Early-Season Diseases in Cotton

April 12, 2022


  • Cotton seedlings can be infected by several different fungal pathogens that may result in reduced yield potential.

  • Other stress factors, such as insect and nematode injury, environment, and soil conditions can impact the severity of disease.

  • Utilizing the best agronomic practices and fungicide seed treatments can reduce potential yield losses from early-season diseases.


Early-season diseases may occur in all soil types but are more often found in wet and poorly drained soils. Reduced tillage systems, soil compaction, planting to deep slowing emergence, and flat planting (without beds) may contribute to an increased incidence of soil borne diseases. Nematode and thrips damage can delay seedling growth and intensify damping-off caused by Pythium species. Symptoms of early seedling injury include decayed seeds or seedlings, delayed and uneven emergence, girdling of seedling stems, and rotted roots. Damaged seedlings are pale to chlorotic, stunted, slower growing, and may die within a few days after emergence. The taproot is often destroyed, leaving only shallow-growing lateral roots to support the plant.1

Management tactics2

Seed bed preparation. Maintain soil pH above 5.5 and below 7.0 to help insure good, even seedling emergence. Low levels of phosphorus and potassium retard seedling emergence. Ensure that pH and soil nutrient levels are adequate for the optimum growth, yield, and quality.

Soil Temperature. Plant when soil temperature is above 65 °F, at a 4-inch depth, and 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 by optimizing soil temperatures at planting on soils that cannot be bedded, such as those in a conservation tillage program.

Seed Quality. Plant seeds that have adequate warm test and a cool test germination percentage. In general, the warm germ test (about 86° F) will estimate the percent emergence under highly favorable conditions, while the cool germ test (64 ° F) will estimate emergence under more typical, somewhat adverse conditions. The minimum acceptable percent germination percentage for cotton planting seed are 80% on the warm test and 50% on the cool test. The warm germination test percentages are printed on most seed tags. Growers should ask their seed dealer for the warm and cool germ test results for each lot of seed, and should only plant seed that germinates well, especially when planting early or in heavy soil. Fungicide seed treatments on most commercially sold seed are there to protect seed from rot and are helpful in suppressing disease to achieve a uniform stand.

Planting. Planting seed too deep can extend the time required for emergence, increasing the risk of infection by plant pathogens.2

Scouting. Scouting for symptoms of early-season issues such as diseases and insects can help identify potential problems, which may help in the future and in some cases allow time to apply a remedy for the current season.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 possible pathogens carried on the seed or soil-borne pathogens that may directly come in contact with the seed. Systemic fungicides are taken up by the seedling to provide protection from certain types of pre- and post-emergence fungi causing damping off symptoms. 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.

Identification of early-season cotton diseases

Click on the disease for more information

Rhizoctonia Infection
Figure 1. Rhizoctonia infection. Photo courtesy of Clemson University - USDA Cooperative Extension Slide Series, Bugwood.org.

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.

Pythium Infection
Figure 2. Pythium infection. Photo courtesy of Howard F. Schwartz, Colorado State University, Bugwood.org.

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 Infection
Figure 3. Fusarium infection. Photo courtesy of Clemson University - USDA Cooperative Extension Slide Series, Bugwood.org.

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.

Blcak root rot
Figure 4. Black root rot. Photo courtesy of G.J. Holmes, Bugwood.org

Black root rot

  • Region: Texas, Arizona, Missouri, Alabama
  • The tap root and exterior of hypocotyl turn black (Figure 4).
  • Does not usually cause plant death, but can kill lateral roots, stunt plants, and delay flowering.
  • Occurs more often in clay soils than sandy soils.4,5

Ascochyta blight of cotton
Figure 5. Ascochyta blight. Photo courtesy of Clemson University - USDA Cooperative Extension Slide Series, Bugwood.org.

Ascochyta blight of cotton

  • Region: Cotton Belt
  • Also referred to as wet weather blight or cotton stem canker
  • 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.


1 Koenning, S. and Collins, G. 2016. Disease management in cotton. 2016 Cotton Information. North Carolina State University. http://cotton.ces.ncsu.edu/.

2 Roberts, P. Editior. 2021. 2021 Cotton production guide. The University of Georgia Cooperative Extension Service. http://www.caes.uga.edu/.

3 Boyd, M.L., Phipps, B.J., and Wrather, J.A. 2004. Cotton pests scouting and management. University of Missouri Extension. IPM 1025. http://extension.missouri.edu/.

4 Texas Plant Disease Handbook. Cotton Gossypium hirsutum. Texas A&M AgriLife Extension. http://plantdiseasehandbook.tamu.edu/.

5 Cotton seedling disease identification. The National Cotton Council. http://www.cotton.org/.