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Alliums, Botrytis Neck Rot

Botrytis neck rot of alliums, caused by the fungus Botrytis allii, affects onions,garlic, leeks and shallots. This pathogen is different from the one that causes Botrytis leaf blight. Botrytis neck rot primarily appears after harvest in onions and garlic that are not cured or stored correctly. The most common causes of severe losses are excessive nitrogen application, which delays crop maturity and curing, irrigation or rain late in the season, inadequate or improper curing, and improper storage. The pathogen is soil- and seed-borne.


In onion, the disease is more apparent after harvest, while bulbs are in storage. Initially, soft neck tissue will become water-soaked and a yellow discoloration will move down from the neck into the leaf scales. Bulbs break down to a soft mass. A gray mold develops between the onion scales, later producing small to large black sclerotia (overwintering structures), which develop as a solid layer around the neck. Extensive development of sclerotia is best seen on maturing bulbs just before and during harvest.

In garlic, the disease usually appears first on necks near the soil line, and may occur any time after spring greenup when weather is conducive for disease development. The disease causes the most losses when it starts early in the season. The fungus moves rapidly into the succulent tissue of the bulb neck, producing a water-soaked appearance. A gray mold develops on the surface of or between garlic scales, later producing black sclerotia around the neck. Secondary infections by other organisms may follow.

Life Cycle:

Botrytis allii overwinters in the soil on bulb residue or as sclerotia, dense masses of mycelia surrounded by a weather-resistant black rind that can survive long-term in soil. In the spring, sclerotia germinate and directly infect bulbs or produce asexual spores, which are dispersed in the air. Spores and sclerotia that come in contact with tissue of susceptible hosts may initiate new infections, especially if the tissue is wounded. Under prolonged moist conditions, the pathogen can also produce spores on infected dead or dying leaves. After harvest, topped onions and garlic can become infected if the cut edge comes in contact with spores or soil containing sclerotia. Often, plants will become infected in the field but will remain symptomless until they are in storage.

Cultural control:


For more general information on proper harvesting, topping, and curing of onions, please click here.

  • Practice a crop rotation of at least 3 years.
  • Plant only disease-free seed. Most seed produced in the US is from arid environments and does not usually carry B. allii. Seed produced in Europe is more likely to be infested.
  • Follow growing practices that hasten curing:
  • Do not apply nitrogen fertilizer later than ~8-9 weeks after seeding
  • Plant onions at proper spacing: 2-4 rows/bed, 9”-18” between rows, and 6-9 plants/foot or plants 3”-4” apart in the row.
  • Allow tops to mature well (at least half of leaves brown), then lift or undercut the onions. In dry weather, cure onions on the ground 6-10 days.
  • Destroy crop residues after harvest.
  • Be sure onions are well dried and necks tight (i.e. the tissue does not slide when you roll the neck between your fingers) before topping. Botrytis can move through green tissues into bulbs but cannot move through dry tissue.
  • Minimize bruising and mechanical injury in topping and storage.
  • Store in a well-ventilated area at 32°F or slightly warmer. Use higher temperatures if humidity cannot be held below 75%.


For more general information on proper harvesting, topping, and curing of garlic, please click here.

  • Plant disease free cloves.
  • Avoid frequent and excessive irrigation.
  • Inspect garlic for symptoms and signs of the disease during the season and at harvest. A hand lens can help with this.
  • Allow the tops to mature well, then lift or undercut the garlic. Pulling bulbs out when they are tight in the ground can open wounds at the stem-bulb junction.
  • Minimize bruising during harvest and topping. Don’t remove dirt from roots by banging bulbs against hard surfaces—shake or rub the root-end gently.
  • If dry weather prevails, cure garlic on the ground for 6-10 days. Otherwise, cure in a well-ventilated area at 70-80°F.
  • When topping, minimize bruising and mechanical injury.
  • Store cured garlic in a well-ventilated area at temperatures of 32°F, or just slightly higher.
  • Destroy crop residues after harvest

Chemical Control

There are several fungicides labeled for neck rot control, and fungicides applied to control Botrytis leaf blight may also decrease neck rot incidence.  For information on chemical control of this disease in onion, please see the New England Vegetable Management Guide website.

Crops that are affected by this disease:


--adapted by G. Higgins and S. Scheufele, October 2016, from Alliums, Post Harvest and Storage Diseases, adapted by A. Cavanagh & R. Hazzard, information form Oregon State Extension. 2016 information also from Compendium of Onion and Garlic Diseases, eds. H.F. Schwartz and S.K. Mohan.


Last Updated: 
October 2016

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