Resistance genes versus fungicides

Western wheat growers could potentially recoup $108 million worth of yearly losses caused by fungal disease


Cereals
WA DPIRD researcher Dr Michael Francki in a field trial plot at the Northam research facility. PHOTO: Evan Collis

WA DPIRD researcher Dr Michael Francki in a field trial plot at the Northam research facility. PHOTO: Evan Collis

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Newly discovered disease-resistance genes could save growers.

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Western region wheat growers could potentially recoup $108 million worth of yearly losses caused by the fungal disease Stagonospora nodorum blotch through the use of newly discovered disease-resistance genes.

It is something of a global anomaly that Stagonospora nodorum blotch (SNB) disease on wheat is such a problem to western region wheat crops. In eastern states – and many parts of the world – SNB is not as prevalent a disease of wheat as the other major fungi, yellow spot and Septoria tritici blotch.

In contrast, in the west SNB is rated as the second most significant necrotrophic fungal disease of wheat. It decreases yields annually by nine per cent on average – at a cost of $108 million to growers – due to leaf death in adult plants and reduced grain fill. The yield cost means WA wheat growers face an extra disease burden that is especially onerous in productive, high-rainfall areas.

Given the anomalous impact, it is not surprising that WA pre-breeders are leading the world in identifying useful forms of genetic resistance to SNB.

That work is so advanced that scientists are on the verge of directly isolating not one but a small pool of resistance genes to both protect new wheat varieties and ensure resistance does not break down in the future.

That work is being undertaken at the WA Department of Primary Industries and Regional Development (DPIRD) and the State Agricultural Biotechnology Centre at Murdoch University. It is led by WA DPIRD’s Dr Michael Francki and involves field trials at WA DPIRD’s Northam, Katanning and Manjimup, WA, research stations.

Dr Francki notes that while cultural and fungicide management practices can decrease SNB severity, he nonetheless targeted genetic resistance to this necrotrophic disease in the early 2000s as a way to decrease on-farm production costs and reduce fungicide dependence.

The search for resistance started by bringing together a diverse pool of wheat germplasm sourced from both Australia and overseas. He paid particular attention to winter wheats that were known to express SNB resistance in US grain-growing environments. He also included internationally bred wheat sourced from GRDC’s CIMMYT Australia ICARDA Germplasm Evaluation (CAIGE) program.

“What we were interested in was SNB resistance that was effective under environmental conditions experienced by WA wheat growers,” Dr Francki says.

“We could have tested for resistance genes in the glasshouse or our Perth nursery. But that’s not necessarily telling us the value of the resistance in production environments for WA growers. Instead, we established field-based protocols that can identify broad-spectrum SNB resistance that is useful to growers.”

The field-based disease-screening protocols became the foundation for a gene-discovery program that has the potential to change the way growers manage SNB production risks.

To date, it has detected only ‘minor’ SNB-resistance genes, meaning one gene alone is insufficient to protect wheat crops. The pre-breeders, however, have identified optimal combinations of two, three or more minor genes that have proven effective against SNB under WA production environments.

Marker Strategy

Incorporating a combination of genes into commercial wheat-breeding programs can be complex. To facilitate uptake of the resistance genes by wheat breeders, genetic maps were used to develop DNA markers that can quickly and cheaply detect the genes in hundreds of breeding lines.

Resistant germplasm and DNA markers were then made available to commercial wheat-breeding companies for use in developing new varieties. However, Dr Francki says uptake by the commercial sector has been hindered by difficulties implementing the new resources.

“What is lacking is an effective strategy to translate our knowledge, resources and capabilities in order to improve uptake of project outputs in commercial breeding, which is vital to maximise return on pre-breeding investment to the grain grower in the form of new varieties with suitable SNB resistance,” Dr Francki says.

We spent a lot of time developing our protocols and can now set up disease-screening capabilities in different crop production environments that present different pathogen populations and levels of disease intensity. - Dr Michael Francki

His team, therefore, is focused on developing a new partnership model that offers an effective technology-transfer strategy to help overcome barriers to commercial applications.

“Breeders can struggle with the field-based testing and selection,” Dr Francki says. “We spent a lot of time developing our protocols and can now set up disease-screening capabilities in different crop production environments that present different pathogen populations and levels of disease intensity.

“We can also contribute relevant expertise when devising breeding strategies to move the SNB resistance genes into a commercial breeding program.”

The WA DPIRD team is now exploring options to work in close conjunction with breeding companies, with the aim of moving SNB-resistance genes into breeding material. Included is support for field-based evaluation that is needed to select the suitable SNB resistance during variety development. This is especially important given that SNB is not included in national disease rating programs or the National Variety Trials.

“We need to have a strong and cohesive working relationship with commercial breeders if we are to effectively use the genetic resources and markers we have developed,” Dr Francki says. “We need to come together as a highly integrated team to share knowledge, resources and the methods developed in this project, especially with regards to the breeding, evaluation and selection strategies needed to deliver new resistant wheat varieties that maintain yields under SNB epidemics. A new pre-breeding–commercial breeding partnership model to effectively translate R&D outputs into new varieties will need financial investments from partner organisations and other industry stakeholders to succeed.”

To make inclusion of SNB-resistance genes an even better proposition for breeding companies, Dr Francki has also extended his wheat germplasm collection in order to identify additional resistance genes. Those extra genes provide insurance against the future breakdown of the first generation of gene-based crop protection.

He is also tapping into other global resources including the wheat genome sequence developed by the International Wheat Genome Sequencing Consortium to rapidly home in and isolate the individual disease-resistance genes. This would then permit the development of diagnostic markers that can identify gene variants with different resistance properties.

The gene discovery work is underway in conjunction with research fellow Dr Dora Li at Murdoch University.

“While identifying combinations of resistance genes that are broadly effective in grain production environments is pivotal, the prospect of directly isolating the resistance genes is also really exciting,” Dr Francki says.

“We are quietly confident that we will find the genes. That then creates new opportunities to optimise gene combinations that are the most valuable to the wheat industry. In the meantime, we want to build cohesive relationships and partner with breeders to get the first generation of the trait into new commercial cultivars. That’s the major focus.”

  • More information: Dr Michael Francki at michael.francki@dpird.wa.gov.au

GRDC Research Code: DAW00248

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