Soybean Disease Update

2020 Crop Production Clinic Proceedings

Soybean Disease Update

The 2019 growing season was difficult for many producers. Many fields experienced significant flooding, and those that didn’t were still indirectly affected. Plants under stress due to environmental factors, such as extreme temperature and moisture are more susceptible to disease, and many were under stress due to the unique environmental conditions in 2019. While most of Nebraska was relatively cool and wet throughout the year, certain areas of the state still experienced drought conditions. This wide range of weather conditions provided favorable conditions for development of several soybean diseases. The excessive rains early in the season led to many growers planting in less-than-ideal conditions which led to a range of root and stem rots. These cool, wet conditions at planting created ideal conditions for damping off and bacterial blight. Cool conditions during flowering resulted in white mold being a common problem. White mold is typically found in the northern part of the state, however this year it was detected into the south-central region. Frogeye leaf spot was a serious problem in some areas and continues to increase its spread across the state. While typically controlled well with QoI Fungicides (FRAC group 11), resistance to this fungicide mode of action was detected in Nebraska. Below is a summary of common soybean diseases of 2019. Additional information 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. Phytophthora, Pythium, Rhizoctonia, and Fusarium species are common in Nebraska and can kill developing soybeans, or cause damage that affects the plant’s ability to reach its yield potential. Pythium was common in 2019 due to cooler soil temperatures. It is difficult to distinguish these pathogens in the field and samples may need to be sent to the UNL Plant & Pest Diagnostic Clinic to determine which seed treatment fungicides are warranted (if any).

When assessing whether seed treatment fungicides should be used to manage seedling diseases consider:

  • History of stand or emergence problems
  • No-till
  • Early planting
  • Poor seed quality

Phytophthora Root and Stem Rot (Phytophthora sojae)

Phytophthora root and stem rot is caused by a soilborne pathogen that is present in many Nebraska fields. The pathogen primarily survives as dormant spores in the soil or in infested crop debris. Disease development is favored by soil temperatures above 60°F and high soil moisture. Dry conditions followed by heavy rain events can result in more disease development. This disease is most common in low-lying areas of the field, in poorly drained or compacted soils, and in soils with high clay content. However, it is not limited to these sites or conditions. During wet seasons, Phytophthora may occur on well-drained hillsides.


Symptoms associated with infection by Phytophthora sojae include seed rots, pre- and post-emergence seedling damping off, and stem rot at various growth stages. The stem rot phase is identified by a dark, brown/black discoloration that extends from below the soil line to 6 inches or more above the soil line. The taproot may be dark brown as it becomes rotted. Leaves on older, infected plants become chlorotic between the veins, followed by a general wilt and death. Dead petioles and leaves remain attached to the plant.

Management of Phytophthora Root and Stem Rot

  • Genetic Resistance: Use resistant varieties with a combination of good partial resistance and an Rps gene(s). Partial resistance alone will not be as effective during early growth stages or under high disease pressure.
  • Cultural Practices: Anything that will improve soil drainage will reduce disease pressure.
  • Seed Treatment Fungicides: Seed treatment fungicides containing mefenoxam or metalaxyl should be used. A higher rate may be needed for Phytophthora control vs Pythium control.

Bacterial Blight (Pseudomonas savastonoi)

Bacterial blight generally occurs early in the season, but may occur whenever environmental conditions are favorable. The bacterium overwinters on infected plant residue and is splashed onto leaves. Development of this bacterial disease is favored by cool wet weather (70 – 80°) and often continues until hot and dry conditions limit development. Outbreaks may occur after strong winds, rainstorms, and hail events. The summer of 2019 did not have extended periods have high heat, which made bacterial blight a serious problem throughout the growing season.


Young plants may be infected early, but symptoms often don’t appear until mid-season. Young plants may be stunted and die. In the later growth stages symptoms include angular lesions with a yellowish-green water-soaked “halo” around the edge (Figure 1). Eventually, the center of the lesions falls from the leaves resulting in a ragged appearance. Young leaves are most susceptible to infection and older leaves may remain intact. Lesions on the pods may cause them to become shriveled, however seeds usually do not show symptoms.

Management of Bacterial Blight

  • Genetic Resistance: Soybean varieties vary in their response to bacterial blight. Highly susceptible varieties should not be considered in fields with a history of bacterial blight.
  • Cultural Practices: Crop rotation and incorporating residue into the soil will help decrease disease development. To prevent spread, limit cultivation to periods when the foliage is dry.
  • Chemical Application: Copper fungicides are labeled for control of bacterial blight on soybeans, but must be applied early in disease cycle to be effective. Normally, chemical control is not necessary for this disease.
Bacterial blight of soybean
Figure 1. Bacterial blight of soybean appeared to be more common and severe in 2019, likely due to favorable weather conditions. Look for small, irregular reddish-brown lesions surrounded by yellow haloes that can later grow together to produce larger lesions and dead areas that fall out. Lesions tend to start in the upper canopy.

Frogeye Leaf Spot (Cercospora sojina)

Frogeye leaf spot is a foliar fungal disease that is becoming more prevalent in Nebraska. Yield loss estimates due to this disease have been reported as high as 30% nationally, but Nebraska losses are estimated to be less than 20% loss in highly susceptible varieties. This residue-borne disease is most common on continuous soybeans, especially in reduced and no-till situations. The primary source for disease is infested residue, infected seed, and airborne spores. If the 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 often occurs after flowering in the upper canopy. Symptoms begin as small, dark spots on leaves. The spots enlarge to a diameter of ¼ inch with gray to brown centers with a reddish purple margin (Figure 2). Lesions may coalesce to create irregular patterns of blighted leaves. Pods and stems may also be infected. Stem infections are long, narrow, dark lesions with flattened centers that generally develop later in the season.


  • Genetic Resistance: Soybean varieties vary in their resistance to frogeye leaf spot.
  • Cultural Practices: Crop rotation and incorporating residue into the soil will decrease disease potential
  • Fungicide Applications: Fields with a history of this disease may benefit from a fungicide application at the R3 – R4 growth stage. Typically QoI fungicides (strobilurin; FRAC group 11) have been successfully used to manage frogeye leaf spot, however fungicide resistance has been documented in samples collected from fields in 10 Nebraska counties (Figure 3). Successful management with foliar fungicides will require use of products containing active ingredients representing 2 or 3 fungicide classes instead of or in addition to those in the QoI Group 11. A combination of management strategies is more likely to provide satisfactory reduction in disease severity.
Frogeye leaf spot lesions
Figure 2. Frogeye leaf spot lesions are gray to brown and have red to purple margins and usually begin in the upper canopy.
Map of QoI (FRAC Group 11) fungicide resistance
Figure 3. QoI (FRAC Group 11) fungicide resistance was confirmed in soybean samples with frogeye leaf spot collected from 10 (yellow shaded) Nebraska counties in 2019. Samples were tested from only 1-2 fields in these 10 counties and 98% of C. sojina isolates (111 out of 113) had reduced sensitivity to QoI fungicides.

Soybean Cyst Nematode (Heterodera glycines)

Soybean cyst nematode is the most damaging pathogen of soybeans in North America and can cause substantial yield loss when left unmanaged. The nematode can also worsens other soybean diseases. Soil sample analysis is the only way to confirm the presence of the nematode.


Soybean cyst nematode can cause yield losses of 30% with no visual symptoms. When present, symptoms occur in patches throughout the field and include yellowing, stunting, and reduced canopy closure. Small, white to yellow lemon-shaped female nematodes may be observed with the naked eye on roots six weeks after planting.

Management of Soybean Cyst Nematode

  • Genetic Resistance: Resistant cultivars are available, although over 90% come from the same source, PI 88788. This source of resistance is becoming less effective as nematodes adapt. It is recommended to test nematode population densities by sampling at least every 6 years to monitor population changes. If populations are continuing to increase on PI 88788 resistance, consider 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 slow population increases.
  • Weed Mangement: Soybean cyst nematode can infect several annual weeds such as henbit, purple deadnettle, and field pennycress. Management of these weed species may help slow nematode reproduction.
  • Nematicides: Several seed treatment nematicides are available and may help protect seedlings from nematode infection for the first few weeks. Nematodes may continue to increase later in the growing season.

Sclerotinia Stem Rot (White Mold) (Sclerotinia sclerotiorum)

Sclerotinia stem rot, also known as white mold, is caused by a residue-borne pathogen that can persist in soil for an indefinite amount of time. Due to cool conditions at flowering, white mold was a serious problem for the fourth time in five years. Saturated soils and full canopies favor emergence of apothecia (mushroom-like bodies) from sclerotia (hard, black survival spores). Apothecia produce millions of spores over a 7- to 10-day period. During favorable weather conditions, these airborne spores can spread to other fields in the area.

Spores primarily infect through senescing flowers, but can also infect through wounded plant tissue. Free moisture on the plant surface is required for infection to occur. Flowers on the tips of small pods provide a common entrance for fungal infection. During harvest, the survival structures (sclerotia) are scattered back into the soil, providing inoculum for future seasons.


Symptom development begins at pod development and may include the leaves wilting, turning gray-green before becoming brown, curling, and dying. Observing stems and pods for white mycelium and sclerotia is important to differentiate this disease from other stem and root diseases. Early stem or pod water-soaked lesions occur near colonized flowers. Within a few days, diseased stem areas are killed, becoming tan and eventually bleached. This bleached stem will have a pithy texture and is easily shredded. Infected plant parts often have white, fluffy mycelium during humid conditions and sclerotia on the surface, or embedded in the stem tissue. Stem and pod infections generally occur 6 – 14 inches above the soil line, basal infections may also occur. Infection occurs after flowering has initiated.


  • Genetic Resistance: Soybean varieties vary in their response to Sclerotinia, however the resistance is incomplete and disease may still occur.
  • Cultural Practices: Narrow rows favoring canopy closure may result in more Sclerotinia stem rot. Avoid or minimize irrigation during flowering. Implementing at longer rotation with corn and wheat has been shown to reduce disease potential.
  • Fungicide Application: Foliar fungicides applied at the beginning of flowering (R1 growth stage) have been shown to provide better control than applications at beginning of pod set (R3 growth stage). Fungicide applications after this period may not provide control.

Late Season Diseases

Anthracnose Stem Blight (Colletotrichum truncatum)

Anthracnose pod and stem blight developed late in 2019, as was the case in 2018. While rarely a threat to yield, warm and wet weather during pod-fill and just prior to harvest favor this disease. The pathogen overwinters in infected crop residue or in seed. Infection occurring during planting or early pod development can become severe and yield limiting.


Foliar infections may result in red discoloration of veins, leaf rolling, and defoliation. As the plants mature, stem infections develop between the R5 – R7 growth stages. Lesions are irregularly-shaped and blotchy (Figure 4). Under magnification, the center of the lesions will contain fungal structures with pointed, black spines and spores may be visible. Seed may or may not have visible symptoms.

Management of Anthracnose Stem Blight

  • Genetic Resistance: Soybean varieties vary in their response to Anthracnose stem blight, but there are no known sources of resistance to this disease.
  • Cultural Practices: Crop rotation to a non-legume and tillage may reduce survival of the fungus and disease pressure in following years.
  • Seed Quality: Use of high-quality, certified seed (when available) helps to manage this disease.
  • Fungicide Applications: Fungicides are typically not necessary for Anthracnose stem blight. If application is desired, available products should be applied during the early to mid-reproductive stages.

Pod and Stem Blight (Diaporthe sojae)

Pod and stem blight is a part of the Diaporthe disease complex, which also includes Phomopsis seed decay and stem canker. Infection may occur early in the season, however symptoms are often not evident until late in the season as the plants mature. Warm, humid conditions while the plant is maturing favor disease development, especially in early maturing varieties. Wet conditions that delay harvest may lead to more severe disease.


Aside from the leaves, most plant parts can become infected by the fungus causing pod and stem blight. The most diagnostic characteristic is the development of small, black fungal pycnidia that can be in distinct rows on infected stems (Figure 4). These rows are often most visible at, or near the nodes. Symptoms are best observed late in the season during the pod fill stage (R6 – R8). Planting infected seed may lead to disease development in seedlings.

Management of Pod and Stem Blight

  • Genetic Resistance: There is no resistance to this disease. Planting a later maturing cultivar may reduce the likelihood of disease development.
  • Cultural Practices: Crop rotation to a non-host (corn or small grains) and tillage may help break down infested crop residue, decreasing disease in future seasons.
  • Seed Quality: Do not plant seed with a high incidence of infection (germination rates will be reduced).
  • Fungicide Application: Foliar fungicides applied near R5 may reduce infection, but may not impact yield.
The fungus causing pod and stem blight
Figure 4. The fungus causing pod and stem blight produces tiny distinct black fungal pycnidia that can be visible in distinct rows of “dots” on soybean stems. In contrast, symptoms of anthracnose can include dark irregularly-shaped blotchy lesions (also visible in the photo on the lower stem).

Online Master of Science in Agronomy

With a focus on industry applications and research, the online program is designed with maximum flexibility for today's working professionals.

A field of corn.