Stamp out disease! What do you need to know?

Developing an Integrated Disease Management strategy for your farm

Effective disease management should be integrated within the management of the whole farm, focusing on the host, the potential pathogen, and the environment. The implementation of basic disease management strategies, even where a significant disease problem is not evident, will reduce the risk of future outbreaks.

It is important be informed about what  diseases are present and where they occur on your farm to implement management strategies which can assist with minimising the severity and spread of diseases. Growers and agronomists can  conduct their own early and late season disease surveys to monitor and record findings allowing comparison over time. Farm staff should be trained to look for and report unusual symptoms in the crop. Contact your state department cotton pathologist for assistance in identifying suspected diseases and to confirm pathogen strain.

Pathogen control

Come Clean Go Clean:

Prevention is better than cure. Preventing a pathogen from entering your farm is far easier than managing a disease.  Managing machinery and vehicle movements within the farm and implementing a strategy for ensuring clean movement of machinery and vehicles onto and around the farm will minimise the risk of moving disease from field to field, farm to farm, and region to region. Ensure that you communicate your Come Clean Go Clean requirements to all staff, contractors and visitors before they reach the farm. It also pays to minimise spillage and loss when transporting modules, hulls, cotton seed or gin trash. More information on Come Clean Go Clean can be found on the biosecurity page of this site, and in the CottonInfo Come Clean Go Clean fact sheet

Control alternative hosts and volunteers: 

Implementing a host free period prevents the buildup of disease inoculums and carryover of disease from one season to the next. The pathogens that cause Verticillium wilt, Fusarium wilt, Black root rot, Tobacco Streak virus and Alternaria leaf spot can also infect common weeds found in cotton growing areas. A host free period is particularly important in the control of disease such as Cotton Bunchy Top that can only survive in living plants. Controlling alternative hosts, especially cotton volunteers and ratoons helps reduce the risk of disease outbreak.

Crop residues: 

Crop residues should be managed to minimise carryover of pathogens into subsequent crops. Incorporate crop residues as soon as possible after harvest, except where Fusarium wilt is present. Where Fusarium wilt is present, residues should be slashed and retained on the surface for at least one month prior to incorporation. Fusarium wilt can also survive and multiply on the residues of non-host crops such as cereals, some legumes and canola. Current recommendations are that residues of all crops should be incorporated or removed as soon as possible after harvest.    

Crop rotations: 

Successive crops of cotton can contribute to a rapid increase in disease incidence. A sound crop rotation strategy should be employed, using crops that are not hosts for the pathogens present. The Cotton Rotation Finder (listed under tools, below), the Australian Cotton Production Manual, and the Cotton Pest Management Guide can assist in understanding how rotation crops will impact disease load. 

Insect vectors: 

Diseases caused by a virus or phytoplasma can often be prevented by controlling the vector that carries the pathogen. For example, Cotton Bunchy Top (CBT) can be transmitted by aphids feeding on infected plants then migrating to healthy plants. Appropriate IPM should always be considered when controlling pests. 




Managing the host crop:

A healthy crop is more able to express natural resistance to disease.  Strong seedling vigour can also assist the plant to cope with pathogens. A balanced approach to crop nutrition, especially with nitrogen and potassium, will make plants less susceptible to disease. Both deficiencies and excesses can create favourable conditions for the development of diseases such as Verticillium wilt and Alternaria leaf spot. Excess nitrogen greatly increases the risk of boll rot, particularly in fully irrigated situations.

Resistant varieties: 

A particular plant may be immune, resistant or susceptible to disease. The term ‘tolerant’ implies reasonable yield performance despite the presence of disease. Disease risk is greater in back to back fields increasing the importance of planting resistant varieties. There are a number of varieties that have good resistance to Verticillium wilt or Fusarium wilt, with the levels of resistance indicated by higher V-rank or F-rank respectively. In addition to resistance, consider the seedling vigour of a variety particularly when watering up or planting early. 

Managing environmental conditions:

Altering row or plant spacing, changing irrigation method or frequency, or changing sowing date are means of manipulating environmental conditions to be less conducive to infection and disease spread in the host plant. 


Planting into well prepared, firm, high best will optimise stand establishment and seedling vigour. Carefully positioned fertiliser and herbicides in the bed prevents damage to plant roots. Fields should have good drainage and not allow water to back-up and inundate plants. Ideal soil temperatures for cotton establishment are 16–28 degrees celcius. Temperatures below this can result in slow emergence and increased chance of attack from soil pathogens such as the Black root rot pathogen and insects. Where possible delay planting until conditions are suitable.

Irrigation scheduling:  

Applying water prior to planting provides better conditions for seedling emergence than water after planting, as the water can drop the soil temperature further. Root systems weakened by disease can show water stress early in the season, and should be irrigated accordingly. Waterlogging should be avoided, particularly later in the season when temperatures are cooler.

Agronomic management:  

High planting rates can compensate for seedling mortality but a dense canopy favours development of bacterial blight, Alternaria leaf spot and boll rots. Avoid rank growth and a dense canopy with optimised nitrogen and water and the use of growth regulators where required. Considering an early planting date, or a delayed harvest, may be an appropriate response to various disease problems. In fields where Fusarium and/or Verticillium wilt is present, avoid inter row cultivations after seedling stage as mechanical damage to the roots provides a site for infection by the pathogen.

So, what should you do on your farm?

  • Monitor crops for disease symptoms - this information is valuable and is used to identify where the disease occurs on the farm and its impact over time.
  • Where pathogens are known to be present, plant resistant varieties where possible to assist in controlling diseases.
  • Utilise industry pathology services when unusual symptoms or new disease are present. Use this form to send a plant sample for diagnosis. Ensure all farm personnel, contractors and visitors, where possible, are made aware of diseases on farm and unusual disease symptoms are reported. 
  • Implement an integrated disease management strategy across the whole farm, with tactics including optimal planing date and temperature, nutrition and irrigation. 
  • Control volunteer and ratoon cotton throughout the year.
  • Manage crop residues and consider crop rotations based on best practice for diseases present in the field.
  • Ensure vehicles, equipment and people have followed Come Clean Go Clean principles.

visit the myBMP Disease Management module for more information on disease management

Where should I go for more information?

Cotton pathologists:

Dr Linda Smith – QLD Department of Agriculture and Fisheries 
Phone: 07 3708 8456
Mobile: 0457 547 617

Dr Duy Le – NSW Department of Primary Industries
Phone: 02 6799 1530
Mobile: 0439 941 542

CottonInfo Technical Lead:

Amanda Thomas - Extension Technical Lead for Disease
Mobile: 0417 226 411