Causes and Management of Early-season Cotton Diseases


  • Cotton seedling diseases are caused by several different soil fungi and can significantly reduce yield potential.
  • Insect and nematode populations, environment, and soil conditions can impact disease probability and pressure.
  • Implementing good management practices and use of seed treatments can reduce potential damage from early-season diseases.


Early-season diseases occur in all soil types, but occur more often in wet and poorly-drained soil conditions. Conservation tillage, compacted soil, flat planting, and planting too deep can contribute to a higher incidence of disease. Nematode and thrips damage can delay seedling development and intensify damping-off. Symptoms include decayed seeds or seedlings, delayed emergence, partial or complete girdling of seedling stems, and root rot. Damaged seedlings are pale, stunted, slower growing, and can die within a few days after emergence. The taproot is often destroyed, leaving only shallow-growing lateral roots to support the plant. Stands may be slow-growing with skips in the rows.1


Soil Prep. Prior to planting, be sure the soil pH is within the 6.0 to 6.5 range. Apply fertilizer according to soil test results to help speed germination. For more information refer to the Agronomic Spotlight - Cotton Fertility​.

Plant when soil temperature is above 65 °F at a 4-inch depth, with a favorable 5-day weather forecast. Germinating cotton seeds can be injured when soil temperatures fall below 50 °F. Planting into raised beds may improve soil temperature and drainage. It is important to mitigate potential disease risk on soils that cannot be bedded, such as those in a conservation tillage program.

Seed Quality. Plant high-quality seed with standard germination test results of at least 80%, or cool germination test results of above 70%.2

Planting. Planting seed too deep can extend the time required for emergence, increasing disease opportunities.2 For more information refer to the Agronomic Spotlight - Cotton Planting and Stand Establishment​.

Scout. Scout for symptoms of early-season diseases while scouting for early-season insect damage.3

Seed Treatments. Fungicide seed treatments can provide cotton seedlings with adequate broad-spectrum protection from early-season diseases. Seed treatment fungicides may be either protectants or systemics. Protectant fungicides protect the seed from a possible disease carried on the seed or soil diseases that may be in direct contact with the seed. Systemic fungicides are taken up by the seedling to provide protection from certain types of pre- and post-emergence damping off. Most commercial cotton seed sold is pre-treated with both protectant and systemic fungicides.

Premium seed treatment packages with higher use rates are available to help provide more complete and consistent protection in high disease pressure situations.

Figure 1. Rhizoctonia damage. Source: Clemson University - USDA Cooperative Extension Slide Series,

Rhizoctonia solani.

  • Region: Cotton Belt
  • Described as “sore-shin” due to the reddish-brown lesions girdling the stem at the soil line.
  • Stem may be weakened at lesion site and plant growth may be stunted (Figure 1).
  • Plants injured by sand blasting are particularly susceptible to this pathogen.
  • Less dependent on wet, cool conditions and can be found in either wet or dry soils with warmer soil temperatures.
Figure 2. Pythium root damage. Source: Howard F. Schwartz, Colorado State University,

Pythium spp.

  • Region: Cotton Belt
  • Typically has a water-soaked, almost translucent lesion at the soil line.
  • Can have a peeled back outer root layer creating a ‘wire root’ appearance (Figure 2)
  • Problematic in soils saturated for an extended period.

Fusarium spp.

  • Region: Cotton Belt
  • Causes wilted plants even in adequate soil moisture.
  • Plants may be stunted with interveinal chlorosis in the leaves.
  • Vascular tissue inside stem may be brown and damaged, limiting soil moisture and nutrient uptake.2
  • May be found in conjunction with root-knot nematode infestations, as nematodes can injure young roots and increase severity of disease.
Figure 4. Symptoms of Thielaviopsis basicola. Source: Texas A&M University.

Thielaviopsis basicola

  • Region: Texas, Arizona, Missouri, Alabama
  • Also called “black root” as tap root and exterior of hypocotyl turn black.
  • Typically does not cause plant death, but can kill lateral roots, stunt plants, and delay flowering.
  • Occurs more often in clay soils than sandy soils.4,5
Figure 5. Cotton seedlings infected by Ascochyta gossypii. Source: Clemson University - USDA Cooperative Extension Slide Series,

Ascochyta gossypii (Phoma exigua)

  • Region: Cotton Belt
  • Cotyledons may turn brown and die prematurely (Figure 5).
  • Hypocotyl can also be attacked, killing affected plants.
  • More common in foggy conditions and when night temperatures are in the 50’s.1
  • Usually sporadic and plants may recover once warm, dry weather returns.
  • Also referred to as Ascochyta Blight, Wet Weather Blight or Cotton Stem Canker.

1 Koenning, S. and Collins, G. 2016. Disease management in cotton. 2016 Cotton Information. North Carolina State University.

2 Whitaker, J., Culpepper, S., Freeman, M., Harris, G., Kemerait, B., Perry, C., Porter, W., Roberts, P., Shurley, D., and Smith, A. 2017. 2017 Cotton production guide. The University of Georgia Cooperative Extension Service.

3 Boyd, M.L., Phipps, B.J., and Wrather, J.A. 2004. Cotton pests scouting and management. University of Missouri Extension. IPM 1025.

4 Texas Plant Disease Handbook. Cotton Gossypium hirsutum. Texas A&M AgriLife Extension.

5 Cotton seedling disease identification. The National Cotton Council.

Web sources verified 02/14/18.

ID 140512014102

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