Fungicide Use in Field Crops: Web Book

4.4: Fungicide Resistance

4.4: Fungicide Resistance

Impact of Fungicide Resistance

Pathogens on field crops have been managed with fungicides since the 18th century. Copper and sulfur-based fungicides were used in the 19th century, while mercury-based fungicides were used in the early 20th century until animal toxicity concerns were revealed. The contact fungicides mancozeb (FRAC code M3; Dithiocarbamates and relatives) and captan (FRAC code M4; Phthalimides), which were only effective if applied prior to infection, were marketed in the 1940s and 1950s. Apparent risk of fungicide resistance was low, since these fungicides have multiple sites of action.  

In recent decades, fungicides with systemic properties, specific modes of action, and the ability to inhibit many different fungi have proven to be highly effective for disease control. These include the quinone outside inhibitors (FRAC code 11; QoIs). Increased reliance on these fungicides, coupled with the fact that fungi can more easily overcome a specific mode of action than multi-site activity, has resulted in the emergence of fungicide resistance. After only four years of use, populations of the causal pathogen of frogeye leaf spot of soybean, Cercospora sojina, already exhibited resistance to QoI fungicides. Conversely, it may take decades for other fungicides to lose efficacy due to pathogen resistance. Extensive use of a specific fungicide mode of action or active ingredient increases risk of resistance developing. Sunflower, soybean, sugar beet, and potato farmers have all experienced the loss of fungicide products resulting from the selection of fungicide resistant pathogens and widespread development of fungicide resistance within fungal pathogen populations.

Development of Fungicide Resistance

A fungal population becomes resistant to a fungicide through selection pressure. Over time and with repeated use of the same fungicide active ingredient, less sensitive individuals within a pathogen population will multiply and eventually make up the majority within that population (Figure 4.8). As a pathogen population exhibits less sensitivity to a fungicide product, that product becomes a less valuable, or even useless, pest management tool. 

Figure 4.8. This diagram illustrates how fungicide resistance occurs. The fungicide resistant genetic variant (red hexagon) is not controlled by a fungicide application. As use of the same fungicide active continues for successive applications, the resistant genetic variant survives and multiplies, eventually reducing the effectiveness of the fungicide.

Attributes of the chemical product and pathogen determine the risk of selection for fungicide resistance. Fungal plant pathogens with a high degree of genetic variability in the population are at greater risk for fungicide resistance. This greater degree of genetic variability often is observed in plant pathogens with polycyclic life cycles (repeating spore stages) and those that reproduce sexually. Increased genetic variability increases the chances that a genetic variant with reduced sensitivity to a fungicide will occur within the pathogen population. Fungicides with multi-site activity are less likely to select for resistant pathogens than those with a single-site mode of action. Applicators cannot control the genetic variability within a pathogen population, but can take measures to reduce selection pressure related to fungicide choice.     

Reducing Risk of Fungicide Resistance

The risk of fungicide resistance development can be reduced using a few standard practices such as use of integrated pest management, mixing and alternating fungicides, and following label recommendations. The best way to ensure long-term effectiveness of a fungicide is to make sure a fungicide program includes all of these fungicide resistance management practices.                                                            


In order to assess if a fungicide has performed as desired, field scouting should be conducted after an application. There are multiple reasons why a fungicide may not work as expected, but identification of potential resistance is important. If fungicide resistance is suspected, the first step is to contact local extension personnel or representatives from the fungicide manufacturer.

In order to monitor fungicide resistance, researchers use laboratory analyses to establish a baseline level of pathogen sensitivity to a fungicide. The baseline sensitivity level is the sensitivity to a particular fungicide of a fungal population that has not been previously exposed to that fungicide (or fungicides with the same mode of action This baseline level provides a comparison point that researchers can use when monitoring pathogen populations suspected of being resistant, or becoming less sensitive to a fungicide active ingredient as time passes. This is accomplished by periodically testing pathogen populations in a laboratory. 

Integrated Pest Management (IPM)

An IPM program includes using multiple disease management methods, and regular field scouting, local and regional disease monitoring. Using recommended fungicides if disease risk is high is part of IPM. Because fungicides are important components of field crop disease management programs, it is necessary to protect the long-term effectiveness of these tools. IPM practices are implemented to help preserve this effectiveness (Figure 4.9). For more information about  fungicide use as part of IPM, see Section 1.2.

Using fungicides only when warranted due to disease risk and scouting observations is a way to help ensure that fungicides will continue to be useful for as long as possible. Every time a fungicide is applied, fungal plant pathogens are exposed to the fungicide. Application of a fungicide when it is not warranted due to low disease risk or scouting observations will unnecessarily expose the fungal pathogen population to the fungicide and speed up the selection of resistant (insensitive) individuals within the population. Fungicide application when disease risk is low also decreases the probability of a positive return on investment.

The same fungicide products or active ingredients may be registered for many field crops. This is important to consider if these crops are part of the same rotation. Keep in mind the need to rotate modes of action as well as products and active ingredients, as different fungicides may have the same mode of action.

Figure 4.9. Integrated Pest Managment (IPM) includes the use of many tools to reduce disease losses and also helps to delay development of fungicide resistance. Using disease-resistant plant varieties is one such tool. The corn hybrid on the left is susceptible to northern corn leaf blight, while the hybrid on the right is resistant.

Image: Albert Tenuta

Alternating and Mixing Fungicides

Use of fungicide products that contain a single active ingredient can increase selection pressure for fungicide resistant pathogen populations compared to using premix products or tank mixing products with active ingredients that have distinct modes of action. If a resistant fungal propagule is not killed by one fungicide mode of action in the tank mix, the other fungicide mode of action should kill it, reducing survival of propagules that can increase to become resistant populations. This only works if both fungicides have the ability to manage the target pathogen. For example, mixing two products such as flutriafol (FRAC code 3; DMI) and fluazinam (FRAC code 29; Oxidative phosphorylation uncouplers), would not be effective for resistance management when trying to control frogeye leaf spot, as only one of these exhibits activity against the causal pathogen. However, mixing flutriafol and thiophanate-methyl (FRAC code 1; MBC) would be effective as both are able to control the pathogen that causes frogeye leaf spot. 

Use different modes of action when more than one fungicide application is needed during a single season. Applications should be timed to be most efficacious for disease management when fungicides are alternated.

Label Recommendations

It is important to remember that the “label is the law” regarding fungicide application. Fungicide labels may have a resistance management section which should be followed carefully. The label contains important information regarding application restrictions such as permissible number of single season applications, or if back-to-back applications are allowed.

Sublethal doses of fungicide may increase risk of pathogen desensitization to an active ingredient. This makes following label rates an important part of slowing resistance development, as well as ensuring proper disease control.

Cross-resistance occurs when a fungal organism exhibits resistance to multiple fungicides in the same FRAC code, as is often the case when a fungus exhibits resistance to one of the fungicides within that FRAC code.

Managing Fungicide Resistance

Using the same fungicide with the same mode of action/FRAC code season after season or several times within the same season could result in the target pathogen becoming resistant to the chemical family. A pathogen can develop resistance to one chemical family but still be very sensitive to another. Therefore, to reduce the risk of a pathogen developing resistance, rotate among chemical groups and/or families within the same season or during successive growing seasons for control of the same disease. Also, some types of fungicides have a higher risk of resistance developement than others. See Section 2.2 for fungicide resistance risk classification.

Fungicide resistance management is an important part of field crop production. The following guidelines can help minimize the risk of resistance:

Spray when needed

  • Do not make unnecessary fungicide applications. There should be a tangible, defined reason for application, as opposed to emotion- or tradition-based applications. 
  • Only use chemical control when necessary and consider implementing an integrated pest management strategy, including cultural control (e.g., crop rotation, disease- resistant varieties, scouting, use of certified seed, etc.) or biological control, which will also help reduce the risk of a pathogen developing resistance to a fungicide.
  • Scout fields regularly, noting incidence and severity of diseases. Use this information to develop a field history for future disease management decisions.
  • Be willing to accept some level of disease. A completely clean crop is not necessary to maximize yield or economic returns.

Healthy plants help

  • Ensure good agronomic practices are in place to minimize fungicide need.
  • Plant disease-resistant hybrids/varieties whenever possible. 
  • Maintain proper soil fertility. 
  • Utilize a crop rotation that fits your area and field history. 
  • Avoid sites with a history of high disease pressure. 

Fungicide selection is important

  • Use a pre-mix fungicide or tank-mix high-risk fungicides with fungicides that have different modes of action, are active against the targeted disease(s), and have similar lengths of residual activity. 
  • Alternate fungicides with different modes of action when multiple applications are required during a season. 
  • Do not apply the product at rates lower than the recommended rate on the label. 
  • Be sure to follow the rates, restrictions and other application instructions on the fungicide label. 
  • Do not exceed the total number of applications or total amount of material allowed per year for each product.

Fungicide timing is important

  • Apply fungicides preventively or early in the disease cycle and when disease risk is high. 
  • Avoid fungicide applications at late stages of disease development, especially with high-risk fungicides, as these increase the risk of selecting for resistance. 

Monitor after application

  • Monitor disease progression following fungicide application (Figure 4.10). This is a way to check for potential fungicide resistance. If the fungicide is found to be ineffective, this may be an indicator of resistance. However, other reasons can cause fungicide failure and should be ruled out first.  

Figure 4.10. Check disease progression after a fungicide application, making sure to follow the fungicide label for re-entry interval of the sprayed field.

Image: Iowa State University Integrated Pest Management

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4.4: Fungicide Resistance