Are the conditions right for sclerotinia in canola?

There are a few points to remember when considering a fungicide application for sclerotinia in canola this year:

  • In order for sclerotia to germinate and produce apothecia, they require at least 10 days of moist soil conditions (surface soil – as we aren’t concerned with sclerotia that are buried more than an inch or two below the surface).
  • Spores cannot infect leaves and stems directly – they grow on senescing tissue (i.e. canola petals) and then spread to the leaves and stems.
  • Dew/rainfall after petal drop is required for the pathogen to spread from the infected petals to the stem. Petals that dry up in leaf and branch axils without any moisture will not spread the infection.
  • The recommended timing for a fungicide application for sclerotinia management in canola is 20-50% bloom. This is because typically the canopy has filled in after 50% bloom. Petals can still be infected after 50% bloom, but when they fall, they tend to land on upper branch axils. Infection that only affects minor upper branches will not have a large impact on yield. If a crop is stagey or the canopy thin, infected petals may land on lower leaf and branch axils even after 50% bloom and infect the main stem. As long is there are petals present on the plants there is potential for infection to occur, the question is where will those petals land when they fall?
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Should I Spray my Sunflowers for Sclerotinia Headrot?

Sclerotinia in sunflowers can be frustrating and devastating, especially in the form of headrot. Headrot is very weather related. It needs rainfall to wet soils stimulate sclerotia to produce apothecia mushrooms and ascopores. Ascospores once on disk petals, need prolonged wetness to allow the infection and growth of the fungus on the petals and spread into the sunflower head tissue.

It takes approximately 14 days after a “ground soaking” rainfall for the mushrooms to appear and produce ascospores.  In 2016, most areas in Manitoba have saturated soils, making an ideal environment for apothecia emergence, which could be the start of the lifecycle to cause sclerotinia head rot in sunflowers.

Weather data can be used in combination with a risk calculator to determine if a fungicide is needed.  You can find the Manitoba Agriculture calculator here

It has only been in the past couple of years that sunflower growers have had fungicide registered to control headrot.  With limited use of use, control has been not always been what was expected.  The fungicides available are protectant and work to protect plant when disease infection potential present.  If there was infection prior to application, or, if pressure remains high after application, control may be less than expected.

National Sunflower Association of Canada has put out a bulletin talking about sclerotinia headrot control in sunflowers in 2015 and can be found at


Submitted by: Anastasia Kubinec, Manitoba Agriculture, Oilseed Crop Specialist


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Over the Course of Time: Manitoba Canola Diseases 2009-2014

Canola is one of the most economically important crops produced in Manitoba and yield robbers such as canola diseases need to be identified in order to apply best management practices. For many years, sclerotinia has been the most significant canola disease in Manitoba. However, in recent years the prevalence (% of fields infested) and incidence (% plants infected per field) of blackleg have been increasing.

Disease incidence and severity will change from year to year based on use of genetic resistance in varieties, environmental conditions, and agronomic practices such as crop rotation and fungicide use. Annual surveys of commercial canola crops provide valuable information on the distribution of disease, impact of farming practices on severity and incidence, help agronomists and farmer prioritize where future resources need to be directed, and can provide an early-warning system that provides information on the occurrence of disease/pesticide breakdown.

For more information on the annual Manitoba canola disease survey including methods, results from 2009 to 2014, and further discussion, please view the attached poster which was presented at the 2014 Manitoba Agronomists Conference:

Over the Course of Time Manitoba Canola Diseases 2009_2014 (Kubinec et al., 2014)

For more information on canola diseases in Manitoba, and information on various types of control methods, please visit MAFRD’s website at
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When is the Best Time to Spray Sunflowers for Head Rot?

With the registration of fungicides for sclertotinia head rot control in sunflowers, growers have an excellent management tool for reducing the impact of an economically devastating disease.

As the products and use is new to many growers, there are a number of question on timing.

  • Sunflower staging : Target the R5.1 to R5.2 stage (10-20% disk flowers open)
  • Field staging: 50-80% of heads at R5.1 to R5.2
  • Number of applications: Depends of product. If registered and conditions good for infection a second application can be made 12-14 days after the first application


Expert advice from Dr. Khalid Rashid, Pathologist with AAFC Morden, who has tested the head rot fungicides and sunflower staging timing for over 10 years is that:

“The growth stage of R5.1-R5.2, until end of flowering( 3 weeks window) is the most susceptible stage.  The main factors for susceptibility are the availability of ascospores from mushroom production in adjacent fields (less are produced in the sunflower fields), and there is humidity in the air and on the sunflower heads, for ascospores to germinate and infect the heads.    Sometimes, a second application 2 weeks after the first application may further reduce the disease infections.   In some years/some fields get high late infection after the end of flowering due to a flux of ascospores production late in the season coupled with favourable humidity/rain conditions.”

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Assessing Canola for Swathing Timing? Why Not Look for Diseases Too!

Prepared by Anasatsia Kubinec, MAFRI Oilseed Crop Specialist

Once your canola comes out of flower the countdown is on to swathing and then harvest. 

The prime stage to be swathing is at 50-60% seed color change.  On the plants that looks like the bottom 1/3 of the plants pods have mostly black/brown seeds, the middle 1/3 has 50% brown/black seeds and the top 1/3 seeds are firm when rolled between your fingers and at there are some seeds that can be found to have spots started turning brown.

While out there staging for swathing, scout for the diseases your canola field has too.  Scouting at this stage does not mean control, but it will give you and idea of diseases the crop has and how you can plan for your next canola crop in that field.

Examine the plants from root to top.  What do you see:

Leaves – yellowing and lesions – could be blackleg, look also for black pepper spots that could be blackleg (raised black spots that don’t rub off or smear).  No black spots – it could be alternaria which will also have concentric rings in the lesion.  Just yellow but lesion look ‘water-soaked’, that may be the start of sclerotinia

Stems – grey/white lesions – does the spot ‘shred’ when you scratch the lesion, then is is probably sclerotinia.  Does the lesion have black pepper spots and does not shred – then it is probably blackleg. Is there entire portion of the stem that are grey and hollow, but not shredding or no black spots?  Then is may be grey stem. 

Base of plant – see pinching?  It could be a root rot.  If you cut through the base of the stem and see blackening in the base that is blackleg.

Get what you see confirmed by your agronomist or take the plants to your local MAFRI office to be confirmed.  Then write the diagnosis down.  Management options like longer time between canola crops, variety selection and fungicide use can be integrated into your future cropping plans and reduce the amount, and severity of the above diseases in the future.

For more information also see Canola Council of Canada CANOLA WATCH for July 31, 2013

SCLEROTINIA on STEM – note the shredding. Photo from Anastasia Kubinec, MAFRI

BLACKLEG on STEM – see black pycnidia or “pepper spots.” Photo from Anastasia Kubinec, MAFRI

BLACKLEG found when cutting through canola crown.
photo from Anastasia Kubinec, MAFRI


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Plan Ahead to Reduce Head Rot in Sunflowers

Prepared by Anastasia Kubinec, MAFRI Oilseed Crop Specialist

Sclerotinia Head Rot in sunflowers costs growers money.  It will reduce yields due to small and diseased seeds as well as seeds falling on the ground before the combine can pick them up.  It also reduces the quality of the saleable product leading to price reductions at the delivery point.

Fungicides are registered for the suppression of Head Rot in sunflowers just like products are available for suppressing sclerotinia in canola.

Application timing is R5.1 with a second application 7 to 14 days after the first application if environmental conditions and pressure remains high.  

See in pictures sunflower stages at:

With the weather lately being more conducive to the development of sclerotinia, you may want to speak with your retail the availability of a fungicide for your cropping needs.  The fungicide products that are registered for use in sunflower to control Sclerotinia Head Rot are the same ones registered for use in canola, pulses and other crops.

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Should I Spray My Canola a Second Time for Sclerotinia?

Prepared by Holly Derksen, MAFRI Field Crop Pathologist

Probably not. We only see consistent results from a fungicide application to help control sclerotinia in canola when the application is made prior to the 50% bloom stage. Even if your canola has been flowering for a long period of time this year if your bloom stage is past 50% it is unlikely that you will see a benefit from a fungicide application at this stage.

Petals that are present in the later flowering stages may become infected with sclerotinia, but at this stage your canopy has filled in so when these petals fall they are landing in upper leaf axils. Infection of the stem in these upper portions is unlikely to have a big yield effect. However, at 20-30% bloom – that key timing for a sclerotinia fungicide application – petals that fall land on lower leaf axils and are more likely to cause infection on the main stem and potentially wipe out an entire plant. In any year, one well-timed fungicide application, at 20-30% bloom (but definitely prior to 50% bloom!), will provide the best economic return (assuming there is disease pressure).

For more information, check out Real Agriculture’s Canola School Episode on Sclerotinia Control – Assessing Bloom and Why 50% Bloom Can Be Too Late

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Manitoba Sclerotinia Risk Assessment Update

MAFRI currently does not produce sclerotinia risk maps like we do for Fusarium Head Blight, as we do not have a proven and consistent model to forecast sclerotinia risk. 

Since Manitoba producers grow multiple sclerotinia susceptible crop (canola, soybean, sunflower, dry bean, etc.), the inoculum is present in the environment, but risk and disease development is dependent on a combination of inoculum as well as day/night temperature, precipitation, crop canopy and soil moisture, which can vary from field to field.

 Scout and monitor your fields, you may be at greater risk and require a fungicide application if you have the following conditions:


  • Ground is damp to wet and,
  • Canopy is moderately closed to closed (i.e. you cannot see the ground through the leaves), and
  • Canopy is still damp to wet when walking through the field at 10am (i.e. your pants are wet), and
  • Field is at 20 – 50% flowering (you are wanting to cover the petal so when it falls into a humid canopy, it won’t be a viable food source for the sclerotinia to start on).

 Conditions can change throughout flowering.  If the canopy is somewhat open and dry at 20% flower you may not feel that you need to spray, but if there is a rainfall event and the canopy is wet at 30 – 40% flower, you may want spray then.

 Dry Bean:

  • Ground is damp to wet and,
  • Canopy is moderately closed and is continuing to close, and
  • 50 – 80% of the Field has started to flower (at least one open flower per plant)
  • Dry bean may require a second application at full flower, depending on the precipitation, temperature and canopy moisture

 Sunflower (for Sclerotinia Head Rot only) :

  • Ground has been damp to wet for the past week, and
  • Plants are at R5 (sunflower face is open with ray petals out, but pollination has not yet started)

Spraying for sclerotinia in soybean is not being considered at this time as flowering has not yet occurred. Damage and economic loss in soybean has only occured in one growing season on record. Sclerotinia development can occur under extreme wet and cool conditions, or the crop is significantly lodged and further information will be posted if these conditions do occur later on in the 2013 growing season. 

Canola Council of Canada July 3, 2013 New Release – Moisture Raises Sclerotinia Stem Rot Risk                                                    

NSDU Sclerotinia Risk Map  Please note this is based on temperature and precipitation only and is not based on individual field conditions


Prepared by:  Anastasia Kubinec – MAFRI Oilseed Crop Specialist  and  Holly Derksen – MAFRI Field Crop Pathologist

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Managing Wheat and Canola Disease With Fungicides

With rainfall throughout the province in the past week and crops advancing into heading/flowering, the need for fungicide crop protection products to protect canola and wheat crops is probable.  The attached document outlines ideal conditions for disease development, and management timing based on crop stage.

It is important to note that fungicides work to control disease, spraying in the absence of disease is an extra cost without the yield benefit.

Managing Disease with Fungicide Fact Sheet: Fungicides Fact Sheet

Prepared by Holly Derksen, MAFRD Field Crop Pathologist

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Why Do Sunflowers Do Poorly After Canola?

We don’t know all the reasons that sunflowers seem to do so poorly after canola, but the most likely culprit  is sclerotinia.  Sclerotinia kills or greatly reduces sunflower yields in three ways, throughout the season – basal rot (early), mid-stalk (mid-summer) and head rot (late summer).  Canola is also a host for the disease and sclerots from a previous year infection would be present and germinating  in very close proximity to the sunflower plants.  This would provide prime opportunities to cause multiple plants to be infected at different times in a growing season.  Yields  reported to MASC (MB Agricultural Services Corp.) in the Harvest Acreage Reports from 1998 to 2007, show sunflowers after canola yielding 87% as compared to the overall average sunflowers yield.

Other issues contributing to the yield reduction may also include common insects between crop species grown in succession, herbicide carryover, soil moisture availability and nutrient availability. 

For more information on growing sunflowers see:

Specifically on Sclerotinia in sunflowers: 

Information on Re-cropping Restrictions for Residual Herbicides see the Guide to Field Crop Protection at:


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