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Fusarium diseases

Onion (Allium cepa) is an important horticultural crop which is cultivated by every agricultural nation in the world with an annual production of 78.5M tonnes and a value of £9,500M. It is the second most valuable vegetable crop in the world behind the tomato and in the UK, production is valued at approx. £110M per year. Onions are a staple crop and deliver a range of health benefits including anticarcinogenic, antithrombotic and antibiotic effects.

Fusarium basal rot (FBR) caused by Fusarium oxysporum fsp. cepae (FOC) and Allium white rot (AWR) caused by the fungus Sclerotium cepivorum and are two major soilborne diseases of onions and other Allium crops. Both diseases are very difficult to control as they form long-lived survival structures which remain in the soil for many years; chlamydospores for F. oxysporum and sclerotia for S. cepivorum. FOC infects roots directly through germination of spores in the soil and predominantly causes a bulb rot on onions later in the season or more often in store. However, the pathogen can also cause symptoms at any stage of plant development. It is an increasing problem for onion growers in the UK and globally it is predicted to worsen under current climate change models. S. cepivorum sclerotia germinate and infect roots through hyphae in response to specific chemical compounds released from onion roots. This results in wilting and subsequent plant death during the growing season with more sclerotia being produced and returned to the soil.

The overall aim of our research is to characterise these and other onion pathogens using molecular methods, understand their biology and develop alternative and more sustainable ways of reducing their impact for onion growers.

A recently awarded BBSRC HAPI project in collaboration with Richard Harrison at East Malling Research and industry partners Hazera Seeds and AHDB Horticulture is investigating both the genetic basis for pathogenicity in FOC and for new sources of resistance in onion. An accompanying PhD project being carried out by Sascha Jenkins is investigating the pathogenicity of Fusarium spp. on pea.

Fusarium Basal Rot Research
  • Molecular and biological characterisation of FOC isolates and basis for pathogenicity
  • Identifying and characterising new sources of resistance to FBR on onion
Allium White Rot Research
  • Dormancy and other factors affecting germination of S. cepivorum sclerotia
  • Epidemiology and effect of environmental conditions on S. cepivorum and its interaction with microbial antagonists
  • Biological control of AWR using Trichoderma spp. and composts

Research Projects


Selected Publications
  • Taylor A, Vágány V, Jackson AC, Harrison RJ, Rainoni A, Clarkson JP (2016) Identification of pathogenicity-related genes in Fusarium oxysporum f. sp. cepae. Molecular Plant Pathology 17, 1032–1047.

  • Taylor A, Vagany V, Barbara DJ, Thomas B, Pink DaC, Jones JE, Clarkson JP (2013) Identification of differential resistance to six Fusarium oxysporum f. sp. cepae isolates in commercial onion cultivars through the development of a rapid seedling assay. Plant Pathology 62, 103-11.
  • Clarkson JP, Scruby A, Mead A, Wright C, Smith B, Whipps JM (2006) Integrated control of Allium white rot with Trichoderma viride, tebuconazole and composted onion waste. Plant Pathology 55, 375-86.
  • Coventry E, Noble R, Mead A, Marin FRM, Perez JA, Whipps JM (2006). Allium white rot (Sclerotium cepivorum) suppression with composts and Trichoderma viride in relation to sclerotia viability. Phytopathology 96, 1009-1020.
  • Clarkson JP, Mead A, Payne T, Whipps JM (2004) Effect of environmental factors and Sclerotium cepivorum isolate on sclerotial degradation and biological control of white rot by Trichoderma. Plant Pathology 53, 353-62.
  • Clarkson JP, Payne T, Mead A, Whipps JM (2002) Selection of fungal biological control agents of Sclerotium cepivorum for control of white rot by sclerotial degradation in a UK soil. Plant Pathology 51, 735-45.
  • Clarkson JP, Whipps JM, 2002. Control of sclerotial pathogens in horticulture. Pesticide Outlook 13, 97-101.

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