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).

Figure 1. Cotton standing with stunting and damping off symptoms

Plant Disease Insect Clinic

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Figure 1. Cotton standing with stunting and damping off symptoms

Plant Disease Insect Clinic

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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.

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.

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

Figure 2. Sore shin on cotton seedlings.

NC State Plant Pathology

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Figure 2. Sore shin on cotton seedlings.

NC State Plant Pathology

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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.

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.

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*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 ↲

• The NC State University Plant Disease and Insect Clinic provides diagnostics and control recommendations.
• The NC State Extension Plant Pathology Portal provides information on crop disease management.
• The North Carolina Agricultural Chemicals Manual provides pesticide information for common diseases of North Carolina. The manual recommendations do not replace those described on the pesticide label, and the label must be followed.
• For assistance with a specific problem, contact your local N.C. Cooperative Extension agent.