How to Manage Pests

UC Pest Management Guidelines


Seedling Diseases

Damping-off: Pythium spp.
Soreshin: Rhizoctonia solani
Black root rot: Thielaviopsis basicola
Fusarium wilt: Fusarium oxysporum f. sp. vasinfectum

(Reviewed 5/13, updated 5/13)

In this Guideline:

Symptoms and Signs

Pythium causes water-soaked lesions on the roots or hypocotyl of infected seedlings. Lesions may collapse and turn light brown. Girdled plants often die. Pythium may rot seeds and seedlings before germination or emergence through the soil.

The main symptoms of soreshin, caused by Rhizoctonia solani, are sunken lesions on the hypocotyl, which are oval- to irregular-shaped and reddish brown. Girdled plants often die.

Black root rot, caused by Thielaviopsis basicola, is characterized by a dark brown to black discoloration and reduced diameter of the taproot of infected seedlings. As the plant ages, healthy tissue replaces decayed tissue, but affected plants may be stunted.

Virulent strains of Fusarium oxysporum f. sp. vasinfectum, the cause of Fusarium wilt, can also kill seedlings. Laboratory analysis is often needed for correct diagnosis of the presence of Fusarium spp. and the exact race of Fusarium.

Comments on the Disease

All seedling diseases are caused by soilborne fungi common to most cultivated soils. The diseases are generally more severe during cool, damp weather that delays seedling growth. As cotton plants grow, they become more resistant to attack.


To reduce seedling diseases, make sure that conditions at planting favor rapid germination and seedling growth so that cotton seedlings quickly outgrow the most vulnerable stage and infection is less likely. Fungicide seed treatments can usually prevent severe losses caused by seedling diseases as long as growing conditions are reasonably good.

Cultural Control

Always use the highest-quality seed you can afford. If possible, select seed that has shown a high rate of germination in a cold test. If you must use lower-quality seed, plant as late as possible to allow the soil to warm up. Regardless of seed quality, never plant if rain or cold weather (i.e. less than 15DD) is expected during the 4 or 5 days following planting. Follow UC Cotton Planting Forecasts issued during the planting season to plant into the most optimal conditions.

Use an adequate seeding rate so that the loss of a few plants to seedling diseases will not leave skips that must be replanted. Don't plant deeper than 2 inches because excessive depth delays emergence and exposes more hypocotyl surface to invasion by fungi.

Soil that is too wet at planting or during germination favors seedling diseases. To avoid excess moisture, allow preirrigated beds to drain adequately before planting, and don't irrigate up the crop during cool weather. Firming wheels on planters operated in wet soil often create a shallow compacted layer that aggravates seedling disease problems. Roots growing through compacted layers may develop constricted, weakened areas vulnerable to infection by fungi and may restrict growth later in the season.

Rotate cotton with sorghum and small grains to reduce inoculum of Pythium and Rhizoctonia.

Monitoring and Treatment Decisions

Always use seed treated with fungicides effective against Rhizoctonia solani and Pythium spp. In cooler areas, especially in early plantings, it is advisable to include a material effective against Thielaviopsis basicola. Supplemental fungicides applied to the soil at planting provide extra protection when cool, wet weather is likely after planting, in fields with a history of severe seedling disease, and in fields that must be replanted due to seedling disease. Assess stand establishment to determine if your crop is growing satisfactorily. Guidelines for stand assessment are available in the online version of this guideline.

Common name Amount to Use
(example trade name) (rate/100 lb seed)

Calculate impact of pesticide on air quality
Bee precaution pesticide ratings
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To treat for PYTHIUM:
  (Apron XL LS) 0.32–0.64 fl oz/100 lbs of seed
  COMMENTS: Apply as a seed treatment to machine-delinted or acid-delinted cottonseed.
To treat for RHIZOCTONIA:
  (Baytan 30) 0.25–0.75 fl oz/100 lbs of seed
  MODE OF ACTION GROUP NAME (NUMBER1): Demethylation inhibitor (3)
  COMMENTS: Higher rates are only for areas with a history of severe seedling disease problems.
  . . . or . . .
  (Nu-Flow M-HF) 1.25–1.75 fl oz/100 lbs of seed
  MODE OF ACTION GROUP NAME (NUMBER1): Demethylation inhibitor (3)
  (Baytan 30) 1–3 fl oz/100 lbs of seed
  MODE OF ACTION GROUP NAME (NUMBER1): Demethylation inhibitor (3)
  COMMENTS: Higher rates are only for areas with a history of severe seedling disease problems.
  . . . or . . .
  (Nu-Flow M-HF) 1.25–1.75 fl oz/100 lbs of seed
  MODE OF ACTION GROUP NAME (NUMBER1): Demethylation inhibitor (3)
1 Group numbers are assigned by the Fungicide Resistance Action Committee (FRAC) according to different modes of actions (for more information, see Fungicides with a different group number are suitable to alternate in a resistance management program. In California, make no more than one application of fungicides with mode of action Group numbers 1, 4, 9, 11, or 17 before rotating to a fungicide with a different mode of action Group number; for fungicides with other Group numbers, make no more than two consecutive applications before rotating to fungicide with a different mode of action Group number.



[UC Peer Reviewed]

UC IPM Pest Management Guidelines: Cotton
UC ANR Publication 3444


  • R. M. Davis, Plant Pathology, UC Davis

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