling diseases.

Photo Credits: University of Minnesota Extension

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