Single test improves stubble-borne disease management

Photo of man sitting in field with hat on.

Northern New South Wales grower and agronomist Drew Penberthy thinks a new soil-sampling strategy to help better predict crown rot risk in the northern grain-growing region has the potential to provide labour and cost savings.

PHOTO: Clarisa Collis


Northern New South Wales grower and agronomist Drew Penberthy is road-testing new research findings on a DNA-based soil test to help better predict crown rot risk in northern farming systems.

For Drew, this on-farm exploration of GRDC-funded research has meant a more rigorous approach to soil sampling on his 2200-hectare grains operation at Bellata, 40 kilometres south of Moree.

The research by the South Australian Research and Development Institute (SARDI) and the NSW Department of Primary Industries (DPI), with a focus on fine-tuning soil-sampling, has the potential to provide cost savings, Drew says.

“New soil sampling techniques for the PreDicta B® test could provide savings in terms of the preparation and analysis of stubble testing for crown rot,” Drew says.

This is because a new soil-sampling strategy developed by researchers to lift the accuracy of testing for crown rot risk using SARDI’s PreDicta B® test might allow northern growers to combine tests for both crown rot and root lesion nematodes.

Drew, who also runs a business that provides stubble testing for crown rot and soil testing for root lesion nematodes, says most growers in the northern grains region undertake two separate tests for these cereal pathogens. These include a PreDicta B® test for root lesion nematodes and a stubble test through Crown Analytical Services for crown rot.

Speaking at a recent GRDC Grains Research Update, NSW DPI senior plant pathologist Dr Steven Simpfendorfer said researchers had worked on improving the reliability of the PreDicta B® test in assessing crown rot levels before sowing.

Photo of man in hat sitting at microscope

Dr Steven Simpfendorfer: new guidelines for soil sampling.


“In recent years, while PreDicta B® has shown to be reliable for assessing root lesion nematode populations, it has been perceived by industry to be less reliable in assessing crown rot risk in the northern grains region,” Dr Simpfendorfer said.

“This is potentially due to the crown rot fungus being stubble-borne while PreDicta B® is a soil-based test.”

It is this challenge – to use a soil test to identify the risk of a stubble-borne pathogen – that has led Drew to modify his own soil-sampling regime.

Before seeding this season, Drew collected 15 soil cores from last year’s cereal rows at different locations – to account for varying levels of crown rot inoculum across paddocks.

At each location, he also added a single, short piece of stubble to the soil core samples so a combined test could be made, increasing the accuracy of testing for crown rot using PreDicta B®.

In the past, Drew has collected these samples randomly from between the previous season’s cereal rows before seeding as part of a PreDicta B® test to predict root lesion nematode levels for the season ahead.

Before seeding, he also collected samples of stubble over his property to help determine the risk of crown rot pressure using a separate stubble-plating test.

If this more intensive approach to soil sampling proves effective, it could allow him to avoid the need for a separate stubble-plating test for crown rot.

Dr Simpfendorfer says new guidelines for soil sampling draw on the results of a cereal pathogen survey of 248 paddocks in central and northern NSW from 2010 to 2012.

The three-year survey enabled researchers to measure the DNA levels of the crown-rot-causing Fusarium pathogen at sowing against the infection levels that had developed by harvest.

These comparisons showed that adding stubble to soil samples might overestimate the level of crown rot risk, but, on the other hand, reduce the likelihood of underestimating risk or a “failure to warn” in situations where the disease could hit yields.

Overestimation of risk is considered a preferable outcome because it gives growers the opportunity to select disease-resistant varieties and vary crop sequencing to help reduce crown rot pressure prior to seeding.

Adding stubble to soil samples is also expected to improve risk prediction following wet conditions in summer, which tend to result in higher survival of the Fusarium pathogen in above-ground residues (first nodes) compared with below-ground residues (crowns).

Dr Simpfendorfer says collecting cores from different depths in the soil, down to 15 or 30 centimetres, had a minor effect on PreDicta B® testing to detect crown rot pathogen levels in northern soils. However, the test results were less reliable where samples were not taken from the previous season’s cereal rows.

This finding is significant because it was previously thought that soil sampling to a deeper depth in the northern grains region, down to 30cm (instead of down to 10 or 15cm in other grain-growing regions) might reduce the accuracy of PreDicta B® testing.

Dr Simpfendorfer now urges growers to provide soil-depth information when sending samples to SARDI for PreDicta B® analysis because the study also showed that some disease pathogens are more concentrated at the soil surface.

For example, the Fusarium pathogen that causes crown rot was found to be more prevalent near the soil surface, while populations of the Pratylenchus thornei species of root lesion nematode were found at varying soil depths down to 30cm.

Drew says the new insights to help better assess disease risk before seeding have added to his existing on-farm strategy to minimise pressure from crown rot and root lesion nematodes, the combined effects of which can reduce wheat yields by 60 per cent.

For Drew, this research-based strategy has involved reducing the family’s area planted to chickpeas, which can lead to increase levels of root lesion nematodes in subsequent cereal crops. This chickpea country has been replaced with faba beans and canola because these break crops tend to reduce the combined effects of the pathogens in following cereal crops.

The Penberthys have also reduced their area planted to durum wheat in dry seasonal conditions when the crop is more susceptible to cereal disease, and switched to high-yielding wheat varieties with better disease resistance such as LongReach Lancer, Suntop and LongReach Spitfire.

Seeding crops earlier to encourage stronger plant root systems and reduce the risk of heat stress during grain-filling is another component of their strategy that assists in reducing losses from root lesion nematodes and crown rot, Drew says.

More information:

Drew Penberthy,
0427 255 752,;

Dr Steven Simpfendorfer,
0439 581 672,;

Dr Alan McKay, SARDI,
08 8303 9375,



Perennial wheat on the drawing board


E-help just a click away

GRDC Project Code DAS00137, DAN00143

Region North