1. Plant Disease
  2. Host and Disease Descriptions

Onion (Allium cepa)-Neck Rot

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Latest revision: 
March 2024

By C. M. Ocamb and D. H. Gent

Cause Botrytis aclada (= B. allii), a fungus that overwinters on plant debris in soil, on infected bulbs, and as sclerotia in soil. The pathogen also can be seedborne. The disease is seen primarily in storage. Most common causes of severe losses are excessive nitrogen, which delays crop maturity; irrigation and/or rain late in the season; inadequate or improper curing; and improper storage. Infection is through neck tissue or wounds in bulbs. Some bulb infections may arise from symptomless leaf infections, but often the fungus directly enters the neck via airborne spores when onions are topped before soft, susceptible top tissues dry properly.

Symptoms Disease is more apparent after harvest, while bulbs are in storage. At first, soft neck tissue looks water soaked, and a yellow discoloration moves down the neck into the scales. Bulbs break down to a soft mass. A gray mold develops between the onion scales, later producing small to large black bodies (sclerotia), which develop as a solid layer around the neck.

Cultural control

Bulb onions:

  • Allow tops to mature well, then lift or undercut the onions. In dry weather, cure onions on the ground 6 to 10 days.
  • Increase the length of onion necks at harvest.
  • Minimize bruising and mechanical injury in topping and storing.
  • Store in well-ventilated houses at 32°F or slightly higher. Use higher temperatures if humidity cannot be held below 75%.
  • Practice a crop rotation of at least three years.

Seed onions:

  • Bury culls and onion debris from onion crops in nearby fields.
  • Avoid planting new seedlings within several miles and/or downwind from current seed crops.
  • Practice a crop rotation of at least three years.
  • Use seed treated with commercial fungicide.

Chemical control

  • Carboxamide (Group 7) formulations are registered for use. Do not make more than two (2) sequential applications before alternating to a labeled fungicide with a different mode of action.
    • Fontelis at 16 to 24 fl oz/A on 7- to 14-day intervals. Preharvest interval is 3 days. 12-hr reentry.
  • Chlorothalonil as numerous formulations (Group M5) are registered for use and appear very effective on Botrytis in studies conducted by Cornell.
    • Bonide Fung-onil is available for home gardens. H
    • Bravo Ultrex at 0.9 to 2.7 lb/A on 7- to 10-day intervals for dry bulb onions. Do not apply within 7 days of harvest. 12-hr reentry.
  • Copper formulations (Group M1) offer limited control.
    • Cueva at 0.5 to 2 gal/100 gal water on 7- to 10-day intervals. May be applied on the day of harvest. Poorcontrol as a stand-alone product. 4-hr reentry. O
  • Iprodione formulations (Group 2) are registered.
    • Rovral 4 Flowable at 1.5 pints/A on 14-day intervals. For dry bulb onions only. Do not apply within 7 days of harvest. 24-hr reentry.
  • Mancozeb formulations (Group M3) are labeled.
    • Dithane F45 Rainshield at 1.5 quart/A on 7- to 10-day intervals can be used on seed crops only. Washington and Oregon only (SLN WA-220008, SLN OR-090016). 24-hr reentry.
    • Roper DF Rainshield at 3 lb/A on 7-day intervals can be used on dry bulb onions and at 2 lb/A on 7- to 10-day intervals for Allium seed crops. Oregon and Washington seed crops only (SLN OR-130003, SLN WA-1300003). 24-hr reentry.
  • Omega 500F (Group 29) at 1 pint/A on 7- to 10-day intervals. Do not use an adjuvant. Preharvest interval is 7 days. 12-hr reentry.
  • OSO 5% SC (Group 19) at 3.75 to 13 fl oz/A on 7- to 14-day intervals. Can be applied the day of harvest. 4-hr reentry. O
  • Regalia (Group 5) at 1 to 4 quarts/A plus another fungicide on 7- to 14-day intervals. Preharvest interval is 0 days. 4-hr reentry. O
  • Scala SC (Group 9) at 9 or 18 fl oz/A on 7- to 14-day intervals. Appears very effective on Botrytis in studies conducted by Cornell. When applying alone, do not make more than two (2) consecutive applications of Scala SC without alternating to an equal number of applications of a fungicide from a different resistance management group. Do not apply within 7 days of harvest. 12-hr reentry.
  • Premixed fungicides are available for use. Do not make more than one (1) application of any Group 11 fungicide before alternating to a labeled fungicide with a different mode of action.
    • Dexter Max (Group M3 + 11) at 3.2 lb/A on 7-day intervals for dry bulb onion. Do not apply to exposed bulbs. Pre-harvest interval is 7 days. 24-hr reentry.
    • Dexter Xcel (Group M3 + 11 + 3) at 48 to 72 fl oz/A on 7- to 10-day intervals for dry bulb onion. Do not apply to exposed bulbs. Preharvest interval is 7 days. 24-hr reentry.
    • Gavel 75DF (Group 22 + M3) at 1.5 to 2 lb/A on 7-day intervals for dry bulb onions. Do not apply within 7 days of harvest. 48-hr reentry.
    • Luna Experience (Group 7 + 3) at 8 to 12.8 fl oz/A on 10- to 14-day intervals. Do not make more than two (2) applications before alternating to a fungicide in different FRAC groups (non-Group 7 and non-Group 3). Preharvest interval is 7 days. 12-hr reentry.
    • Luna Tranquility (Group 7 + 9) at 16 to 27 fl oz/A on 7- to 14-day intervals. Do not make more than two (2) applications before alternating to a fungicide in different FRAC groups (non-Group 7 and non-Group 9). Preharvest interval is 7 days. 12-hr reentry.
    • Merivon Xemium (Group 7 + 11) at 8 to 11 fl oz/A on 7- to 14-day intervals. Do not make more than two (2) applications before alternating to a fungicide in different FRAC groups (non-Group 7 and non-Group 11). Preharvest interval is 7 days. 12-hr reentry.
    • Miravis Prime (Group 7 + 12) at 11.4 fl oz/A on 7-day intervals. Do not make more than two (2) sequential applications before alternating to a labeled fungicide with a different mode of action. Preharvest interval is 7 days. 12-hr reentry.
    • Pristine (Group 7 + 11) at 14.5 to 18.5 oz/A. Preharvest interval is 7 days. 12-hr reentry.
    • Quadris Opti (Group 11 + M5) at 1.6 to 3.2 pints/A or Quadris Top at 12 to 14 fl oz/A. Do not apply within 7 days of harvest. 12-hr reentry.

Biological control

  • Actinovate AG at 3 to 12 oz/A as a foliar spray on 7- to 14-day intervals. 4-hr reentry. O
  • Actinovate Lawn & Garden at 1/2 to 1 teaspoon/gal water. H O
  • Double Nickel LC at 0.5 to 4.5 pints/A for soil application on 14- to 28-day intervals. Can be applied the day of harvest. 4-hr reentry. O
  • Prestop WG at 3.5 oz/5 gal water (0.5% suspension) on 3- to 6-week intervals. Apply only when no aboveground harvestable food commodities are present. 4-hr reentry. O
  • Serenade Opti at 14 to 20 oz/A on 7- to 10-day intervals. Applications can be made up to and the day of harvest. 4-hr reentry. O
  • Stargus at 2 to 4 quarts/A plus a nonionic surfactant on 7- to 10-day intervals. Preharvest interval is 0 days. 4-hr reentry. O

Reference Chilvers, M.I, and du Toit, L.J. 2006. Detection and identification of Botrytis species associated with neck rot, scape blight, and umbel blight of onion. Online. Plant Health Progress doi:10.1094/PHP-2006-1127-01-DG.

Hoepting, C. A. 2017. Efficacy of fungicide treatments for control of Botrytis leaf blight and Stemphylium leaf blight on onion, 2016. Plant Disease Management Report: Report No. 11:V127.