An international team of scientists has developed a new method to improve the accuracy of gene mapping in complex organisms.

This is a breakthrough that could enhance research into fungal diseases affecting crops like wheat.

Research scientists at Rothamsted Research are involved with this project.

Using an advanced bioinformatics tool, researchers have re-assessed the genome of the fungal pathogen responsible for septoria leaf blotch.

This is a disease that causes significant wheat yield losses across Europe.

The researchers’ findings highlight major flaws in previous genetic analyses and offer a more precise picture of the fungus’ genetic structure.

Gene mapping

Until now, predicting genes in complex organisms has been a challenge, even with vast amounts of genetic data available.

Past efforts to map the genes of the fungus produced inconsistent results, with different studies identifying between 10,900 and 13,200 genes, yet only a third of these findings matched across datasets.

To address this, the research team developed a new tool that combines multiple gene prediction methods with real biological evidence from fungal RNA sequences.

The updated analysis identified 13,414 ‘high-confidence’ genes, improving the accuracy of previous research and shedding new light on how the fungus regulates its genes.

The research team, led by French scientists, compared four different gene prediction datasets for the same septoria strain, each generated independently by researchers in The Netherlands, Germany, US, Australia, and UK (Rothamsted Research).

Dr. Jason Rudd who led Rothamsted’s contribution to the study, commented: “Whilst many differences were observed, when each gene was analysed in detail, we were able to form a consensus on the most accurate structure of each and every one of them, as well as identify previously hidden genes, and structural gene variants.”

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This approach has given rise to the release of a “gold standard” open community reference resource for septoria, which will accelerate research efforts to identify exploitable weaknesses in the pathogen.

The study also revealed new insights into how the pathogen’s genes are structured and expressed, particularly in regions that influence when and how they are activated.

This could help scientists better understand how the fungus adapts in wheat to different environments, potentially paving the way for more effective disease control strategies.

Dr. Rudd concluded: “Accurate genome mapping is a crucial step in tackling fungal diseases, which are becoming an increasing threat to global food security.

“By refining gene prediction techniques, we hope we can improve our ability to monitor and combat these pathogens before they cause further damage to crops.”

Biofungicide pilot trials

Meanwhile, the coming years will see arable farmers in the UK getting independent data on biofungicide performance in crop protection programmes.

This is thanks to a series of Agriculture and Horticulture Development Board (AHDB)-funded pilot trials.

Replicated field trials will test the effectiveness of biofungicides against septoria tritici in winter wheat over two cropping years (2025/2026 and 2026/2027).

A consortium with a strong track record of delivering trusted, independent research to support effective crop disease management has been appointed to lead the research.

Biofungicides are a type of biopesticide and regulated as plant protection products. They are used most frequently in high-value horticultural markets.

The pilot trials will generate evidence to maximise their performance in disease management programmes for cereals.

AHDB lead crop protection scientist Sacha White said: “Biofungicides have good potential for the arable sector but their biological nature means they need particularly careful integration in crop protection programmes.

“Additionally, biopesticide activity is often established in controlled environments.

“This work will specifically examine evidence of efficacy in field conditions, where numerous factors can impact their performance, such as weather, disease progression, and the wider spray programme.”

The pilot trials will focus on septoria tritici control due to the economic importance of this disease in UK winter wheat, the availability of biofungicide products with disease-management potential and the relatively high number of preliminary research findings.

Biofungicides will be tested in line with the manufacturer’s recommendations on two varieties with different levels of resistance to septoria tritici – a moderately resistant and a moderately susceptible variety.

This will be done as part of conventional winter wheat fungicide programmes.

The trials will also vary conventional fungicide dose to help reveal the point at which biofungicides start to contribute to disease control and yield gains.

The consortium, which includes SRUC, ADAS and NIAB, already manages an extensive network of efficacy trials as part of AHDB’s long-term fungicide performance research and has strong connections with the agrochemical industry.

Gene mapping

Biofungicide pilot trials

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