Developing disease prediction of onion basal rot using a quantitative molecular test

Losses due to Fusarium basal rot of bulb onions caused by the fungus Fusarium oxysporum f.sp. cepae (FOC) continue to increase for UK growers with plants becoming diseased both in field and store. We previously developed a DNA-based quantitative molecular diagnostic (qPCR) assay for FOC and the aim of this project is to evaluate the feasibility of using this test pre-planting to assess disease risk for growers. To do this, we will define a relationship between FOC inoculum level, the results of the qPCR test and disease development for different soils using an artificially inoculated system under controlled conditions. The results will indicate whether pathogen-free or low pathogen onion field sites can be identified with confidence and hence whether a pre-planting soil test to assess basal rot disease risk is feasible. In addition, we will determine the rate of FOC root colonisation to examine whether pathogen detection in onion seedlings before symptoms appear could also help inform crop management and harvest / storage decisions. Finally, we will also explore the hypothesis that soil factors such as the level of soil organic matter and the composition of the microbial community influence the rate of basal rot disease development and begin to investigate the key groups of organisms potentially involved using an amplicon sequencing approach. The project addresses the priority pathogen F. oxysporum and the key research area of pathogen detection as outlined in the call. 

Aim:  The main aim of the project is to define relationships between FOC inoculum level, the amount of FOC DNA as measured by a quantitative (q)PCR test and onion basal rot disease development for different soils. A secondary aim is to examine onion root colonisation by FOC and determine the capacity of different soils to reduce the rate of FOC disease development and identify the components of the microbial community that may be responsible. 

Objective: 

1. Determine the effect of different FOC inoculum levels on onion basal rot disease development for different soils 
2. Quantify the amount of FOC DNA for different inoculum levels using qPCR in different soils and define relationships with onion basal rot disease development
3. Determine the rate of onion root colonisation by FOC for different soils 
4. Establish the potential of amplicon sequencing to quantify levels of FOC inoculum for different soils and identify components of the microbial community that may reduce the rate of onion basal rot disease development