Diagnostic tests to assess Fusarium disease risk, select rotation crops and monitor microbial communities


Findings:  The work carried out in this project builds on work carried out in the previously funded project FV POBOF 452 and CP 196.

  • Objective 1: A clear relationship between FOL4 inoculum concentration, pathogen DNA levels and Fusarium wilt disease development in lettuce was established. This was help determine the risk of disease development from qPCR analysis of soil samples.
  • Objective 2: FOC could be detected in soil samples from commercial onion fields using qPCR during the season but results were variable due to relatively low levels of basal rot developing. No FOC was detected at planting suggesting a different approach to utilising qPCR is required to better assess disease risk.
  • Objective 3: Molecular qPCR diagnostics was effective at detecting FOC in onion bulbs even in the absence of visible symptoms. This approach is therefore promising for assessing if bulbs might develop basal rot before they go into store.
  • Objective 5: A method was successfully developed to examine FOL4 inoculum build up in sterilised and non-sterilised soil after successive lettuce crops. This will be used to test different treatments to suppress proliferation of the pathogen.
  • Objective 6: Amplicon sequencing was successfully employed to quantify FOL4 alongside other components of the soil microbial community


Project code:
CP 204
01 April 2020 - 28 February 2023
AHDB sector cost:
Total project value:
Project leader:
Dr John Clarkson


CP 204_Report_Annual_2021 CP 204_GS_Report_Annual_2021 CP204_Report_Annual_2022 CP204_Growers Summary_Report_Annual_2022

About this project

Aim: To use molecular methods to determine the risk of Fusarium disease in a number of horticultural crops, select effective rotation crops and monitor F. oxysporum pathogens and associated microbial communities in soil.

  1. Define a relationship between the amount of Fusarium DNA, Fusarium inoculum and disease development in soil
  2. Evaluate the use of molecular diagnostics to detect and assess the risk of Fusarium disease in onion, lettuce and Narcissus
  3. Evaluate the use of molecular diagnostics to determine the presence of FOC in harvested onion bulbs to assess the risk of disease development in store or pre-planting.
  4. Determine the colonisation of non-host plants by oxysporum pathogens to identify suitable rotation crops
  5. Investigate the feasibility of establishing Fusarium-suppressive microbial communities and biological control agents in protected cropping systems
  6. Employ amplicon sequencing to quantify oxysporum pathogens alongside suppressive components of the soil microbial community
  7. Evaluate crop protection products for control of FOC in field experiments