Early Season Disease Scouting

(Updated: April 13, 2026, 8:26 a.m.)
Soybean seedlings

Early Season Disease Scouting

While the spring is a busy time of the year for growers getting their crops in the ground, it can also be a busy time for pathogens that infect newly emerging seedlings. There are several seedling diseases that can reduce plant stand and ultimately reduce yield in severe cases.

Common seedling diseases of corn include Pythium Seedling Blight, Fusarium Root Rot, and Rhizoctonia Seedling Blight. Soybean seedling diseases include these same three, with the addition of Phytophora Root Rot.

Disease Profiles

  • Pythium Seedling Blight: Caused by Pythium spp. which is a fungal-like organism known as an oomycete. This disease is characterized by poor root development and seedlings becoming mushy and rotten. Oomycetes are also known as “water molds”, which given the name, indicates these pathogens thrive in water. Conditions that favor the development of Pythium Seedling Blight are often cool, poorly drained soils, however some species of this pathogen can survive in warm, saturated soils as well.
  • Fusarium Root Rot: Caused by the fungal pathogen Fusarium spp. This disease is characterized by poor root development with dark-colored patches, yellowing discoloration of cotyledons, wilting, and damping-off. When a seedling is experiencing damping-off, it often shows symptoms such as girdling of the stem where it looks thin and thread-like or the seed fails to emerge at all. Fusarium Root Rot is most likely to occur during stressful conditions and is not restricted to young plants.
  • Rhizoctonia Seedling Blight: Caused by the fungal pathogen Rhizoctonia solani. This disease is characterized by damping-off and seedlings having reddish-brown, sunken in patches around the stem at soil level. Rhizoctonia Seedling Blight is most likely to develop in warm, moist field conditions with plants already experiencing stress and is not restricted to young plants.
  • Phytophthora Root Rot: Caused by the fungal-like pathogen Phytophthora spp., which is another oomycete. Seedlings experiencing symptoms of Phytophthora Root Rot often have mushy stems, which lead to wilting. Conditions that are most likely to favor Phytophthora Root Rot include warm, saturated soils.

Management

Because these pathogens produce structures that allow them to overwinter in crop residue and pathogens such as Rhizoctonia solani and Fusarium spp. have a wide host range, which allows them to infect several types of crops, crop rotation may not always be effective. The use of a fungicidal seed treatment can help protect the seedling from disease, but keep in mind not every seed treatment protects against all seedling diseases. Scouting and documentation of field history is essential for seed treatment selection. Planting practices such as seeding rate, seed depth, and planting during optimal conditions can help the seedlings emerge and establish stands quickly. An integrated approach is the best option when working to mitigate disease risk.

Sources:

https://content.ces.ncsu.edu/north-carolina-organic-commodities-production-guide/chapter-3-crop-production-management-corn#:~:text=Corn%20generally%20requires%20from%20120,for%20a%20nutrient%20management%20plan.

https://cropprotectionnetwork.s3.amazonaws.com/scouting-for-soybean-seedling-diseases-filename-2021-02-09-124605.pdf

https://content.ces.ncsu.edu/soybean-seedling-diseases

https://cropprotectionnetwork.org/encyclopedia/seed-decay-and-seedling-blight-of-corn