Onion neck rot

This fungal disease develops during storage, and can cause severe losses of onion and shallot bulbs. Prevention of neck rot depends on the use of appropriate cultural techniques, particularly in relation to conditions at harvest and during storage.

Onion neck rot
Onion neck rot

Quick facts

Common name Onion neck rot
Scientific name Botrytis allii
Plants affected Onions and shallots (occasionally garlic)
Main symptoms Decay of bulbs from the neck downwards, with copious grey mould and hard, black resting bodies
Caused by Fungus
Timing Symptoms appear during storage. Infection occurs during growth and harvesting of the crop

What is onion neck rot?

Onion neck rot is a disease of onions and shallots caused by the fungus Botrytis allii. Plants infected by the fungus usually appear perfectly healthy whilst the crop is growing. Symptoms are not usually seen on the

bulbs until they have been in store for several weeks. In general, onion cultivars with white bulbs are more likely to be attacked than those which have red or yellow bulbs.



You may see the following symptoms:

  • Bulbs are usually first affected at the neck, although the decay can spread downwards to affect the whole bulb. Occasionally, symptoms develop at the side or the base of the bulb if there has been physical damage at this point
  • Scales of diseased bulbs become soft and brown, giving them a ‘cooked’ appearance
  • A dense grey mould growth develops, producing huge numbers of spores
  • This is often accompanied by hard, black, crust-like structures (the resting bodies or sclerotia of the fungus)
  • Affected tissues gradually dry up so that the bulb suffers from a dry rot and eventually becomes sunken and mummified


Non-chemical control

Cultivation of the crop

  • Ensure that seed or sets are obtained from a reputable company
  • Practice crop rotation, and don’t grow onions for three years in soil where the disease has occurred
  • Aim to produce hard, well-ripened bulbs. Avoid excessive use of nitrogen and late (i.e. after July) application of fertiliser
  • Water the crop regularly during dry spells


  • It is very important that the bulbs are kept dry during the harvesting period, and that the foliage and necks dry quickly
  • The ripe bulbs should be pulled up and laid on their sides with the roots exposed to the sun
  • Cover the bulbs temporarily if rain threatens, or better still dry them under cover in a greenhouse or open shed


  • Don’t attempt to store damaged or thick-necked bulbs – use them immediately
  • Twist off the tops and store in a cool, dry place with good air circulation, e.g. wire netting, slatted shelves, strings hung from rafters
  • Check the stored bulbs regularly and remove any that are decaying or sprouting prematurely

Chemical control

There are no fungicides available to gardeners for the control of onion neck rot. However, several seed companies now treat their seed to reduce infection.


The neck rot fungus can contaminate both seed and sets, and also persists in the soil on debris and as sclerotia (resting bodies). Plants grown from contaminated seed are infected almost as soon as the seed germinates. Spores produced on the affected plants can spread the fungus through the crop, but infected plants usually remain symptomless during the growth of the crop.

The bases of the older leaves eventually become infected, and the fungus spreads from here into the neck of the bulb. High levels of neck rot developing in store are often the result of factors during growth, harvesting and storage that favour the pathogen. These include:

  • Dull, wet weather during growth of the crop
  • Delayed maturity due to late application of fertilisers
  • Excessive use of nitrogen
  • Damage due to careless cultivation or an irregular water supply
  • Growing successive crops in the same soil
  • Harvesting during wet conditions
  • Attempting to store damaged or thick-necked bulbs
  • Storage of bulbs in warm, damp conditions

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