Virus diseases in Carrots: The UK experience. Adrian Fox Fera Science Ltd

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1 Virus diseases in Carrots: The UK experience Adrian Fox Fera Science Ltd

2 What is Fera Science Ltd?

3 Carrot virus research in Europe (up to 2012) Scotland: Carrot Motley Dwarf complex Hogweed virus 6 (and others ) Netherlands: Carrot Motley Dwarf complex HV6 (Carrot yellow leaf virus) Parsnip yellow fleck Germany: Carrot Yellow leaf virus Carrot thin leaf virus England: Parsnip Yellow fleck virus Carrot Red leaf virus Carrot red leaf associated viral RNA

4 Current state of Knowledge Carrot necrotic dieback virus (Formerly Parsnip yellow fleck virus Anthriscus strain) Important early season disease Sporadic outbreaks Associated with seedling death Stunted, misshapen roots in mature plant infections Needs Anthriscus yellows virus (AYV) for transmission Carrot is not a host AYV therefore NO onward transmission in carrot crops Source: AAB DPV394

5 Current state of Knowledge Carrot Motley Dwarf disease Three pathogen complex Carrot red leaf virus (CtRLV), Carrot mottle virus, Carrot red leaf associated viral RNA Needs CtRLV for aphid transmission CAN be spread from carrot to carrot Causes reddening of leaves and mottle Thought to cause splits in roots called kippering

6 Rooting out the cause of internal browning

7 Viral browning of carrots (HDC FV382a) Conventional PCR of affected & unaffected carrots showed no association with expected viruses Stocks of carrots rejected due to the presence of internal necrosis linked to viruses. Real-time PCR demonstrated a strong association between CYLV and necrosis, suggesting that removal of this virus would reduce necrosis by 96% samples positive affected unaffected PYFV CRLV CRLaV CMoV CYLV Negative Virus MiSeq sequencing identified Carrot yellow leaf virus in necrotic samples. Sequencing also detected a Closterovirus (CtCV-1) and a Torradovirus (CaTV-1) plus several other viruses which were new to science. Adams et al. (2014) Carrot yellow leaf virus Is Associated with Carrot Internal Necrosis. PLoS ONE 9(11): e doi: /journal.pone

8 AHDB FV382b and Defra projects : understanding the novel viruses

9 Field sampling 2014 Field Margin and Road N Hedgerow CYLV 23% CTV 25% DUAL 9% Total Virus 39%

10 Relative virus incidence Carrots 2015 (Two regions) 250 CMD CYLV CaTV CtCV Virus % Stamford Bridge Stamford Bridge Late Sutton of the Forest Elvedon Estate Highman 'Healthy' Highman 'Infected' Yorkshire (North) Norfolk (East)

11 Sources of virus? Cow Parsley (Anthriscus sylvestris) Hogweed (Heracleum sphondylium) Ground Elder (Aegopodium podagaria) Hemlock (Conium maculatum) Rough Chervil (Chaerophyllum temulum) Alexanders (Smyrnium olusatrum)

12 Warwick Crop Centre weed samples 1555 samples UK Wide sampling Collected over 3 years ( ) 10 species sample locations per year Previously tested for CtRLV, PYFV, AYV RNA extracts retained at Warwick (-80 o C) PYFV and CtRLV findings sequenced to look at population genetics Many wild hosts, few carrot Cow Parsley only Carrot/Wild Carrot Carrot red leaf virus from Defra IF0188

13 % Proportion of positive virus cases Relative proportion of viruses in weeds = 472 virus cases 2012 = 174 virus cases CtRLV PYFV AYV CYLV CtCV-1 CaTV

14 Viruses detected by host species 60 Percentage infection (%) Alexanders Cow Parsley Ground Elder Hemlock Hogweed Rough Chervil CRLV PYFV AYV CYLV CtCV-1 CaTV

15 Aphid Transmision of CaTV-1 and CtRLV

16 Aphid vectors of carrot viruses Virus Vectors? Transmission mode? CMD: Carrot red leaf virus (CtRLV), Carrot mottle virus (CMoV) and carrot red leaf associated viral RNA (CtRLVaRNA) Parsnip yellow fleck virus (PYFV) requires helper -Anthriscus yellows virus (AYV) Carrot yellow leaf virus (CYLV) Carrot torrado virus (CaTV) C. Aegopodii M. persicae C. aegopodii C. pastinacae C. aegopodii C. pastinacae C. theobaldi M. persicae M. persicae C. aegopodii Circulative, persistent non-circulative, semi-persistent non-circulative, semi-persistent Carrot closterovirus-1 (CtCV-1)???

17 Sources of carrot viruses. From Cow parsley AYV PYFV Aphids/Eggs on winter host Aphids Migrate Pick up Virus Transmit to Carrot From Carrots CtRLV (CMoV) (CtRLVaRNA) CaTV-1?

18 Knowledge gaps Relative influence of peach-potato aphid in carrot crops Aphicide resistance status for willow-carrot aphid How much does this species contribute in the field in the UK? should we worry about this.? Can we spray the right chemical at the right time? Epidemiology of CYLV and CtCV-1 Is crop to crop transmission the major concern (e.g. CMD)? Is weed to crop transmission the major concern (e.g. PYFV)? When is the virus coming in? How long is it being spread within crop throughout the season? Can we tailor crop management practices to minimise virus risk?

19 So what does this all tell us? 250 CMD CYLV CaTV CtCV1 200 PYFV possibly underreported Virus% Stamford Bridge Stamford Bridge Late Sutton of the Forest? Elvedon Estate Highman 'Healthy' Highman 'Infected' due to sampling time Highest incidence viruses may come from carrot as a source Is the source overwintered carrots or volunteers? Virus control appears to be breaking down. Length of season? Vector resistance? Limited range of control measures?

20 The principles of plant virus management : Plant clean seed Grow in absence of vectors Grow in absence of virus reservoirs Isolate from similar crops Use resistant (or tolerant?) varieties

21 Acknowledgements Dr Derek (Dez) Barbara ( ) Zurine Rozado s Carrot torrado virus PhD work conducted under UK Government-Defra Plant Health Capability funding Initial carrot necrosis work and Carrot yellow leaf virus work funded by AHDB-Horticulture (FV382a & b) Fera Staff in Virology, the MTU and Applied Entomology Staff of Warwick Crop Centre