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Soybean seed and seedling diseases

Seed and seedling diseases of soybean are common and significant problems. They can decrease plant populations that result in replanting and production losses. Several different pathogens can cause these diseases, and the most common tend to be FusariumRhizoctoniaPhytophthora, and Pythium. They can kill and rot seeds before germination or cause seedling death. They are most common when soil is very wet in the first few weeks after planting and in heavy, poorly-drained soils.


Evidence of seed and seedling diseases is usually seen when seedlings don't emerge or they die or are stunted. Infection and damage prior to emergence is common but difficult to identify. Factors other than disease can also cause these problems, so it is important to look closely to determine the cause(s). Different seedling diseases may cause different symptoms, but similarities can make them difficult to distinguish.

Phytophthora can attack and rot seeds prior to emergence, and can cause pre- and post- emergence damping off. It produces tan-brown, soft, rotted tissue. At the primary leaf stage (V1), infected stems appear bruised and soft, secondary roots are rotted, the leaves turn yellow, and plants frequently wilt and die.

Pythium can attack and rot seeds and seedlings prior to emergence and can cause post-emergence damping-off under wet conditions. The characteristic symptom of most Pythium infections is soft, brownish-colored, rotting tissue. Thus, Pythium causes symptoms similar to Phytophthora in seedlings, and can only be distinguished by laboratory examination. Although Pythium causes most damage to seeds and seedlings, roots of established plants can be rotted and plants may be stunted.

Rhizoctonia can damage seeds and plants prior to or after emergence. In seedlings and older plants, a firm, rusty-brown decay or sunken lesion on the root or on the lower stem is a characteristic symptom. The infections can be superficial and cause no noticeable damage, or they can girdle the stem and stunt or kill plants.

Fusarium is also a common pathogen that can damage seeds and seedlings. It causes light to dark brown lesions on roots that may spread over much of the root system and may appear shrunken. Fusarium may attack the tap root and promote adventitious root growth near the soil surface and may degrade lateral roots.

For more information, see the sections on Phytophthora root and stem rotRhizoctonia root and stem rot, and Fusarium root rot.

Conditions and timing that favor disease

General conditions that promote seed and seedling disease diseases include wet, poorly-drained, and compacted soils. However, the different pathogens have different optimal conditions. For example, Phytophthora and Rhizoctonia are favored by wet and warm soils, whereas Pythium is typically favored by wet and cool soils. Seed and seedling diseases may be enhanced by slow germination and growth of soybeans, poor quality seed, and plant stress.

Causal pathogen

  • Most of the important seed and seedling diseases of soybeans are soilborne, although the role of seedborne inoculum is not well understood. They are spread primarily with soil and water, but can also be spread with dirty seed. Most are probably indigenous soil inhabitants in soybean fields. They can generally survive for long periods in the soil, often associated with plant debris.
  • The most important pathogens involved in seed and seedling diseases of soybeans in the Midwestern U.S. are fungi or fungal-like organisms: Fusarium spp, Rhizoctonia solaniPhytophthora sojae, and Pythium spp. In some situations and locations, other soilborne or seedborne pathogens that may be important include MacrophominaColletotrichum, and Phomopsis.
  • Phytophthora sojae is a fungal-like pathogen that survives in soil for up to five to 10 years in association with decomposed soybean tissues. Soybean is the only known crop host for this pathogen. It is favored by saturated, warm soil.
  • Pythium is a soilborne, fungal-like pathogen. Several different species damage soybeans. The various species of Pythium that infect soybean have a wide host range that can include corn and many other crops. Pythium tend to be favored by cool and soil, but some species may do more damage in warm soils.
  • Rhizoctonia solani is a common pathogen with a wide host range. The most common strains of this pathogen (anastamosis groups, AG) that infect soybean are AG-2-2 and AG-4. AG groups can have different optimal conditions for infection.
  • Fusarium seed and seedling blight of soybean is caused by a complex of different species that may prefer different conditions. For example, some species may prefer warm and dry soils and others may prefer cool and wet soils. Some Fusarium species may also have a broad host range that includes corn and wheat.

Disease management

Seed and seedling diseases of soybean are difficult to manage, and the different pathogens and diseases require different management approaches. Thus, accurate diagnosis can help in managing them.

In general, these diseases can be reduced by planting good-quality seed in well-drained, non-compacted fields. Delaying planting until soils are warmer than 55 degrees F and relatively dry to allow for rapid emergence and growth can be beneficial. Crop rotation and tillage may be of some benefit. Genetic resistance in soybean varieties is only clearly available for managing Phytophthora infections.

Fungicidal seed treatments may reduce seed and seedling diseases. Seed treatments with two or more active ingredients should typically be used. For example, products containing mefenoxam (ApronXL®) or metalayl (Allegiance®) can be effective against Pythium and Phytophthora, and products containing fludioxonil (Maxim®) or a strobilurin product (azoxystrobin, trifloxystrobin, or pyraclostrobin) may help to reduce damage from true fungi such as Fusarium and Rhizoctonia.

Dean Malvick, Extension plant pathologist

Reviewed in 2018

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