Seedling Diseases and Management in Cotton

I’ve had a few questions this week about cotton seedling diseases and thought it worthwhile to share a section of the 2019 Georgia Cotton Production Guide from Dr. Bob Kemerait.  The section on seedling diseases and management can be found on pages 107-109 of the guide.  It can also be found below.  

If you have any questions about particular treatment options or need help diagnosing issues, contact your local UGA County Extension Agent.

Here’s to a great 2019 Georgia cotton crop,




Seedling Diseases
Seedling diseases are widespread but typically not a major problem in Georgia cotton in most years. However, economic loss to seedling diseases can be significant at specific locations, especially when weather conditions are cool and wet at planting time and the grower is not able practice good crop rotation. Seedling diseases are caused by fungi that either survive on the seed or that live in the soil and infect seeds or developing seedlings. By far, the most common cause of seedling disease in Georgia is the fungus Rhizoctonia solani; however Pythium spp. and Fusarium spp. May also damage young plants. Generally as the young plant matures it becomes less susceptible to infection by these pathogens.

Seedling diseases are differentiated by the stage of development of the seed and young plant when symptoms occur.

  1. Seed rot is the first disease in this sequence and is easily identified by the presence of decayed seed; however the problem is often detected only after the grower notices “skips” in the stand. Seed rot may be caused a number of different fungi that can exist either in the soil or on the seed itself.
  2. The second disease in this sequence is pre-emergence damping-off where a fungal pathogen attacks the young seedling after germination but before it cracks the soil surface. Like seed rot, pre-emergence damping-off results in skips in the stand.
  3. Post-emergence damping-off occurs once the seedling has emerged from the soil. It is identified by the presence of a brown lesion at, or just below, the soil line that will eventually expand and girdle the young, succulent stem. Once the stem is completely girdled, the young plant will quickly wither and die. In the case of “hill-dropped” cotton, it is a common that if one seedling in a hill is diseased, all of the seedlings will be affected. Post-emergence damping-off is often referred to as “soreshin” in Georgia and is caused by the fungus Rhizoctonia solani. It is perhaps the most common seedling disease of cotton in the state and the one with which growers are most familiar. Although seedling disease caused by Pythium spp. is less common, it still occurs and is characterized primarily by a water-soaked root rot, either before or after emergence. As will be discussed later, it is important to identify the pathogen(s) that is/are responsible for seedling disease in a field as Rhizoctonia solani and Pythium spp. may not be controlled by a single fungicide

Management of Seedling Diseases
Control of seedling diseases of cotton begins with the use of a fungicide seed treatment. All commercial seed sold in Georgia is pre-treated with at least two fungicides. Growers should never plant cotton seed that has not been treated with a fungicide. Seed companies continue to incorporate more effective chemistries in their fungicide seed treatment package. Growers can reduce the effect of seedling diseases by avoiding conditions in which seeds/seedlings are at risk to damage from fungal pathogens. Cool, wet weather at planting and low soil temperatures produce an environment that not only slows germination and emergence, but may also favor fungal growth and infection. Pythium can be especially troublesome in saturated soils; Rhizoctonia solani is less dependent on soil moisture or temperature. NOTE: Growers should avoid planting cotton seed when rain and colder soil temperatures are likely, even if seedling disease is not an issue. Rapid germination and vigorous growth by the seedling are factors which help to insure the survival of the young plants. Slower growth early in the season gives the fungal pathogens more time to infect the vulnerable seed and seedling. The sooner the seedling develops hard, “woody” tissue, the less likely it is to be penetrated and rotted by fungi.

Good management practices to reduce the chance of disease include the following:

  • Plant in warm soils where the temperature at a 4-inch depth is above 65°F and where the 5-day forecast doesn’t call for cooler or cooler/wetter weather. NOTE: Cotton growers should NOT plant cotton if at all possible when conditions are cool and wet or if the forecast calls for such conditions soon after planting, even if they plan to use additional fungicide treatments!
  • Plant seed on a raised bed since soil temperatures in the bed are generally slightly warmer than surrounding soil and drainage is likely to be better. Cotton planted in conservation tillage is not grown on raised beds, thus potentially increasing the threat from seedling disease.
  • Avoid planting seed too deeply. Seed that is planted too deeply results in longer periods before the young seedling cracks the soil surface, increasing the likelihood of seedling disease.
  • Correct soil pH with lime (pathogenic fungi are more tolerant to acidic soils than are cotton seedlings; pH should be in the range of 6.0 to 6.5).
  • Fertilize according to a soil test so as to promote rapid seedling growth; however care should be taken to avoid “burning” the seedling with excessive rates of at-plant fertilizers.
  • Avoid chemical injury through the use of excessive amounts or improper application of insecticides, fungicides, or pre-plant herbicides.
  • Plant only high quality seed as indicated by the percent germination in the standard seed and cool germination tests. Preferably, cool germination test results should be above 70%, though 60-69% is still adequate. Additional seed treatment fungicides such as Dynasty CST, Trilex advanced, and Acceleron, beyond the “base” treatment can significantly reduce the amount of seedling disease, increase stands, and potentially improve final yields where conditions are favorable for disease development. However, significant outbreaks of seedling diseases are a sporadic problem. Because we cannot reliably predict which years will have greater amounts of seedling disease, growers can become justifiably frustrated when trying to determine the economic benefit of the additional fungicide.

As significant yield losses to seedling disease are sporadic in Georgia, UGA Extension does not recommend an additional fungicide treatment for each and every cotton field. Numerous field trials have been conducted by researchers at The University of Georgia assessing the benefits of seed treatments, hopper box treatments, and in-furrow fungicides. It has been very difficult to document significant yield benefits from these products despite increases in stand that may occur.

When a grower is assessing the need for additional protection from seedling diseases, he should note the following:

  • Any field with a history of cotton seedling diseases should be considered a prime candidate for the use of these additional fungicides and seed treatments.
  • This is especially true when a poor history is combined with any combination of the following: a. cool, wet weather at planting, b. poor seed quality, c. conservation tillage (which tends to keep the soil cooler and perhaps moister than conventional tillage), d. a low seeding rate, or e. the use of an in-furrow insecticide or nematicide. The risk for losses to seedling disease increases in fields where multiple factors, as described above, apply.

Final note on seedling diseases: It is important to understand that fungicides which are effective on Rhizoctonia solani may not be effective on Pythium spp., and vice versa. For example, PCNB is active against Rhizoctonia but not Pythium. Metalaxyl, mefenoxam, and etridiazole are active on Pythium spp. but not Rhizoctonia.

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