UC Management Guidelines for Root and Crown Rots and Damping-off Diseases (2022)

UC Pest Management Guidelines

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Root and Crown Rots and Damping-off Diseases

Pathogens: Phytophthora capsici, Pythium aphanidermatum, and other Pythium spp.

(Reviewed 12/09, updated 11/12, pesticides updated 6/16)

In this Guideline:

  • Symptoms and signs
  • Comments on the disease
  • Management
  • Publication
  • Glossary


Damping-off is primarily caused by Pythium spp. Seedlings affected by damping-off fail to emerge or fall over and die soon after emergence. Stems usually have a dark, shriveled portion at the soil line. Damping-off is generally limited to areas where drainage is poor or where soil is compacted, but whole fields can be affected, especially in early plantings exposed to rain.

Root and crown rot is primarily caused by Phytophthora capsici. Symptoms on affected pepper plants include rapid wilting and death of pepper plants. Close examination of the roots and stems is necessary to confirm the cause of disease. The disease can develop at any stage of pepper plant growth. Taproots and smaller lateral roots show water-soaked, very dark brown discoloration of surface, cortical, and vascular tissues. Very few lateral roots remain on diseased plants and the tap roots may also be shorter compared to those of healthy plants. The most striking difference between healthy and diseased plants is the total amount of root tissue. Stems are usually infected at the soil line. Stem lesions first become dark green and water-soaked, followed by drying and turning brown. A lesion can girdle a stem, resulting in wilting of plants above the lesion and subsequent death. Under some conditions, P. capsici can also cause a brown foliar blight on pepper.

Another important soilborne disease of pepper in California, Verticillium wilt, causes foliar symptoms similar to those seen in root and crown rot diseases; however, Verticillium wilt does not cause any browning or rotting of the root surface and cortex. In contrast, the xylem tissues of main stems and roots of Verticillium dahliae-infected pepper show brown to black streaking and discoloration.


Disease caused by P. capcisi can develop at any stage of growth, but once pepper seedlings reach the 2- or 3-leaf stage, they generally are no longer susceptible to infection by Pythium spp. However, Pythium spp. can cause root rot when peppers are grown on plastic mulch.

"Damping-off" is a general term for the death of seedlings in damp conditions, either before or after emergence. It is mainly an early-season problem, causing greatest losses in cool, wet soils. Because almost all California pepper production uses transplants, this disease is of more concern in the greenhouse if potting soil is contaminated or overwatered.

Although infection is most common under cool conditions, P. capcisi can infect seedlings in warmer soils. Damping-off due to Pythium spp. may increase where green manures such as volunteer grain are worked into the soil just before planting. Damping-off does not necessarily carry over from one season to another in the same places, but appears only when and where conditions favor infection.

Neither P. capcisi nor Pythium spp. is seedborne. However, both can survive in soil for long periods as thick-walled oospores. Contaminated transplants or soilborne inoculum are sources of primary infections. Irrigation water often disseminates fungal propagules from infested areas to other parts of the field. Thus, irrigation can significantly increase the incidence and severity of root and crown rot in pepper. Increased frequency and duration of irrigation favor disease development.

Water, temperature, and soil texture are the major factors affecting the development of damping-off and root and crown rot. The presence of water is mandatory; soil saturation for as little as 5 to 6 hours can result in infection, and susceptible varieties can become severely diseased in as little as 5 days. Optimum temperature for plant infection is 75° to 92°F (24° to 33°C). Symptoms usually appear following a warm, wet period. The disease is severe in fine-textured (clay) soils that drain slowly and in highly compacted soils. Severely infected fields may have nearly complete loss of plants.

Infections that occur late in the season may reduce vigor and yield of plants without killing them. In addition, if the foliage wilts during the hottest time of the day and exposes fruit to the open air, such fruit can become sunburned and therefore unharvestable.


Factors that influence the development of damping-off and root and crown rot diseases in peppers in a given season include varietal susceptibility, amount and frequency of irrigation, and soil compaction and drainage. Crop rotation, proper irrigation, and clean transplants are critical in managing this disease. Fields that have a history of root and crown rots may need fungicide treatments at planting.

Cultural Control

The disease can be effectively prevented by:

  • Using clean transplants
  • Proper field and seedbed preparation
  • Good water management
  • Employing a 2-year crop rotation that exclude susceptible plants
Soil and bed preparation

Practices that reduce or alleviate soil compaction may improve control; for example, growing plants on raised beds. If possible, avoid planting when the soil is cool. Seeds germinate faster and seedlings are more vigorous when the soil is warm: thus they are less likely to be damaged.


Use sprinklers during germination to better control irrigation and lessen the chance of infection. In heavy soils that are poorly drained, root and crown rot may be reduced by irrigating every other row on each irrigation or by carefully managing drip irrigation.


Commercial cultivars with acceptable levels of resistance to the disease are available. However, in general peppers are very susceptible to these diseases.

Treatment Decisions

Fungicides are sometimes used preventively in fields with histories of root rot or problems with drainage. Use a fungicide seed treatment to prevent damping-off.

Common name Amount per acre REI‡ PHI‡
(Example trade name) (hours) (days)
When choosing a pesticide, consider its usefulness in an IPM program by reviewing the pesticide's properties, efficacy, application timing, and information relating to resistance management,honey bees (PDF), and environmental impact. Not all registered pesticides are listed. Always read the label of the product being used.
(Ridomil Gold SL) 1 pt (soil-applied) 48 7
0.5 pt (foliar) 48 7
COMMENTS: Apply at planting and make two subsequent post-directed applications at 30-day intervals. Do not exceed 1.5 pt/acre per crop season (soil applied) or 0.5 pt/acre per crop season (foliar application). Mechanically incorporate or sprinkler-irrigate to move the pesticide into the root zone. Do not use for peppers grown in greenhouses.
(Presidio) 3–4 fl oz 12 2
COMMENTS: A tank mix with a labeled rate of another labeled fungicide product with a different mode of action must be used for resistance management.
(various products) Label rates See label See label
COMMENTS: Research on the use of this pesticide has not been conducted in California, but field experience suggests that it may provide control in a preventive program. Multiple applications are necessary to achieve control.
Restricted entry interval (REI) is the number of hours (unless otherwise noted) from treatment until the treated area can be safely entered without protective clothing. Preharvest interval (PHI) is the number of days from treatment to harvest. In some cases the REI exceeds the PHI. The longer of two intervals is the minimum time that must elapse before harvest.
1 Group numbers are assigned by the Fungicide Resistance Action Committee (FRAC) according to different modes of actions. Fungicides with a different group number are suitable to alternate in a resistance management program. For fungicides with mode-of-action group numbers 1, 4, 9, 11, or 17, make no more than one application before rotating to a fungicide with a different mode-of-action group number; for fungicides with other group numbers, make no more than two consecutive applications before rotating to fungicide with a different mode-of-action group number.


UC IPM Pest Management Guidelines: Peppers
UC ANR Publication 3460


S. T. Koike, UC Cooperative Extension, Monterey County
R. M. Davis, Plant Pathology, UC Davis
K. V. Subbarao, USDA Research Station, Salinas

Acknowledgment for contributions to Diseases:
B. W. Falk, Plant Pathology, UC Davis

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