Soybean Disease Update

Soybean Disease Update

In 2018 an array of weather conditions led to the development of several soybean diseases. Excessive early season moisture and heavy rains during the season resulted in many fields being impacted by Phytophthora root and stem rot. Frogeye leaf spot developed early in some areas and continues to build in the state with more fields being affected. Below is a summary of some of the most common diseases of soybean in 2018. Additional information on disease identification can be found at the UNL CropWatch website in the Plant Disease Management Section.

Early Season Diseases

Several pathogens are involved in damping off seedling diseases. The most common in Nebraska are Fusarium, Phytophthora, Pythium, and Rhizoctonia. All four are capable of killing the developing soybean seedling or causing damage that affects the plant’s ability to achieve its full yield potential.

The following criteria can help you assess the use of seed treatment fungicides to manage seedling disease problems. (If these conditions are part of your production system, your risk is greater.)

  • History of a stand problem
  • No-till
  • Early planting date when soils are cool
  • Poor seed quality

Phytophthora Root and Stem Rot (Phytophthora sojae)

Phytophthora root and stem rot of soybean are caused by a soilborne fungus that is present in many Nebraska soybean fields. The pathogen survives primarily as “resting” spores in the soil or in association with infested crop debris. Disease development is favored at soil temperatures of 60oF and high soil moisture. We have observed that dry conditions followed by heavy rain events can result in higher amounts of Phytophthora. This is most likely due to the higher soil temperature and plants being slightly stressed. It is most common in low areas of a field, in poorly drained or compacted soils, and in soils with high clay content, although it is not limited to these sites or conditions. It also may occur on well-drained hillsides during wet growing seasons.


Symptoms associated with Phytophthora sojae infections include seed rots, pre- and post-emergence damping off of seedlings, and stem rot of plants at various growth stages. The stem rot phase is easily identified by the dark brown color on the exterior surface of the stem and lower branches. Discoloration of the stem extends from below the soil to 6 inches or more above the soil line. The taproot turns dark brown and the entire root system may be rotted. Leaves on older infected plants become chlorotic between the veins followed by general wilting and death. Leaves remain attached.

Management of Phytophthora Root and Stem Rot

  • Genetic Resistance. Use resistant varieties. A combination of good partial resistance and an Rps gene are recommended. Partial resistance alone will not be as effective during early growth stages or under high disease pressure
  • Cultural Practices. Anything that can be done to improve soil drainage will reduce disease pressure.
  • Seed Treatment Fungicide application. Seed treatment fungicides containing mefenoxam or metalaxyl should be used. A higher rate may be necessary for Phytophthora control versus Pythium control.

Frogeye Leaf Spot (Cercospora sojina)

Frogeye leaf spot is a fungal disease that is becoming more common in Nebraska. Yield loss estimates due to frogeye leaf spot have been reported as high as 30% nationally with extensive leaf blighting, but for Nebraska loss would be estimated at less than 20% loss in highly susceptible varieties. The disease is most severe when soybean is grown continuously in the same field, particularly in fields where tillage is reduced, since this is a residue-borne disease. The primary source for this disease is infested residue, infected seed, and airborne spores. In areas where this disease has been observed in past years, it will typically show up again if weather conditions are favorable.


Infection can occur at any stage of soybean development, but most often occurs after flowering and is typically in the upper canopy. Initial symptoms are small, dark spots on the leaves. Spots eventually enlarge to a diameter of about ¼ inch and the centers of the lesions become gray to brown and have a reddish purple margin. Individual leaf spots can coalesce to create irregular patterns of blighting on the leaf. In addition, stems and pods can also be affected. Stem infections appear later in the season and are long, narrow, dark lesions with flattened centers. Pod lesions are circular to elongate, slightly sunken, and reddish brown in color.

Management of Frogeye Leaf Spot

  • Resistance. Soybean varieties vary in their resistance to Frogeye leaf spot.
  • Cultural Practices. More severe in continuously cropped soybean fields.
  • Fungicide application. Application of fungicides to manage frogeye leaf spot in Nebraska is typically not warranted in most fields. Fields with a history of frogeye should be watched carefully and if disease develops, a QoI (strobilurin) fungicide should be applied at the R3 (pod set) – early R4 growth stage. Fungicide resistance can occur to QoI fungicides. Using products with mixed modes of action will reduce the risk of developing resistance.

Soybean Cyst Nematode (Heterodera glycines)

Soybean cyst nematode is the most damaging pathogen of soybean in North America. The nematode can cause substantial yield loss when not managed and can worsen some other diseases of soybean. Soil sample analysis is the only way to confirm the presence of the nematode.


Soybean cyst nematode may cause up to 30% yield loss with no other visible symptoms. When symptoms are present, they often appear in smaller patches in the field and may include yellowing, stunting, and reduced canopy closure. Tiny, white to yellow lemon-shaped female nematodes may be observed with the naked eye on roots during mid-season.

Management of Soybean Cyst Nematode

  • Resistance. Many resistant cultivars are available, although 90-95% come from PI 88788 which is becoming less effective as nematodes adapt. It’s now recommended to test soybean cyst nematode populations by sampling at least every six years to monitor population changes as an indicator for reproduction on soybeans with PI 88788. In Nebraska, almost half (47%) of the populations were capable of reproducing on PI 88788 when last tested. It’s recommended to occasionally rotate to a different source of resistance, such as Peking (PI 548402) or Hartwig (PI 437654).
  • Cultural Practices. Crop rotation to non-host crops (corn, grain sorghum, alfalfa, or small grains) helps to slow population increases.
  • Weed Management. Soybean cyst nematode can infect several annual weeds, such as henbit, purple deadnettle, and field pennycress) and lead to minor population increases, so management of these species may help slow nematode reproduction.
  • Nematicides. Several seed treatment nematicides are available and may help to protect seedling plants from nematode infection for their first few weeks, possibly resulting in a yield increase. Although, nematodes may continue to increase later during the season.

Late Season Diseases

Anthracnose Stem Blight (Colletotrichum truncatum)

Anthracnose stem blight is another fungal disease that developed late in 2018. The disease is rarely a threat to yield and often develops just prior to harvest. Warm and wet weather favors disease development. The pathogen overwinters in infested crop debris or in seed. Infection that occurs at flowering or soon thereafter during early pod development can become severe and yield limiting.


Red to dark-brown lesions with irregular shapes may appear on petioles and stems during the early reproductive stages. Infected petioles may become defoliated and cause yield loss. Leaf infections may lead to red discoloration of veins, leaf rolling, and defoliation. As plants mature, black fungal reproductive structures may develop on stems, late in the season between R5-R7. Under magnification, these structures’ pointed black spines and spores may be visible. Seed may or may not have visible symptoms.

Management of Anthracnose Stem Blight

  • Resistance. Soybean varieties vary in their susceptibility, but there are no known sources of resistance.
  • Seed Quality. Use high-quality, certified seed when available, to manage Anthracnose stem blight.
  • Cultural Practices. Crop rotation with non-legume species and tillage may help to reduce survival of the fungus and disease pressure during the subsequent year(s).
  • Fungicides. Fungicides are usually unnecessary, but are available and should be applied during the early to mid-reproductive stages for best efficacy, as needed.

Pod and Stem Blight (Diaporthe sojae)

Pod and stem blight disease is part of the Diaporthe disease complex, which also includes Phomopsis seed decay and stem canker. Although infection may occur earlier in the season, the disease is often not evident until late season. Warm, humid conditions near plant maturity favor development of the disease, especially in early maturing cultivars. Likewise, delayed harvest may lead to more severe disease, as was observed during fall 2018 when very wet conditions delayed harvest.


Most parts of the plant can be infected (except the leaves), including the leaf petioles, nodes, pods, and seed. The most diagnostic characteristic of the disease is the development of small, black fungal pycnidia in distinct rows on infected stems. Symptoms are best observed late season during R6-R8. Planting infected seed can lead to disease development in seedling plants that can develop reddish-brown lesions and with rotted or deformed buds.

Management of Pod and Stem Blight

  • Resistance. There is no resistance to the disease, although planting a later maturing cultivar will reduce the chances of developing disease.
  • Seed Quality. Do not plant seed with a high incidence of infection (whose germination rates are reduced).
  • Cultural Practices. Crop rotation to a non-host crop (corn or small grain) or tillage may help to promote degradation of infested crop debris.
  • Fungicides. Foliar fungicides applied near R5 stage may help to reduce infection, but may not have an impact on yield.

Cercospora Leaf Blight and Purple Seed Stain (Cercospora kikuchii)

Although Cercospora leaf blight is common in the southern states, the disease is becoming increasingly common in northern U.S. states and can cause substantial yield loss. Purple seed stain is caused by the same fungus and can cause seed-quality issues and impact the marketability of food-grade soybean.


Cercospora leaf blight symptoms usually begin developing on the leaves and petioles during seed set. Dark red lesions begin in the upper canopy on the petioles and purple to bronze discoloration occurs on upper leaves that are exposed to sunlight. Affected leaves may develop a leathery feeling and defoliate under severe disease pressure, leaving bare petioles. Purple seed stain symptoms may be pink to purple small or large spots on seed coat surfaces, or seeds may have no symptoms at all.

Management of Cercospora Leaf Blight and Purple Seed Stain

  • Resistance. Some commercially available cultivars are available with resistance to Cercospora leaf blight, but there are no known sources of resistance to purple seed stain.
  • Cultural Practices. Rotation to non-host crops (corn, alfalfa, or a small grain) and tillage to bury infested crop debris and promote degradation.
  • Fungicides. Fungicides applied during the pod-fill stages may reduce Cercospora leaf blight, but the pathogen may be resistant to some fungicides, especially QoI (formerly known as strobilurins). Applications at this time also may reduce the incidence of purple seed stain.

Charcoal Rot (Macrophomina phaseolina)

Charcoal rot is more common in non-irrigated fields during times of drought stress. The disease can develop in plants growing in areas prone to drought stress, such as on the tops or sides of hills, non-irrigated pivot corners, compacted areas, sandy areas, or near trees at field edges. The fungus causing charcoal rot has a wide host range and disease may develop in several other species, such as corn, grain sorghum, sunflower, and alfalfa.


Patches of affected plants may yellow or wilt in the field and eventually die. The fungus causing charcoal rot produces copious amounts of tiny black survival structures inside infected stems and roots. Microsclerotia give the tissue the discolored appearance of charcoal dust for which the disease is named, although they may not be visible until plant death or maturity. Symptoms may be more severe in the presence of soybean cyst nematode.

Management of Charcoal Rot

  • Resistance. Resistance is limited in varieties adapted for northern climates (MG 0-III).
  • Cultural Practices. Soybeans produced in no-till systems tend to have less charcoal rot than those in conventional tillage. Irrigation can offset disease pressure by reducing moisture stress, although the fungus can still infect plants under irrigation. Crop rotation with a non-host, like wheat, for one to two years can reduce overwintering inoculum.
  • Nematode Management. Managing soybean cyst nematode will help to reduce the severity of charcoal rot.

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