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

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

TEF Tree: Fusarium species

Fusariumoxysporumcomplex

Onion

Non-pathogenic

PeaTomatoBanana

Daffodil

OtherFusariumspecies

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

A28 JB4 M9FU

S1 R3CB3

A1/2 55A21

S1B224 84

FUS3

FUS2

K3BRO2

A230

10

20

30

40

50

60

70

F. oxysporum isolate

Perc

enta

ge o

f oni

on b

ulb

dise

ased

Pathogenicity: basal rot on bulbs

Non-pathogenic Intermediate Pathogenic

SIX genes vary in F. oxysporumFusarium species Host Secreted in xylem (SIX) genes

1 2 3 4 5 6 7 8 9 10 11 12 13 14F. oxysporum f.sp. cepae (pathogenic) OnionF. oxysporum f.sp. cepae (pathogenic) LeekF. oxysporum f.sp. cepae (intermediate isolate) OnionF. oxysporum (non pathogenic) Onion F. oxysporum f. sp. lycopersici (race 1) TomatoF. oxysporum f. sp. lycopersici (race 3) Tomato

F. oxysporum f. sp. phaseoli (race 4) BeanF. oxysporum f. sp. pisi (race 1) PeaF. oxysporum f. sp. pisi (race 2) PeaF. oxysporum f. sp. pisi (race 5) PeaF. oxysporum f. sp. pisi (genome) Pea

F. oxysporum f. sp. lini LinseedF. oxysporum f. sp. narcissi DaffodilF. oxysporum f. sp. freesia FreesiaF. oxysporum f. sp. cubense Banana

F. proliferatum OnionF. redolens Onion

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. cubense

F. oxysporum f.sp. freesia

F. oxysporum f.sp. lilii

SIX gene separates F. oxysporum ‘forms’

FOC resistance: seedling test

0

10

20

30

40

50

60

70

80

90

Surv

ival

(%)

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

Resistant line Inoculated Uninoculated

1 2 3 4 5 6 7 8 9 10 110

10

20

30

40

50

60Resistant LineSusceptible Line

Resistance score

Perc

enta

ge o

f pla

nts

Genetic markers for FOC resistance

• Resistant and susceptible individuals are being genotyped

• Genetic markers associated with resistance will be identified

Percentage of individual plants with different resistance scores

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 High

Oat High

Sunflower Low

Wheat Low

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 sections96 hours post inoculationPathogenic 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