Does neck length at harvest affect bacterial bulb rot?

If onions are topped when the neck tissue is still moist and green, the potential for internal bulb rot increases if the necks are clipped too short.
Onions should be topped or clipped to leave a neck length of at least 2 inches (to minimize the risk of bacterial bulb rot.

Why does leaving a longer neck length reduce risk of internal bacterial bulb rot?

Bacterial pathogens of onion require moisture to infect and spread. The moister the neck tissue, the greater the risk of infection. Bacterial pathogens do not infect or spread through dried tissue.
Bacteria that end up on the tip of a freshly cut, 1-inch neck have a shorter distance to travel to the bulb than on the tip of a freshly cut 4-inch-long neck.
Longer necks are more likely to dry fully and halt the spread of bacterial infection before the bacteria enter the bulb.

Top/clip onion necks to at least 2 inches long (preferably 3-4 inches).
Consider field curing for longer before topping bulbs, if the neck tissue is still moist.

When harvesting manually:

Avoid transferring bacteria from the roots to the neck: clip the necks before the roots or sterilize the blades between clipping the roots and necks.
Do not clip roots too close to the basal plate, to avoid damage to the bulb that might enable bacteria to enter the bulb.

Topping onion necks to a length of 1 inch resulted in 4 to 5 times more internal bulb rot (19%) than onions that were clipped to a 3-inch or 5-inch neck length (4.0-4.5% bulb rot incidence).
Topping onion bulbs very close to the shoulder or leaving a short neck (1 inch long) resulted in significantly more bulb rot (18.0-18.5% bulb rot incidence) than topping necks to a 2-inch or 3-inch length (10.0-11.5% bulb rot).

Dutta, B., and Tyson, C. 2022. Evaluation of neck-clipping length on post-harvest incidence of external and internal bacterial bulb rot in onion, Georgia, 2021. PDMR 16:V107.
Dutta, B., Greene, R. and Tyson, C. 2023. Evaluation of neck-clipping length on post-harvest incidence of external and internal bacterial bulb rot in onion, Georgia, 2022. (Accepted for publication, we’ll add the pdf to Alliumnet as soon as it’s ready.)
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2022. Effects of late-season cultural practices on bacterial leaf blight and bulb rot in an onion crop, Pasco, WA, 2021-22. Plant Disease Management Reports 16:V149.