1. How will new Fusarium research help control in the future?
Dr John Clarkson, Warwick Crop Centre, University of Warwick

2. Outline Background: F. oxysporum and onion basal rot
Identification and diagnostics
Resistance
Management and control: rotations

3. Fusarium oxysporum
A fungal complex that includes important plant pathogens causing vascular wilts and root rots
Formae speciales (f. spp.) are ‘special forms’ specific to different hosts
Many plants affected: onion, leek, tomato, lettuce, pea, bean, potato, brassicas, strawberry, apple, pepper, coriander, spinach, banana, carnation and narcissus
There are also many non-pathogenic isolates of F. oxysporum

4. Fusarium basal rot Caused by Fusarium oxysporum f. sp. cepae (FOC)
One of the biggest problems for UK onion growers and set producers
Infects roots and basal plate
Causes damage at any stage of plant development but mainly at harvest / in store
Produces chlamydospores which can survive for many years in the soil

5. FOC identification
Why? Identifying and quantifying FOC would allow testing of seed, sets, bulbs and soil to assess risk of disease
Different Fusarium species can be difficult to distinguish on agar
Species can be identified by DNA sequencing of a standard ‘housekeeping’ TEF gene (translation elongation factor)
BUT TEF does not distinguish different pathogenic forms of F. oxysporum or non-pathogenic isolates

6. TEF Tree: Fusarium species
F. oxysporum (non pathogenic)
F. proliferatum
F. fujikuroi
F. sacchari
F. redolens
F. avenaceum
F. tricinctum
F. equiseti
F. culmorum
F. poae
F. solani
F. oxysporum f.sp. narcissi
F. oxysporum f.sp. cepae (pathogenic on onion)
F. oxysporum f.sp. pisi race 2
F. oxysporum f.sp.lycopersici race 1
F. oxysporum f.sp. cubense
Fusarium oxysporum
complex
Onion
Non-pathogenic
Pea
Tomato
Banana
Daffodil
Other
Fusarium
species

7. Fusarium pathogenicity genes
14 Secreted In Xylem (SIX) genes are associated with pathogenicity in Fusarium oxysporum f. sp. lycopersici (tomato pathogen)
We looked for SIX genes in F. oxysporum isolates from onions and assessed pathogenicity

8. Pathogenicity: basal rot on bulbs
Non-pathogenic Intermediate Pathogenic

9. SIX genes vary in F. oxysporum
Fusarium species
Host
Secreted in xylem (SIX) genes 1 2 3 4 5 6 7 8 9 10 11 12 13 14
F. oxysporum f.sp. cepae (pathogenic)
Onion
F. oxysporum f.sp. cepae (pathogenic)
Leek
F. oxysporum f.sp. cepae (intermediate isolate)
F. oxysporum (non pathogenic)
F. oxysporum f. sp. lycopersici (race 1)
Tomato
F. oxysporum f. sp. lycopersici (race 3)
F. oxysporum f. sp. phaseoli (race 4)
Bean
F. oxysporum f. sp. pisi (race 1)
Pea
F. oxysporum f. sp. pisi (race 2)
F. oxysporum f. sp. pisi (race 5)
F. oxysporum f. sp. pisi (genome)
F. oxysporum f. sp. lini
Linseed
F. oxysporum f. sp. narcissi
Daffodil
F. oxysporum f. sp. freesia
Freesia
F. oxysporum f. sp. cubense
Banana
F. proliferatum
F. redolens

10. SIX gene separates F. oxysporum ‘forms’
F. oxysporum f.sp. dianthi
F. oxysporum f.sp. narcissi
F. oxysporum f.sp. lini
F. oxysporum f.sp. canariensis
F. oxysporum f.sp. pisi race 1
F. oxysporum f.sp. lycopersici
F. oxysporum f.sp. cepae
F. oxysporum f.sp. lilii
F. oxysporum f.sp. cubense
F. oxysporum f.sp. freesia

11. FOC resistance: seedling test
Add susceptible resistance bar
Susceptible Resistant
Onion Line

12. FOC resistance: bulb test
Selected onion lines also screened for FOC resistance on mature plants / bulbs
Good agreement between seedling and bulb tests
Susceptible line
Inoculated Uninoculated
Resistant line

13. Genetic markers for FOC resistance
Percentage of individual plants with different resistance scores
Resistant and susceptible individuals are being genotyped
Genetic markers associated with resistance will be identified

14. Some management strategies…
Seed/set fungicide treatments give short term control
Avoid plant stress which can enhance basal rot
Cure and dry harvested bulbs quickly
Assess risk of basal rot in store by splitting samples of bulbs at harvest and / or ‘hotboxing’
Biocontrol work (Ralph Noble) identified some potentially useful products but further development is needed – new products coming to market
Optimise rotations – do some cropping patterns encourage or suppress Fusarium?

15. FOC colonises other plants
Crop species
FOC colonisation
Onion
High
Maize
Oat
Sunflower
Low
Wheat
Leoni C, De Vries M, Ter Braak CF, Van Bruggen AC, Rossing WH, Fusarium oxysporum f.sp. cepae dynamics: in-plant multiplication and crop sequence simulations. European Journal of Plant Pathology 137,

16. Onion root cross sections 96 hours post inoculation
Pathogenic isolate
Non-pathogenic isolate

17. Summary
The presence of SIX genes in FOC correlated with pathogenicity on onion and could form the basis for a diagnostic to help assess disease risk
Genetic markers for FOC resistance and pre-breeding onion lines are being developed
FOC may colonise non-host crop plants which may influence rotation strategies in the future

18. Acknowledgements Andy Taylor Alison Jackson Graham Teakle Sascha Ott
Laura Baxter
Patrick Schafer
Ruth Schafer
Beatriz Lagunas
Alessandro Rainoni (Erasmus)
Richard Harrison
Andrew Armitage
Reinout de Heer
Tosca Ferber
Hans van den Biggelaar