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Adrian Fox Carrot viruses Carrot viruses • • • • • • • • • • • • • • • • • • Alfalfa mosaic alfamovirus Arabis mosaic nepovirus Beet pseudo-yellows (?) closterovirus Carrot latent nucleorhabdovirus Carrot mosaic (?) potyvirus Carrot mottle mimic umbravirus Carrot mottle umbravirus Carrot red leaf luteovirus Carrot red leaf associated viral RNA Carrot temperate 1 alphacryptovirus Carrot temperate 2 betacryptovirus Carrot temperate 3 alphacryptovirus Carrot temperate 4 alphacryptovirus Carrot thin leaf potyvirus Carrot yellow leaf (?) closterovirus Cassava green mottle nepovirus Celery mosaic potyvirus Celery yellow net (?) virus • • • • • • • • • • • • • • • • Clover yellow vein potyvirus Coriander feathery red vein nucleorhabdovirus Cucumber mosaic cucumovirus Galinsoga mosaic carmovirus Heracleum latent trichovirus Lettuce infectious yellows (?) closterovirus Oat blue dwarf marafivirus Okra mosaic tymovirus Parsnip mosaic potyvirus Parsnip yellow fleck sequivirus Poplar mosaic carlavirus Potato black ringspot nepovirus Strawberry latent ringspot (?) nepovirus Tobacco ringspot nepovirus Tomato black ring nepovirus Tulip X potexvirus Parsnip yellow fleck virus (PYFV) • PYFV carrot isolates to Cow Parsley reservoirs • Requires Anthriscus yellows virus (AYV) for transmission C/CP• Results from FV382 suggest this virus is not involved in internal browning • Carrot is not susceptible to AYV Direct carrot to carrot H/P transmission not a factor Work carried out under HDC/HortLINK FV228 Carrot red leaf virus (CtRLV) • Carrot red leaf virus needed for transmission of CMD viruses • Most carrot isolates form a distinct ‘carrot’ group • Weed group isolates from: Carrot Cow parsley, Hogweed, Pignut, Sweet Ciceley, Wild Parsnip, Hemlock, Rough Chervil, Wild Carrot and Carrot (limited) Carrot to carrot major factor in CMD Work carried out at Warwick Crop Centre under Defra IF0188 Weed Simplifying the complex... Salix spp. Cow Parsley? Or AYV + PYFV Umbelliferous weeds Aphids on winter host Aphids Migrate Carrots under straw?? Pick up Virus Transmit to Carrot CtRLV (CMoV) (CtRLVaRNA) Carrots? 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. 100 90 80 70 samples positive real-time PCR demonstrated a strong association between CYLV and necrosis, suggesting that removal of this virus would reduce necrosis by 96% affected 60 unaffected 50 40 30 20 10 0 PYFV CRLV CRLaV CMoV Virus CYLV Negative MiSeq sequencing identified Carrot yellow leaf virus in necrotic samples. Sequencing also detected a Closterovirus (CtCV) and a Torradovirus (CaTV) plus 5 other viruses which were new to science. 2014: tracking down the viruses 2014 : Wild hosts of new viruses (2012 weed samples) Species Hogweed Cow Parsley No. of fields No. Of sampled Samples CaRLV CMoV CaRLaVRNA PYFV CYLV CtCV CaTV 1 1 1 9 59 (1.7%) (1.7%) (1.7%) 8 3 7 (25.9%) (11.1%) (29.6%) 7 27 Hemlock 1 1 Rough Chervil 2 3 1 (33%) Total 9 90 9 • • • • • 1 0 1 3 8 0 CaRLV, CMoV & CaRLV = Carrot Motley Dwarf PYFV = Parsnip yellow fleck virus CYLV = Carrot yellow leaf virus (NEW - linked to root necrosis) CtCV = Carrot closterovirus (NEW – similar to CYLV) CaTV = Carrot toradovirus (NEW – unknown incidence and impact) 2014 Field sampling (HDC FV 382b + Defra Funding) • Samples from carrot crops – 100m x 100m blocks • • • Sampled in season to assess infection levels and assess foliar symptom development; Roots sampled at end of season to assess levels of necrosis against infection To be repeated on a broad geographic basis in 2015 Comparative virus health of 3 fields (N.Yorks) 70 60 50 40 Positive Negative 30 20 10 0 Strensall Sand Hutton Sutton on the Forest Relative virus incidence between 3 fields (N. Yorks) High Roans Field Field Margin and Road N 208 219 230 241 252 263 274 285 297 308 198 209 220 231 242 253 264 275 286 298 309 199 210 221 232 243 254 265 276 287 299 310 200 211 222 233 244 255 266 277 288 300 311 201 212 223 234 245 256 267 278 289 301 312 202 213 224 235 246 257 268 279 290 302 313 203 214 225 236 247 258 269 280 291 303 314 204 215 226 237 248 259 270 281 292 304 315 205 216 227 238 249 260 271 282 293 305 316 206 217 228 239 250 261 272 283 294 306 317 207 218 229 240 251 262 273 284 295 307 318 23% 25% 9% Hedgerow CYLV CTV DUAL 197 Ongoing work • Transmission studies and Koch’s postulates (HDC) • Incidence of carrot viruses (HDC) • Weed hosts of novel carrot viruses (Warwick samples) • Defra PhD studentship: The crop ‘virome’: - Virus ecology of carrot crops CaTV: Characterisation and impact Quantifying the effects of asymptomatic infection ‘Candidatus Liberibacter solanacearum’ The ‘Zebra chip’ pathogen ‘Candidatus phytoplasma asteris’ Aster Yellows Phytoplasma SOURCE: Nisbet C, Ross S, Monger WA, Highet F, Jeffries C, 2014. First report of 'Candidatus Phytoplasma asteris' in commercial carrots in the United Kingdom. New Disease Reports 30, 16. Acknowledgements • This project was carried out with funding from HDC project FV 382 (a & b) • Funding from Defra Plant Health Capability is supporting Zuri Rozado PhD studentship • Howard Hinds (Root Crop Consultancy Ltd) • Rodger Hobson (Hobson Farming Ltd) • Fera staff in Virology, The Molecular Technology Unit and Applied Genomics team • Andy Aspin (Bacteriology – Fera)