Shallot

As with any clustered allium, one maggot has several bulbs within reach once it is inside. Lift and destroy the whole affected cluster, and never keep bulbs from it for replanting.

Individual plants yellowing and wilting while their neighbors look fine, and - on pulling one - small white maggots with brown, slimy rot in the bulb base, shank or stem.

There is no rescue for a maggot-riddled bulb. Pull and destroy infested plants rather than composting them, and never save affected bulbs for replanting. Beneficial nematodes drenched into the soil help suppress the larvae in a bed you have to keep using.

Rotate alliums yearly, cover the crop with row fabric through the fly's spring egg-laying window, space plants out rather than growing them in dense rows, and never plant into fresh manure, which draws the flies in.

The larvae of a small gray fly - the onion fly is the same insect - that lays its eggs at the base of allium plants. The white maggots tunnel into the bulb, shank or stem base, and the damage they leave opens the door to soft rot, so the plant yellows, wilts and collapses into a mush. It is worst in cool, wet springs, in unrotated allium beds, and in dense rows where the maggots can work from one plant to the next.

Rust shrinks the whole bulb cluster rather than a single bulb, so leaf area matters more here than on a single-bulb onion. Space the clusters properly and go easy on nitrogen.

Orange-red raised dots and streaks on the leaf blades, worst in humid spells and on crowded, poorly spaced or congested plantings.

Strip or shear off the worst-affected leaves early and let clean growth come back, improving airflow at the same time. A bulb crop usually still matures, so harvest on schedule rather than writing it off - rust rarely reaches the bulb itself.

Give wide spacing and full sun so the leaves dry quickly, avoid overhead watering and excess nitrogen, divide congested perennial clumps, and rotate alliums on a three-year cycle. Rust-tolerant varieties are available in some allium crops.

A fungal disease that raises bright orange pustules on allium leaves. The pustules destroy green tissue, and since those leaves are what feed the bulb, a heavy infection shrinks the crop or weakens the clump. It builds in humid weather, in crowded plantings and in high-nitrogen soil, and it rarely reaches the bulb itself.

Stunted, swollen or twisted plants; soft, spongy bulbs with cracked or discolored basal tissue; bloated leaf bases.

None in-season. Destroy infected crops, hot-compost nothing from them, and rest that bed from alliums for 4+ years.

The whole defense is clean stock: certified seed, sets, and transplants, and never replant from a suspect crop.

Microscopic worms that live inside onion tissue, causing bloated, twisted, stunted growth and soft, cracked bulbs - spread almost entirely through infected planting stock and seed.