Current Status and Challenges

Virus control in horticultural Alliaceae


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%.

For information sources, see here.

What follows below, are the most important viruses.

Viral disease in onion

What is it? 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.

Official name: 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.

How to recognize it: 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%.

IPM solutions: 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

What is it? 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.

Official name: 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.

How to recognize it: 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.

IPM solutions: 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

What is it? 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).

Official name: 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 Alliaceae.

IPM solutions: 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.


Current Status and Challenges

Pest control in horticultural Alliaceae


Allium vegetables such as onion (Allium cepa), garlic (Allium sativum) or leeks (Allium porrum) are important commercial crops, which are grown all over the world. They are generally used as vegetables and spices. Allium vegetables are valuable sources of many health-promoting compounds, which act as natural medicine for treating high blood pressure or regulating blood sugar. They also possess antibiotic and antiviral properties. Onion bulbs are also rich in minerals, proteins and Vitamin C. These crops are attacked by many pests and diseases, which cause significant economic losses. Allium vegetables protection is based mainly on agrotechnical practices and pesticides, which pose a serious threat to the environment. Some bio pesticides and biological methods of protection are also used.

What follows below, are the most important pests.

Stem and bulb nematode

What is it? Polyphagous nematode is a serious pest of onions and garlic, as well as other plants. All life stages develop in the soil. The nematode penetrates plants through injuries, vents and also actively using enzymes.

Official name: Ditylenchus dipsaci can persist in soils for many years (anabiosis), therefore the recommended interval of interruption is at least five years.

IPM solutions: There are some agrotechnical procedures and physical methods (solarization) that prevent nematode infestation of plants. One of them is crop rotation. Emphasis is also placed on quality and healthy seedlings and tolerant or resistant cultivars. Different types of seedling staining are used. Research today focuses on filamentous or endoparasitic fungi that can be used as biological control agents for nematodes, but do not appear to be widely used. Farmers should use and combine all available methods to create an integrated system of protection and not rely solely on pesticides. It is highly recommended to rotate crops with a suitable cover crop (see here), which may have a potential for “SMART” technologies to help farmers organize an overview the crops and fields and alert them at the end of the preferred sowing interruption.

Allium leaf miner

What is it? This fly is an important pest especially of leeks and scallions, but attacks also onions and garlic, while it has become invasive in the US.

Official name: Phytomyza gymnostoma 

How to recognize it: The larvae bore into stems and bulbs and so, it is very difficult to control them. Larvae pupate in leeks in hundreds of individuals which is a big deal for market. What’s more, the affected plants are more susceptible to secondary infections and rots. More information available here.

IPM solutions: The main recommendation is consistent removal of crop residues in order to interrupt the life cycle of the pest. Infested plants should not even be composted. Only few pyrethroid-based insecticides are registered for direct protection. A key aspect is to anticipate the flight waves of adults, before they can lay their eggs. Plants can be protected by covering with an insect-proof mesh. The flight wave occurs twice a year, first in March to April and then in October to November. Sticky boards were evaluated as ineffective. Monitoring relies exclusively on visual inspection of crops. Research can focus on the development of a degree day model to predict the emergence of populations. Defining attack patterns in the fields is also one of the options where “SMART” technologies could be used.


What is it? Thrips are important pests of leeks and onions and several other crops in most parts of the world.

Official name: Thrips tabaci

How to recognize it: They thrive during hot and dry years. In Central Europe, they have about 5 generations a year. Adults overwinter in soil, compost and plant residues. Nymphs and adults usually congregate in dense masses. They rasp the leaves of onion and suck the sap, which affects the yield of bulbs. Deformities on the leaves and chlorosis make fresh onions unmarketable. The threshold is three thrips per green leaf. More information available here.

IPM solutions: Common management strategies are cultivation practice like crop rotation, post-harvest residues removal, use of spray irrigation and some others. Sky blue sticky traps are attractive for adults and they can be used for monitoring. There is a fairly wide range of pesticides and some biopesticides that can be used (spirotetramat, dimethoate, synthetic pyrethroids, cyantraniliprole, neem soap, spinosad, Beauveria bassiana). Thrips have plenty of natural nemies including coccinellids, hoverflies, lacewings, bugs of the genus Orius, predatory thrips and entomopathogenic fungi. Regular monitoring of the crop is essential for timing of the protective intervention. “SMART” technologies can focus on monitoring thrips in the field (automatic traps) and monitoring water stress in order to optimize irrigation, which can be combined with the application of some (bio) pesticides.

Onion fly

What is it? Thrips are important pests of leeks and onions and several other crops in most parts of the world.

Official name: Delia antiqua 

How to recognize it: They overwinter as pupae, which hatch in spring. It usually has 3 generations per year. First generation larvae are the most harmful ones. The most vulnerable are directly sown onion stands, because the plants are small and they can be destroyed easily by maggots. Infested bulbs of older plants are unmarketable and susceptible to rots. Even harvested plants which are left to dry in field before storage, can be found by adults, who will lay their eggs. Later the larvae bore into these bulbs, which makes them also vulnerable to storage rots.

IPM solutions: The control is challenging. Common procedures include crop rotation and spatial distancing from last year’s fields (≥1.2 km), use of covering nets to prevent oviposition (on a small scale) and pesticides that are applied during adult flights and egg laying. After this period, foliar sprays are not effective at all. Systemic insecticides, seed treatments and drenches are more likely to be more effective, but many active ingredients have been banned in EU. Onion flies can develop resistance to pesticides.

Monitoring and forecasting the occurrence of root-feeding flies is the basis for successful control of the pest. First flight activity in spring can be detected by inverted-screen cone traps baited with damaged onions. Accurate prediction of second-generation flight is more difficult. Yellow sticky traps placed at the field edges can be used. Some research was done also on attractiveness of other colours, indicating that bright blue, violet and white traps can be even more attractive than the yellow traps. Sticky traps can be combined with volatile organic compounds (VOC) that are attractive to flies. Visual control of the plants is also recommended. Infested plants can be easily identified by yellowing and wilting leaves. Damage from first generation larvae can be seen in mid-to-late June. Larvae can spread through soil and infest neighbouring plants, which creates patches in field. Infested plants must be destroyed in order to reduce the population density of the next generation, which is even harder to detect.

In Europe there are plenty of natural enemies of the onion fly. Parasitoid wasps Trybliographa rapae attack onion fly larvae, rove beetles (Aleochara bilineata) larvae parasitize onion fly pupae and adult beetles feed on larvae and pupae of the fly. The maggots are also attacked by range of entomopathogenic fungi and nematodes (Neoaplectana). Among them, Metarhizium anisopliae and Beauveria bassiana are available as commercial plant protection products, but in field conditions their use has certain limits (application, temperature, UV, humidity etc.).

“SMART” technologies should focus on improving existing monitoring systems, as the right timing of interventions is essential. Second-generation larvae must also be spotted and destroyed in the field, which is a chance for smart technology, as outbreak patterns may be visible from the air.

For information sources, see here:

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Leek moth

What is it? It is a moth attacking leek cultivations. Depending on the number of generations per year, it is considered either a serious or minor pest. In America, the specie is invasive. The pest is active from April to October.

Official name: Acrolepiopsis assectella

How to recognize it: Damage is caused by larvae that attack onions, garlic, leeks, chives, shallots and other alliums. They bore into the leaf tissue and form mines, and occasionally they also feed on bulbs. Affected plants may appear distorted and are more susceptible to plant pathogens. The damage is usually greatest at the edges of the field. Female start laying eggs when night temperatures reach 10°C-12°C.

IPM solutions: Pheromone traps are used to monitor adult flight waves. Insecticidal control is possible with the right timing of application, which is 7-10 days after the peak of adult flight observed by traps. Spraying is also recommended, if 1 in 25 plants throughout the field is damaged. Bt-based products and organophosphates are usually used. Good cultivation practice is important – crop rotation, disposal of post-harvest residues, disposal of infested plants etc. Lightweight floating row covers can also protect developing plants from leek moth damage. Since the moths fly only at night, growers can remove the covers during the day. Leek moth has a range of natural enemies. Parasitoid Diadromus pulchellus has also been released in Canada.

“SMART” technologies may be used to improve the forecasting and monitoring process.

For more information sources, see here.

Turnip moth

What is it? The pest is polyphagous, but it can seriously damage onions in fields. Larvae develop in the soil near the host plants and are therefore hidden for a long time.

Official name: Agrotis segetum

How to recognize it: Larvae have nocturnal activity, then they are coming out of the soil and feed on the above-ground leaves. When they are discovered, it is often too late. They are particularly harmful to directly sown vegetables in the summer, which can be completely destroyed. A larva often cuts one plant and quickly moves on to other plants and continues cutting. Therefore, relatively small populations of cutworms can destroy entire stands of crops.

IPM solutions: The larvae thrive in drier conditions. Eggs and young larvae are sensitive to moisture and fungal diseases, so they can be reduced by targeted spray irrigation. Entomopathogenic nematodes – Steinernema feltiae are available commercially for cutworm control, but the use is not suitable for large field areas. Insecticide treatment is not effective in general, because there is only a short window, when the larvae are small and feed on the above-ground leaves. Bt-based products are suitable for the first instars larvae. Pheromone traps are an effective tool for monitoring flight waves and can also reduce adult population a bit. Careful visual inspections in the field are recommended. Adult moths are able to travel long distances, so it is not clear where the damage will occur.

“SMART” technologies can help predict the occurrence of larvae by identifying drier parts of fields where there is a higher probability of possible outbreaks, so locating pests would be easier.


SMART technologies may be efficiently assist in applying monitor of pests in Allium vegetables. Traps’ use is suggested for some of the species, while prediction of pests’ spreading and can contribute in the proper application of biopesticides and further plant protection products.

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