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Chapter 2: Disease Management

2.1 General Principles

For a vegetable to become diseased, several conditions must be present: a susceptible host plant, a pathogenic organism, a good method of distributing the organism, and the proper environment for it to exist, enter the plant, and thrive. When these conditions are met, infection occurs, and a disease agent becomes established. The choice of a proper management tactic must be based on accurate knowledge of the pathogen causing the disease; its life cycle; time of infection; the part of the plant involved; the method of agent distribution; past, present, and future environmental conditions; and certain economic considerations. Effective management techniques include: use of resistant varieties; use of recommended rotations; sterilization of soil with steam or chemicals; use of clean seed, either certified or grown in disease-free areas; treatment of seed with heat or chemicals; control of insects and weed hosts; monitoring of weather conditions; use of biological control agents; and proper timing and application of fungicides or nematicides.

Effective management of vegetable diseases requires preventing disease or, if this is not feasible, slowing the spread of disease once it occurs. What can be done to prevent disease outbreaks or reduce the risk of early-season epidemics? Nine procedures and the current estimated percentage of importance of each toward vegetable disease control, have been recommended for many years: rotating crops (30%), spraying when necessary (20%), treating the seed (15%), using clean seed (10%), planting resistant varieties (5%), controlling weeds (5%), aerating the soil properly (5%), draining and fertilizing the soil (5%), and practicing good sanitation (5%). It is unlikely that all diseases of a particular crop can be controlled by simply following these procedures. Nevertheless, the extent of disease and the concomitant costs of controlling them can be significantly reduced by following as many of these procedures as possible. Note that this estimate indicates that spraying is only responsible for 20 percent of disease control. Using the other disease control techniques, which contribute 80 percent of disease control cannot only greatly improve disease control, but also reduce the costs of spray materials and result in better quality crops.

2.2 Diagnosis of Disease

The first step in disease management should be accurate diagnosis. It is important to differentiate between infectious diseases (e.g. those caused by fungi, bacteria, viruses, and nematodes that can spread from plant to plant) and noninfectious diseases or disorders (e.g., damage caused by mites and insects, physiological disorders, air pollutants, nutrient imbalances, and herbicide injury). Growers who have a reasonably good understanding of plant diseases, their symptoms, and the infectious and noninfectious disorders that can affect a particular crop, are more likely to make the correct disease control decisions. Numerous fact sheets and bulletins with full-color illustrations have been developed by Cornell faculty to assist growers in making accurate disease diagnoses. (See references in each disease section). In addition, samples can be sent to the Plant Disease Diagnostics Clinic in Ithaca (607-255-7850).

2.3 Disease Management Tactics

2.3.1 Crop Rotation and Tillage

Rotating fields to different crops each year cannot be overemphasized as one of the most important and easily implemented disease control strategies. This practice avoids the buildup of certain plant pathogens in the soil. The longer the rotation, the less likely that an early-season disease outbreak will occur. Because pathogens usually attack members of the same plant family, it is best to avoid planting successive crops belonging to the same family. Choices of unrelated crops to be rotated include beans to sweet corn, leafy vegetables to cucurbits, cucurbits to crucifers, and crucifers to sweet corn. Rotating beans with a grain crop such as barley, oats, rye, wheat, or field corn or with a forage crop is very beneficial for root-rot control. One or two years in a grain crop is often long enough to prevent severe root rot when the field is not heavily infested.

Some soilborne diseases are not readily controlled by rotation. Such diseases are caused by pathogens that produce structures that can withstand the effects of time and nonhost crops. Examples include clubroot of crucifers, Phytophthora blight, and Fusarium wilt of several crops. Other pathogens have such a wide host range that they can survive indefinitely because so many crops and weed species serve as hosts. These pathogens include Sclerotinia, Rhizoctonia, Verticillium and ropt-knot nematodes. Other pathogens are not affected by rotation because they overwinter in southern states, and new inoculum is blown into the area every year. This group includes sweet corn rust and downy mildew of cucurbits.

Many pathogens can overwinter successfully in association with plant debris and are unable to survive once the crop residue decomposes. Destruction of current-season crops can eliminate reservoirs for overlapping plantings. Fall tillage is important because it reduces the amount of inoculum that survives the winter.

2.3.2 Disease-resistant Varieties

The use of disease-resistant varieties is among the most economical and reliable methods of disease control. Although resistant varieties are not available for all diseases of vegetable crops, this option should be used whenever possible. Resistant varieties exist for asparagus, bean, cabbage, cucumber, muskmelon, pea, potato, spinach, sweet corn, and tomato diseases that are important in the northeastern states. The list of disease-resistant varieties will surely increase in the coming years. An advantage of using varieties that are resistant to soilborne disease can be the long-term decline in the pathogen population in the soil when used in combination with adequate crop rotations. Use of varieties resistant to foliar diseases can prevent expenditures and potential environmental consequences of fungicide applications.

Tables of Disease Resistant Varieties

2.3.3 Healthy Transplants and Seed

A basic rule for controlling plant diseases is to begin each growing season with healthy seed and transplants. A crop established with infected or infested plant material may contaminate an entire field and remove it from production for many years. Introduction of diseased material as primary inoculum into a field will greatly increase the chance of early-season epidemics, resulting in reduced yields, poorer quality products, and added costs for chemical control. Although diseases may occasionally be introduced via seed from commercial companies, seed companies are the most reliable source of plant material. Saving vegetable seed from the previous year's crop is a certain way of perpetuating a disease from season to season. So too is growing transplants for a friend with seed from his or her "private stock." In recent years, many vegetable operations have diversified, combining growth of bedding plants, maintenance of stock propagating material, and production of local vegetable transplants, often within close proximity. The potential for spread of vegetable and ornamental plant diseases has been documented with tomato spotted wilt virus and its vector, the western flower thrips. Another example is powdery mildew (two different species) spread to tomato and cucurbits from ornamental plant sources. Although local transplant production allows a more flexible production schedule, proper hardening of plants, and a reduced risk of introducing southern soilborne and foliar diseases, there may be offsetting disadvantages such as the risk of spreading seedborne diseases and other diseases endemic to northern states or harbored within the plastic houses.

Seed treatment is generally important to obtain and hold good stands, especially when soil moisture and temperature conditions are unfavorable during the germination period. Many seed suppliers treat seed before it is sold. If the seed has not been treated by the supplier, the grower can treat it. Seed treatment is especially necessary for beans, beets, onion, carrot, sweet corn, and peas; available materials are discussed under these crops.

The use of healthy transplants and seeds can help growers avoid many costly and environmentally damaging fungicide applications later in the season. Often, once a disease gets started in a field as a result of poor quality transplants or seeds, crop damage or yield loss will result no matter how many rescue treatments are applied.

2.3.4 Other Cultural Practices

Other practices can be followed to make conditions less favorable for development and spread of disease. These include planting after soils have warmed, selecting well-drained fields, improving soil health, using raised beds, reducing plant densities, scheduling overhead irrigation when foliage will dry soon afterwards, controlling weeds, and avoiding root pruning and stem injury by cultivating too deep or too close to plant stems. For example, steps to minimize the severity of white mold for beans would include planting rows in an east-west direction; using wide row spacing to promote drying of soil and reduce moisture in the plant canopy; not planting in shaded areas and small fields surrounded by trees that reduce air drainage; and not planting in fields that drain slowly and have a history of white mold. Steps to minimize white mold from the cabbage crop would also require the removal of ragweed and velvetleaf from the field.

2.3.5 Disease Scouting

Scouting, or systematically monitoring fields for the presence of pests, is an important aspect of any disease management program for vegetables. Recommended scouting procedures are available for many disease pests and are specifically designed to detect diseases when they reach economically damaging levels. See the references in each disease section to obtain manuals describing disease scouting techniques. Most often, when scouting for diseases, one should make sure to look for symptoms of the disease on a few plants in many areas of the field. Proper diagnosis and recognition of symptoms is important for successful disease scouting.

2.3.6 Weather Monitoring and Pest Forecasting

During the last 15 to 20 years considerable research in plant pathology has been dedicated toward developing mathematical models of plant disease development which can be used to forecast disease outbreaks. Most often these forecasting systems are driven by environmental factors such as temperature, leaf wetness, rainfall, and relative humidity. To most effectively use the forecasting models, the weather conditions near the fields need to be monitored regularly, and then the data need to be run through the computer models. In the past, data collection has been a time consuming and expensive process. Innovations in weather data collection, the use of personal computers, and the development of the Internet have allowed weather data collection for disease forecasting models to become affordable. There are two types of data available to farmers - data that is collected on electronic instruments placed in fields and retrieved by phone lines and data which is extrapolated to local conditions using mathematical equations from central collection sites. In order to make use of the first type of data, growers must obtain software for their own computer or subscribe to a service which connects to their weather instrument and interprets the data into disease predictions for them. In order to make use of the second type of data, growers must subscribe to a service which owns the mathematical models for extrapolation. In many cases, the use of the models will result in fungicide application savings which pay for the data acquisition costs.

Among the forecasting programs available are potato and tomato early and late blight, onion programs for Botrytis leaf blight, Alternaria and downy mildew; and white mold of snap beans. In addition, weather monitoring information can be useful for analysis of crop growth and yields.

For more information on weather-based disease forecasting services see the Network for Environment and Weather Applications site (NEWA). NEWA makes daily disease forecasts for a number of pests of vegetable crops in New York based on weather data collected in growers' fields.

2.3.7 Threshold

Both disease scouting information and weather information require the use of disease thresholds to be useful. Thresholds are levels of disease or disease conducive weather beyond which it is recommended that growers take some action to avoid economic loss from crop disease. Many common crop diseases occurring in New York have threshold information available for them. This information is listed in the disease management tables under each crop.

2.3.8 Biological Control

Research has shown that some fungi and other organisms show activity against specific pest organisms, including both diseases and insects. Some of these organisms have been commercialized and are now available in the marketplace. These products can be quite effective when used properly and offer several advantages over chemical controls, including reduced environmental impact and increased worker safety. Often, biocontrols work more slowly and must be used in combination with other control techniques to be effective. Sometimes fungicides are active against both the pest organism and the biocontrol organism. For this reason, growers should attempt to minimize chemical control applications when trying to make use of biocontrols.

2.3.9 Chemical Control

As the profit margin for successful farming continues to shrink, growers are beginning to look at all production costs in an effort to reduce expenses. Today, as never before, the decision to use chemicals to control diseases can either save a crop from certain economic loss or result in a loss of financial resources. Making the proper decision may depend on the grower's knowledge of the disease in question. With this basic information and by reading labels, the grower can select the appropriate material for treatment. Growers can save money and avoid crop loss by making use of scouting, weather monitoring, disease forecasting and thresholds as described above, before making the decision to apply a chemical disease control agent. Minimizing the use of these agents is also a method for growers to practice good environmental stewardship.

Bactericides. In general, there are two types of bactericides: copper compounds and antibiotics. However, products that can induce systemic acquired resistance (SAR) in plants have been shown to affect the development of bacterial diseases (i.e. Actigard). Similarly, some conventional fungicides have shown activity in the suppression of bacterial diseases (i.e. Tanos). All of these products can play a role in reducing the incidence of early- and midseason bacterial epidemics. They are most effective when used in conjunction with cultural practices, including rotating crops, using disease-free seed and transplants, sanitizing or using new stakes when crops are trellised, modifying irrigation methods, and regulating activities in a field when bacterial diseases are present. Copper compounds are most effective when disease incidence is low at the time of the initial application and if protection can be maintained during extended periods of weather favorable to disease. Antibiotics serve a similar purpose in certain crops. Because rain helps spread bacterial diseases, an extended period of dry weather will often arrest an epidemic.

Fungicides. Fungicides can be classified as protectants and eradicants. Protectant fungicides act as a chemical barrier to infection by plant pathogenic fungi. They must come into direct contact with a germinating spore or growing mycelium to be effective in preventing subsequent spore germination and infection. They may be used as seed or soil treatments or as foliar sprays. Because these fungicides are not site specific and can control a diverse group of pathogenic fungi, they are used widely for disease control. Additional terms used to describe protectant fungicides are preventive, contact, and broad spectrum. Because protectant fungicides are not absorbed by the plant per se, they do not destroy or burn out existing infections. Once an infection has occurred, a lesion will develop and may produce more spores despite the presence of the protectant fungicide. To be effective, a protectant fungicide must be applied repeatedly during the season and in such a manner as to provide maximum spray deposition and coverage. Eradicant fungicides have been developed for the control of a limited number of fungi. They are also called systemic fungicides because they are absorbed into the plant and are able to eradicate existing infections. Their main advantage is that they can be applied after infection has occurred and still be effective; because they move systemically within the plant, coverage is less critical; and eradicant fungicides do not need to be applied as often as other fungicides. A major limiting factor of eradicants is that their more specific mode of action may lead to the development of new strains of some pathogens that are resistant to the fungicide. Improper use of these materials, such as initiating sprays when disease is well-established, can enhance the development of fungicide resistance. Tank mixing with a protectant fungicide helps maintain the effectiveness of the eradicant.

Fungicides have been arranged by Group Names or Chemical Groups and assigned a Group Code Number by the Fungicide Resistance Action Committee (FRAC), especially to indicate their ability to develop resistance to populations of fungi. The vegetable fungicides that are "at risk" include the following groups:

Group 1 benzimidazoles (ex. thiabendazole, Mertect, and the previous product benomyl, Benlate) and thiophanates (ex. thiophanate-methyl, Topsin M);
Group 2 dicarboximides (ex. iprodione, Rovral and the previously registered product vinclozolin, Ronilan);
Group 3 DeMethylation Inhibitors (DMIs) imidazoles (ex. triflumizole, *Procure and triazoles (ex. myclobutanil,  Rally; propiconazole, Quilt and Tilt; and the previously registered product triadimefon, Bayleton);
Group 4 phenylamides, acylalanines (metalaxyl, Ridomil and mefenoxam, Ridomil Gold or Ultra Flourish);
Group 7 carboxamides (ex. flutolanil, MonCoat and † Moncut; boscalid, Endura)
Group 9 anilinopyrimidines (ex. cyprodinil, Vanguard and pyrimethanil, Scala);
Group 11 Quinone outside Inhibitors (QoI) (ex. azoxystrobin, Quadris; pyraclostrobin, Headline and Cabrio; trifloxystrobin, Flint and Gem
Group 12 phenylpyrroles (ex. fludioxonil, Maxim);
Group 13 quinolines, (ex. Quintec, quinoxyfen);
Group 14 aromatichydrocarbons (ex. quintozene (PCNB), Blocker)
Group 15 cinnamic acids (ex. dimethomorph, Forum);
Group 17 hydroxyanilides (ex. fenhexamid, Decree);
Group 21 Quinone inside Inhibitors (Qil), cyanoimidazole (ex. cyazofamid, Ranman);
Group 22 benzamides (zoxamide, * Gavel);
Group 25 glucopyranosyl antibiotic (ex. Streptomycin) (ex. streptomycin sulfate, Agri-mycin 17,and Agricultural streptomycin,and Firewall
Group 27 cyanoacetamideoximes (cymoxanil, Curzate);
Group 28 carbamates (ex. propamocarb, * Previcur Flex).

Do not apply fungicides in these groups exclusively in a disease control program. Fungicides in these groups should be rotated with broad spectrum (multi-site Groups M1, M3, M5 given below), or used in combination with another group of fungicides to delay the development of resistant strains of fungi.

Resistance problems are generally not recognized for the following groups:

Group 29 2,6-dinitroanilines (ex. fluazinam, Omega)
Group 30 organo tin compounds, tri phenyl tin compounds (ex. fentin hydroxide, *Super Tin or *Agri Tin)
Group 33 phosphonates, ethyl phosphonates (ex. fosetyl-Al, Aliette), and phosphorous (ex. phosphorous acid, ProPhyt and Phostrol);
Group 40 carboxylic acid amides (ex. dimethomorph, Forum; mandipropamid, Revus);
Group 43 pyridinylmethly-benzamides (ex. fluopicolide, *Presidio;
Group M (multi-site activity):
Group M1 inorganics (ex. coppers, Kocide, Champion, or OLF; and sulfur, Microthiol Disperss);
Group M2 inorganics (ex. sulfur, Microthiol Disperss or OLF);
Group M3 dithiocarbamates (ex. mancozeb, *Dithane DF, Manzate, Penncozeb; *Roper; metiram, Polyram; thiram; ziram, Ziram 76DF; Group 4 phthalimides, captan (seed treatment only);
Group M4 phthalimides, captan (seed treatment only);
Group M5 chloronitriles (ex. chlorothalonil, Bravo,  Echo);
Group P1 (host plant defense induction) benzo-thiadiazole (ex. acibenzolar-S-methyl, Actigard)
Group B Biologicals (ex. fungal and bacterial species, Contans, Serenade and Sonata).
Not Classified (ex. mineral oils, organic oils, and potassium bicarbonate)

Combinations of fungicides are becoming more common as manufacturers expand their fungicide portfolios with different modes of action (MOA). This has allowed the combination of products to backstop in case one of the active ingredients has developed fungicide resistance for a particular pathogen as illustrated with Quadris Opti and Quadris Top because of azoxystrobin resistance to early blight fungus in both potato and tomato.

Premixed components which utilize a multisite active fungicide like chlorothalonil and mancozeb has led to products like Ridomil Gold Bravo, Catamaran, *Gavel, ManKocide, and a large number of potato seedpiece treatment products.

The combination of fungicides with different MOA chemistry has resulted in products like Switch (9cyprodinil + 12 fludioxonil), Inspire Super (3difenoconazole + 9cyprodinil), Tanos (11famoxadone + 27 cymoxanil) and several more, and seems to be the trend for future products.

Do not use "at risk" fungicides as a rescue treatment for disease control. "At risk" fungicides should be used in a full season disease control program or not at all. Applying "at risk" fungicides only after a disease is present in a field, increases the chances for the development of resistant populations of plant pathogenic fungi.

The need for a fungicide spray depends on several factors, including plant stress (caused by fruit load or lack of good fertility); weather conditions conducive to fungal spore germination and infection (moisture and temperature); stage of crop development; levels of host resistance; and levels of pathogen inoculum.

Nematicides and Fumigants. These chemicals reduce populations of nematodes and soilborne fungi. Fumigants are usually applied before the crop is planted, whereas most of the non-fumigant nematicides are applied shortly before or during planting. They are most effective when used in combination with cultural control strategies such as crop rotations and resistant varieties. However, the cost-benefit of using such fumigant nematicides varies greatly from crop to crop and their application may be restricted to only custom-applicators.

A number of factors have a pronounced effect on the success or failure of soil fumigation. Six are given below.

Soil preparation prior to fumigation. Soil should be plowed deeply (ten inches or more) in order to incorporate previous crop debris as thoroughly as possible and to prevent turning up nonfumigated soil during fitting in the spring. This should be followed by disking or any other means of fitting which will leave the soil in seedbed condition. Clods and poorly incorporated debris will provide "chimneys" through which fumigant can escape prematurely from the soil.

Soil moisture. The soil should be neither too wet nor too dry. A good rule of thumb is that moisture content is most favorable when soil will just "ball" in one's hand when pressure is applied. If soil is excessively dry and irrigation is available, moisture supplementation before fumigation is recommended.

Soil temperature. The optimal temperature for most fumigants is 50° to 70°F. At warmer temperatures, fumigants dissipate thoroughly and rapidly, nematode larvae (which are easier to kill than eggs) have emerged, and all nematode stages can be more effectively controlled.

Crop debris. Undecomposed residues from previous crops prevent distribution of fumigant through the soil, irreversibly absorb fumigant, interfere with application equipment, prevent proper sealing of the soil surface, and protect nematodes and nematode eggs from fumigant action. Rake, burn, or deeply incorporate debris prior to fumigation.

Sealing of soil surface. It is essential that fumigated soil be thoroughly sealed as soon after application as possible. This can be achieved by means of equipment such as a cultipacker, chain harrow or float, or by means of spray irrigation or plastic sheets.

Interval between fumigation and planting. Under average conditions, with a soil temperature of ± 50°F, a minimum of three weeks is regarded as necessary between fumigation and planting to prevent phytotoxicity to potatoes. See fumigant labels for specific recommendations.

A plastic film seal will increase the efficacy of soil fumigants. Soil fumigants are injected to a depth of 6 to 8 inches. Immediately after application, soil should be dragged, rolled, or cultipacked to delay loss of fumigant.

At least 2 to 3 weeks should intervene between the application of most soil fumigants and the time a crop is planted. See manufacturers label recommendations for specific crops and fumigants.

One week after application, work soil to a depth of several inches so that gasses may escape. Severe injury killing of sensitive plants may occur if the fumigant has not sufficiently dissipated.

To determine if it is safe to plant into fumigated soil, collect a soil sample from the treated field (do not go below the treated depth). Place the sample in a glass jar with a screw top lid. Firmly press numerous seeds of a small seeded vegetable crop (lettuce, radish, etc.) on top of the soil and tighten the lid securely. Repeat the process in another jar with nonfumigated soil to serve as a check. Observe the jars within 1 to 2 days. If seeds have germinated, it is safe to pant in the field. If seeds have not germinated in the fumigated sample and have germinated in the nontreated sample, then the field is not safe to plant. Rework the field and repeat the process in a few days.

Owing to a reduction in nitrifying bacteria by the fumigants, at least 50% of the nitrogen in the initial fertilizer application should be in the nitrate form.


Maintained by Abby Seaman, New York State IPM Program. Last modified 2017.

This information is based on the Cornell Integrated Crop and Pest Management Guidelines for Commercial Vegetable Production, Cornell Cooperative Extension.


Stephen Reiners, SIPS Horticulture Section, Cornell AgriTech at Cornell University; Editor; cultivar selection and fertility
Lynn Sosnoskie, SIPS Horticulture Section, Cornell AgriTech at Cornell University; weed management
Bryan Brown, NYSIPM Program, Cornell AgriTech at Cornell University; weed management
Paul D. Curtis, Natural Resources, Cornell University; wildlife management
Michael Helms, Pesticide Management Education Program, Cornell University; pesticide information
Margaret T. McGrath, Plant Pathology, Long Island Horticultural Research and Extension Center, Riverhead, NY; disease management
Brian A. Nault, Entomology, Cornell AgriTech at Cornell University; insect pest management
Abby Seaman, NYSIPM Program, Cornell AgriTech at Cornell University; integrated pest management

Special Appreciation

Special appreciation is extended to the following for their contributions to this publication: George S. Abawi, Robin Bellinder, Helene R. Dillard, Donald E. Halseth, Michael P. Hoffmann, Andrew J. Landers, Curt Petzoldt, Anu Rangarajan, Anthony M. Shelton, Christine D. Smart, John Wallace, and Thomas A. Zitter.