title: Carrot yellow leaf virus is associated with carrot internal necrosis.
abstract: Internal necrosis of carrot has been observed in UK carrots for at least 10 years, and has been anecdotally linked to virus infection. In the 2009 growing season some growers had up to 10% of yield with these symptoms. Traditional diagnostic methods are targeted towards specific pathogens. By using a metagenomic approach with high throughput sequencing technology, other, as yet unidentified causes of root necrosis were investigated. Additionally a statistical analysis has shown which viruses are most closely associated with disease symptoms. Carrot samples were collected from a crop exhibiting root necrosis (102 Affected: 99 Unaffected) and tested for the presence of the established carrot viruses: Carrot red leaf virus (CtRLV), Carrot mottle virus (CMoV), Carrot red leaf associated viral RNA (CtRLVaRNA) and Parsnip yellow fleck virus (PYFV). The presence of these viruses was not associated with symptomatic carrot roots either as single viruses or in combinations. A sub-sample of carrots of mixed symptom status was subjected to MiSeq sequencing. The results from these tests suggested Carrot yellow leaf virus (CYLV) was associated with symptomatic roots. Additionally a novel Torradovirus, a novel Closterovirus and two novel Betaflexiviradae related plant viruses were detected. A specific diagnostic test was designed for CYLV. Of the 102 affected carrots, 98% were positive for CYLV compared to 22% of the unaffected carrots. From these data we conclude that although we have yet to practically demonstrate a causal link, CYLV appears to be strongly associated with the presence of necrosis of carrots.
authors.affiliation: Centre for Crop Protection, Food and Environment Research Agency, Sand Hutton, York, United Kingdom.
authors.forename: Ian P
authors.initials: IP
authors.lastname: Adams
authors.affiliation: Centre for Crop Protection, Food and Environment Research Agency, Sand Hutton, York, United Kingdom.
authors.forename: Anna
authors.initials: A
authors.lastname: Skelton
authors.affiliation: Centre for Crop Protection, Food and Environment Research Agency, Sand Hutton, York, United Kingdom.
authors.forename: Roy
authors.initials: R
authors.lastname: Macarthur
authors.affiliation: Centre for Crop Protection, Food and Environment Research Agency, Sand Hutton, York, United Kingdom; University of York, York, United Kingdom.
authors.forename: Tobias
authors.initials: T
authors.lastname: Hodges
authors.affiliation: RootCrop Ltd., Hoveringham, Nottinghamshire, United Kingdom.
authors.forename: Howard
authors.initials: H
authors.lastname: Hinds
authors.affiliation: Centre for Crop Protection, Food and Environment Research Agency, Sand Hutton, York, United Kingdom.
authors.forename: Laura
authors.initials: L
authors.lastname: Flint
authors.affiliation: Department of Plant Pathology, Assam Agricultural University, Jorhat, India.
authors.forename: Palash Deb
authors.initials: PD
authors.lastname: Nath
authors.affiliation: Centre for Crop Protection, Food and Environment Research Agency, Sand Hutton, York, United Kingdom.
authors.forename: Neil
authors.initials: N
authors.lastname: Boonham
authors.affiliation: Centre for Crop Protection, Food and Environment Research Agency, Sand Hutton, York, United Kingdom.
authors.forename: Adrian
authors.initials: A
authors.lastname: Fox
mesh_terms: D017790:Closterovirus / Q000145:classification / Q000235:genetics*; D018552:Daucus carota / Q000821:virology*; D016679:Genome, Viral; D050884:HSP72 Heat-Shock Proteins / Q000235:genetics; D009336:Necrosis; D010641:Phenotype; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics
chemical_list: D050884:HSP72 Heat-Shock Proteins; D014764:Viral Proteins