Exploiting next generation sequencing technologies to understand pathology and resistance to Fusarium

Onion is a major crop across the world and as such is the second most valuable vegetable crop tomato. Fusarium oxysporum f. sp. cepae causes basal rot of onion. In the UK alone postharvest losses due to F. oxysporum f. sp cepae are estimated to be worth £11million per year.

The Harrison lab is part of a collaborative BBSRC-funded project to investigate the basis of pathogenicity in Fusarium oxysporum f.sp. cepae and the factors contributing to resistance in onion.

 Major project aims:

  • Identify effectors produced by Fusarium oxysporum f.sp. cepae, which shut down plant defence.
  • Identify resistance genes  produced by onion, which recognise pathogen effectors and promote plant defence response. Identify molecular markers associated with these resistance genes.
  • Produce new onion populations segregating for resistance to Fusarium oxysporum f.sp. cepae


  • Molecular markers for pathogen effectors can then be used as tools to screen for and identify Fusarium oxysporum f.sp. cepae pathogens.
  • Molecular markers associated with resistance genes can be used to identify resistance in onion cultivars.
  • Onion lines segregating for resistance and pre-breeding onion lines will be used by partners in industry to develop novel resistant onion cultivars.

NIAB EMR is responsible for performing genome sequencing for a large set of Fusarium oxysporum isolates, generating transcriptome sequence data and determining the structure of genes within these genomes.  Effectors and resistance genes will then be identified through analysis of this genomic data. Partners at Warwick Crop Centre (University of Warwick) are screening these isolates for virulence on a diverse set of onions and related species, as well as understanding how Fusarium genes are turned on/off during the course of infection.

Principal Investigator: Richard Harrison

ResearcherAndrew Armitage, Bethany Greenfield

Funder: BBSRC

Duration: 2014-2016


Warwick Crop Centre

John Clarkson 

Andy Taylor

Graham Teakle

Sascha Ott


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