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

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

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

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

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

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

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

Pathogenicity: basal rot on bulbs Non-pathogenic Intermediate Pathogenic

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

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

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

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

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

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?

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, 2013. Fusarium oxysporum f.sp. cepae dynamics: in-plant multiplication and crop sequence simulations. European Journal of Plant Pathology 137, 545-61.

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

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

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