Stem Rust Fungus

Puccina graminis is the scientific name for stem rust fungus, which affects wheat and barley crops. Wheat makes up much of the staple diet in 97% of countries. Between barley and wheat, they make up 25% of the world’s food supply, and help keep billions of people from being malnourished.

Over the years, the fungus has caused devastation numerous times; the fungus can effect fields that are nearing harvest, and can reduce crop yields by up to 80%, Different strains effect different crops, but the strain that effects wheat is the most damaging to human food stocks.


Stem rust is a parasitic fungus- it feeds on living tissues of its host. It can infect either cereal plants or Berberis (Barberry), a genus of shrubs which grow freely in temperate and sub-tropical regions. It forms five different types of spores.

The disease is transmitted when spores from infected plants are carried to other crops by the wind. It can also be transmitted if it’s grown in soil where an infected plant previously was. It can pass thousands of miles in certain conditions through soil. The pattern of the infection is used to determine the source (a fan of infection implies it’s local, overall coverage for a distant field).

Mode of Infection

Spores need water in order to germinate. They use hypha (thread-like structures) to penetrate the stomata of the leaves or stem of the plant to gain access to water, and in turn, to other internal tissues. Hypha secrete enzymes such as cellulases which digest plant cells and then they absorb nutrients into the fungus. The hyphae branch to form a mycelium that feeds and grows, hidden in the stem or leaves of healthy-looking plants.

The fungus grows best in hot days (25-30°C), mild nights (15-20°C), and wet leaves (from rain, dew or irrigation). The spore relies on this water to germinate.

Pathogenic Effects

Symptoms start 7-15 days after the plant has become infected. Rust-red pustules break through the epidermis of the stem of leaf, which can contain up to 100,000 similarly coloured spores; any of these can be blown by the wind to infect more plants.  This can happen many times over a crop’s growth cycle, until black spores (which can last over a winter) are finally formed. It’s at that stage that the crop itself becomes blackened and worthless.


  • Absorbs nutrients, reducing crop yield
  • Pustules break the epidermis, making transpiration more difficult for the plant to control; their metabolism becomes less efficient; the plant is more likely to dry out; secondary infections become more likely
  • Mycelium grows into vascular tissue, absorbing water and nutrients; interference of supply to crop
  • Weakens stems so plants are more likely to be damaged or topply due to the weather, reducing harvest efficiency

Controlling Stem Rust in Wheat

Stem rust is fast-acting upon its host. Some farming practices encourage its spread;

  • High nitrate soils favour the fungus; fertilisers encourage the fungus.
  • Many farmers in HICs deliberately avoid disturbing the soil; if there are any spores in the soil, they are likely to be near the top where they can more easily infect the next crop
  • Regular irrigation provides both water for the plants to grow, and the virus.

To avoid the virus, start by avoiding such practices, where possible. Then;

  • Use bigger spaces between plants to reduce moisture and increase distances for spores to have to travel
  • Reduce fertiliser application
  • Use earlier-maturing crops which avoid the time of maximum spread
  • Remove wild Berberis so part of the life cycle is interrupted, reducing further spread

Fungicides can be used to control the growth of stem rust, but the cost of this can make it uneconomic to grow the crop at all.

Genetic Resistance

The main method of fighting the fungus historically has been to just develop more hardy breeds of crop. In the mid 1900’s, scientists discovered genes that hep gives resistance to rust attacks, especially Sr31. Wheat strains were breed to have this variant that were very resistant to the fungus, and by the ’70s, the virus seemed to be under control.

In 1999, an unknown strain of wheat stem rust fungus appeared in Uganda, known as Ug99. This strain can overcome almost all of the known resistance genes in wheat; Sr31 has no protective effect. The spores have been covered to other East African countries, and even as far as Yemen and Iran, and are continuing to spread. Scientists have calculated that 80-90% of wheat could be susceptible to this strain.

Scientists are working to develop new strains of resistant wheat to prevent Ug99 from spreading into some of the most important wheat-growing areas of the world. A package of genes have been found that can be engineered into various varieties, giving resistance to all stem rust strains and infections. However, the cost, environmental and ethical concerns in some countries about GM crops (many of which can be counter-acted by sterilising plants carrying the modification, though this creates a dependancy on the original supplier and can hinder development in LICs) mean that this solution is not yet widely adopted.