Allium vegetables such as onion (Allium cepa), garlic (Allium sativum) or leek (Allium porrum) represent valuable sources of well-known health promoting compounds. Alliums are historically one of the most widely-consumed vegetables across the world. The total annual production of onion reached 103.5 million tonnes in 2019, garlic production was reported to be 30.6 million tonnes, leek and other alliaceous vegetable 4.2 million tonnes (see here), with an estimated average price 200 USD per ton. The data indicate the high value of the Allium vegetables market. Pest attack and phytopathogen infection cause losses that are estimated to be up to 50%. They impact not only yield, but also product quality. Among them viral diseases are a common phenomenon and they may significantly reduce the yield by 20-60%.
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What follows below, are the most important viruses.
Viral disease in onion
A number of diseases affect onion crops, caused, inter alia, by systemic pathogens including viruses. The viruses known to infect onion belong to the genera Allexivirus, Carlavirus, Potyvirus, and Orthotospovirus. Among them, potyviruses and orthotospoviruses induce the most important damage to this crop. In particular, Onion yellow dwarf virus – OYDV, genus Potyvirus, family Potyviridae, characterized by a ssRNA (+) genome, is one of the 14 viruses reported to infect onion, with a worldwide distribution in onion and Allium spp.. It induces severe symptoms like yellowing, dwarfing and stem twirling, in early infections reducing bulb weight and size by up to 40%, with a seed loss up to 50%. Serology methods using enzyme-linked immunosorbent assay (ELISA), and dot immunobinding assay (DIBA) are common methods to detect viruses, with polymerase chain reaction (PCR). Multiplex assays which save time and labour are available now. As viruses are transmitted by vectors, e.g., aphids or thrips, sticky traps are recommended to monitor the occurrence of the vector. It is advisable to analyse the insect through barcoding to detect the presence of dangerous species (see Grode et al., 2019).
Garlic viral diseases
Viral diseases represent a substantial obstacle in garlic cultivation. Garlic is a vegetatively propagated species, thus, once infected, the viral particles are spread within the host to different regions. Virus-free propagating material, which is still not common, represents an option. However, the viruses are also spread by vectors such as eriophyid mites or aphids. Garlic is attacked by a so called “virus complex” consisting of different viral strains. The most frequent virus is the onion yellow dwarf virus (OYDV), which together with leek yellow stripe virus (LYSV) belongs to the genus Potyvirus. Another important genus is Carlavirus, which includes Garlic common latent virus (GCLV) and Shallot latent virus (SLV). Another important virus belongs to the Carlaviruses. In general, 13 different viruses have been well described in detail and others have been newly reported. Infected plants provide lower yield and the products are of lower quality. These viruses produce characteristically similar symptoms and the strains need to be somehow differentiated one from another. Some countries require virus-free seedlings. Diagnostic techniques, mostly individual-laboratory based, are available. Only a minute amount of plant material is necessary for the analysis and so-called multiplex reactions allow for rapid screening of the virus particles in any part of the plant. The laboratory providing such a service should be accredited for the purpose. Additionally, insect monitoring is advisable using e.g., insect traps to warn of likely virus transmission in the fields.
Other Allium vegetables
Viruses infecting Alliaceae are widespread throughout the world and affect a great number of Allium species, causing significant yield losses. Apart from onion and garlic also the presence of virus has been recorded in leek (A. porrum), chives (A. asclonicum) and elephant garlic (A. ampeloprasum). Among the potyviruses affecting Allium spp., Onion yellow dwarf virus (OYDV) and Leek yellow stripe virus (LYSV) have been detected worldwide. Carlaviruses have been identified as other harmful factors in the Alliacea. Protection of the plants against vectors and the use of healthy seeds represent the most effective prevention methods.
Allium vegetables are often clonally propagated, which increases the risk of viral infection. Modern tools allow for virus-free seedling production and efficient monitoring of the process using ELISA or PCR, multiplex /PCR or LAMP based tests. Along with decision support systems, diagnostic tools will increase the cleanliness of production. In order to prevent direct infection in the field nowadays farmers use sticky traps and identify the presence the dangerous species using bar coding and take the necessary measures to protect the fields. SMART devices improve all over efficiency.