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Common Soybean Diseases

  • There are multiple, common soybean diseases that may be encountered during a growing season, and many are described here with symptoms and some management tips.
  • When managing most soybean diseases, variety selection is a critical component.

Stem Canker

Stem canker is a disease in soybeans found widely where infections occur, resulting from multiple fungi in the genus Diaporthe. Diaporthe-Phomopsis disease complex is also responsible for Phomopsis seed decay, pod and stem blight as well as stem canker. The fungi can survive in residue or in the soil for several years. Seed infection can sometimes be responsible for spreading, but most often results from infested residue. There are also multiple weed species such as black nightshade, curly dock, morningglory and others that can serve as hosts for the disease, although they will not often show symptoms.

Infection requires extended periods of moisture and can occur across a wide range of temperatures. Fungus spores will splash on plant tissue from rain events and infect during early vegetative stages even though symptoms will not be visible until later reproductive plant stages.

Examples of Stem Canker disease in soybeans
(Left) Figure 1. Stem canker (Right) Figure 2. Stem canker zonal lines near canker lesion.


Correct diagnosis can be difficult due to multiple diseases that can cause similar symptoms. Key symptoms include:

  • Patchy, dead plants later in the season with dried leaves still attached to petioles.
  • Reddish-brown lesion spots that start small at base of stem branching and expand to form slightly sunken cankers – lesions may expand over several nodes or girdle stem, killing the plant (Figures 1 and 2).
  • Sometimes top dieback can occur when canker forms on upper 4-6 internodes, killing only the top of the plant.
  • Interveinal chlorosis and necrosis of leaves may occur, similar to sudden death syndrome and brown stem rot.

Pod and Stem Blight

Soybean pod and stem blight is caused by the Diaporthe-Phomopsis disease complex and is found throughout most soybean-producing areas of the U.S. Other common, associated diseases are Phomopsis seed decay and stem canker. This disease favors wet conditions for development and survives similarly to stem canker.

Close up of Stem Blight symptoms in soybeans
Figure 3. Stem blight.


  • The characteristic sign of pod and stem blight is the linear rows of black specks on the stem – these black specks are pycnidia, the fruiting structures that contain the spores for the fungal pathogen (Figure 3).
  • The pycnidia will only be present on plant tissue that is dead.
  • Pods may become infected showing scattered pycnidia too and will have infected seed – the infected seed will appear shriveled, cracked and have a white, chalky mold on it.
Table 1. Symptom expression summary table of soybean diseases.

Brown Stem Rot

Brown stem rot (BSR) is caused by the fungus Cadophora (Phialophora) gregata, of which there is an A and B genotype. Infection occurs through plant roots before colonizing vascular tissue, stems and leaves. Genotype A causes both stem and leaf symptoms. Genotype B usually only results in stem symptoms. Foliar symptoms are suppressed when temperatures are high, often making it difficult to determine the cause of dying plants. The BSR fungus survives in infected soybean residue, but unlike SDS, it doesn’t form any long-term survival structures.

Alt text: Brown stem rot symptoms in soybean leaf and stem.
(Left) Figure 4. Brown stem rot foliar symptoms (Right) Figure 5. Brown stem rot (left) healthy stem (right); Source: D. Malvik, Univ. of Minnesota.


  • Foliar symptoms have interveinal yellowing and browning of leaves similar in appearance to SDS (genotype A only) (Figure 4).
  • Dark, brown and discolored pith that extends from lower stem upwards, but sometimes appears only at nodes (Figure 5).
  • Diseased plants will retain leaves after death, whereas SDS-affected plants typically drop leaves rapidly.
  • Roots will not be affected, whereas SDS will show root infection.
  • Diseased plants often occur in clusters of individual plants among healthy plants.


  • Variety selection
  • Crop rotation
  • Burying residue via tillage
  • Managing soybean cyst nematode (SCN), if present

Sudden Death Syndrome

Sudden death syndrome (SDS) in soybeans is caused by Fusarium virguliforme, a soilborne fungal disease. It is one of the most significant disease pathogens impacting soybean performance. F. Virguliforme overwinters on crop residue and infects the plant’s root system early in the season, although symptoms rarely occur until late in the season after toxins from the disease begin to move up throughout the canopy. The risk of SDS infection is greatest when there is significant early season moisture followed by mid-summer rains saturating the soil. Poorly drained, compacted and SCN-prone soils are favorable for this disease.

Picture example of sudden death syndrome in soybeans
Figure 6. Sudden death syndrome.


  • Chlorotic spots between veins on the leaves begin to form in the uppermost canopy.
  • Yellow spots coalesce to form chlorotic yellow-brown interveinal leaf scorching similar to BSR (Figure 6).
  • Uniquely different from BSR, SDS-infected plant leaves fall off early and leaf petioles remain attached to the plant.
  • Lower stem infection will result in cortex (outside edge of split stem) turning gray-brown in color, while inner pith of stem remains a normal green-white appearance.
  • Fuzzy, powdery white or cobalt blue growth appearance on outer surface of roots can be observed under wetter soil conditions. Distinctly different from BSR, which does not affect roots.


Since infection occurs much earlier than actual symptoms, in-season fungicide applications have limited value, however there are multiple options for minimizing future infections:

  • Variety selection
  • Seed treatments such as Saltro® fungicide
  • Improving soil water drainage
  • Minimizing stresses such as compaction
  • Delay planting of high-risk fields until soils warm
  • Manage SCN
  • Harvest in timely manner

Charcoal Rot

Charcoal rot, also called dry weather wilt, affects soybeans throughout the U.S. and is caused by the fungal pathogen Macrophomina phaseolina.

Microsclerotia, the survival structures of the pathogen, overwinter on dry soil or infected plant residues. The disease infects the roots of soybean plants early in the growing season and remain latent until favorable conditions occur for disease development. Environmental conditions favorable for charcoal rot development are high temperatures and dry soil conditions during the reproductive stages.

Close up example showing charcoal rot in stems
Figure 7. Charcoal rot.


  • Appear as patches of stunted plants later in season after R1 crop stage.
  • Yellowing leaves followed by wilting and browning leaves that eventually die.
  • A unique identification key is that dead leaves remain attached to the plant, unlike SDS-affected plants that drop leaves but retain the petiole.
  • Lower portion of the stem and tap root will have a light gray or silver discoloration.
  • Tiny black specks of microsclerotia are visible on the outside as well as inside of lower stem and root with an appearance of fine charcoal powder sprinkles (Figure 7).

Management Tips

  • Select soybean varieties that are less susceptible to charcoal rot.
  • In fields with history of charcoal rot, avoid high populations to help conserve soil moisture and make sure fertility levels are adequate to reduce plant stress.
  • Crop rotation to small grains may help reduce inoculum, however corn is susceptible to charcoal rot and does not help to reduce infected residue.

Cercospora Leaf Blight and Purple Seed Stain

Cercospora leaf blight is caused by the fungus Cercospora kikuchii, a close relative of frogeye leaf spot. Warm, humid conditions of 80°F greatly increase fungal sporulation. The pathogen overwinters on crop residue and/or seed. Yield loss may occur if the disease infects leaves early in the season, but the loss is usually less than 10%. Seed discoloration may result in dockage in sale price if more than half the load is discolored.

Examples of cercospora (purple) seed stain
(Left) Figure 8. Cercospora leaf blight (Right) Figure 9. Cercospora seed stain.


  • Infection not usually visible until R4.
  • Leaf symptoms range from light purple small spots to larger, irregularly shaped patches on the upper surface (Figure 8).
  • Leaves develop a purple to bronze discoloration that can resemble a sunburn appearance on the uppermost leaves – the color will deepen and may take on a leathery appearance.
  • Infected pods often show a noticeable purple discoloration or staining of the seed; however symptomology may not be present even though seed is infected (Figure 9).


  • Rotating to crops other than soybeans and incorporating residue may help reduce inoculum and future disease.
  • Plant tolerant varieties
  • Consider an application of Miravis® Neo, Miravis Top, or Trivapro® fungicide at R1-R3 to help control Cercospora and consider a second application at R3-R5.

Frogeye Leaf Spot

Frogeye leaf spot (FLS), caused by the fungus Cercospora sojina, can be easily mistaken for other diseases or herbicide injury. There is a chance for significant yield impact from this disease when it appears during or just after flowering and favorable environmental conditions are present to allow continued development. Late-season occurrence (post-R5.5) usually has minimal yield impact. Frogeye leaf spot also has growing cases of resistance toward the Qol (Group 11) class of fungicides (strobilurins are the most well-known type in this class), making it imperative to be conscientious about fungicide choice and use.

Figure 10. Frogeye leaf spot.


  • Produces circular lesions, beginning as small, circular and dark watersoaked marks on the leaf tissue, but will become larger, more angular, and lighten in color throughout the season, fading from gray to brown to tan, and surrounded by a thin, purple margin (Figure 10).
  • Lesions may also be found on the pods and stems, where they will sometimes appear more oblong on pods and elongated on stems than on the leaves.
  • Tiny, dark fruiting bodies may be seen in the center of the spots.
  • Severe infection can cause premature defoliation.
  • Infection is most prevalent from R1-R7 (flowering through early maturity), mostly impacting the upper canopy of the crop, but can be seen in earlier growth stages.


  • Plant a Golden Harvest® soybean variety containing the Rcs3 gene, the only gene currently available that is resistant to all strains of the frogeye leaf spot fungus.
  • Residue management may help mitigate future impacts of a previously infected field.
  • Tillage and crop rotation may help break up and lessen overwintering host residues in the field.
  • Consider using a fungicide with multiple, effective modes of action, such as Miravis® Top fungicide, to help manage strobilurin-resistant FLS infections.

White Mold

Sclerotinia stem rot, more commonly called “white mold,” is a very common and widespread soybean fungal disease caused by Sclerotinia sclerotiorum. Losses from this disease may be extreme depending on the year and the amount of inoculum in the soil. White mold infections occur at flowering and thrive in saturated wet soils, high humidity and temperatures lower than 85°F. White mold symptoms aren’t prevalent until later in the season and may be harder to manage at that point in time. It is important to identify as early as possible to manage effectively.

Figure 11. White mold.


  • Gray-to-white lesions at nodes will later develop into fluffy white growth on soybean stems (usually developing R3-R6) (Figure 11).
  • Dark black sclerotia appear along the stem or bean pods.
  • Bleached or light-colored stems occur as soybeans become dry or die.
  • Dead brown leaves attached to stem are seen after severe disease progression.


  • Plant Golden Harvest soybean varieties with favorable Sclerotinia white mold ratings.
  • Improve air movement within canopy to minimize development by choosing varieties with upright growth, increasing row width and reducing seeding rates.
  • Consider crop rotation of 2-3 years to corn, small grains or forage legumes.
  • Control broadleaf weeds which can serve as alternate hosts.
  • If fields have a history of this disease or experience prime, consistent environmental conditions for disease growth, consider a fungicide application of Miravis® Neo or Miravis Top fungicide close to the R1 growth stage.

All photos are either the property of Syngenta or used with permission.


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