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Finding a solution to fusarium basal rot

Dr Andrew Taylor and Dr John Clarkson, Warwick Crop Centre

Published Fenbruary 2014

The onion is a staple ingredient, has extensive health benefits and, in the UK alone, the industry is worth approximately £110 million. But Fusarium Basal Rot (FBR, caused by the fungus Fusarium oxysporum), a disease little known outside the industry, has the potential to threaten that situation. Dr Andrew Taylor and Dr John Clarkson are working to find an environmentally friendly and sustainable solution to this global problem.

A staple ingredient of many world cuisines, onions also offer a range of health benefits including anticarcinogenic, antithrombotic and antibiotic effects. Onions rarely arouse excitement amongst foodies but imagine a world without them. As well as being tasty and healthy, the ‘tear-inducing’ vegetable is a vitally important horticultural crop.

Taylor examines an onionDespite their obvious value and health benefits, increasingly onion crops are being blighted by a disease called Fusarium Basal Rot (FBR). Last year alone, losses due to FBR were estimated at £11 million in the UK. It’s not only the UK that’s affected; the soil-borne disease is having a significant impact on onion production globally.Cultivated by every agricultural nation in the world, each year more 78.5 million tonnes are produced, with an economic value of around £18,673 million. In the UK, around 350 tonnes of onion are produced every year with a value of approximately £110 million.

“The problem with FBR is that it can affect the root of the onion at any stage in the plants development, causing seedling death or resulting in the bulb rotting in more mature plants,” explains Dr Andrew Taylor. “Typically this results in rotting bulbs at harvest and in store. However we’re seeing increasingly severe cases where entire onion fields are lost.”

Recent harvests have been challenging for UK onion growers with higher than normal average temperatures leading to increased losses. Andrew warns that unfortunately the problem is likely to get worse: “FBR likes warm, wet conditions, and based on current climate change predications, the UK is becoming more conducive to this disease.”

Until recently there has been little investment in research into ways to prevent and reduce the damage caused by FBR. Research at the Warwick Crop Centre, which began in 2009, means that that we now have an increased understanding of FBR and why current attempts to the treat the disease have had mixed results.

Dr John Clarkson: “Fusarium oxysporum produces tough, long-lived spores that can survive in soil for many years. This explains why attempts to control the disease through long rotations, soil sterilisation and drenches with fungicides have had limited success.”

Some of these methods also impact on the environment, and with legislation restricting pesticide use in a number of countries, Andrew and John are focussing on developing disease resistant varieties of onion.

“Identifying and developing disease resistant onions is much more of an environmentally- friendly and sustainable approach,” says John.

Developing disease resistant onions is also welcomed by those in industry, including Alastair Findlay, Chairman of the British Onions R&D Committee. "FBR is soil borne and its severity is linked to climatic conditions. Infection of the crop results in breakdown in store and and rejection by customers. The opportunity for future genetic resistance to FBR would be warmly welcomed by onion producers and a major advance in consistent quality onion production," said Alastair.

The team at Warwick Crop Centre have been researching the problem since 2009 as part of a Defra-funded ‘Vegetable Genetic Improvement Network’ (VeGIN) project. Different onions lines were screened for resistance using a glasshouse-based seedling assay. Results were verified in tests with mature bulbing onion plants.

The onions grown in the glasshouse were exposed to a highly virulent strain of Fusarium, allowing the team to identify a range of resistance responses in onion lines from an extensive diversity collection. This ‘differential resistance’ in the diversity set ranged from ‘highly susceptible’ through to ‘moderately resistant’ and ‘highly resistant’ lines. By the end of 2012, several highly resistant onion lines had been verified over several independent experiments.

A new collaborative project funded by BBSRC as part of the Horticulture and Potato Initiative (HAPI) sets out to develop this research further and will start in April next year.

“One of the main aims of the work will be to use next generation DNA sequencing approaches to identify the genetic basis for Fusarium resistance so that DNA-based markers can be developed to accelerate the breeding of new resistant onion varieties.

This research should provide us with the information, tools and resources to understand the genetics that control resistance. This will allow resistance genes to be tracked throughout the breeding process and new onion lines to be rapidly genetically screened for resistance.”

Another aim of the research will be to identify the genes which enable particular strains of F. oxysporum to specifically attack onions. This could potentially help address the general question of how different strains of the fungus attack different crops. This information might also help scientists to develop diagnostic tools to test soil for the disease.

The team are acutely aware that alongside developing disease resistant onions, they also need to develop varieties of onion that will meet agricultural and consumer needs too, as John explains: “The new varieties we develop need to have characteristics that are essential for commercial production such as high yield, uniform bulb size, and ability to store well.

Although this is a long term goal, we have made significant progress towards finding a solution to a globally important onion disease which threatens current and future food security.”


 Dr Andrew TaylorDr Andrew Taylor (pictured above) is the principal plant pathology researcher based at the Warwick Crop Centre, which is part of the School of Life Sciences, University of Warwick. His research interest focuses on plant pathology. He is currently working on a Defra-funded project looking at resistance to Sclerotinia disease in brassicas and is also involved in research on the dynamics of cavity spot disease in carrots. From November 2013, he will begin a five year HDC fellowship which will allow him to further his plant pathology skills by working with a wider range and pathogens and hosts.


Dr John ClarksonDr John Clarkson is a research leader also based at the Warwick Crop Centre. John is a plant pathologist with almost 20 years research experience. John specialises mainly in vegetable crops, initially working on brassica and allium foliar pathogens before focussing more recently on soilborne diseases. These include major pathogens such as Sclerotinia, Fusarium and Pythium species and his interests cover plant pathogen biology, ecology and diversity as well the use of biological control and disease forecasting for disease management. John is involved in a range of different individual and collaborative projects encompassing basic, strategic and applied research which are funded by government, research councils and industry. John also teaches on the Crop Protection module, a core feature of several MSc courses at the School of Life Sciences and supervises several PhD students.