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What's to Blame? A Lesson in Plant Disease Diagnosis​

Lauri A. Lutes and Jay W. Pscheidt

De​​pt. of Botany & Plant Pathology, Oregon State University, Corvallis, OR


Many plant pathology-related careers require skills in systematic diagnosis, from growers to field representatives and extension agents to individuals with specialized training working in academia, the government, and industry. Similar to detective work, diagnosing disease problems requires a close attention to detail to determine an accurate diagnosis.

In this case, a scenario unfolds in which a grower noticed an issue with their crop, then mentioned it to a field representative that contacted the regional extension specialist who contacted the state extension pathologist for additional help and expertise. As anyone that has played the childhood game of “telephone” can relate, information passed through this chain can allow for information to be lost, added, or misinterpreted by the time it reaches the final individual. Even if the information was presented directly, careful attention to detail still must be paid for a proper diagnosis.

So, put on your detective hat, open your mind, be cautious not to jump to conclusions, and have fun. Happy Diagnosing!​


The overall goal is to engage students in a simulated plant disease diagnosis scenario, allowing them to gain disease diagnostic experience in order to cultivate critical thinking skills and prepare for plant pathology-related careers. Specific objectives are: 

  • Systematically diagnose the cause of a plant disease and identify the causal agent
  • Understand the challenges and importance of plant pathogen diagnosis

​All objectives may not be accomplished in every class. The depth of coverage is dependent on student level and the emphasis and direction of the specific class.​​​


  • Farmer/Grower – Bailey Williams
  • Field Representative – Alex Nguyen
  • Regional Extension Agent – Morgan Khan
  • Extension Plant Pathologist – Dr. Jennifer Martinez​


  • Enation – a leaf symptom associated with plant viruses in which an abnormal outgrowth of plant tissue appears on the underside of a leaf
  • Grafting – the process of joining two plants together to grow as one
  • Rootstock – a rooted plant onto which another variety (the scion) is grafted
  • Scion – a young plant shoot or twig used for grafting onto a rootstock


​​​Click here for part A

​Click here for Par​t B​​​


​​​​Case Summary

This activity emphasizes a systematic approach to plant disease diagnosis by allowing students to investigate a true-to-life scenario involving a commercial sweet cherry grower in the Pacific Northwest region of the U.S. Students will be able to practice solving a plant disease mystery using a perennial crop model and make management recommendations based on their diagnosis.​​

​​Suggestions on how to use this case

This active learning activity is designed to be implemented in a lab or classroom where students can converse with their peers. Ideally, students would be working in an environment where they can sit in small groups of 3 to 5.

If the diagnostic process has not yet been introduced to the students, it is important to first review the content in the Background Information section.

After the background information has been presented, Part A can be introduced to the students. Before reviewing the Discussion Break questions in the groups, students should have the opportunity to develop their own responses to the questions. After students have time to work individually, the small groups (3 to 5 students) should discuss the ideas collectively. This facilitation design follows the “Think/Pair/Share” method, where students have time to think on their own, discuss their ideas with a partner or small group, and then share their ideas aloud to the entire class. The questions are designed to be used at this point to get students thinking more critically by discussing prompts with peers. The Group Activity for each part of the case is designed to allow students to work collaboratively with their peers to address/solve a problem.

Only after Part A has been completed, should Part ​B be presented to the students, as Part B contains some answers to Part A. Depending on classroom time, the email prompt activity in Part​ B could be used as an individual or group take-home assignment to allow students more time to provide a thoughtful response.

As a final wrap-up, several prompts were written for students to reflect on the activity and think more deeply about the importance and implications of disease diagnosis and management. Due to the number of suggested questions, it may be most effective to assign each group to discuss 2 to 3 questions and then share their responses with the class.

Possible Adaptations

This case study was designed to be adaptable to any disease problem with the same cast of characters to make the problem relevant to an emerging local disease problem or laboratory activity of interest. Changes would need to be made to the initial email correspondence and conversation transcript, as well as location-specific information to make the disease relevant.

Instead of having a virus focus, this activity could be a preliminary assignment that would segue well into a fungal culturing activity where students have to decide which media to make to facilitate an accurate diagnosis. 

An alternative to the images in the email used to present the disease of interest may be using a live sample rather than photos or videos. This live sample could be presented after the first discussion prompt in Case Part A​ where students are asked what information would be useful for diagnosis. A possible response may be seeing a live sample instead of an image, which could be used as an introduction to a “sample submission.”


We would like to thank professors Dr. Chris Mundt and Dr. Russ Ingham and the BOT 552 Plant Disease Management students at Oregon State University for participating in the pilot of this case study and providing helpful feedback for improvements before publication.


When it comes to diagnosing disease problems, you can easily get distracted if you do not have a plan of attack. The following steps outline a disease diagnosis approach:

Systematic Disease Diagnosis​

  1. ​​​​Identify the host. (Common/Latin name)

    Without identifying the host, you cannot accurately narrow the disease possibilities that are known on that specific host. However, it is also important to note that new pathogens in new regions are constantly being discovered, so try to keep an open mind that the disease-causing pathogen may not have been described on that host yet. 

  2. Describe symptoms and signs. (Primary/secondary symptoms and signs)

    When observing the diseased sample (or image of the sample), make careful observations of the symptoms observed using common symptom descriptors: blight, blotch, burn, canker, chlorosis, curl, dieback, dwarfing, enation, epinasty, etiolation, fasciation, flagging, gall, mosaic, mottle, necrosis, phyllody, ringspot, rot, rugose, russet, scab, scorch, shot hole, stunting, water soaking, wilt, witches broom, and/or yellowing. Are there secondary symptoms (e.g. wilting of leaves, early senescence)? The signs of a plant disease are physical evidence of the pathogen. For fungal pathogens these may include: leaf rust, stem rust, sclerotinia (white mold), or powdery mildew. Bacterial signs include: bacterial ooze, water-soaked lesions, and bacterial streaming in water from a cut stem. Signs are not observable for viruses without the aid of an electron microscope, which could be used to visualize virus particles.

  3. Describe the damage pattern. (In the community (e.g. orchard, field, section of landscaping), on individual plant, AND on individual plant part)

    Begin by observing the entire community (field, orchard, etc.) before assessing the damage pattern in the individual and parts of the individual.

  4. Identify if there is evidence of damage spread. (Date of onset, year-to-year changes)

    The time of year when a disease is noticed can provide clues to the causal agent. If a consistent or irregular pattern is noted, these can be clues as to whether an abiotic or biotic source causes the symptoms observed, respectively.

  5. Identify the cultural or site conditions. (When, where, if/how was sample collected)

    Knowing when and where a disease problem is observed can be useful in identifying a pathogen of interest. Some signs and symptoms are only observable at certain times of year. If a sample is collected, it also important to note how and when this sample was collected, as the integrity of the sample will be affected by prolonged storage, especially without refrigeration.

  6. Determine possible diagnosis. Be sure to include references! (Common name, scientific name)

    Use the best resources you have available to make a diagnosis. A good place to start is the most current version of Westcott’s Plant Disease Handbook. Other regional handbooks may also be available online, for example, the Pacific Northwest Plant Disease Management Handbook.

  7. Indicate certainty of identification. (Certain, most likely, or tentative)

    As with any science, there is always a spectrum of certainty. Based on what is known about a host and pathogen and the resources available, decide how confident you are in your diagnosis.

  8. Identify other possible causes.

    If you are not certain of your diagnosis, or you suspect there may be more than one causal agent, identify what the other cause or causes may be.

  9. Describe what you would do to confirm the diagnosis and distinguish similar pathogens.

    In order to be more confident in your diagnosis, there are many tools available for confirmation. What type of media would you use to isolate a bacterial or fungal pathogen to differentiate it from another? What types of assays are available to confirm the presence (or absence!) of a virus? It is also important to note that a specific diagnosis isn’t always needed. Sometimes it isn’t practical (or cost-effective) to diagnose the specific virus (or fungus or bacterium) when the management of the disease would be the same regardless of the pathogen species. 

  10. Determine possible control measures. Be sure to include references!

    Based on the diagnosis and the context of the situation, you can now determine a disease management plan. Also, keep in mind that some growers or homeowners may be interested in different types of products such as conventional vs. organic.


Green, J. 2003. A Systematic Approach to Diagnosing Plant Damage. Oregon State University. Plant Disease Diagnosis. Plant Health Instructor.

Horst, R. K. 2013. Westcott’s Plant Disease Handbook. 8th edition. Dordrecht: Springer Netherlands.

Pscheidt, J. W. 2018. BOT 533 Plant Disease Diagnosis: Unknown Plant Disease Diagnosis Sample Sheet.

Pscheidt, J.W., and Ocamb, C.M., senior editors. 2018. Pacific Northwest Plant Disease Management Handbook. Corvallis, OR: Oregon State University.