Fusarium: Investigations into the control of basal rots in crops


Fusarium species cause some of the most devastating diseases in agriculture and horticulture with both specialist and generalist pathogenic species that affect single or multiple hosts respectively. F. oxysporum is one the most important species with many pathogenic ‘forms’ that are specific to particular crops. These are particularly challenging to identify as even molecular approaches cannot easily distinguish between the different pathogenic or non pathogenic isolates. This, together with the fact that there is a wide diversity of other pathogenic Fusarium species that can often occur together in a disease complex, has hampered both our understanding of the epidemiology of these important pathogens, as well as the development of effective disease management strategies. The main aim of this proposal is to develop tools and approaches to detect, identify and quantify multiple Fusarium species and also assess the relationship between inoculum level and disease development with a focus on onion, leek, narcissus and column stocks. DNA-based tests will be developed for key Fusarium pathogens and ‘next generation’ amplicon sequencing techniques developed and employed to understand the dynamics and interaction of multiple pathogenic and non-pathogenic Fusarium species concomitantly, against the background of the wider microbial community. This ‘Fusarium community’ approach will have wide application across multiple crop types in agriculture and horticulture in understanding how different Fusarium species and complexes proliferate or decline in response to rotations, environment and application of control treatments, such as biopesticides. Such accurate identification and analysis of Fusarium has not been possible before and it is only with recent advances and use of the latest information and technology (such as whole genome sequencing) that the aims of this proposal can be addressed. The work outlined here is an essential first phase in underpinning a longer-term programme of Fusarium research that aims to improve our fundamental knowledge of Fusarium diseases and develop new management approaches across multiple crops.    
Benefits to Industry
Identification of the major Fusarium species affecting leeks (already known for onion, narcissus and stocks).
Development of specific diagnostic DNA based tests for F. oxysporum on onion, leek, narcissus and column stocks. These could be used to test seed, sets,    bulbs, plant material or soil for each pathogen. This information could then be potentially used to assess disease risk in nurseries, in the field or in store. 
Development of DNA based methods for studying the dynamics of multiple Fusarium species. Testing of this approach will lead to preliminary data on the      complex of Fusarium species and other microorganisms associated with infected crops of onion, leek, narcissus and stocks. This approach is generic and      would allow ‘pathogenic communities’ of Fusarium to be identified and quantified for any crop or rotational situation affected by this group of pathogens.      This is therefore directly relevant to all crops suffering from Fusarium problems, the main ones being onion, leek, Narcissus, stocks and other cut flowers,      tomatoes, cucumbers, sweet peppers, peas, cereals and potatoes.  
Quantification of the effect of F. oxysporum inoculum level on disease development for FOC, FOM and FON. This will allow DNA based tests to be                  calibrated with inoculum levels that result in significant Fusarium disease development. 
Characterised Fusarium isolate collections from multiple crops for future research use.
All the above benefits will form the foundation for further research on optimising rotations and other control measures for Fusarium.   
Project code:
01 April 2017 - 30 September 2018
Total project value:
Project leader:


POBOF 452_Report_GS_Annual_2018 POBOF 452_Report_Annual_2018 FV POBOF 452_Report_Final_2019_0 FV POBOF 452_Grower Summary 2019

About this project

To develop molecular tools for identifying and quantifying Fusarium species
To determine the effect of Fusarium inoculum concentration on disease development for key crops 
Objectives for each aim:
To develop molecular tools and resources for identifying and quantifying Fusarium species
1.1: Collect, identify and test pathogenicity of different Fusarium spp.
1.2: Develop specific quantitative (real-time) qPCR tests for F. oxysporum f.spp. affecting onion, leek, narcissus and column stocks.
1.3: Develop a DNA barcoding approach for analysis of Fusarium communities
1.4: Develop Fusarium infested areas for onions and stocks 
To determine the effect of Fusarium inoculum concentration on disease development 
2.1: Determine the effect of F. oxysporum inoculum level on disease development in onions 
2.2: Determine the effect of F. oxysporum inoculum level on disease development in stocks
2.3: Determine the effect of F. oxysporum inoculum level on disease development in Narcissus
2.4: Quantify colonisation of F. oxysporum on onions, stocks and Narcissus