Cotton Seedling Diseases

Cotton Disease Information Note No. 1
Steve Koenning, Plant Pathology Extension Specialist


Figure 1. A poor stand of cotton seedlings.

Seedling diseases (Figure 1) cause an estimated average annual yield loss of 5% and are usually the major disease problems in cotton production in North Carolina. Several soilborne fungi are responsible; however, cultural and environmental factors that delay seed germination and seedling growth make the problem more severe.

Environmental Factors Influencing Seedling Diseases

Seedling disease occurs more frequently under cool, wet conditions and seems to be more prevalent on sandy, low-organic-matter soils. Environmental factors are very important in influencing the development of seedling diseases (Table 1). Other factors, such as planting too deep, poor seed bed conditions, compacted soil, nematode or insect infestations, and misapplication of soil-applied herbicides such as dinitroanalines, may increase the problem. Seedling diseases tend to be more severe in reduced tillage situations and when beds are absent. Planting on beds elevates the seed allowing for more rapid emergence, especially after heavy rains. Plants are more prone to attack by pathogens when stressed by an inhospitable environment, insects, or other causes. As a result, contagious diseases are often associated with insect infestations and poor growing conditions. Damage from thrips in particular can delay seedling development and enhance damping-off diseases caused by various fungi.

Fungi Causing Seedling Diseases

Figure 2. sore shin of
cotton seedlings.
Several species of fungi can cause seedling disease, but the primary agents are Rhizoctonia solani, Pythium spp., Phoma exigua (Ascochyta), and Fusarium spp. These disease causing organisms can attack the seed before or at germination. They also can attack the young seedling before or after emergence. Symptoms include seed decay, decay of the seedling before emergence, partial or complete girdling of the emerged seedling stems, and seedling root rot. Seed and seedling disease is characterized by a soft, watery rot. Damaged seedlings that emerge are pale, stunted, slower growing, and sometimes die within a few days. Examination of infected seedlings may reveal dark lesions on the stem and root. Often the taproot is destroyed, and only shallow-growing lateral roots remain to support the plant. The "sore shin" phase of seedling disease is characterized by reddish brown, sunken lesions at or below ground level (Figure 2). These lesions enlarge, girdle the stem, and cause it to shrivel. Seedling diseases do not usually kill the entire seedling population, but rather result in uneven, slow-growing stands with skips in the rows. In some years, replanting is necessary. Poor stand establishment causes problems with the management of other pests and may reduce yields.

The most common fungi associated with seedling diseases in North Carolina are Pythium spp. and Rhizoctonia solani. Often both fungi can be found on the same seedling. The same fungus may cause seed decay, seedling root rot, or both. However, Pythium spp. and Fusarium spp. usually attack the seed and below-ground parts of young seedlings, while R. solani usually causes sore shin. Rhizoctonia solani and P. exigua may attack seedlings from the time they emerge until they are about 6 inches tall. After this stage, the stem becomes woody, and subsequent infection rarely occurs unless the stem is injured.

Pythium spp.

Several species of fungi in the genus Pythium can cause seedling disease in cotton as well as several other crops. Pythium spp. are generally classified as water molds. These fungi produce spores that can actively move in soil water. In general, Pythium is more commonly the causal fungus if the soil has remained saturated for several days or is poorly drained. Mefenoxam (Ridomil Gold) or Etridiazole (ETMT, Terrazol) are necessary to control seedling disease caused by Pythium spp.

Rhizoctonia solani

This fungus typically causes sore shin, and is more common on sandy, well-drained soils. Plants injured by sand blasting are particularly susceptible to this pathogen (Figure 2). Fungicides containing PCNB (Terrachlor) or Iprodione (Rovral) are generally effective against Rhizoctonia solani.

Phoma exigua (Ascochyta gossypii)

Figure 3. Post-emergence damping off caused by Phoma exigua.

This fungus can cause post-emergence damping off. This disease is characterized bypremature dying of cotyledons which turn brown and shrivel (Figure 3). This disease has been observed when night temperatures are in the 50's and foggy or misty conditions occur (see also Cotton Disease Information Note No. 2). Fungicides have not been evaluated as to their efficacy against this fungus.


Various species of fungal genus Fusarium are typically found on diseased seedlings. Seed applied fungicides are generally effective in managing Fusarium spp.

Seedling Disease Management

A control program for seed and seedling diseases is based on preventive rather than remedial treatments. The program uses fungicides along with cultural practices to make conditions more favorable for the young cotton and less favorable for the disease-causing organisms. Poor quality seed with low germination should be avoided.


Fungicides (Table 2) are a primary component in a program to manage cotton seedling diseases. Be sure to plant only fungicide treated seed. Using in-furrow fungicides may give further benefits. Be sure to follow label recommendations since formulations change from year to year. In particular, Ridomil Gold generally is applied at lower rates than Ridomil.

Seed Treatment

All cotton seed offered for sale in North Carolina is treated with fungicides. Seed treatments are categorized as protectants and systemics. Protectant fungicides, such as captan or thiram, provide surface protection from disease organisms carried on the seed and from organisms found in nearby soil that cause seed rot. Systemic fungicides, such as carboxin (Vitavax) or mefenoxam (Ridomil Gold), are absorbed through the seed coat of the germinating seed and are taken up by the young seedling. Systemic fungicides provide temporary protection from certain types of preemergence and postemergence damping off. For specific fungicide recommendations and formulations refer to the NC Agricultural Chemicals Manual. In most years, seed treatment fungicides are sufficient for controlling seedling disease, unless the quality of the seed is low or weather conditions are unfavorable for germination. If additional fungicide is desired, it is best to use an in-furrow treatment. Hopper-box seed treatments are also available. However, coverage and effectiveness are much better with in-furrow sprays or granules.

In-Furrow Fungicide Treatment

Protection obtained with seed treatment may not last long enough for the cotton seedlings to grow to a stage where their susceptibility to diseases is reduced. An in-furrow fungicide is suggested for fields with a history of seedling disease problems, when planting early, or when cool, wet weather is expected shortly after planting. In-furrow treatments also are helpful if the seed quality is questionable. Fungicides, however, are not a substitute for high-quality seed and good planting conditions. In-furrow fungicides will not be profitable in most years; however, if conditions are less than optimal, they can result in better and more uniform stands. Better stands may translate into higher yields. There are two methods for applying in-furrow fungicides: in-furrow sprays or in-furrow granules.

An in-furrow spray is a very effective method, but it is not practical for most growers who use their spray tanks and pump to apply preemergence herbicides as they plant. For best results, apply the fungicide through two cone-type nozzle tips. Mount the front nozzle just behind the seed drop outlet to treat the soil around the seed. Direct the rear nozzle to spray soil as it tumbles into the seed furrow with a small amount of spray striking the top of the covered row.

Using an in-furrow granular fungicide is practical and effective. Nearly all cotton planters already have one applicator box for systemic insecticide applications. A second applicator is a relatively inexpensive addition. If a second applicator cannot be added, combination treatments (insecticide and fungicide on the same granule) may be available (check with your dealer). Granules should be placed in the bottom of the seed furrow and mixed with the covering soil.

Hopper Box Treatments

Soil fungicides cannot be applied very well by the hopper-box method with acid delineated seed unless the seed and fungicide are properly layered in the hopper box. When mixed well with seeds, some fungicide will fall out with each seed to treat the soil around it. Fungicides may reduce the seeding rate by 10 to 20 percent, so you must calibrate the planter with the seed and fungicide mixture to get the desired rate. The hopper-box method, while less expensive than in-furrow sprays and in-furrow granules, however, is sometimes less effective. When used properly, the hopper-box method may give better results than seed treatments alone.

Additional Seed Treatments

The addition of more seed treatment to treated seed is not generally recommended. This may result in more handling of seed that may cause mechanical damage. Most cotton seed is treated with three or more fungicides which are sufficient to protect against the spectrum of disease causing fungi that commonly occur in North Carolina. Additional seed treatment is likely to add more fungicide that is already present on the seed.

Table 1. Point system for determining the need for in-furrow fungicides. This point system is only a guide as to the probability of receiving a benefit from application of an in-furrow fungicide.

Soil Temperature < 65 = 75
5 Day Forecast - Colder and wetter = 50
Seed Quality - Cold germ < 59% = 75
Field History - Severe disease = 100
Tillage - Minimum tillage = 50
Row Preparation - Beds absent = 75
Seeding Rate - Less than 3-4/foot of row = 100
Poorly Drained Soil = 50
If total exceeds 200, consider using an in-furrow fungicide

Table 2. Fungicides for control of cotton seedling diseases. These materials are generally used in combinations. For specific fungicide recommendations and formulations refer to the NC Agricultural Chemicals Manual.

Common Name
Biological Spectrum
Diseases Controlled
Mefenoxam Ridomil, Ridomil Gold, Apron Pythium, Phytophthora Pythium damping off
Pentachloronitrolbenzene PCNB (PC, Terraclor) Rhizoctonia Sore shin
Iprodione Rovral Broad spectrum Sore shin
Etridiazole ETMT, Terrazole Broad spectrum Pythium, Sore shin, Fusarium
Azoxystrobin* Quadris Broad spectrum Pythium?, Sore shin, Fusarium
Bacillus subtillus (a bacterium)** Kodiak Broad spectrum Pythium, Sore shin, Fusarium
Trichoderma harzianum (a fungus)** T-22 Broad spectrum

Pythium, sore shin,

*Not currently labeled for use on cotton.
**Little information on the efficacy of these biological pesticides is available.

Other Links

Cotton Pest Management Strategic Plan for the MidSouth
NC Agricultural Chemicals Manual

Recommendations for the use of chemicals are included in this publication as a convenience to the reader. The use of brand names and any mention or listing of commercial products or services in this publication does not imply endorsement by the North Carolina Cooperative Extension Service nor discrimination against similar products or services not mentioned. Individuals who use chemicals are responsible for ensuring that the intended use complies with current regulations and conforms to the product label. Be sure to obtain current information about usage and examine a current product label before applying any chemical. For assistance, contact your county North Carolina Cooperative Extension Service agent.

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