Anthracnose (Onion smudge) (Colletotrichum circinans)

It usually appears in fields just before harvest and continues to develop during storage period. Under warm and wet soil conditions, it can cause seedling damping-off. The most common symptom is the small dark green or black stains (dots) on outer scales of bulbs. The dots develop concentric rings. In severe cases, the fungus attacks the living tissue causing a collapse of fleshy scales. On coloured onions, the fungus is restricted to the neck of the bulbs making the flattened leaves colourless. The fungus survives on onions, sets and in the soil. Warm moist conditions favour development of the disease.
Optimum temperature for infection is from 23.9 to 29.4° C. White onions are very susceptible to the disease. Reduced market value results from marred bulb appearance and bulb shrinkage. It also attacks leeks and shallots.

Bacterial soft rots (Erwinia carotovora subsp. carotovora)

This is a big cause of loss in storage onions. Bacteria Erwinia carotovora subsp. carotovora) can enter the neck tissue as plants mature and then invade one or more scales. At this stage, the affected tissues are water-soaked and pale yellow to light brown. As the rot progresses, the invaded fleshy scales become soft.

Diseased bulbs can be diagnosed by pressing on the bulb: a watery, foul-smelling fluid often can be squeezed from the neck of diseased bulbs.

Bacterial soft rot bacteria enter only through wounds. Onion maggots (Delia antiqua) may carry the bacteria and introduce them while feeding. Onions with mechanical injuries, bruises or sunscald under warm, humid conditions are particularly susceptible to bacterial soft rot. Soft rot can affect many vegetables including carrots, celery, potato and parsnip.

Downy mildew (Peronospora destructor)

It attacks young plants, appearing as white specks, usually confined to the oldest leaves of young plants. A greyish white mould develops rapidly in cool damp weather and progresses down the sheath, and plants eventually fall over and dry up. Optimum temperatures for fungal growth are between 13 and 20° C. Because of the temperature requirements of the fungus, the disease is more serious in higher cooler areas.
The fungus survives in seeds, bulbs, sets, and on plant debris. Spores are carried long distances by air currents. The fungus can infect onion, Welsh onion, Egyptian onion, garlic, shallot, leek and possibly some other species of Allium.

Fusarium basal rot (Fusarium oxysporium f.sp. cepae)

The above ground symptoms constitute yellowing of leaf blades at the tip. The yellowing at later stages covers the whole blade. The affected leaves shrivel and decay. Diseased plants can be easily pulled out because the root system is rotted. Affected roots are dark brown, flattened, hollow and transparent. When diseased bulbs are cut vertically, a brown discolouration is evident. The fungus survives in any soil moisture that permits crop growth. Infection is facilitated by injuries to root system, Losses can occur in the field and in storage.

The disease is most prevalent where onions are grown under high temperature conditions. Although of no economic importance the disease could attack garlic, shallots, chives and leeks. It also can survive in weed, Oxalis corniculata.

Leafminers (Liriomyza spp.)

Leafminers may cause damage to green onions. Damage is largely cosmetic, and mining on leaves may cause rejection of marketed onions, but generally does not affect plant growth. Damage in dry onions and garlic is of little concern unless populations become high to prematurely kill foliage.

Onion fly (Delia antiqua)

The larvae of the onion fly, also called onion maggot is a major pest of onions. The maggot is small (about 8 mm in size when fully grown), white-cream coloured. It eats the lateral roots, then tunnels into the taproot and sometimes bores into the base of the stem. Attacked leaves wilt and the leaves turn bluish. The plants become shrivelled or eventually die. The maggots feed just above the base of seedlings killing them. A maggot can attack several seedlings in succession. This causes poor plant establishment resulting in many gaps in the field.
The maggots are also found inside developing onion bulbs. Their feeding exposes the plant to infection by diseases such as bacterial soft rot. Pupae are light to dark-brown in colour, and about 7 mm in length. Pupae are found in the soil near the base of the plant. The adult is a brownish grey fly, somewhat smaller than house flies. When at rest, they keep their wings folded one over the other. Adult flies do not cause damage. They lay eggs in the soil surface near the germinating plants.
Onion maggots are adapted to cool, wet weather, so usually they are less of a problem during hot dry periods. They prefer soils heavy in organic matter. The onion maggot attacks plants related to onion such as leeks, shallots and garlic.

Onion rust (Puccinia porri)

Affected leaves show small reddish to dusty orange spots (pustules). These later turn black and are covered until maturity by leaf epidermis. Leaves that are heavily infected turn yellow and die prematurely. A new crop of leaves may develop and the bulb size is usually reduced. The fungus attacks also leek, shallot and some wild species of Allium. The disease is favoured by high humidity coupled with moderate to low temperatures. Also excessive nitrogen in the soil favours disease development.

Purple blotch (Alternaria porri)

Purple blotch attacks onion, garlic, leek and other Allium crops. Initially, small white sunken spots develop on the leaves. These enlarge and under moist conditions, turn purple with a yellowish border and are often covered with a sooty deposit of spores. After 3-4 weeks the leaves turn yellow and collapse. Bulbs may also be attacked, mainly at the neck. This can be seen as a yellow to reddish watery rot.
A good timing of sowing or transplanting can minimise purple blotch attack by A. porri, depending on the local environmental conditions. The fungus requires rain or persistent dew for reproduction. It can grow through a wide temperature range of 6 to 33.8° C. Optimum temperature of fungal growth is 25° C.

Slippery skin (Pseudomonas allicolai pv. allicola)

There are no symptoms on the outer surface of bulbs during early stages of disease development. When the bulb is cut open lengthwise, one or more of the inner scales can be found water-soaked or appears as if it has been cooked. The rot does not progress crosswise in the bulb. After the decay has progressed, the tissue begins to dry, the onion shrivels and secondary organisms can enter and cause a wet rot. The base of the bulb can be pressed hard enough to cause the centre core to slip out at the top, and for this reason the disease is known as slippery skin. The disease is favoured by high moisture.

Sour skin (Pseudomonas cepacia)

In contrast to soft rot and slippery skin, infected scales are not water-soaked but are slimy and yellow. Symptoms usually visible only after onions are dug. The upper portion of the bulb shrinks, and in advanced stages of the disease, the outer dry skin readily slips off during handling while the centre of the bulb still remains firm. Outer layer of scales often becomes darkened and almost orange. Decay of inner scales leads to a soft rot that has a sour, vinegar-like odour. The disease is favoured by wet warm conditions.

Onion thrips (Thrips tabaci)

The onion thrips are major pests of onions throughout Africa. The onion thrips attack an extensive range of crops, including cereals and broadleaved crops. They are tiny (1 mm in length), slender and very mobile insects. Adult thrips are pale yellow to brown in colour. Immature thrips are whitish to pale yellow. Both immature and adult thrips pierce the upper surface of the leaves and feed on the plant sap, generally on the developing leaves, deep inside the plant. This results in white and silvery patches on the leaves.

The excreta of the thrips are clearly visible as small black dots on the silvery leaves. Severe infestations can cause browning of the leaf tips, slowing of plant growth, distortion of leaves and bulbs, and reduction in bulb size. Although thrips feeding during the early bulbing stage is the most damaging to yields, thrips must be controlled before onions reach this stage so that populations do not exceed levels that can be adequately controlled. Onions can tolerate higher thrips populations closer to harvest.

White bulb rot (Sclerotium cepivorum)

The disease occurs mainly in the field and seldom causes injury in storage. The disease is called white rot because of characteristic basal bulb rot where the tissue is covered with white mat of fungal growth. Later numerous rounded black fungal bodies (sclerotia), each about the size of a pin's head, develop. The leaves of diseased plants decay at the base, turn yellow, wilt, fall over and die. The older leaves are the first to die. The roots of affected plants are usually rotted making the plants easy to pull.
Optimum temperature range for infection is from 15 to 18.3° C. The fungus survives in the soil as sclerotia and also in diseased onion sets and wild onion. It is most severe in light cool moist soils. Its host range includes Welsh onion, garlic, leek, shallot and some species of wild onion.