Crown rot an update on latest research

Author: | Date: 24 Jul 2015

Take home messages

  • Impact of crown rot on yield and quality is a balance between inoculum levels and soil water
  • The balance is heavily tipped towards soil water yet most management strategies tend to focus solely on combating inoculum, sometimes to the detriment of soil water
  • Cultivation (even shallow) distributes infected residue more evenly across paddocks and into the infection zones below ground for crown rot. This IS NOT good!
  • Some of the newer wheat varieties appear promising in that they provide improved tolerance to crown rot
  • PreDicta B® is a good technique for identifying the level of risk for crown rot (and other soil-borne pathogens) prior to sowing within paddocks. However, this requires a dedicated sampling strategy and IS NOT a simple add on to a soil nutrition test


Crown rot, caused predominantly by the fungus Fusarium pseudograminearum is a significant disease of winter cereals in the northern region. Infection is characterised by a light honey-brown to dark brown discolouration of the base of infected tillers, while major yield loss from the production of whiteheads is related to moisture stress post-flowering.  It is critical that growers understand that there are three distinct and separate phases of crown rot, namely survival, infection and expression. Management strategies can differentially effect each phase.

Survival: the crown rot fungus survives as mycelium (cottony growth) inside winter cereal (wheat, barley, durum, triticale and oats) and grass weed residues, which it has infected. The crown rot fungus will survive as inoculum inside the stubble for as long as it remains intact, which varies greatly with soil and weather conditions as decomposition is a very slow process.

Infection: given some level of soil moisture the crown rot fungus grows out of stubble residues and infects new winter cereal plants through the coleoptile, sub-crown internode or crown tissue which are all below the soil surface. The fungus can also infect plants above ground right at the soil surface through the outer leaf sheathes. However, with all points of infection, direct contact with the previously infected residues is required and infections can occur throughout the whole season given moisture. Hence, wet seasons favour increased infection events by the crown rot fungus when combined with the production of greater stubble loads significantly builds-up inoculum levels.   

Expression: Yield loss is related to moisture/temperature stress around flowering and through grain-fill. This stress is believed to trigger the crown rot fungus to proliferate in the base of infected tillers, restricting water movement from the roots through the stems, and producing whiteheads that contain either no grain or lightweight shrivelled grain. The expression of whiteheads in plants infected with crown rot (i.e. still have basal browning) is restricted in wet seasons and increases greatly with increasing moisture/temperature stress during grain-fill. Focus attention to crops around trees within a paddock or along tree lines. Even in good years whiteheads associated with crown rot infection are likely to be seen around trees. This is due to the extra competition for water.

How to manage crown rot

Crop rotation

The most effective way to reduce crown rot inoculum is to include non-susceptible crops in the rotation sequence. The crown rot fungus can survive for two to three years in stubble and soil. Growing a non-host crop for at least two seasons is recommended to reduce inoculum levels. This allows time for decomposition of winter cereal residues that host the crown rot fungus. Stubble decomposition varies with the type of break crop grown – their canopy density and rate of the canopy closure as well as row spacing, the amount of soil water they use and seasonal rainfall. Trials in the northern region have indicated that faba beans and canola are better break crops for crown rot than chickpeas.


Growers may cultivate their stubble for a range of reasons e.g. to reduce trash load prior to sowing. However, the effect of cultivation on crown rot is complex as it potentially impacts on all three phases of the disease cycle.

Survival: stubble decomposition is a microbial process driven by temperature and moisture. Cultivating stubble in theory increases the rate of decomposition as it reduces particle size of stubble, buries these particles in the soil where microbial activity is greater and the soil environment maintains more optimal moisture and temperature conditions compared to the soil surface or above ground. However, cultivation also dries out the soil in the cultivation layer, which immediately limits the potential for decomposition of the incorporated stubble. Decomposition of cereal stubbles is a very slow process that requires adequate moisture for an extended period of time to occur completely. A summer fallow (even if extremely wet and stubble has been cultivated) is not long enough!

Infection: as covered earlier, the majority of infection sites with crown rot are below ground and physical contact between an infected piece of residue and these plant parts is required to initiate infection. Cultivation of winter cereal stubble harbouring the crown rot fungus effectively breaks the inoculum into smaller pieces and spreads them more evenly through the cultivation layer across the paddock. Consequently, the crown rot fungus has been given a much greater chance of coming into contact with the major infection sites below ground as the next winter cereal crop germinates and develops. In a no-till system the crown rot fungus becomes confined to the previous cereal rows and is more reliant on infection through the outer leaf sheathes at the soil surface. This is why inter-row sowing with GPS guidance has been shown to provide around a 50% reduction in the number of plants infected with crown rot when used in a no-till cropping system. Cultivation or harrowing negates the option of inter-row sowing as a crown rot management strategy.

Expression: extensive research has shown that cultivation dries out the soil to the depth of cultivation and reduces the water infiltration rate due to the loss of structure (macropores etc). The lack of cereal stubble cover can also increase soil evaporation. With poorer infiltration and higher evaporation, fallow efficiency is reduced for cultivated systems compared to a no-till stubble retention system. Greater moisture availability has the potential to provide buffering against crown rot expression late in the season. Like crown rot management and all farming practices, cultivation is a balancing act between perceived benefits and costs.

Stubble burning

Burning removes the above ground portion of crown rot inoculum but the fungus will still survive in infected crown tissue below ground so it is not a ‘quick fix’ for high inoculum situations. Removal of stubble through burning will increase evaporation from the soil surface and impact on fallow efficiency. A ‘cooler’ autumn burn is therefore preferable to an earlier ‘hotter’ burn as it minimises the negative impacts on soil moisture storage whilst still reducing inoculum levels.

Reduce water loss

Inoculum level is important in limiting the potential for yield loss from crown rot but the overriding factor dictating the extent of yield loss is moisture/temperature stress during grain-fill. Any management strategy that limits storage of soil water or creates constraints that reduce the ability of roots to access this water will increase the probability and/or severity of moisture stress during grain-fill and exacerbate the impact of crown rot.

Grass weed management

Grass weeds should be controlled in fallow periods and in-crop, especially in break crops, as they host the crown rot fungus and can also significantly reduce soil moisture storage. In pasture situations grasses need to be cleaned out well in advance of a following cereal crop as they serve as a host for the crown rot fungus.

Row placement

In a no-till system the crown rot fungus becomes confined to the previous cereal rows and is more reliant on infection through the outer leaf sheathes at the soil surface. This is why inter-row sowing with GPS guidance has been shown to provide around a 50% reduction in the number of plants infected with crown rot when used in a no-till cropping system. Further research conducted by NSW DPI has also demonstrated the benefits of row placement in combination with crop rotation and the relative placement of break crop rows and winter cereal rows within the sequence to limit disease and maximise yield (Verrell 2014 GRDC Updates). Sowing break crops between standing wheat rows which are kept intact then sowing the following wheat crop directly over the row of the previous years break crop ensures 4 years between wheat rows being sown in the same row space. This substantially reduces the incidence of crown rot in wheat crops, improves establishment of break crops (esp. canola) and chickpeas will benefit from reduced virus incidence in standing wheat stubble.

Soil type

Soil type does not differentially affect the survival or infection phases of crown rot. However, the inherent water holding capacity of each soil type interacts with expression by potentially buffering against moisture stress late in the season. Hence, yield loss can be worse on red soils compared to black soils due to their generally lower water holding capacities. Any other sub-soil constraint e.g. sodicity, salinity or shallower soil depth effectively reduces the level of plant available water which can increase the expression of crown rot.

Cereal crop and variety choice

All winter cereal crops host the crown rot fungus. Yield loss varies between crops and the approximate order of increasing loss is oats, barley, triticale, bread wheat and durum.
Barley is very susceptible to crown rot infection and will build up inoculum but tends to suffer reduced yield loss through its earlier maturity relative to wheat. Late planted barley can still suffer significant yield loss especially when early stress occurs within the growing season.
Bread wheat varieties appear to differ significantly in their level of yield loss to crown rot with newer varieties in the northern region (Sunguard, Suntop, LRPB Spitfire, LRPB Lancer and Mitch) appearing to suffer less yield impacts compared to the widely grown EGA Gregory. NSW DPI trials from a total of 23 sites in 2013/14 conducted across the northern region indicate that this can represent a yield benefit of around 0.50 t/ha in the presence of high levels of crown rot infection.

However, variety choice is NOT a solution to crown rot with even the best variety still suffering up to 40% yield loss from crown rot under high infection levels and a dry/hot seasonal finish. All current durum varieties are very susceptible to crown rot and should be avoided in medium and high risk situations.

Sowing time

Earlier sowing within the recommended window of a given variety for a region can bring the grain-fill period forward and reduce the probability of moisture and temperature stress during grain-fill. Earlier sowing can increase root length/depth and provide greater access to deeper soil water later in the season, which buffers against crown rot expression. This has been shown in previous NSW DPI research across seasons to reduce yield loss from crown rot. Earlier sowing however can place a crop at risk of frost damage during its most susceptible time. Sowing time in the northern region is a balancing act between the risk of frost and heat stress. However, when it comes to crown rot, increased disease expression with delayed sowing can have just as big an impact on yield as frost. The big difference from NSW DPI trial work is the additional detrimental impact of later sowing on grain size in the presence of crown rot infection.

Interaction with root lesion nematodes

Root lesion nematodes (RLNs) are also a wide spread constraint to wheat production across the region. Two important species of RLN exist throughout the northern region, namely Pratylenchus thornei (Pt) and P. neglectus (Pn). Previous surveys of the northern NSW have found that Pt is more widespread and generally at higher populations than Pn. RLNs feed inside the root systems of susceptible winter cereals creating lesions and reducing lateral branching. This reduced the efficacy of the root system to extract soil water and nutrients which subsequently can exacerbate the expression of crown rot. Varieties with reduced tolerance of Pt can suffer significantly greater yield loss from crown rot if both of these pathogens are present within a paddock.

How do I know my level of risk for crown rot and RLN?

PreDicta B® is a DNA based soil test which detects levels of a range of cereal pathogens that is commercially available to growers through the South Australian Research and Development Institute (SARDI). Because the crown rot fungus is stubble-borne, normal soil samples are unreliable and disease detection is highly sensitive to the sampling technique used. Follow the specific protocols for how to collect samples for crown rot testing (further paper in these proceedings).

If you are not willing to follow the recommended PreDicta B® sampling strategy then DO NOT assesses disease risk levels prior to sowing.

Further reading

GRDC Grains Research Update paper (July 2014) on Managing crown-rot through crop sequencing and row placement, Andrew Verrell, NSW DPI


This paper includes some older information conducted in collaboration with Northern Growers Alliance as acknowledged in the text and crop sequences in combination with row placement research was conducted by Dr Andew Verrell (NSW DPI). This information has been presented in greater detail at previous GRDC Updates with full reports available at Technical assistance provided by Robyn Shapland, Finn Fensbo, Karen Cassin, Kay Warren, Rod Bambach, Peter Formann, Stephen Morphett and Jim Perfrement are gratefully acknowledged.

The research undertaken as part of this project is made possible by the significant contributions of growers through both trial cooperation and the support of the GRDC, the author would like to thank them for their continued support. The project is co-funded by the NSW state government through the NSW DPI who are also thanked for their support in fully funding the position of Dr Simpfendorfer and laboratory and other infrastructure costs.

Contact details

Steven Simpfendorfer
Ph: 0439 581 672

Varieties displaying this symbol beside them are protected under the Plant Breeders Rights Act 1994.

GRDC Project code: DAN00175