BT&C, Inc.

Identification of Plant Diseases

Introduction

Food is important.  Anyone who has ever gone hungry knows that.  In the United States, most of us are fortunate to not experience hunger, however up to 20% of school aged kids can be at risk of hunger.  Generally, there is sufficient food in the United States, but the distribution of that food is not uniform.  One reason that there is sufficient food is due to science.

All food starts with sunshine.  Plants are the backbone of our food supply.  If you lived on candy bars and lobsters, you are still relying on plants.  Sugar from sugarcane or sugar beats is used to make candy bars, while lobsters dine on microscopic algae that grow using sunlight (algae are technically not plants, but grow using light as do plants).  As plants (and algae) are the source of all food, there is an immediate interest in making plants heartier and producing greater yields when harvested.  Scientists, in such jobs as plant pathologists, botanists, breeders, and biochemists, are responsible for keeping plants healthy and making them better.

Many different types of scientists work together to develop crops and keep them healthy. Plant breeders and geneticists develop new varieties of crops with desirable traits, such as higher yields, better nutrition, resistance to disease, or the ability to tolerate drought and heat. Molecular biologists and biotechnologists study plant DNA and can use techniques such as genetic engineering and gene editing to introduce or improve useful traits. Plant physiologists study how plants grow and respond to their environment, including water, temperature, nutrients, and sunlight.

Other scientists concentrate on keeping crops healthy after they are planted. Plant pathologists study diseases caused by fungi, bacteria, viruses, and other microorganisms, while entomologists study insects that can damage crops. Soil scientists and agronomists study soil fertility, fertilizers, irrigation, and farming practices that help crops grow efficiently. Weed scientists help control plants that compete with crops for water, nutrients, and sunlight. Together, these scientists help farmers produce healthy crops while dealing with pests, diseases, changing weather, and the need to feed a growing population.

There are many scientists involved with putting food on our tables.  In this story, you will take on the role of a plant pathologist.

Scenario

Zea mays, commonly known as corn, is a very important commodity crop.  In 2025, approximately 17 billion bushels of corn were produced with a value of $70 billion USD.  It is used for everything from corn bread to animal feed to gasohol to paper.  Basically, it is important to the livelihood of many people.  A plant pathologist’s job is to protect crops, such as corn.

Corn, and all crops, are constantly being threatened by microorganisms that can harm plants.  These harmful microbes are referred to as pathogens, and include viruses, bacteria, and fungi.  These pathogens can attack a plant at different stages of their development, such as during germination and development of the shoots and leaves, to killing flowers and infecting fruit and vegetables.  Plant diseases can be devastating to the plant and the farmer, and indirectly to the consumer.  It is possible for entire crops to be lost to plant disease.  The plant pathologist is one of many scientists whose role it is to prevent the loss of plants to disease.

Picture yourself as a plant pathologist.  You receive a call from a farmer who is worried that one of his fields is infected with a disease they don’t recognize.  The farmer describes plants that emerge from the soil without a problem, but as the season progresses, the plants become stunted and eventually wilt and die.  This problem was observed during the previous growing season, but it was limited to a few square yards of corn.  This year the problem spread to a much larger area.  The farmer is asking for your help so they can identify the problem and take steps to prevent the issue next year.

What do you do?

Three Options

  1. Travel out and collect the sample

The farmer requests a site visit. Your first responsibility is not simply to find the diseased corn plants. It is to understand the field pattern and collect representative evidence that can distinguish a disease from injury, herbicide damage, nutrient stress, drought, poor drainage, or other abiotic causes.

Before the visit, prepare a field kit containing sample bags or containers, waterproof labels, a marker, gloves, a hand lens, a measuring tool, a camera or phone, a field map, and a cooler. Create sample codes before collecting material so that every sample can be linked to its location, tissue type, plant condition, and collection time. Wear field clothes and a hat, and boots if the soil is muddy.

At the site, you should:

  1. Map the affected area and describe whether symptoms are random, clustered, row-associated, edge-associated, or related to low areas, water movement or waterlogged soils.
  2.  Uproot the plants and compare symptomatic with apparently healthy at the same growth stage. Describe the symptoms (leaf spot, blight, yellowing or mosaic, stalk rot, ear rot, root rot, root knot, stunting or wilting).
  3. Examine aboveground and below ground symptoms (roots, crowns, lower stems, vascular tissue, and ears).
  4. Record the number of affected plants, percent symptom severity (leaf area or whole plant), plant growth stage, and any evidence of insects, wounds, or any plant pathogen signs (fungal structures (rust pustules, smuts and pink, green and black molds on corn ears), bacterial ooze (cut plant section immersed in water exuding cloudy mass) nematode (egg masses on root galls), and viral systemic symptoms (mosaic, mottling, yellowing).
  5. Interview the farmer about crop rotation, seed source, irrigation, drainage, fertilizer and pesticide use, tillage, weather, and the date when symptoms first appeared.
  6.  Collect representative symptomatic plants, plants at the advancing edge of the problem, healthy comparison plants, and other samples only when they address a specific hypothesis.

Student Report: An annotated field map, symptom record, field-history summary, sample inventory, and preliminary differential diagnosis.

Conceptual bridge: Field observations provide the context needed by diagnosticians. A DNA result is difficult to interpret when the laboratory does not know where the sample came from, which tissue was affected, or how the disease was distributed.

  • Have a diseased plant sent to you that can be used for classical and genetic analysis

Instead of visiting the farm, you or as class team receive a plant sample. This pathway shows that molecular diagnosis begins before DNA extraction, with symptom description, proper sampling, labeling, preservation, and documentation.  Request the farmer to ship fresh plant disease samples to your address by keeping them in plastic bags (brown paper bags preferred) in dry condition. Do not place moistened paper towels inside bags as these will only allow deterioration and decay in transit.

When the sample arrives, review the submission information: host, location, symptoms, collection date, tissue submitted, disease pattern, crop history, and management practices. Then compare the contents with the sample inventory, record the condition of the material, and assign a laboratory identification code. Healthy comparison material and symptomatic tissue should be kept clearly distinguished. The instructions should be followed for storage and processing; excess moisture and prolonged warm storage can cause deterioration and misleading results. Store the samples in the fridge until processing.

Use the current SYNERGY Plant DNA Extraction Kit protocol to extract DNA from approved plant-associated material. The lesson should emphasize the purpose of each stage: tissue disruption, removal of debris and inhibitors, recovery of nucleic acids, and preservation of an extract suitable for downstream testing.

You should:

  1. Include healthy plant material as a comparison and an extraction blank to detect contamination.
  2. Record starting material, final elution volume, DNA concentration, purity measurements, extract appearance, and any deviations from the protocol.
  3. Explain that total DNA concentration measures nucleic acid from all material in the extract and does not identify a pathogen.
  4. Use ITS sequencing or fungal-specific PCR when a fungal pathogen is suspected, and 16S-based methods when a bacterial pathogen is suspected. Viruses require a separate nucleic-acid and assay strategy.
  5. Compare the molecular result with the field observations. Detecting pathogen DNA supports presence but does not by itself prove that the organism caused the disease.

Optional Activity: Fungal and bacterial isolation from plants using tissue planting technique on culture media (potato dextrose agar for fungi) and streaking on nutrient agar for bacteria) when resources are available.

 Student Report: A sample-receipt record, DNA extraction data sheet, molecular identification report, interpretation of controls, and recommendation for additional testing if the result is inconclusive.

Conceptual bridge: A plant pathologist identifies biological material, but the result becomes meaningful only when integrated with symptoms, field pattern, sample quality, and disease history.

  • Survey the area and see if there are other farmers with a similar problem

The third pathway is more epidemiological. Investigate whether the disease is isolated to one field or occurs in neighboring fields. You do not need to identify the pathogen immediately. Your first task is to determine how disease is distributed and which conditions are associated with it.  Ask the farmer about the incidence of the same symptomatic plants in other neighboring fields. Check if the symptoms are similar and if they are spreading.

Design a survey by defining the area being studied, the sampling unit, and what counts as a diseased plant. Record healthy, symptomatic, and dead plants rather than only counting diseased plants. Record crop variety, planting date, soil type, drainage, irrigation, crop rotation, weather, and management history.

Students should then:

  1. Create a map showing affected and unaffected fields or field zones.
  2. Calculate disease incidence as the proportion of plants showing symptoms in a defined population.
  3. Estimate disease severity using a consistent rating scale or the proportion of tissue affected.
  4.  Compare disease frequency in wet and well-drained areas, low and high portions of fields, or fields with different varieties and management histories.
  5.  Look for clustering, gradients, edge effects, and relationships to water movement or field operations.
  6. Distinguish association from causation. A common factor in affected fields may be a risk factor, but it does not automatically cause the disease.
  7. Use the survey to identify the fields and tissues that should receive priority for laboratory testing.

Student Report: A survey protocol, data table with sample sizes, disease map, incidence and severity calculations, interpretation of risk factors, and targeted sampling recommendation.

Conceptual bridge: Epidemiology tells the team whether the problem behaves like an isolated event or a spreading disease and helps determine where diagnostic sampling will be most informative.

Integrating the evidence

After completing their assigned pathway, teams exchange results. The class must decide whether the evidence supports an infectious disease, an abiotic disorder, or a combination of factors. Students should identify what is known, what is uncertain, and what additional evidence is needed.

  1. Field observations show symptoms, affected tissues, and spatial pattern but they do not identify the causal organism.
  2. DNA extraction and sequencing can show whether target genetic material is detectable, but detection alone does not prove causation.
  3. An epidemiological survey can show distribution, incidence, severity, and possible risk factors, but it cannot establish a definitive diagnosis without biological or molecular confirmation.

Final Task

Prepare a plant health report for the farmer. State the leading diagnosis or differential diagnosis, summarize the evidence, explain limitations, and recommend the next action. Possible recommendations include additional sampling, laboratory confirmation, sanitation, crop rotation, drainage improvement, resistant varieties, vector management, or consultation with an extension plant pathologist.

Assessment questions

  1. Why is a field pattern important before a sample is sent to a diagnostic laboratory?
  2. Why should a diagnostic laboratory receive both symptomatic and healthy comparison material?
  3. What is the difference between detecting a pathogen and proving that it caused disease?
  4. How can an epidemiological survey help a plant pathologist decide which samples to test?
  5.  Which additional scientist would you involve next, and what question would that scientist help answer?