Exploiting Next Generation Sequencing Technologies to understand Pathology and resistance in Fusarium


CP 116 - Exploiting Next Generation Sequencing Technologies to understand Pathology and resistance in Fusarium

Start Date: 
Completion Date: 
Project Leader: 
Dr John Clarkson, University of Warwick
CP 116

HDC project cost: £44,348 (total project cost: £85,348)


Project summary:

Onion (Allium cepa) is an important horticultural crop which is cultivated by every agricultural nation in the world with an annual production of 78.5M tonnes and a value of $24,698M. It is the second most valuable vegetable crop in the world behind the tomato and in the UK, production is valued at approx. £110M per year. Onions are a staple crop and deliver a range of health benefits including anticarcinogenic, antithrombotic and antibiotic effects. Despite its value, research into genetic improvement of onion is limited as there are still few resources available. One reason is that compared to some other crop species, onion has very large diploid genome (16 Gbp per 1C organised into 8 chromosomes; cf. wheat=17.2 Gbp, maize=2.3 Gbp, rice=340 Mbp) which complicates genetic studies. However, recently onion ESTs have been used to produce a preliminary map.

Soilborne diseases caused by Fusarium oxysporum formae speciales (isolates adapted to specific hosts, f. spp.) are major constraints to the production of many horticultural food crops worldwide including onion, leek, lettuce, tomato, brassicas, asparagus, cucurbits, peppers, coriander, spinach, basil, beans, peas, strawberry, watermelon and banana and also affect economically important non-food crops such as carnation and narcissus. F. oxysporum was recently identified as the 5th most important plant pathogenic fungus based on its economic and scientific impact. F. oxysporum f.sp. cepae (FOC) is one of the most important pathogens of onion crops and infects the roots and/or basal plate at any stage of plant development. This causes a damping-off symptom on seedlings and a basal rot on more mature plants resulting in severe pre- and/or post-harvest losses. In the UK, FOC is recognised mainly as being a problem at harvest and in store but in severe cases entire crops can be lost in the field. Economic losses due to FOC on onion are estimated at £10-11 million per year the pathogen is becoming increasingly prevalent on leek crops (value £37M per year). FOC infection is favoured by warm temperatures and is predicted to get worse in Europe due to climate change. FOC produces long-lived chlamydospores that survive in the soil for many years and hence control approaches have previously relied on the use of soil sterilisation, drenches with fungicides or seed treatments. These approaches have largely been unsuccessful, have undesirable environmental effects and are threatened by legislation governing restrictions in pesticide use.

Although an important pathogen, non-pathogenic isolates of F. oxysporum also commonly occur in the soil as saprophytes while some have been identified as biocontrol agents and endophytes. The genetically heterogeneous nature and lack of reliable morphological characters in F. oxysporum means that distinguishing pathogenic and non-pathogenic isolates and different f. spp. is difficult and can only be done through pathogenicity testing on different hosts which is time-consuming and expensive. Molecular biotyping methods have been investigated but standard approaches (e.g. DNA fingerprinting, multilocus genotyping) have failed to reliably identify different f. spp. The factors which determine the host specificity and pathogenicity of different F. oxysporum f. spp. are poorly understood although more recent studies have identified the role of secreted effector proteins and mobile pathogenicity chromosomes in F. oxysporum f. sp. lycopersici, the f. sp. infecting tomato (FOL). If the genetic basis for pathogenicity could be similarly identified in FOC, then this information could be utilised to provide molecular tools for distinguishing it from other f. spp. and non-pathogenic isolates and also for detection in soil, onion seeds and sets as part of developing a risk assessment strategy for onion growers.

In the absence of effective control measures for Fusarium basal rot, identifying resistance in onion is extremely desirable but the lack of genetic resources and robust screening methods and the variability in FOC isolate pathogenicity has hindered progress and until recently only partial resistance was found in A. cepa. However, using a rapid and repeatable onion seedling bioassay and a highly pathogenic FOC isolate we have identified onion lines with much greater levels of resistance than current commercial cultivars. Moreover, this resistance was also evident in further tests at a mature bulb stage.


Aims and objectives:

In this proposed research, we will examine the genetic basis for FOC pathogenicity and resistance to this fungus in onion.
The major expected outcomes of the project are:
1) the identification of FOC pathogenicity/effector genes which could be used as markers to distinguish this pathogen from other F. oxysporum f. spp. or non-pathogenic isolates,
2) the identification of FOC resistance loci and associated genetic markers in onion for use in breeding programmes, 3)the production of new onion populations segregating for FOC resistance and pre-breeding onion lines to enable the development of basal rot resistant onion cultivars for the industry.
The project addresses the HAPI research challenges as follows.
Pathogens: the project will lead to an improved understanding of the interactions between F. oxysporum f. spp. and their hosts through examining the genetic basis for pathogenicity in FOC and resistance in onion leading to new options for disease control.
Seed quality and soil health: as FOC is seed and soilborne, identifying markers for pathogenicity will allow the development of diagnostic seed and soil tests which will help assess disease risk.
Changing Seasons: FOC is likely to become more prevalent in the UK with climate change and hence there is an increasing need for new control strategies.
The project also addresses the HAPI requirement for cross-cutting research by delivering impact at different stages in the onion crop supply chain.
The proposal also aligns with the BBSRC crop science strategic priority area of sustainability, particularly with respect to reducing inputs and reducing waste and also through accelerating translational research by generating pre-competitive crop germplasm improvement to underpin commercial plant breeding. In addition it addresses the data driven biology priority area through the use of next generation sequencing to identify and understand natural variation in genes controlling traits.