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Diagnosing and Managing Fruit Tree Trunk Injuries

Apple tree with a canker suspected to be black rot. 
Photo used by permission of the grower.
Author: Annie Klodd, University of Minnesota Extension Educator - Fruit Production. 

Reviewed by: Dr. Bob Blanchette and Dr. Brett Arenz, UMN Department of Plant Pathology

The Great Lakes Fruit Workers Group contributed research-based information to inform this article.


A number of factors including diseases, herbicide damage, insect/animal activity, and winter injury can all contribute to trunk cankers on fruit trees. To complicate things further, these factors can interact. 

For example, winter injury can cause cracks in the trunk, which pathogens can then enter and infect the tree. Treatment of existing trunk cankers is not always possible, but identifying the cause will lead to determining management steps to prevent it from happening again.

Diagnosing fruit tree trunk cankers

Because the causes of trunk cankers are complex, they often cannot be diagnosed reliably by a simple online search or comparing the symptoms to photos. Tree fruit experts, plant pathologists, and Extension educators are more than happy to assist in diagnosing injuries on fruit trees.

This process often involves examining evidence like photos and spray records, and then sending a sample to a university plant diagnostic clinic for identification. The University of Minnesota offers these services at the Plant Disease Clinic. Many other state universities have their own clinics as well.

The clinic will examine the sample via microscope to determine whether a disease is contributing to the problem. On occasion, they may need to make isolations to get pathogens into pure culture, and DNA sequencing can sometimes also be needed to firmly identify the species involved in the disease.

I encourage fruit growers to reach out to me or your local Extension Educator to assist with this process, because we will help provide follow-up information on "next steps" once the problem is diagnosed (more information below).

A high quality, close up photo of an undiagnosed apple tree injury. Photo permission from the grower.

When reaching out to an Extension educator for help identifying a trunk canker, please send photos:
  • Include close-up photos that clearly show the symptoms. 
  • Cut into the bark, and take a photo that shows the wood right under the bark.  
With the photos, please include information about:
  • Irrigation (was the tree irrigated or not)
  • When you first noticed the canker
  • Variety & root stock
  • Does it extend from a wound
  • Herbicides sprayed 
  • Depending on the appearance of the symptoms, we may also ask you what geographical direction the injury is occurring at, and if it is consistent among the affected trees.

If a number of trees are impacted, the grower may be asked to cut down the trunk of one of the impacted trees so that the lab can examine the interior wood. Trunk diseases leave visible discoloration on the interior wood that is helpful and sometimes even necessary to examine for diagnosis.

Potential causes of trunk cankers:

(These descriptions are meant for informational purposes, and are not enough to diagnose the problem)

Black rot (Diplodia seriata): Black rot causes black, blotchy discoloration on the tree trunks and limbs. It is commonly introduced by winter injury. Black rot cannot be treated once it infects the wood, except by pruning out affected limbs.

Fire blight (Erwinia amylovora): A bacterial disease that infects apple blossoms and wounds and moves into the tree. Fire blight causes a "shepherd's crook on small twigs. Antibacterials are used to prevent infection of wounds and flowers. Once the bacterium infects a branch it must be cut out of the tree to prevent infection into the trunk which would require removing the tree.  Some cultivars have resistance, such as Honeycrisp, which is not particularly susceptible to fire blight.

Botryosphaeria dothidea: This is one of the many trunk disease fungi that can cause cankers and tree decline. It gradually kills the tree by girdling the wood and preventing water, carbon, and nutrient transport. Diagnosis requires cutting into the interior wood with a plug or a cross section, and conducting culturing and DNA analysis to identify the pathogen.

Winter injury: Trunk injuries are a symptom of winter damage, and they can be an avenue for subsequent disease development. This occurs frequently with quick periods of freezing temperatures in the late fall, before the trees have hardened off for the winter. Once winter injury is present on tree trunks, pathogens can infect by entering the injured tissues. For example, black rot, mentioned above, could get its start through a winter injury canker.

Cankers directly under a branch may be due to winter injury, as that area is highly sensitive to cold stress in the fall, winter, or spring.

The winter injury that promoted canker development may have occurred several years before the grower notices it, as it grows and becomes infected over time. Therefore it is helpful to know the first time the canker was noticed, but also to keep in mind that if the damage could have originated from a past year.

Herbicide injury: Over the last decade, fruit researchers have discovered that application of glyphosate on or near the trunks of apple trees can contribute to apple trunk injury and disease cankers. Glyphosate application to weeds around the trunk can drift onto the trunk, and frequent contact with the trunk can cause cracking and wounds on the bark. Those wounds can let in disease, and is thought to have led to outbreaks of Botryosphaeria infection in the Northeast.

Cornell University fruit tree researchers also observed that glyphosate that drifts onto lower leaves can make those limbs more susceptible to winter injury, even if the leaves show no visible symptoms. Based on informal on-farm observations, researchers are also examining whether paraquat may impact trunk damage, but this has not been confirmed. Source: Cornell Scaffolds newsletter, March 30, 2020.

For citations and more information on this, read Effects of Glyphosate on Apple Tree Health, a publication from Cornell University.

The complex nature of trunk cankers necessitates a combination of:
  1. Working with an Extension educator, plant pathologist or fruit tree specialist to explore potential causal factors
  2. Submitting a sample to a plant disease clinic to identify or rule out the involvement of plant diseases.
Photo: Annie Klodd, University of Minnesota.


What to do about fruit tree cankers:

In general, the next steps after diagnosing the cause of a trunk canker depend on the diagnosis. Please either contact me directly (kloddann@umn.edu), or contact your local Extension educator, to work through the next steps based on the plant disease clinic report.

If the canker contains black rot or another fungal disease, there are no fungicides to stop the canker from progressing. Trunk diseases, once they enter the wood, are not impacted by fungicides.

If we feel that herbicide application may have led to canker development, we can re-visit your weed management program or discuss strategies to prevent drift from neighboring fields.

If the canker is consuming a large part of the trunk and impacting the health of the tree, the tree will either need to be removed or allowed to live out its remaining years as it declines in health. The grower can also attempt to regrow the tree from the base by cutting off the entire trunk well below the canker and re-growing the tree from a water sprout that comes up from the cut stump. The formation of water sprouts is not guaranteed, however, and it is usually more feasible to plant a new tree. This decision depends on the scale of the orchard and goals of the grower.

Author: Annie Klodd, University of Minnesota Extension Educator - Fruit Production. 

Reviewed by: Dr. Bob Blanchette and Dr. Brett Arenz, UMN Department of Plant Pathology

The Great Lakes Fruit Workers Group contributed research-based information to inform this article.

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