NC State Extension Publications


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Seed and seedling diseases are one of the top three major disease problems in North Carolina cotton. These diseases are caused by several different species of soilborne fungi found in every cotton-growing county in the state. Primary cotton seedling diseases in North Carolina include Fusarium wilt (Fusarium spp.), Phoma blight [Phoma exigua (Ascochyta gossypii)], root rot (Pythium spp.), soreshin (Rhizoctonia solani), and black root rot (Thielaviopsis basicola).

Cotton standing with stunting and damping off

Figure 1. Cotton standing with stunting and damping off symptoms

Plant Disease Insect Clinic

Environmental Factors Influencing Seedling Diseases

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Although seedling diseases can be caused by numerous pathogens, these pathogens are most severe when cultural and environmental factors delay seedling emergence and growth. Seedling diseases occur more frequently during cool, wet weather and are more prevalent on sandy, low-organic-matter soils. Other factors that may lead to more severe disease include reduced tillage, planting too deep, absent or poor seedbed conditions, compacted soil, and misapplication of soil-applied herbicides. Damage to the root and crown of cotton seedlings due to nematode or insect infestations also leave plants more susceptible to seedling diseases. Damage from thrips, in particular, can delay seedling development and enhance damping-off diseases caused by various fungi.


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Seedling diseases cause characteristic signs and symptoms that help differentiate them from each other. Identifying the problem fungi in a field as well as the risk factors they are associated with (Table 1) will help inform management strategies.

Table 1. A list of major seedling disease reported in North Carolina cotton
Seedling Disease Primary Causal Fungal Signs & Symptoms Major Risk Factors*

Fusarium wilt

Fusarium spp.

  • Chlorosis (Yellowing), Stunting

  • Wilting

  • Brown streaks running down stem to roots

Ascochyta blight

Phoma exigua

  • Premature browning and death of cotyledons

  • Black cankers and streaks on main stem

  • Cold, wet weather

  • Night temperatures between 50 - 60°F

  • Plants less than 6 inches tall

Pythium root rot

Pythium spp.

  • Seed rot

  • Water soaked lesions

  • Damping off

  • Cold, wet weather

  • Poorly drained soils

  • Water saturated soils (several days)


Rhizoctonia solani

  • Sunken reddish-brown lesions on hypocotyl (soreshin) (Figure 2)

  • Girdling and seedling collapse

  • Stunting in surviving seedlings

  • Cold, wet weather

  • Plants less than 6 inches tall

Black root rot

Thielaviopsis basicola

  • Loss of mycorrhizal symbionts

  • Rotting of the cortex tissue

  • Thinner, dark brown to black, discolored taproot

  • Stunting

  • Cold, wet weather

*these risk factors are generally associated with the diseases, though there may be other environmental factors that contribute to disease severity (see Table 2)

Photo of cotton seedlings with "sore shin" phase of disease

Figure 2. Sore shin on cotton seedlings.

NC State Plant Pathology

Disease Cycle

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Survival spores of seedling disease fungi can survive in soil and crop debris for years. Survival structures of Fusarium, Phoma, and Thielaviopsis are chlamydospores. Survival structures of Pythium are oospores, and of Rhizoctonia are sclerotia. In the presence of developing roots and root exudates, survival spores begin to germinate into infecting spores and enter the roots through direct penetration or wounds. The fungi produce spores on infected plants, which serve as the source of secondary inoculum dispersed by wind and splashing rain. Spores will return to soil and persist as survival spores on dead plants and debris.

Disease Management

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Cotton seedling disease management is based on preventative rather than curative treatments. As cotton plants grow to around 6 inches, the stem becomes woody and infection is less likely to occur unless injured.

Cultural Practices

  1. Select seeds with high rates of germination. Seeds with lower germination potential should be planted later when conditions are not as cool or wet.

  2. Planting on beds elevates the seed, allowing for more rapid emergence and improved water drainage, especially after heavy rains.

  3. Low or no-till cotton may increase the frequency and severity of seedling diseases since reduced tillage preserves inoculum that overwinters in crop debris. When planting in reduced tillage situations, using an in-furrow fungicide should be considered.

  4. Rotating crops should also be considered to help prevent the buildup of cotton seedling diseases.

  5. Sanitize and rinse equipment after use to remove soil and spores and prevent spread of soilborne fungi.

Chemical Control

  1. All cotton seed offered for sale in North Carolina are treated with fungicides and insecticides, which are often sufficient for disease management unless the quality of the seed is low or weather conditions are unfavorable for germination.

  2. Assess risk factors (Table 2) for seedling disease development and consider an in-furrow fungicide if threshold is exceeded (Table 3).

  3. Systemic fungicides provide temporary protection (about 5 weeks from planting) from certain types of pre-emergence and post-emergence damping-off.

  4. Control for nematodes in cotton to reduce damage to seedlings.

Table 2. Point System for Determining the Need for In-Furrow Fungicides*
Factor When It Matters Points*
Soil temperature Less than 65°F 75
5-day forecast Colder and wetter 50
Seed quality Cold germination less than 59°F 75
Field history Severe disease 100
Tillage Minimum tillage 50
Row preparation Absent beds 75
Seeding rate Less than 3 to 4 per ft of row 100
Poorly drained soils Consistently saturated 50

*This point system is only a guide as to the probability of cotton seed benefitting from an application of an in-furrow fungicide.

**If total exceeds 200, consider using an in-furrow fungicide

Table 3. In-furrow fungicide options for control of seedling diseases. Table may not represent a complete list of all products registered for control of cotton seedling diseases in North Carolina, and inclusion of the products in the list does not endorse efficacy. Please refer to product labels for application methods, regulations, and compliances.
Fungicide Active Ingredient Rate of Formulation Remarks
Ridomil Gold SL mefenoxam 0.075 to 0.15 oz/1000 row ft Efficacy on Pythium and Phytophthora spp.
Headline SC pyraclostrobin 0.1 to 0.8 fl oz/1000 row ft Efficacy on Rhizoctonia solani
Quadris azoxystrobin 0.4 to 0.8 fl oz/1000 row ft Efficacy on Pythium spp. and Rhizoctonia solani
Proline prothioconazole 0.4 to 0.5 fl oz/1000 row ft Efficacy on Rhizoctonia solani and Fusarium spp.
Priaxor fluxapyroxad + pyraclostrobin 0.1 to 0.6 fl oz/1000 row ft Efficacy on Rhizoctonia solani and Fusarium spp.

Useful Resources

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Assistant Professor and Extension Field Crop Pathology Specialist
Entomology & Plant Pathology

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Publication date: Sept. 6, 2017
Revised: Sept. 29, 2023

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Recommendations for the use of agricultural 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 NC State University or N.C. A&T State University nor discrimination against similar products or services not mentioned. Individuals who use agricultural 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 regulations and examine a current product label before applying any chemical. For assistance, contact your local N.C. Cooperative Extension county center.

N.C. Cooperative Extension prohibits discrimination and harassment regardless of age, color, disability, family and marital status, gender identity, national origin, political beliefs, race, religion, sex (including pregnancy), sexual orientation and veteran status.