The secret life of crown rot: what happens after harvest?

Take home messages

  • A preliminary survey of cereal stubble from 2017 showed that in the northern region (NSW and Qld) the crown rot fungus is commonly present from the crown up to 18 cm, with detection up to 33 cm within tillers at harvest
  • However, moist conditions can promote further growth of the crown rot fungus post-harvest in inoculated cereal stubble (increasing by almost 1 cm up from the crown per day at 100% humidity)
  • Inoculum levels in post-harvest stubble are not static and may fluctuate as different weather patterns are experienced
  • Planting different bread wheat, durum wheat and barley varieties may not be useful for supressing inoculum growth in stubble after harvest
  • Reducing cereal stubble height may limit inoculum build-up in crown rot affected paddocks by restricting the capacity for further fungal growth post-harvest. This could also help reduce dispersal of infected residues when harvesting shorter break crops such as chickpea, but field validation of this management option is required.


Crown rot is a significant disease of winter cereal crops in northern NSW and southern Qld. The disease is estimated to cause $37 m loss to wheat production and $6 m loss to barley production each year in this region (Murray and Brennan 2009a, 2009b). In Australia, Fusarium pseudograminearum (Fp) is the dominant fungal species causing crown rot (Backhouse et al., 2004). The fungus infects through the roots, crown, lower stem or leaf sheaths of growing plants. Once infection has been established, fungal mycelium can colonise the entire stem (Mudge et al., 2006) and survive in these residues for at least three years after initial infection (Summerell and Burgess, 1988). Stubble retention practises help preserve inoculum in stubble and have contributed to an increase in the incidence of crown rot globally in the last three decades (Kazan and Gardiner, 2018).

To date, a large effort has been made to investigate the pathogenic (infectious) phase of crown rot in winter cereals in Australia (e.g. disease mechanisms, disease impacts, yield loss analyses, breeding etc.). However, stubble-borne pathogens such as Fp spend the majority of their life cycle in their saprophytic phase (i.e. surviving in stubble after the plant matures and dies). This phase has received much less research attention over the years, even though inoculum survival in stubble is a major challenge for crown rot management. Specifically, there is limited knowledge about the drivers of Fp saprophytic growth.

To begin investigating this problem and benchmark the natural incidence of crown rot inoculum at different heights within stubble, a preliminary survey was conducted using cereal stubble collected from the 2017 harvest through the National Paddock Survey (BWD000025) and National Variety Trials (NVT).

Vertical colonisation of cereal stubble - preliminary survey data

Segments (1.5 cm in size) were taken from main tillers at 4 cm intervals (at 0 cm, 5.5 cm, 11 cm, 16.5 cm) up to harvest height. Segments were surface sterilised and plated on laboratory media to assess the presence of Fp at the different stubble heights. This data was used to approximate how far, on average, the fungus had progressed within stubble in northern (NSW and Qld), southern (Vic and SA) and western (WA) regions (Table 1).

Table 1. Vertical incidence of the crown rot fungus F. pseudograminearum (%) recovered from four different heights in the 2017 post-harvest stubble survey. Incidence was averaged for each region.

Incidence F. pseudograminearum (%)

Stubble sample height (cm)

(n = 27)

(n = 6)

(n = 26)

0 – 1.5 (crown)

5.5 – 7

11 – 12.5

16.5 – 18













Sites in the northern region (NSW and Qld) had higher incidence of inoculum at all stubble heights measured in 2017 compared with the other two regions (Table 1). This ranged from 46% in the crown section and gradually declined to 19% at 16.5 – 18 cm. Inoculum was found as high as 33 cm (tallest sample recieved) but the sample size (n) of stubble intact at this height was insufficient to include in the table of averages.

Inoculum assessment in post-harvest stubble is most routinely isolated from the crown and/or 5 cm up the stem. However, this preliminary survey shows that inoculum is retained within stubble not just in the bottom 0-5 cm, but substantially higher. Almost one in five tillers collected in the north contained inoculum at 18 cm in 2017 (Table 1). Crown rot inoculum retained in stubble around this height could become problematic when pulses such as chickpea are used as break crops due to their lower harvest height requirements. Harvesting of shorter stature break crops could potentially spread crown rot infected cereal residues from previous years into “clean” inter-row spaces where the fungus can more readily infect a new cereal crop sown into this space.

Another concern is that Fp has the potential to further increase in stubble (i.e. the fungus will grow saprophytically up the length of stubble) if conditions are favourable. For example, Summerell and Burgess (1988) observed an increase in inoculum levels at 20 cm above the crown in 18-month post-harvest wheat stubble following a wet summer. They suggested the moisture was facilitating the fungus to grow up the standing stubble. However, it is still unknown exactly what environmental conditions are required for vertical growth in standing cereal stubble, and how far or fast the fungus will colonise residues under these conditions. Therefore, a controlled environment experiment was conducted to identify if specific cereal stubble types (durum wheat, bread wheat or barley) or moisture conditions (wet, wet then dry and dry) promote Fp growth in post-harvest stubble.

Saprophytic growth in stubble - controlled environment experiment

Factors such as the individual saprophytic fitness of different Fp isolates have previously been investigated in Australia, where certain isolates were faster growing than others (Melloy et al., 2010). However, the effect of different cereal stubble types (e.g. durum wheat, bread wheat or barley) and moisture conditions on saprophytic growth has not been reported. Thus, the following factors were used to further explore Fp saprophytic fitness: moisture conditions (wet, wet then dry and dry), cereal type (durum wheat, bread wheat and barley), and isolate (isolate A from Wongarbon, NSW and isolate B from Horsham, Vic).

Treatments in the controlled environment experiment were randomised in a split plot design, where moisture treatments were randomly assigned to humidity chambers (main plots), while combinations of cereal type and isolate were randomly assigned to plates (sub plots) within each humidity chamber. Each treatment combination, being the combination of moisture treatment, cereal type and isolate, was replicated four times over repeated runs of the experiment.

Stubble of durum wheat (DBA Bindaroi), bread wheat (Suntop) and barley (Commander) were collected from paddocks at the Tamworth Agricultural Institute in 2017. Stubble pieces were sterilised (autoclaved on two consecutive days) and one end inoculated with an agar plug of an isolate (Figure 1a) before being inserted upright onto nail plates to simulate standing stubble (Figure 1b). Each nail plate consisted of four stubble pieces of the same cereal type, infected with the same isolate. Nail plates were subsequently placed into one of three humidity chambers. Humidity chambers were set up to achieve a wet (0.5 L sterile water in the base of a closed 10 L container for five days), wet then dry (as per wet treatment but water drained and lid propped open after 2.5 days) or dry (no water added with container lid propped open) moisture treatment, all run in a room with alternating ultra-violet light (12 h light/12 h dark) at constant 25 °C. Tinytag data loggers (Gemini Data Loggers, Chichester UK) were used to log temperature and relative humidity.

This image shows three different components of a controlled environment experiment on saprophytic growth in stubble -  (a) Sterile stubble inoculated with an F. pseudograminearum agar plug by pressing stubble into the isolate culture. (b) Stubble pieces set vertically onto nail plates after inoculation. (c) Stubble trimmed into 1 cm pieces and plated onto agar for culturing after being subject to wet, wet then dry or dry environments for five days

Figure 1. (a) Sterile stubble inoculated with an F. pseudograminearum agar plug by pressing stubble into the isolate culture. (b) Stubble pieces set vertically onto nail plates after inoculation. (c) Stubble trimmed into 1 cm pieces and plated onto agar for culturing after being subject to wet, wet then dry or dry environments for five days

After five days, tillers were removed and trimmed into eight 1 cm sections, with the inoculated end (0.5 cm of base) discarded. Sections (1 cm – 8 cm) were sequentially plated on laboratory media (Figure 1c) and incubated under alternating ultra-violet light (12 h light/12 h dark) at 25 °C. Each tiller section was scored for the presence of Fp after four days to measure the maximum height achieved.

Results - controlled environment experiment

Moisture conditions significantly affected the extent of Fp colonisation in stubble (Figure 2). After five days, the wet treatment (Table 2) resulted in the highest fungal growth, with a maximum extent of colonisation ranging from 3.8 – 4.2 cm (isolate A) and 4.3 – 4.6 cm (isolate B) (Figure 2). In comparison, the wet then dry treatment resulted in approximately half the growth, 1.7 – 2.2 cm (isolate A) and 1.8 – 2.4 cm (isolate B). The dry treatment promoted the least fungal growth, with average colonisation of 0.4 – 0.5 cm (isolate A) and 0.3 – 0.6 cm (isolate B). The rate of Fp growth observed was equal to almost 1 cm per day under high (100%) humidity in the wet treatment. Temperature was unlikely to have affected colonisation as conditions were similar across treatments (Table 2).

This image is a column graph displaying the saprophytic colonisation (in cm) of cereal stubble (bread wheat, durum wheat and barley) inoculated with F. pseudograminearum (isolates A and B) after five days in a wet, wet then dry or dry environment.

Figure 2. The saprophytic colonisation (in cm) of cereal stubble (bread wheat, durum wheat and barley) inoculated with F. pseudograminearum (isolates A and B) after five days in a wet, wet then dry or dry environment.

Table 2. Average relative humidity and temperature conditions for each moisture treatment  (wet, wet then dry and dry) captured by Tinytag data loggers (averaged across reps).

Moisture treatment

Relative humidity (%)

Days exposed

Temperature (˚C)



0 – 5


Wet then dry



0 – 2.5

2.5 – 5





0 – 5


Although the moisture treatments in this study show the largest effect on saprophytic growth, the interaction between isolate, moisture treatment and cereal type was also significant (P = 0.0364, Figure 2).  However, trends are difficult to ascertain for isolates or cereal types. Both isolates still produced a substantial rate of vertical growth (almost 1 cm per day at 100% humidity) over the five days, with moisture significantly driving saprophytic fitness of Fp.

In summary, wet conditions (i.e. high humidity) appear to have the potential to cause an explosive increase in the saprophytic growth of Fp in cereal stubble. This reinforces that inoculum levels are not static within stubble, and they may fluctuate with different weather patterns during fallow or break crop periods. Furthermore, if moisture conditions allow, Fp is likely to progress up the stem after harvest regardless of stubble type. This means any yield advantages in the presence of high crown rot infection shown by different cereal types (e.g. crown rot tolerance in barley) are unlikely to slow saprophytic growth in post-harvest stubble. This supports existing recommendations that cereal or variety selection can increase yield, but not reduce inoculum levels, under crown rot pressure (Simpfendorfer, 2016).

Implications for crown rot management

One way to restrict the extent of saprophytic growth of Fp within stubble after harvest could be to reduce stubble length (e.g. by lowering the harvest height). This would limit the suitable substrate and resources available for the fungus to colonise, even if moisture conditions are suitable for growth. Reducing pre-planting Fp inoculum by half has been associated with a yield benefit of 6 to 8% in durum wheat, 2 to 9% in bread wheat, and 1% in barley in years conducive to disease development (Hollaway et al., 2013). Keeping inoculum levels low is therefore necessary to reduce the risk of infection and outbreaks, and limit yield loss to crown rot in future cereal crops.

Further controlled environment experiments and field validation of results is required before specific recommendations can be developed. One such recommendation may be to match the harvest height of the cereal crop to the expected harvest height of the next crop in rotation. For example, if planning to sow a chickpea crop next season, the grower may decide to harvest their current cereal crop shorter. This could provide benefit in two ways. Inoculum build up would be limited by removing the available habitat for the fungus and capping saprophytic Fp growth at a lower height. Additionally, when harvesting the break crop (e.g. chickpea), the cereal stubble proportion of header trash would be reduced, thereby reducing the amount of stubble (and potentially Fp inoculum) dispersed. This would help ensure clean inter-row spaces for the next cereal crop to be sown into, with the aim of preventing crown rot infection by avoiding contact between existing Fp stubble inoculum and emerging cereal plants. This type of management strategy may also provide benefits with a range of other stubble-borne cereal diseases including common root rot (Bipolaris sorokiniana), yellow leaf spot (Pyrenophora tritici-repentis) and net blotch (Pyrenophora teres) which all survive in retained cereal stubble.

The trade-off between harvesting low to reduce stubble-borne inoculum levels and the benefits of harvesting high will require further consideration. For example, harvesting high (e.g. 40-60 cm using stripper fronts versus 15 cm using a conventional header) has been shown to increase harvest efficiency and reduce harvesting costs by 37-40% in south-west NSW (Swan et al., 2017). Therefore, early identification of paddocks which would benefit from having reduced stubble height is essential to balancing disease risk and overall profitability.

This paper highlights the importance of being aware of inoculum levels in retained stubble to inform crown rot management decisions. Some seasons (e.g. wet finish) and varieties (e.g. barley) are not always conducive to crown rot expression even when infection is present (Simpfendorfer, 2016). This means inoculum can be found in stubble without observing obvious symptoms (e.g. whiteheads or extensive stem browning). This ‘silent inoculum’ could lead growers to believe they have clean stubble, when in reality there is Fp inoculum waiting to infect the next cereal crop. At present, crown rot diagnostic services through NSW DPI and risk predictors such as PREDICTA®B can be used to determine the presence of crown rot inoculum in suspect paddocks to guide disease management decisions.


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Hollaway GJ, Evans ML, Wallwork H, Dyson CB, McKay AC (2013) Yield loss in cereals, caused by Fusarium culmorum and F. pseudograminearum, is related to fungal DNA in soil prior to planting, rainfall, and cereal type. Plant Dis 97:977-982

Kazan K, Gardiner DM (2018) Fusarium crown rot caused by Fusarium pseudograminearum in cereal crops: recent progress and future prospects. Mol Plant Pathol 19(7):1547-1562

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Mudge AM, Dill-Macky R, Dong YH, Gardiner DM, White RG, Manners JM (2006) A role for the mycotoxin deoxynivalenol in stem colonisation during crown rot disease of wheat caused by Fusarium graminearum and Fusarium pseudograminearum. Physiological and Molecular Plant Pathology 69:73-85

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Murray GM & Brennan JP (2009b). Estimating disease losses to the Australian wheat industry. Australas Plant Pathol 38:558-570

Simpfendorfer S (2016) Crown rot – does cereal crop or variety choice matter? GRDC Update Paper, February 2016. Accessed 09-25-2018

Summerell BA, Burgess LW (1988) Stubble management practices and the survival of Fusarium graminearum Group 1 in wheat stubble residues. Australas Plant Pathol 17:88-93

Swan T, Kirkegaard J, Rheinheimer B, Jones K, Fritsch C, Hunt J (2017) A flexible approach to managing stubble profitably in the Riverina and Southwest Slopes of NSW. Accessed 18-01-2019


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 authors would like to thank them for their continued support. Ms Petronaitis would like to thank both the GRDC and NSW DPI for co-funding her position under Capacity Building (DAN00200), and further funding this research topic under a GAPP PhD scholarship. Ms Petronaitis would like to thank Jenny Wood, Joop van Leur, Gururaj Kadkol and Rick Graham from NSW DPI for providing materials and equipment for experiments. Technical assistance provided by Chrystal Fensbo, Finn Fensbo and Karen Cassin is gratefully acknowledged.

Contact details

Toni Petronaitis                
4 Marsden Park Road, Tamworth NSW 2340
Ph. 02 6763 1219

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GRDC code: DAN00200 – Building Research (Pathology)

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