Holland Red Shallots

A seedling killer caused by several different fungi working together. It hits vegetables, flowers, herbs, microgreens, and cover-crop seedlings the same way — seeds rot before they emerge, or young seedlings collapse right at the soil line. Wet seed-starting mix and poor airflow in seedling trays are the classic conditions.

Triggers: Wet soil or starting mix, poor drainage, seedlings packed too tightly, contaminated trays or media, and stagnant air all favor damping-off.

Risk fades when: Drying the soil surface and improving airflow slows new spread. Collapsed seedlings don't recover, but the rest of the tray can be saved.

Onion maggot is the most important early-season pest of onions, leeks, and garlic in northern temperate regions. Larvae feed on bulb basal plates and roots, killing plants and predisposing damaged bulbs to storage rot. First-generation damage can routinely reduce plant stands by over 50%. Three generations occur annually in northern regions; only the first is typically devastating to a young crop.

Triggers: Three generations per year in northern regions. Overwinter as pupae in soil. Adults emerge late April-May. Adult: small grayish-yellow fly resembling slender housefly. Females lay eggs at soil base of onion plants.

On Holland Red Shallot: Larvae feed on roots and developing bulbs.

Prevention: Rotate crops and avoid planting near fresh allium debris.

Risk fades when: Cool, wet weather favors onion maggot while hot, dry summer weather is detrimental to its survival, so pressure eases during midsummer heat between flights; the first (spring) generation is the largest and most damaging, and destroying culls and crop debris reduces overwintering pupae (Wisconsin Hort, UMaine Extension).

SoilStack treats this entry as allium white rot for field alert purposes, rather than Botrytis neck rot (which is mostly a post-harvest storage issue). White rot is allium-specific and causes yellowing, wilt, decay of the basal plate (where roots attach), white fungal growth, and tiny black poppy-seed-like resting bodies (sclerotia). It thrives in cool, moist soil.

Triggers: Cool moist soil favors infection. Development is optimal around 60-65°F and slows sharply above the upper 70s.

On Holland Red Shallot: Excess soil moisture and poor drainage.

Prevention: Use raised beds or loose soils and stop heavy watering as harvest approaches.

Risk fades when: White rot is markedly inhibited above 78°F and reduced by drying soil, though the sclerotia persist in soil for years.

An allium-specific rust on garlic, onion, leek, shallot, and chives. Produces orange to reddish pustules on older leaves first. Favored by cool, humid weather.

Triggers: Optimal infection is near 59°F with saturated humidity for several hours. The disease stays active in cool 57-75°F weather with dew or high humidity.

Risk fades when: Rust thrives in cool saturated air. Dry foliage or heat above the favorable range lowers new infection pressure.

Aphids are soft-bodied sap-sucking insects that cluster on tender new growth. Most established plants tolerate moderate populations and will outgrow damage on their own, but aphids are the most important plant virus vectors in the garden, transmitting more than 100 plant viruses including potato leafroll, cucumber mosaic, and turnip mosaic. Honeydew excreted while feeding supports sooty mold growth and attracts ants that protect aphids from natural enemies.

Triggers: Optimal development at ~75°F (green peach aphid) per UC IPM Floriculture; melon aphid develops fastest above 75°F. Many species heat-intolerant above 90°F and crash in mid-summer. Soft new growth and over-fertilization with high N favor population buildup. Females give live birth parthenogenetically most of growing season — one generation in ~1 week under optimal conditions.

Risk fades when: Per UC IPM and Clemson HGIC, populations crash in mid-summer heat (>90°F) for many species, return in cooler conditions

The main foliar disease of onions, garlic, leeks and shallots in warm humid weather. It starts on the older, lower leaves as small sunken water-soaked spots with pale centres. Those enlarge into oval lesions, several centimetres long, that turn purple to brown and develop concentric light and dark rings - a zonate bull's-eye that is the diagnostic sign. Ringed lesions that merge or encircle a leaf girdle it, and everything above wilts, collapses and dies back from the tip. Leeks show this as classic leaf-tip dieback. The fungus is a close relative of the one that causes early blight on tomatoes, and behaves much the same way: it overwinters on infected debris and cull piles, spreads by wind and splashing water, and needs persistent leaf wetness to infect. Infection often follows injury - abrasion from blowing sand, damage from another fungus, or the wounds and succulent necks left after topping at harvest. That last route is why curing matters: dry the necks before topping and cure bulbs thoroughly, or the same fungus follows the crop into storage.

Triggers: Alternaria porri overwinters on infected bulbs and crop debris and can be seedborne in onion. Spores are dispersed by rain, irrigation water, wind, and by people and equipment moving through a wet crop. Older leaves are the most susceptible, and tops become more prone as plants mature. Infection often follows injury - from other fungi such as Botrytis, or from sand and dust during windstorms. Colorado State: warm, moist weather after midseason favours Alternaria, and the pathogen enters mature leaves and bulbs through wounds and the succulent necks left after tops are removed. UC IPM uses consecutive nightly leaf wetness above 12 hours as the signal to shorten spray intervals. UMass notes that Stemphylium leaf blight looks nearly identical and needs microscopy to separate, but management is the same.

Risk fades when: Infection stops without free moisture on the leaf. Dry weather and good airflow halt new lesions, but existing ones stay and the leaf tissue above a girdling lesion will not recover. The disease also follows the crop into storage through wounds and wet necks, so curing is part of resolution, not an afterthought.

Golf-ball onions are almost always a day-length problem, not a fertility problem. Onions stop making leaves and start making a bulb when daylight hits a variety-specific threshold: short-day types begin bulbing at 10 to 12 hours, intermediate-day at 12 to 14, long-day at 14 or more. And here is the part that decides everything - Iowa State Extension puts it plainly: bulb size is largely determined by the number and size of the leaves at bulb initiation. Every leaf becomes a ring. Once bulbing starts, no new leaves form, and the onion can only fatten the rings it already has. So a short-day onion planted in the north hits its 10-hour trigger in early spring while the plant is still small, bulbs immediately, and Nebraska Extension calls the result exactly what it is - disappointingly small bulbs. Run it the other way and a long-day onion in the far south may never reach 14 hours and never bulb at all. Crowding does the same thing by another route: plants that never build big tops cannot build big bulbs. Match the variety to your latitude, plant as early as the soil can be worked, and give the tops every week of growth you can before the days get long.

Triggers: Iowa State Extension: short-day cultivars begin forming bulbs at 10 to 12 hours of daylight, intermediate-day at 12 to 14 hours, and long-day cultivars at 14 or more; bulb size is largely determined by the number and size of the leaves at bulb initiation. Nebraska Extension: short-day onions grown in northern regions start bulb development too soon, producing disappointingly small bulbs. UMN Extension: sweet or mild onions are short-day types and will generally develop small bulbs in Minnesota; overcast skies and cool temperatures during the season delay bulb formation. Crowding limits top growth and therefore bulb size. Note that bunching onions (Allium fistulosum) do not form true bulbs at all, and this disorder does not apply to them.

On Holland Red Shallot: Crowding, drought, or too little fertility during leaf growth.

Prevention: Space sets properly and keep growth steady through spring.

Risk fades when: Nothing can be done once bulbing has started - no new leaves form, so no new rings. The bulb will only fatten the rings it already has. Fix it at the next sowing: choose long-day varieties north of roughly the 36th parallel and short-day varieties south of it, intermediate-day in between. Plant as early as the soil can be worked, use transplants rather than direct seed in short-season areas to buy leaf-growth time, and thin to 3 to 4 inches. Small bulbs are perfectly good eating - they just will not size up this year.

A thick-necked onion is a storage failure, not a growing failure - the bulb is usually large and looks fine. The neck is the stem where the leaves join the bulb, and at maturity it is supposed to dry down, shrivel, and seal. When it stays green, fleshy and moist, that open wet neck is a highway for rot. UMN Extension is direct about the cause: too much nitrogen results in late maturity, large necks that are difficult to cure, soft bulbs, green flesh, and poor storage quality. Watering late into the season does the same thing by keeping the plant growing when it should be shutting down. USU adds the discipline - stop nitrogen entirely once bulbs have initiated. The other route to a thick neck is pulling too early, before the tops have fallen and the neck has begun to dry on its own. Whatever the cause, extension guidance is unanimous and worth following: sort thick-necked bulbs out, keep them separate, and eat them first. Put one in a storage crate and it will rot and take its neighbours with it.

Triggers: UMN Extension: onions need a good supply of nitrogen, but too much causes late maturity, large necks that are difficult to cure, soft bulbs, green flesh and poor storage quality. USU Extension: refrain from applying any nitrogen fertilizer once bulbs have been initiated, and undercut onions at maturity. Nebraska Extension: harvest when about two-thirds of the tops have fallen over and dried naturally and the necks have started to dry; onions with a thick neck should not be stored. MSU Extension: thick-necked onions still contain green, moist tissue, will not keep, and if stored with the rest they will rot and may ruin the others. Iowa State: use thick-necked bulbs as soon as possible.

Risk fades when: A thick neck does not cure out. Sort those bulbs into a separate 'use first' pile - they are sound to eat but they will rot in storage and spoil neighbouring bulbs. Cure the rest at 75 to 90°F in a warm, well-ventilated place for two to four weeks until outer scales are dry and the neck is tight; poor curing causes decay regardless. For next season: stop nitrogen once bulbs begin to swell, taper irrigation as tops start to go over, and wait to harvest until about two-thirds of the tops have fallen and the necks have begun drying naturally.

Thrips are tiny (1/16 inch) slender insects with fringed wings that puncture and rasp leaf surfaces, leaving silver stippling with black frass dots. The biggest concern is virus vectoring: western flower thrips is the principal vector of tomato spotted wilt virus (TSWV) and impatiens necrotic spot virus (INSV), which affect more than 600 plant species. Greenhouse and high tunnel infestations can be devastating.

Triggers: Hot dry weather; greenhouse/high tunnel environments. Female lays eggs inside leaf tissue. 2 larval stages feed; 2 non-feeding pupal stages in soil/litter. Lifecycle 10-21 days. Many overlapping generations. Bridge crops (spring wheat, peach, strawberry per NC State) build populations before vegetable hosts available.

Risk fades when: Infestations are worst in hot, dry weather; cool conditions slow development and heavy rain or overhead irrigation knocks populations down sharply, so risk fades as the weather turns cool and wet and rebuilds the following spring (UK Entomology, Cornell IPM).

Onions lose fights with weeds, and they lose badly. The reason is anatomical: an onion has a shallow, sparse root system and upright, narrow leaves that never close a canopy or shade the ground. Nebraska Extension states it plainly - due to their shallow root systems, onions compete poorly with weeds. A weedy onion bed does not just look untidy. Every week of shaded, crowded growth costs leaves, and because bulb size is set by the number and size of leaves at bulb initiation, lost leaves mean a permanently smaller bulb. The window that matters is from emergence through bulb initiation; after the bulb starts sizing, weeds cost less. The catch is that the same shallow roots that lose to weeds are easily severed by a hoe. Cultivate shallowly, close to the surface, and do not hill soil up around the plants. Mulch lightly instead: it suppresses weeds and conserves moisture without root damage.

Triggers: Nebraska Extension: due to their shallow root systems, onions compete poorly with weeds; shallow cultivation is necessary and the soil should not be hilled up around the plants. Light mulch decreases weeds and conserves soil moisture. The critical period runs from emergence through bulb initiation, because per Iowa State Extension bulb size is largely determined by the number and size of the leaves at bulb initiation - leaf growth lost to weed competition cannot be recovered once bulbing starts.

Risk fades when: Leaf growth lost to weeds is not recoverable - once bulbing begins the onion makes no new leaves, so the bulb is capped at whatever top growth survived. Weed early and often rather than waiting for a big clean-up. Cultivate shallowly and close to the surface; onion roots sit just below it and a deep hoe cuts them. Never hill soil up around onions. A light organic mulch suppresses weeds and steadies soil moisture at the same time, which also helps prevent split and double bulbs.