How do I manage crop diseases in a stubble-retained system

Stubble retention can increase the carryover of many crop diseases on the stubble, making disease management an important priority. Every disease is different and will require a different management strategy.

Many stubble-borne diseases are necrotrophic and do not need a living host to survive.

In cereal-dominant rotations a break crop is often the most effective way to manage disease.

The key to managing diseases in a stubble retained system is:

  • Monitor crops and know what the diseases risks are with PreDicta™ B testing
  • Keep inoculum levels as low as possible by rotating with non-host crops and control grass weeds early in break crops
  • Select paddocks with low disease risk
  • Manage summer weeds and the green bridge
  • Stubble management and inter-row sowing can help with some diseases

Fungicides may give economic control for some diseases, but not others.

Practices that reduce surface stubble such as cutting low, incorporation, grazing, and burning to remove infected stubble or mechanical practices that increase the rate of stubble break down can reduce inoculum levels. However, removal of stubble increases the risk or erosion and removes the carbon source associated with biological activity and soil health related benefits.

Photo of crown rot disease in bread wheat showing typical white heads
Crown rot. Source: Marg Evans

Soil-borne diseases

Crown rot

Crown rot is stubble-borne and causes losses during seasons with below-average spring rainfall. Crown rot must be controlled prior to sowing as there is no in-crop control available. Rotation with grass-free break crops will lower inoculum levels, although when inoculum levels are high a two to three-year break from cereal and grass weeds may be required to lower the disease risk. Stubble removal, inter-row sowing and adequate nutrition can also help.

See the GRDC Tips and Tactics - Crown rot in winter cereals


Take-all is retained over summer in roots and crowns. A one-year break with a grass-free break crop will lower inoculum levels. Inoculum declines quickly when no host is present, particularly in moist soil.


Rhizoctonia is not stubble-borne, but has become more prevalent due to the change in practices and reduced cultivation in retained stubble systems. Rhizoctonia can survive and feed on organic matter in the soil, therefore it does not require a living host. A one-year break with a grass-free break crop will lower inoculum levels.

See the GRDC Tips and Tactics – Rhizoctonia

Photo of yellow leaf spot in wheat
Yellow leaf spot in wheat. Source: Luise Sigel

Foliar diseases

Yellow leaf spot

Yellow leaf spot is stubble-borne and dispersed by rain within the paddock, but can also be blown in from nearby paddocks. YLS can persist for two years on stubble, although a one-year break from wheat with pulses or canola will generally lower inoculum levels, except in very dry conditions. Practices that reduce surface stubble such as grazing, tillage or burning will reduce inoculum levels.

See the GRDC Factsheet - Yellow leaf spot


Eyespot is an emerging stubble-borne disease that is increasing in importance due to stubble retention, direct drilling and more cereals in rotations. The fungus can survive in the stubble for two years or more, but break crops will reduce inoculum levels. Burning stubbles can reduce the inoculum level but does not eliminate the disease.

See the GRDC Factsheet – Eyespot in wheat


Septoria spores can travel large distances via wind and aren’t just related to within paddock or within farm management. Stubble reduction by burial, burning or grazing can reduce inoculum, but will not reduce disease caused by spores blown in from other fields early in the season. In most instances, a one-year rotation away from wheat is highly effective in reducing early disease occurrence.

See the GRDC Factsheet – Septoria tritici blotch

Net Form of Net Blotch (NFNB), Spot Form of Net Blotch (SFNB)

Net Form of Net Blotch (NFNB) and Spot Form of Net Blotch (SFNB) can survive on infected barley stubble for up to three years. Manage using a combination of resistant varieties, crop rotation and fungicide management. Reducing stubble residues may also assist in increasing the speed of breakdown on the stubble and reducing the time that the paddock remains as high risk for net blotch.

See the GRDC Barley Southern Region - GrowNotesTM

Chocolate spot and Ascochyta in faba bean

Chocolate spot (Botrityis fabae and B. cinerea) and Ascochyta on faba bean (Ascochyta fabae) can carry over from one season to the next on bean stubble, infected seed and volunteer plants. Manage through stubble reduction, resistant varieties, crop rotation and a sound fungicide program.

See the GRDC Faba bean Southern Region - GrowNotesTM

Blackleg in canola

Blackleg survives on canola stubble, producing fruiting bodies that contain large quantities of airborne spores that have the ability to travel several kilometres.

Never sow canola into last year’s canola stubble. Sow at least 500m away from last year’s stubble to reduce blackleg severity. Use resistant varieties. Two-year-old stubble may cause disease if inter-row sowing canola or if the cultivar resistance has been overcome. Stubble destruction is not effective in reducing blackleg infection.

See the GRDC Factsheet – Blackleg management guide

White grain disorder

White grain disorder survives in cereal stubble residue and spores can move long distances by wind. It is viable for at least two years.

More Information

Farming Systems Groups