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Stubble borne diseases in 2016: what can we expect after a drought year?

Reduced stubble breakdown as a result of two consecutive dry years has increased the risk of transferring disease inoculum to emerging crops planted into stubble this season

Stubble borne diseases in wheat, barley and pulse crops

Article prepared by guest authors Frank Henry, Luise Sigel and Grant Hollaway, Agriculture Victoria

Dry conditions during 2014 and 2015 resulted in a reduced rate of stubble breakdown. Consequently, there is an increased risk of stubble borne inoculum being transferred to crops sown into stubble this season, especially if a susceptible cultivar is sown into it’s respective stubble. The following stubble borne diseases are of increased risk to wheat, barley and pulse crops:

  • Yellow leaf spot (Pyrenophora tritici-repentis) and Septoria tritici blotch (STB) (Zymoseptoria tritici) in wheat.
  • Scald (Rhynchosporium commune), net form of net blotch (Pyrenophora teres f. teres) and spot form of net blotch (Pyrenophora teres f. septoria) in barley.
  • Ascochyta, chocolate spot and botrytis grey mould in pulse crops.

The amount of disease that develops in a crop during the season is influenced by environmental conditions. In general, periods of leaf wetness (rain and dew) combined with cool to mild temperatures and high humidity favour fungal infection.

STB has become the most important stubble borne disease in the high rainfall zone of Victoria. This increase is likely to have arisen from stubble retention, intensive wheat rotations, susceptible cultivars and an environment favourable for this disease. 

Recognising stubble borne diseases in wheat, barley and pulse crops

Early symptoms of scald are grey water-soaked lesions on the leaf blades and sheaths. Net form of net blotch starts as pinpoint brown lesions, which elongate and produce fine, dark brown streaks along and across the leaf blades, creating a distinctive net-like pattern. Symptoms of the spot form of net blotch develop as small circular or elliptical dark brown spots. The spots do not elongate into the net-like pattern.

Symptoms of scald, net form of net blotch and spot form of net blotch on barley (Source: Agriculture Victoria)


The key diagnostic feature of STB is the presence of black dots (fruiting bodies or pycnidia) as shown in the left image below. The first symptoms of yellow leaf spot appear on leaves as small yellow-brown oval spots or lesions (right image below). Lesions may expand to 1 cm in diameter, and are surrounded by a yellow margin.

Symptoms of Septoria tritici blotch (STB) and yellow leaf spot on wheat (Source: Agriculture Victoria)


Initially, ascochyta blight appears as small water-soaked pale spots, but as the disease develops small black dots (fruiting bodies or pycnidia) can be seen in the affected areas. While symptoms of ascochyta are similar on pulse crops, each ascochyta species is specific to its host crop.

Symptoms of ascochyta on chickpea, faba bean and lentil (Source: Agriculture Victoria)


Our advice

Stubble borne diseases will need to be managed carefully during 2016, as stubble from 2014 and 2015 will provide an inoculum source for crops this season.

Take an integrated approach to management by not sowing into infected stubbles, avoiding susceptible varieties, monitoring for disease symptoms and using a foliar fungicide when required.

Monitor wheat crops for symptoms of STB, especially in early-sown susceptible varieties. A foliar fungicide application may be necessary at first node (Growth Stage 31) to suppress disease and protect emerging leaves. Another fungicide application may be required once the flag leaf has fully emerged at GS39 to protect the upper canopy.

Strains of STB have developed with reduced sensitivity to some triazole (Group 3) fungicides. Therefore, it is important to manage fungicides effectively. This can be achieved by rotating fungicides, registered for STB control in wheat, with different active ingredients and using mixtures to reduce selection pressure. 

Yellow leaf spot occurs in winter at early growth stages when the use of fungicides is generally unlikely to provide economic control of this disease. However, where wet conditions are likely to persist and susceptible varieties have been sown, fungicides may provide some suppression. A fungicide application should be made prior to or just after rain, between flag leaf emergence (GS39) and late booting (GS49). This will prevent the disease from moving up onto the flag leaf.

In barley, monitor crops for scald, spot form of net blotch and net form for net blotch during tillering and apply a foliar fungicide at GS31 if necessary. A second application at GS39 may be required if the season is favourable for disease development.

Ascochyta species are crop specific in pulses and will need to be monitored particularly in chickpeas, lentils and faba beans, as there has been a recent change in virulence levels (Pulse Disease GRDC Updates, 2016). Report ascochyta on resistant varieties by contacting your local state department of agriculture.

Chocolate spot in faba beans, and botrytis grey mould in lentil and chickpea crops can infect plants at any stage of development and need to be monitored and managed. It is important to apply fungicides before canopy closure to achieve adequate spray penetration deep into the canopy. A follow up fungicide may be required if conditions are conducive.  


Further information

Cereal disease guides, eXtensionAus

DEDJTR crop disease AgNote series

CropPro diagnostic support for the southern region

Foliar and soil borne diseases of cereals, eXtensionAus



Frank Henry, Regional Research Agronomist, Agriculture Victoria, 915 Mt Napier Road Hamilton 3300

Luise Sigel, Extension Plant Pathologist, Agriculture Victoria, 110 Natimuk Road Horsham 3400

Grant Hollaway, Senior Plant Pathologist Agriculture Victoria, 110 Natimuk Road Horsham 3400 


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