Coronavirus (Covid-19): Latest updates and information
Skip to main content Skip to navigation

BBSRC HAPI: Exploiting next generation sequencing technologies to understand pathogenicity and resistance in Fusarium oxysporum


The soilborne fungus Fusarium oxysporum affects many different crops worldwide and causes some of the most devastating diseases in horticulture. Different forms of the fungus are adapted to different hosts and Fusarium oxysporum f.sp. cepae (FOC) which affects onion is a major constraint to production with losses estimated at £11M per annum in the UK. FOC causes a basal rot which is most damaging as bulbs mature in the field or post-harvest in store. FOC produces long-lived spores, and hence control is difficult and relies on soil sterilisation/pasteurisation, fungicide drenches or seed treatments. However, these approaches may not be effective, and can have negative impacts on the environment. Furthermore, legislation surrounding chemical treatment of crops and seeds is changing and some products may not be permitted in future. Plant resistance to basal rot in onion is therefore highly desirable, but so far successful varieties have not been produced for use in the UK.

Aims and approaches

1. Identify the genetic basis for FOC resistance and identify genetic markers
Previous work identified high levels of basal rot resistance in an onion diversity set as part of the Defra-funded Vegetable Genetic Improvement Network (VeGIN). An onion population segregating for resistance / susceptibility to FOC is being genotyped in order to map resistance. Further onion populations for mapping FOC resistance are being developed by Hazera Seeds as well as pre-breeding material to enable the process of introgressing resistance genes into commercial onion cultivars.
2. Determine the basis for FOC pathogenicity
Whole genome sequencing and direct PCR of potential pathogenicity genes is being carried out for a selection of pathogenic and non-pathogenic F. oxysporum isolates from onion.
3. Examine gene expression in interactions between pathogenic / non pathogenic Fusarium isolates and susceptible / resistant onion lines
RNA sequencing is being used to explore genes expressed by pathogenic and non pathogenic F. oxysporum isolates on both resistant and susceptible onion lines.

Partners and funding

The project is a collaboration led by the University of Warwick (John Clarkson) with East Malling Research (Richard Harrison) and Hazera Seeds (Reinout de Heer). The project is funded by the BBSRC as part of the Horticulture and Potatoes Initiative, with industry funding from AHDB Horticulture and Hazera Seeds.



emr.jpg  bbsrc.jpg  hazera.jpg   ahdb.jpg