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.
Highlights
For at least 10 years UK growers have reported carrot roots exhibiting internal necrosis around the root core extending from crown to tip, and these have been anecdotally associated with the presence of viruses
This paper describes a study of the potential causes of carrot internal necrosis using RT_PCR of common carrot viruses and generation sequencing in carrots with and without symptoms of necrosis and a statistical approach to associate particular viruses with the incidence of necrotic symptoms
The 102 necrotic/symptomatic carrot samples found within the sample were taken for analysis. These roots exhibited a range of symptoms which included cases of internal and external necrosis. (See Figure 1). 99 asymptomatic/ non-necrotic carrots were taken for analysis
Summary
For at least 10 years UK growers have reported carrot roots exhibiting internal necrosis around the root core extending from crown to tip, and these have been anecdotally associated with the presence of viruses. It is difficult to grade out affected carrots because the symptoms tend to be internal. A large proportion of the carrots tested in this earlier study were negative when tested for PYFV or the Carrot Motley Dwarf complex (CMD) of viruses. This finding raised the question of other viruses being a cause of the development of carrot root necrosis
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