Why is my crop patchy? Diagnose soilborne diseases to form strategies for next season
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Widespread locations across WA grainbelt
Crops with symptoms of soilborne disease and nematode pest issues are being widely reported by Department of Primary Industries and Regional Development (DPIRD) researchers and consultants across the grainbelt. DPIRD’s Diagnostic Laboratory Services (DDLS) team have been receiving samples with suspected nematode, or soilborne pathogens, from paddocks ranging across the grainbelt from Geraldton to Albany. In the Geraldton port zone, patches are particularly noticeable in wheat and barley crops. DPIRD staff are sending multiple plant samples to DDLS and so far, the majority in the northern and eastern grainbelt are testing positive for root lesion nematode (RLN) species Pratylenchus neglectus and rhizoctonia. RLN species P. quasitereoides has also been reported in the central and southern grainbelt.
Earlier this year, preseason molecular testing was conducted in paddocks in Katanning, Dalwallinu, Walebing, Broomehill, Pingelly and Yerecoin infested with root lesion nematodes (RLN) Pratylenchus quasitereoides and P. neglectus. The results revealed medium to very high levels of infestation, which meant yield losses were a possibility in these paddocks in a conducive season if a susceptible crop was sown. For more information on nematode risk categories, refer to the South Australian Research and Development Institute’s Predicta® Research Risk categories fact sheet.
Unfortunately, numerous areas within WA’s grainbelt are experiencing a growing season conducive to yield loss due to RLN impacts. The situation is being worsened by late starting rains combined with environmental conditions that cause plant stress, including waterlogging around Albany, Broomehill, Katanning and Esperance and dry conditions in the northern and central growing areas.
Root lesion nematodes
Nematodes are microscopic worm-like creatures that come in many forms and are important to soil biological structure. Plant parasitic nematodes naturally live and feed on the root systems of plants and most plants can tolerate low levels of plant parasitic nematodes without any ill thrift.
Unfortunately, our monoculture cropping systems in WA often includes susceptible crops. Many growers are choosing to reduce the frequency of break crops (such as lupin) in recent years, and instead are growing predominantly cereal-canola. Canola, wheat and barley are susceptible to root lesion nematode. This can cause plant parasitic nematode numbers to accumulate to high levels (e.g. >25,000 nematodes/gram of root) and result in significant yield reductions.
Refer to DPIRD’s 2023 WA Crop Sowing Guide for nematode resistance classifications for different varieties.
Four species of RLN are commonly found in Western Australia: Pratylenchus neglectus, P. quasitereoides, P. thornei and P. penetrans. Other plant parasitic nematodes that have the potential to cause yield loss in WA include the cereal cyst nematode and the burrowing nematode). Therefore, correct identification of nematode type and species is important because the choice of suitable crop and variety to mitigate future crop damage is dependent on knowing which plant parasitic nematode species are present.
Above ground symptoms of plants infected with root lesion nematodes include stunting, poor growth, plants prone to early wilting and lower leaves turning yellow prematurely and dying back from the tips.
Below-ground symptoms often include poor root systems with sloughing of the root cortex, fewer lateral roots or root hairs compared to nearby healthy plants. Brown/dark coloured lesions along the roots are also common. For more information, refer to DPIRD’s diagnosing root lesion nematodes in cereals page.
Management measures rely on reducing nematode numbers over a period of at least one season by growing less susceptible crop varieties, resistant break crops or employing fallow periods. With high nematode populations, a break of more than one season may be needed.
Common WA weeds can also be susceptible to nematodes. Control of summer weeds and keeping weeds under control in-season in infested paddocks are important management practices.
For more information on nematodes refer to:
- DPIRD’s 2018 Protecting WA Crops Issue 12 root lesion nematode newsletter.
- DPIRD’s root lesion and burrowing nematodes: diagnosis and management page.
- GRDC’s root lesion nematode fact sheet.
Other causes of patches in crops
Patches occurring in cereal crops are not unique to RLN. Other factors contributing to these patches include soilborne diseases such as rhizoctonia and take-all, along with non-disease related factors.
There have been several observations of rhizoctonia across the grainbelt including Corrigin, Hyden, Narembeen, Mingenew and Geraldton.
A few occurrences of take-all have been recorded this season, with one case reported at Lake Grace.
Growers that have confirmed their paddock has rhizoctonia, with large amounts of the crop affected this year, should consider implementing a grass-free break crop such as canola, pulse or pasture in 2024. Canola has been shown to reduce the level of disease in the following cereal crop but it will become a problem again in the second year of cereals. For detailed information about management options for rhizoctonia, read the GRDC's tips and tactics rhizoctonia factsheet.
For take-all, a grass-free non-cereal break will reduce the pathogen significantly.
Patches caused by rhizoctonia or RLN are difficult to distinguish from each other without close inspection of the plant roots. They require further laboratory tests to identify the primary cause of the issue.
In some cases, a combination of diseases and nematodes are responsible.
Paddocks with a history of continual cropping to cereals often also have the worst soilborne disease issues.
Growers that have observed poor patches in their crops this season are urged to diagnose and confirm the issue causing the patches in crops. This will help put the right management plan in place for 2024. Predicta B soil testing does not cover all the nematode species, so in addition to soil testing, submitting plant samples to DPIRD’s Diagnostic Laboratory Services (DDLS) is recommended.
How to send plants to be diagnosed
For diagnosis of root disease or nematode problems in-crop, growers and consultants can carefully dig up symptomatic plants from the edge of the patch (not the centre) as well as healthy plants from outside the patches. The department’s YouTube video how to take a plant sample shows the correct method to use.
Plants can be sent to the department’s Diagnostic Laboratory Services by mailing them to
Department of Primary Industries and Development
Reply Paid 83377
3 Baron-Hay Court
South Perth WA 6151
Upcoming field walks
There are two field walks with presentations on the impact of soil tillage on rhizoctonia coming up. The first is on Monday 11 September in Narembeen, and the second is on Wednesday 13 September at DPIRD’s Wongan Hills Research Station. For more information on these events, contact the host grower group Corrigin Farm Improvement Group or refer to the Liebe Group website.
More information
For more information contact Senior Nematologist Sarah Collins in South Perth on +61 (0)8 9368 3612, Plant Pathologist Daniel Hüberli in South Perth on +61 (0)8 9368 3836 or Research Officer Carla Wilkinson in South Perth on +61 (0)8 9368 3862.
Article authors: Cindy Webster (DPIRD Narrogin), Sarah Collins (DPIRD South Perth) and Daniel Huberli (DPIRD South Perth).
Article input: Ciara Beard (DPIRD Geraldton).
Flag smut in wheat
- Mullewa
- Merredin
- Goomalling
- Grass Patch
Department of Primary Industries and Regional Development (DPIRD) Plant pathologists Ciara Beard and Jason Bradley recently found flag smut in wheat near Mullewa and Merredin.
There has also been a report of flag smut in Rock Star wheat near Goomalling. Infected plants had no grain heads in the boot and were experiencing restricted growth.
Flag smut is a fungal disease that occurs across the WA grainbelt but appears to be more common through the medium to lower rainfall regions of the central, eastern and northern grain production zones. Barley, oats and broad leaf crops are not affected by wheat flag smut.
This disease generally occurs only sporadically, usually following successive plantings of susceptible varieties without use of fungicide seed dressings. To check flag smut resistance ratings of wheat varieties, refer to DPIRD’s 2023 Sowing Guide for WA – Wheat. A number of popular varieties grown in WA are susceptible or worse, and are more likely to exhibit higher incidence of disease.
Flag smut infection occurs as the wheat plant germinates and emerges from soil. The fungus grows systemically within the plant, and affected plants are often stunted. Infected leaves may be curled and distorted with long grey-black streaks of flag smut spores (which rub off easily). Initially, the spore masses are invisible under the leaf surface, but between stem elongation and heading, they break through the surface as distinct, long, raised streaks of sooty black spores on leaves and leaf sheaths. Infected plants can tiller excessively, but it's important to note that symptoms do not always occur on all tillers. Flag smut differs from other cereal smut diseases by exhibiting symptoms in the leaves/leaf sheaths rather than the heads. Occasionally, stems can also be infected.
Flag smut is quite common in trace levels in wheat crops, however at higher incidence it can reduce yield because affected tillers do not usually produce grain.
During harvest, flag smut spores are distributed onto the surface of seed or onto the soil. Spores of the fungus can survive in the soil for several years and can be moved to adjacent paddocks by wind, plant debris or equipment. Machinery that has handled contaminated grain should be thoroughly cleaned to avoid contamination of other paddocks/grain.
Seed sown into contaminated soil is at risk of developing the disease, and so is infected seed sown into clean soil.
Managing this disease next season
Spores of this fungus are carried on seed and in soil, so it is important to consider management strategies now to avoid having significant recurrence of the disease in next season’s wheat crops.
This disease is well-managed by registered fungicide seed dressings, use of more resistant varieties (refer to DPIRD’s 2023 Sowing Guide for WA – Wheat) and rotation with nonhost crops (although spores can last for a period of years in soil).
In paddocks contaminated with flag smut and adjacent paddocks, use clean seed treated with a fungicide seed dressing at a registered (high) rate to reduce disease risk. Registered seed dressings are highly effective. Ensure that grain recieves an even, full coverage to maximise protection of all grains sown. Information on which seed dressings are registered for specific diseases is available from DPIRD’s seed dressing and in-furrow fungicides for cereals page.
Further information
Further information is available at DPIRD's diagnosing flag smut of wheat and cereal smuts and bunts management pages.
For more information contact Plant pathologists Kithsiri Jayasena in Albany on +61 (0)8 9892 8477, Ciara Beard in Geraldton on +61 (0)8 9956 8504, Geoff Thomas in South Perth on +61 (0)8 9368 3262 or Andrea Hills in Esperance on +61 (0)8 9083 1144.
Article author: Ciara Beard (DPIRD Geraldton).
Wheat leaf rust update
- Geraldton port zone
This week Department of Primary Industries and Regional Development (DPIRD) Plant Pathologist Ciara Beard discovered a trace of leaf rust in Devil and Vixen wheat crops at Ogilvie and Walkaway near Geraldton, during her inspections for a Grains Research and Development Corporation (GRDC) Disease surveillance project. The affected crops were at grain fill stage and had isolated pustules present on upper leaves, but the pustules were very hard to find. It is worth noting that both Devil and Vixen wheat varieties are rated SVS (susceptible to very susceptible) to leaf rust. This is the first report of wheat leaf rust in the Geraldton port zone received by the PestFacts WA team this season. The first report in WA this season came from the southern grainbelt last month.
In areas where moisture is limited and temperatures are high during this stage of the growing season, leaf rust is not likely to spread rapidly. This is because leaf rust requires 4-6 hours of leaf wetness at optimum temperatures 15-25°C (warm days and dewy nights).
However, this finding is a warning to growers and consultants to keep monitoring crops (including bottom of canopy) for disease, particularly for stem rust which can be much more damaging to yield and is favoured by warm spring conditions (20-35°C). For more information, refer to DPIRD’s managing stem rust of wheat page.
For further information on symptoms and management of wheat leaf rust refer to DPIRD’s 2023 PestFacts WA Issue 12 article leaf rust in wheat and managing stripe rust and leaf rust in Western Australia page.
For a list of registered foliar fungicides, visit DPIRD’s registered foliar fungicides for cereals in Western Australia page and keep in mind harvest withholding periods as the season progresses.
Rust pathotype testing
Growers and agronomists are encouraged to send samples of all rusts for pathotype testing at any time of the year to the Australian Rust Survey. Possible new rust strains need to be continuously monitored for as they have implications for existing varieties, and this will assist wheat breeders in developing new resistant varieties. Infected leaf samples should be mailed in paper envelopes (do not use plastic wrapping or plastic lined packages) along with your details and collection information (location, variety etc.) directly to:
The University of Sydney
Australian Rust Survey
Reply Paid 88076
Narellan NSW 2567.
Optional free reply-paid envelopes can be ordered from The University of Sydney. For further details, refer to The University of Sydney’s Australian Cereal Rust Survey page.
More information
For more information on leaf rusts, contact Plant pathologists Ciara Beard in Geraldton on +61 (0)8 9956 8504, Kithsiri Jayasena in Albany on +61 (0)8 9892 8477, Geoff Thomas in South Perth on +61 (0)8 9368 3262, Kylie Chambers in Northam on +61 (0)8 9690 2151 or Andrea Hills in Esperance on +61 (0)8 9083 1144.
Article author: Ciara Beard (DPIRD Geraldton).
Protecting grain: ensure clean augers, field bins and silos against insects
The Western Australian grains industry is focused on gas-tight sealable storage and fumigation to achieve the federally mandated ‘nil tolerance’ for live insects in exports.
Residual pest populations surviving in empty storages during winter will infest new season grain when it is put into the storages. If eradication of these pests is not undertaken, they may undergo selection for resistance as a result of repeated fumigations.
Gas-tight sealable silos are the preferred system of storage and pressure testing silos should be part of the annual maintenance. It is much easier to replace seals and carry out repairs when silos are empty. It is recommended that inspection and replacement, if necessary, of inlet and outlet seals occurs. In addition, pressure relief oil valves should be checked and topped up with light hydraulic oil if needed.
It is good practice to pressure test sealed silos upon erection, annually and before fumigating with a five-minute half-life pressure test. See the GRDC-supported stored grain information hub website for more details on pressure testing.
Augers, field bins and silos should be thoroughly cleaned of grain residues and treated with a structural treatment, such as fenitrothion or diatomaceous earth. The ground around storages should be cleared of weeds and rubbish to prevent harbouring insects. Old grain residues should be burned or buried deep.
Be aware of withholding periods if you are treating the inside of an empty silo with a registered insecticide such as fenitrothion, to provide residual control before the grain is loaded.
Growers are reminded that the insecticide Fenitrothion is not registered as a seed treatment. Fenitrothion is a contaminant in exported grain. Growers using Fenitrothion as a structural treatment in the weeks prior to harvest should leave the chemical in place for 2-3 days and then wash it off to prevent contamination of any grain that may come into contact with the sprayed surface.
Diatomaceous earth is preferred for in-silo structural treatments. Non-chemical products such as diatomaceous earth (e.g., Dryacide) need at least two weeks before loading grain to be effective. Dryacide is a naturally occurring insecticide and will provide good control for at least 12 months. Diatomaceous earth is non-toxic, but a dust mask and eye protection should be worn as per the label's personal protective equipment requirements.
Nitrogen can be used on its own or in combination with other fumigants for effective insect control. However, note that it requires a very high level of sealing on the silo, and the silo must be initially purged along with very high levels of silo sealing to maintain an environment free of oxygen.
Phosphine is the cheapest form of insect control at around 40 c/tonne. However, growers need to ensure that their silo is a gas-tight sealable silo and meets Australian Standards AS2628-2010.
Phosphine inhalation is very serious and can be fatal. Always read the Label and Safety Data Sheets, wear protective clothing including chemically resistant gloves and a full-face respirator with an appropriate phosphine cartridge. Inform others (including putting up a phosphine warning sign) when a storage facility is under fumigation.
In order to kill grain pests at all stages of their life cycle (egg, larvae, pupae, adult), growers should refer to the phosphine label instructions regarding dosage, treatment, ventilation and withholding times.
Poor fumigation can result in only adult and larval insects being killed, giving the mistaken impression that the fumigation was successful. However, the immature eggs and pupae will not be killed and infestations will likely build up again quickly, selecting for resistant populations.
Fumigating in an unsealed silo or field bin is an off label use. It is not only ineffective (at best killing adults and larvae), but it will also lead to strong resistance developing on your farm.
Managing phosphine resistance
Insect populations with weak phosphine resistance have developed in all grain-growing states of Australia, largely as a result of poor fumigations. Strong resistance is widespread in the eastern states and has started to take hold in the west, so to help minimise the development of strong resistance to phosphine in WA, use well maintained gas-tight sealable silos.
Detecting phosphine resistant grain pests early will make eradication possible and will protect your income. To arrange a free resistance test for grain pests, contact Technical Officer Georgia Keir-Uren in South Perth on +61 (0)418 387 010.
Farmers keeping grain on farm for their own use with silos that are not sealed can use aeration as an alternative method to keep insects in low numbers.
Aeration cooling is an effective tool which can be used in combination after fumigation for maintaining insect population control. While aeration cooling will not kill insects, it will dramatically reduce reproduction provided aeration fans are used in combination with an aeration controller to selectively push cool dry air through the grain in the silo at a rate of 2-3 litres per second per tonne.
Further information
For more information on stored grain management techniques visit;
- GRDC’s supported website stored grain information hub
- GRDC’s grain storage – Storage updates webinar video
- GRDC’s hygiene and structural treatments for grain storage factsheet
- DPIRD’s sealed silos make sense page
- DPIRD's insect pests of stored grain page.
For more information, contact DPIRD Research Scientist Jeff Russell in Northam on +61 (0)8 9690 2229 or Ben White from GRDC grain storage extension team WA on 1800 WEEVIL (1800 933 845).
Authors: The original article was written by Dr Oonagh Byrne (DPIRD South Perth), Dave Cousins (DPIRD South Perth) and Ben White (GRDC) and has since undergone revisions.
Article input: Jeff Thomas (DPIRD Northam), Ben White (GRDC) and David Cousins (DPIRD South Perth).