Diseases in Small Grains: 2024

July 1, 2024 /

By Margaret Smith, PhD
Agronomist

“Why were some of my oat leaves orange, and now they’re brown and dried up? What’s wrong?”

“Can I still treat my wheat for scab?”

“How will I know if my rye or barley has ergot?”

Disease observations on small grains are widespread this year. Unfortunately, treatment options are few at this time of the season. But it’s still worthwhile to know what disease you may have on the farm, what you can expect from now until harvest, and precautions to take while harvesting, marketing, or feeding the grain on the farm.  

The Disease Triangle

For plant diseases, certain conditions must be in place for the disease to take hold. The “Disease Triangle” illustrates that three favorable conditions must coexist to result in disease: 

  • The presence of a pathogen  
  • A susceptible host (plant)
  • Proper environmental conditions 

We usually have adequate pathogens for small grain diseases, but diseases are more prevalent this year due to different environmental conditions that are optimal for many disease organisms: heavy rainfall and high humidity early in the growing season. 

The best disease prevention strategy comes from variety selection for resistance, crop rotation and crop residue management, and appropriate planting timing. Even with best practices, variety resistance is almost never complete, and weather conditions like this year’s can provide infection and disease growth conditions that can overcome moderate resistance in varieties.  

For help with disease identification, possible interventions during harvest, and precautions to take for marketing and feeding grain from diseased plants, click on your crop for more information. 

Harvest Management

Due to the toxic compounds associated with them, the diseases of most concern are Fusarium (also called scab) in wheat, barley, and occasionally in oats; and ergot in rye. Ergot is also an occasional disease in other small grains and grasses (e.g. smooth brome). Scab infected grain kernels and ergot fruiting bodies (sclerotia) are usually lighter than good grain and, in many instances, can be blown out of the combine by increasing your fan speed. This cleaning method, though, is never fully complete and some scab may exist on the outside of heavier grain.  

If specific areas of a field are obviously more heavily infected—such as wetter areas—consider combining around them and leaving the most infected grain in the field to remove later. 

Grain Testing for Toxins

Where fusarium or ergot is confirmed or suspected, have grain tested before using it in feed rations. Fusarium produces three important classes of mycotoxins: trichothecenes, fumonisins, and zearalenones. In addition, in small grains, deoxynivalenol (DON) is often associated with zearalenones and produces vomitoxin. Any of these mycotoxins can cause poor animal performance and, if enough is ingested, illness or death in hogs, cattle and sheep. If grain tests positive, mycotoxin binders can be added to the feed and the affected grain should be diluted in the ration. 

Wheat (Winter or Spring)

See additional online resources below table for identification photos, toxicity levels—if any—in grain and more detailed precautions. 

TABLE 1: COMMON WHEAT DISEASES, MANAGEMENT STRATEGIES, AND PRECAUTIONS TO TAKE WITH HARVESTED GRAIN

DISEASE

SYMPTOMS

SOURCE OF INFECTION

MANAGEMENT

IMPACT ON GRAIN AND YIELD

PRECAUTIONS
Fusarium (Scab) Light tan, light test weight seed (“blasted” seed heads), pink coloration on glumes and/or seeds   Fungal spores from previous or neighboring grain crop residue  Select resistant varieties. Don’t plant after corn or other small grains. Fungicides can be used at flag-leaf stage. Increase fan speed on combine.  Reduces both grain yield and test weight, and food and feed quality. Food wheat must meet grade standards for DON and vomitoxin. Analyze grain for mycotoxins, including DON and vomitoxin, before feeding. Allowable levels in feed are noted in resources below. Mycotoxin binders can be added to feed to protect livestock and improve animal performance.
Loose Smut  Darker brown, deformed seed heads  Seed borne fungus  Select resistant varieties. Use disease-free seed. Don’t save seed from infected fields.  Reduces grain yield.  Has little or no effect on grain quality for food or feed. 
Stinking Smut (common bunt)  Kernels are gray-green. When broken open, they release spores.  Soil-borne spores infect seed as they germinate.   Use disease-free seed. Treat with fungicide. Reduces grain yield.  Grain is non-toxic and safe to feed. Strong odor of infected grain may cause refusal. Dilute grain in feed ration.  
Leaf, stem, and stripe  rusts  Varies depending on the type of rust. Exhibits rusty-colored spores at some point.  Spores blown into the Upper Midwest form southern states in the spring.  Select resistant varieties. Treat with fungicide. Reduces grain yield, and test weight. Variable reduction based on how early plants are infected.  Grain is non-toxic and safe for food and feed. 
Barley yellow dwarf  Leaf discoloration—yellowing—from the leaf tip downward  Virus transmitted to plants via aphids. Select resistant varieties. Aphid control may have some promise.  Test weight may be reduced and result in rejection for malting.  Grain is safe to feed.  

Wheat Resources 

Barley

See additional online resources below table for identification photos, toxicity levels—if any—in grain and more detailed precautions. 

TABLE 2: COMMON BARLEY DISEASES, MANAGEMENT STRATEGIES, AND PRECAUTIONS TO TAKE WITH HARVESTED GRAIN

DISEASE

SYMPTOMS

SOURCE OF INFECTION

MANAGEMENT

IMPACT ON GRAIN AND YIELD

PRECAUTIONS
Fusarium (Scab) Light tan, light test weight seed (“blasted” seed heads), pink coloration on glumes and/or seeds   Fungal spores from previous or neighboring grain crop residue  Select resistant varieties. Don’t plant after corn or other small grains. Fungicides can be used at flag-leaf stage. Increase fan speed on combine.  Reduces both grain yield and test weight, food malting and feed quality. Allowable levels of DON very low for malting. Analyze grain for mycotoxins, including DON and vomitoxin, before feeding. Allowable levels in feed are noted in resources below. Mycotoxin binders can be added to feed to protect livestock and improve animal performance.
Loose Smut  Heads are replaced by masses of olive-brown spores. Seed borne fungus. Seeds are infected during flowering.  Select resistant varieties. Use disease-free seed. Don’t save seed from infected fields.  Reduces grain yield.  Smutty seeds are blown out of the combine. Remaining grain safe to feed. 
Stem Rust  Rust-colored pustules along stems and leaf sheathes  Spores spread from volunteer barley or another alternate host, including barberry.   Select resistant varieties. Eliminate alternate hosts (volunteer barley, barberry). Treat with fungicides.  Reduces grain and forage yields. Grain test weight may be reduced, affecting malting quality.  Grain is safe to feed.
Barley yellow dwarf  Leaf discoloration—yellowing—from the tip downward  Virus transmitted to plants via aphids. Select resistant varieties. Aphid control may have some promise.  Test weight may be reduced and result in rejection for malting.  Grain is safe to feed.  

Barley Resources 

Oats

See additional online resources below table for identification photos, toxicity levels—if any—in grain and more detailed precautions. 

TABLE 3: COMMON OAT DISEASES, MANAGEMENT STRATEGIES, AND PRECAUTIONS TO TAKE WITH HARVESTED GRAIN

DISEASE

SYMPTOMS

SOURCE OF INFECTION

MANAGEMENT

IMPACT ON GRAIN AND YIELD

PRECAUTIONS
Crown rust Rust colored pustules of spores beginning on the lower part of leaves, progressing upward.    Spores blown in on spring southerly winds.  Select resistant varieties. Plant early so that if infected, the impact is reduced. Fungicides can be used when rust detected and/or flag leaf stage of growth  Can result in shriveled seeds and grain yield reductions of 10-50%. Reduces test weight—up to 5 percentage points— and access to food-grade markets.  Oat grain is not diseased and is safe to feed. 
Barley yellow dwarf  Leaf discoloration—red, pink, or purple—from the tip downward  Virus transmitted to plants via aphids. Select resistant varieties. Aphid control may have some promise.  Test weight may be reduced and result in rejection for milling. Grain is safe to feed.

Oat Resources 

Winter Rye

See additional online resources below table for identification photos, toxicity levels—if any—in grain and more detailed precautions. 

TABLE 4: COMMON WINTER RYE DISEASES, MANAGEMENT STRATEGIES, AND PRECAUTIONS TO TAKE WITH HARVESTED GRAIN

DISEASE

SYMPTOMS

SOURCE OF INFECTION

MANAGEMENT

IMPACT ON GRAIN AND YIELD

PRECAUTIONS
Ergot Black fruiting bodies in seed heads that look like mice or rat droppings. These appear to replace the seeds.  Fungal spores from soil blown into open, pollinating flowers.  Don’t continuously crop small grains. Hybrid rye has a much lower incidence of ergot infection than open pollinated rye. Increase fan speed on combine. Reduces grain yield, but the biggest impact is on grain quality. Ergot alkyloids are toxic to both humans and livestock. Ergot presence will result in rejection for food use.  Analyze grain for alkyloid levels before feeding. Allowable levels of ergot in grain for livestock feed are noted in resources below. Feed must be diluted. Don’t feed ergot-infected grain to breeding livestock. 

Winter Rye Resources