Pest & disease factsheet - Botrytis (Onion neck rot)

Disease profile for field vegetable growers, by Professor Geoffrey Dixon.

Symptoms of Botrytis (Onion neck rot) - image: Geoff Dixon
Symptoms of Botrytis (Onion neck rot) - image: Geoff Dixon

Botrytis allii (= Botrytis aclada): onion neck rot

Crops affected

Mainly important on stored onion crops, also affecting other alliums such as garlic, shallot, multiplier onion and leek. Separately, B. bysoidea causes grey neck rot while B. squamosa causes small sclerotial neck rot. 


The causal pathogen is B. allii, which produces copious asexual conidia and rapidly spreads the disease. Affected bulbs become covered with large black resting bodies (sclerotia). 


Principally, this is a seed-borne disease and is also spread via infected onion sets and on shallots. Even where infected seed is stored at low temperatures the pathogen can survive for up to three years in a dormant state. 

When seed germinates B. allii spreads from the seed coat onto developing leaves where it sporulates as the leaves senesce. The pathogen grows from the tips of leaves down inside the tissues and into the developing onion bulb. Alternatively, as the crops mature the necks of onions bend or are mechanically topped, this opens wounds that may be invaded by the pathogen from where it grows down into the bulb scales. Large water-soaked lesions develop on and in the bulbs. These turn light brown as the tissues are destroyed around the necks and bodies of affected bulbs.

Mycelial growth and bulb rotting are accompanied by the appearance of dense mats of grey mycelium carrying the asexual conidial stage of this fungus. Numerous black sclerotia are found when infections are well established. These usually first appear on the shoulders of bulbs but also spread across the entire bulb. Symptoms become obvious after several weeks in store, spreading to the entire bulb, which is often reduced to a mass of soft rotten scales.

The disease may also damage crops while they are in the field, causing a brown rot. B. allii is a weak pathogen that invades through areas of mechanical damage or where growing bulbs have split as a result of wide variations in weather conditions or erratically applied irrigation. All parts of the onion are susceptible to damage from B. allii.

The pathogen B. squamosa is characterised by the production of larger quantities of external mycelium. Normally this fungus solely attacks white-bulbed cultivars.

Both B. allii and B. squamosa will cause leaf-flecking disorders. These are superficial symptoms and the damage is largely of cosmetic importance at this stage, although where weather conditions are very wet such disorders may cause serious neck rotting. 

Weather effects

Neck rot disease is encouraged by periods of excessive rainfall and humid conditions combined with standing water on the leaves. Leaf flecking may progress to a more serious condition following 24 hours at 100 per cent relative humidity and 27°C. While these conditions are unusual in the UK, recent summer weather patterns could provide them. The optimal temperature for growth by these fungi is around 21°C.

Soil conditions 

Soil-borne sclerotia provide sources of inoculum that lead to infection in the field. These can survive for up to two years even on debris that has been ploughed back into the soil. Excessive applications of nitrogenous fertilisers encourage lush foliage growth, which may be invaded more easily by B. allii. Periods of drought followed by heavy rainfall produce uneven growth often accompanied by cracking of leaves and immature bulbs, which provides portals for entry by B. allii.

Integrated disease management

Resistant cultivars

Use resistant or tolerant cultivars where they are available.

Husbandry measures Infected seed is a primary source of B. allii. Only use certified seed free from the pathogen that has been treated with a suitable fungicide. Onion sets should be grown from originally treated seed. The economic threshold for acceptable seed infection is one per cent, but even this may be far too high for the production of good-quality crops. Neck rot is a major problem for growers attempting to produce organic onion crops.

Where crops are mechanically topped prior to harvesting it is advisable to leave at least 10cm of foliage, which can dry thoroughly in the field. This produces a barrier preventing pathogen spread from the leaves into the bulbs. Bulb necks should be thoroughly treated with forced air drying prior to longer-term storage. Alternatively, if weather permits, bulbs should be air dried in windrows after lifting.

This requires extended periods of warm, dry conditions. Bulbs should be collected carefully from the field avoiding bruising, which encourages the aggressive spread of neck rot. Stores used for onions should be held at 75 per cent relative humidity and 0-1°C.

Crop rotation with non-alliums provides opportunities for the breakdown of soil-borne sclerotia by antagonistic microbes.

Wild hosts include crow garlic (Allium vineale) and ramsons (A. ursinum). These should be removed by hand, mechanically or using herbicides where appropriate. All stores and stillages used for onions should be thoroughly cleaned and disinfected before harvesting gets underway.

Biological control

Off label approval for use on stem and bulb vegetables:

Bacillus subtilis and Gliocladium catenulatum


Currently allowable chemical treatments include:

Stem and bulb vegetables (onions/leeks/garlic)

Azoxystrobin + chlorothalonil
Cyridinil + fludioxonil (off-label, EAMU).

Fluoxastrobin + prothioconazole (useful reduction).
Iprodione (off-label, EAMU).
Seed treatment
Thiram (off-label, EAMU).


For use on all fresh-produce vegetable crops growers must in advance of use ensure that a particular commercial agrochemical formulation is legally acceptable for their particular crop/husbandry regime and also accepted by the intended purchaser’s crop-quality standards specification as agreed with the relevant crop technologist.

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