Lucerne Disease Control


Various diseases occur in lucerne which may kill seedlings, reduce yield and shorten the lifespan of the stand. The occurrence and severity of the problem depend on environmental conditions, soil type and crop management. Prevention of disease in lucerne by good management practices is the most effective method. Start by planting Rhizobium-treated, high quality seed of an adapted, disease-resistant cultivar.

Plant it in a weed free seedbed which is well-drained, fertilised and has a pH of 6.5-7.5. Soil fertility must be adjusted according to soil tests before planting and maintained by top dressing. Losses due to disease can be prevented or minimised by using disease-resistant cultivars. There are many cultivars already available which have resistance to a variety of diseases, and new ones are released every year.

Diseases occuring mainly on seed and seedlings:

Fungal diseases

Pythium seed rot, damping-off of seedlings and root rot
(Pythium spp.)

If the seed becomes infected during germination, the contents of the seed become a brown, gelatinous mass inside the seed hull or the radicle and cotyledons become brown and soft immediately after germinating.

If the seed is infected at a later stage of germination, the lesion is more typically restricted to the hypocotyl and root, which look watery and pappy, and eventually disintegrate and disappear. The seedlings wilt or may be stunted with small, dark green cotyledons which die after a couple of days.

If humidity is high, temperature moderate and there is enough soil moisture, a seedling with the primary root infected may survive long enough to form secondary roots above the lesion.


Compensate for possible losses by sowing more seed per ha. Fungicide treatment of seeds is effective. Peronosporales-specific fungicides (e.g. metalaxyl) are available and will protect seeds from the disease. Prepare a firm seedbed and ensure that soil fertility and pH are optimal for growth of lucerne. Plant when soil and climatic conditions encourage rapid germination and early growth of seedlings.

Leptosphaerulina leaf spot
(Leptosphaerulina trifolii)

This disease mainly affects younger leaves, but also attacks the petioles and older leaves. Symptoms on the leaves vary with environment, the physiological stage of the leaf and the age of the plant.

Dark-brown to black lesions 1-3 mm in diameter with a well-defined yellow (chlorotic) ring around them appear on the leaves and petioles. The centre of the lesion is usually paler (tan-colored).

In the case of severe infection the lesions enlarge and merge, the leaves become yellow and fall off. Infection in spring can cause dwarfing. Damp conditions favour the disease. It occurs throughout South Africa.


Resistant cultivars are not available, but some cultivars have less leaf loss than others. As far as allowed by the harvesting schedule, harvesting must take place as soon as possible to prevent leaf loss as well as the accumulation of disease innoculum.

Spring black stem and leaf spot
(Phoma medicaginis)

Leaves, stems and pods, as well as the crown and taproot, can be infected. In the spring, many small dark-brown to black spots develop on the lower leaves, petioles and stems. The lesions vary from the size of a pinhead to 1-2 mm in diameter. Irregular lesions enlarge and merge.

There is no yellow ring around the lesions. Leaves turn yellow, wilt and drop off. Lesions on the petioles and stems enlarge and large areas near the base may become black. Serious infection can result in root rot. The pods become discoloured and crumpled in humid conditions. Cool, humid conditions are favourable to the disease. It occurs country-wide.


Early cutting where the disease is present will prevent leaf loss. There are no highly-resistant cultivars available, but there are a few which are moderately resistant. Use good quality seed produced in dry areas. Seed produced in humid areas must be treated with a fungicide. Leaf-applied fungicides can be used where the disease is serious, but are not always economical.

(Uromyces striatus)

Brown, powdery pustules occur on the underside of leaves and on the petioles.

There are dark-brown patches on the upper side of the leaves and often a well-defined yellow (chlorotic) ring is visible (as in Leptosphaerulina leaf spot). Serious infection can cause leaves to yellow, crumple and fall. In the autumn the pustules become darker as a result of production of spores.

Later there is also the development of elongated pustules on the stems. If the pustules are touched, the spores rub off on one’s skin. This is the only leaf disease in lucerne with this characteristic. Cool humid conditions encourage the disease. It occurs throughout South Africa.


The best method of control is by using rust-resistant cultivars, but few of these are available. Timely cutting reduces leaf loss and the build-up of innoculum.

Common leaf spot
(Pseudopeziza medicaginis Sacc. var. trifolii)

Fairly large (1-3 mm in diameter), circular, brown to black lesions occur on leaves. The margins may be smooth or jagged. The lesions are usually single, but may merge. There is no yellow ring around the lesions (different from Leptosphaerulina leafspot and rust).

A small light-brown raised fruiting body, about 1 mm in diameter, is just visible in the centre of each lesion. Infected leaves become yellow and fall off as the disease progresses. Cool humid conditions favour the disease. It occurs country-wide.


Resistant cultivars are available. Cutting must not be delayed and, if possible, should be done before the leaves fall, to remove innoculum and reduce leaf loss. Control with fungicides is possible but not always economical.

Stemphylium leaf spot
(Stemphylium vesicarium)

Stemphylium leafspot causes two different types of disease symptoms in South Africa.

In the warmer areas the lesions on the leaves are pale to dark brown, slightly sunken, often tan-coloured in the centre, with undefined margins, which sometimes form concentric rings so that they look like a dartboard (as in common leafspot).

They are round, oval or irregular, 0.1- 3 mm in diameter and often surrounded by a chlorotic margin. In cooler areas the lesions are a bleached white or tan colour with a well-defined black margin. They are oval or irregular in shape and 0.5 –2 mm in diameter. In both cases lesions are usually single but can sometimes merge.

Severe infection can cause leaves to drop. Humid conditions favour the disease. It occurs in the Western Cape, Eastern Cape, KwaZulu-Natal, Northwest Province, Gauteng and Mpumalanga.


Cultivars with low to moderate resistence are available. Earlier cutting is recommended if the disease threatens to cause serious leaf loss.

Summer black stem and leaf spot
(Cercospora medicaginis)

Both leaves and stems are affected. Leaf drop, which begins at the lowermost leaves and moves up the stem, is the most obvious symptom. The lesions on the leaf are light to dark brown, round, fairly large (2-5 mm in diameter), with an undefined margin and often surrounded by a chlorotic area as in common leaf spot and Stemphylium leafspot. Lesions occur on both surfaces. Under humid conditions, lesions may become ash-grey due to production of spores inside the lesions.

On the stems, the lesions are dark brown to black, irregular in shape, originally single but later merging. Later they become completely black. Serious infection leads to leaf loss, and lesions cause the stems to become girdled and die off.

Hot, humid conditions are favourable to the disease. It occurs in the central and Eastern Cape, Free State, Northwest Province, Gauteng and Mpumalanga.


Harvest earlier to reduce loss. There are no resistant cultivars available.

Downy mildew
(Peronospora trifoliorum)

The disease first affects the shoots with leaves and stems turning yellow and chlorotic. Affected stems are thicker than healthy ones, with short internodes and often have a bushy rosette-type growth at their tips.

The leaves are often twisted with curled margins. Grey downy sporangia which are visible to the naked eye, occur on the underside of the leaves.  Cool humid weather favours the disease. It occurs in the Western Cape, Eastern Cape. Free State and parts of KwaZulu-Natal.


Resistant cultivars are available and are the most economical means of control.

The fungicide metalaxyl is effective in controlling downy mildew in seedlings. The first cut must not be delayed if downy mildew is present. Harvesting removes the source of innoculum and the young susceptible leaves, and reduces the relative humidity caused by the dense leafy covering. The normal increase in temperature with the advancing season will reduce the chance of downy mildew in the regrowth.

Yellow leaf blotch
(Leptotrochilia medicaginis)

This disease occurs mainly on the leaves and is not common on petioles and stems.

Lesions are green-brown to start with, with an irregular shape, and often lie parallel to the veining. At first, small fruiting bodies are produced within the lesions on the upper leaf surface. Eventually the lesions become dark brown to black and produce black cup-shaped fruiting bodies on both leaf surfaces.


Harvest early to prevent buildup of infected leaves.


Bacterial wilt
Clavibacter michiganense subsp. insidiosum Synonyms: Corynebacterium insidiosumCorynebacterium michiganense subsp. insidiosum and Aplanobacter insidiosum

This disease is recognised by dwarfed yellow-green plants which occur scattered in the land. The infected leaves are malformed and much smaller than healthy leaves, and the teeth along the leaf margin are often cup-shaped or curled up. The stems grow in a rambling fashion. When cut open, the roots are yellow-brown inside (the same as crown-rot/root-rot).

It apparently occurs in the Cape Province, the Free State, Gauteng and Mpumalanga.

Bacterial wilt is the only notifiable disease in lucerne. If it does occur no seed may be produced on the specific lands, either for sale or for export.


Cultivars resistant to bacterial wilt are available. Harvest young stands before older ones if the same implements are to be used. Do not cut when the plants are wet.


Lucerne mosaic virus

The lucerne mosaic virus is transmitted by the blue-green aphid and the spotted alfalfa aphid. It occurs during cold spring and autumn weather; in summer the symptoms are not noticeable. The leaves become pale green- or yellow-speckled, the stems are dwarfed and the leaves and petioles are malformed.

Plants may loose their vigour, and some races cause root necrosis and the death of the plant. Lucerne mosaic virus makes plants susceptible to damage by drought and cold. The degree of yield loss depends on the virus race present and lucerne resistance, on temperature, soil and other environmental factors.


The virus is transmitted by aphids, and can be limited by using aphid-resistant cultivars. It is also transmitted by implements. These should be sterilised if moved from an infected to an uninfected land.

Diseases caused by nematodes

Lucerne stem nematode
(Ditylenchus dipsaci)

Infected stems have swollen nodes and seriously shortened internodes and are generally discoloured. In hot humid conditions, leaves may curl, become malformed and white in colour.


Resistant cultivars are the most important control method. In irrigated arid and semi-arid areas, the stem nematode is only a problem at the first cut. If the lucerne is cut when the upper 50-80 mm of soil is dry, the nematodes can be controlled successfully.

Rotation with a non-host crop such as small grains, maize or beans is also effective in controlling nematodes. There are chemicals which can be used to control nematodes, but their cost makes them uneconomical for lucerne.

Diseases occuring mainly on stems and crowns

Fungal diseases

(Colletotrichum trifolii and C. destructivum)

Colletotrichum trifolii: Symptoms vary from small irregular black areas on stems of resistant plants to large sunken oval to sometimes diamond-shaped lesions on stems of plants which are susceptible. The large lesions are tan-coloured with a well-defined black margin. Small, black fruiting bodies are sometimes visible in the centre of the lesion.

As the lesions enlarge, they may merge, girdle the stem, and kill from one to all the stems of the plant. A clear characteristic is the straw-coloured to pearly-white shoots which are scattered across the field (just as in the case of crown/rootrot). These shoots may form a crook if they are ringed by a large lesion, and will quickly wilt.

The most serious form of anthracnose is the blue-black phase. This can be seen if dead stems are broken off at the crown. If the base of the broken stem is blue-black then it is anthracnose. If it is pale brown then it has Fusarium wilt or Rhizoctonia crown-rot.

Another symptom of anthracnose is the black discoloration and the dying off of petioles. Colletotrichum destructivum: small separated lesions, irregular in form, pale brown to black, occur on the stems. Anthracnose is favoured by hot, humid conditions. It occurs country-wide.


There are resistant cultivars available. All implements should be disinfected before the first cut in the spring, and if they are moved from an infected to an uninfected land.

Rhizoctonia diseases
(Rhizoctonia spp.)

In the root canker phase the fungus invades the taproot near to the area from which the side roots develop. The oval, sunken cankers are tan to grey-brown in colour. The colour is often darker and more intense along the margins than in the centre of the lesion. During the winter the pathogen is inactive and the healed lesions become black.

The plant dies when the lesion invades the root. If it survives, new roots will form which will support the plant the following year. In the crown node rot and crown rot phases, brown lesions appear first on the nodes and young shoots, at or just below ground level.

As the infection develops, the nodes and shoots die, the fungus invades the crown and prevents the formation of new vegetative nodes in the infected tissue.

Sunken white to brown lesions develop at the base of the stem. Brown bands develop in the older, lighter coloured lesions, indicating that the lesion is actively enlarging. Coarse brown fungal hyphae can be seen on the surface of the lesion. Stems which become girdled by lesions die, and these look very like anthracnose, except that they are not blue-black. Seedling losses are more common when conditions are hot and soil moisture is high. The roots and lower parts of the seedling stem shrivel and die.


There are no methods of control known. If the upper shoots show symptoms an early cutting can reduce loss.

Sclerotinia crown and stem rot
(Sclerotinia spp.)

The decayed crown tissue is yellow-brown in the early stages and later becomes dark brown and soft. In some cases the whole plant has decayed by spring and disappears.

Losses may then be attributed to winter damage. The only indication of the disease then, is the fruiting bodies that occur in the dead crown tissue or on the soil alongside the dead plant. During cool, damp weather a cotton-wool-like, webbed growth forms on stems and crowns of infected plants.

Secondary infections occur as it grows across the ground to other plants. Individual shoots wilt, become brown, soft and pappy and disintegrate completely. The cotton-wool-like mycelium is partially visible between the dew-covered shoots, beneath the dense leaf-cover of the lucerne in the early morning.

By midday the mycelium has dried out. If cool weather continues through the spring many other plants will be infected and the stand rapidly thinned out. On infected plants, the mycelium changes to hard dark fruiting bodies.


The occurrence of the disease can be reduced by planting in spring. Cultivation reduces the occurrence of the disease, as it buries the fruiting bodies. There are no resistant cultivars available. Burning the stand in the autumn can help control sclerotinia. Harvesting in autumn controls the disease by causing the soil surface to dry out and reducing relative humidity in the leaf cover.

Clean seed should be used for planting.


Crown galls
(Agrobacterium tumefasciens)

Crown gall is rare in lucerne and should not present a serious problem. Irregular, convoluted galls occur on the crown-shoots at or just beneath the soil. Affected plants loose vigour and begin to die slowly. The disease is uncommon on lucerne and its true impact cannot yet be established.


There is no information available about control. The disease should not become a serious problem on lucerne.

Witches broom
(mycoplasma-like organism)

This disease is characterised by the development of masses of short thin shoots from all parts of the crown and from the axils along the branches. Hundreds of thin stems are found on infected plants and a large, heavily-infected crown may have up to 3000 of them, closely packed together.

Marginal chlorosis of the small, rounded, often crinkled leaves, and an overall pale-green color of the thin succulent stems, give the dwarfed plants a yellowish colour. Some infected plants have green flowers.

Sometimes infected plants appear to be recovering slowly during cooler periods in spring and winter, but the symptoms recur rapidly when temperatures, together with moisture stress, begin to rise.


There are no practical methods to control the disease, but area-specific removal of old sick plants, re-sowing, and the maintenance of dense productive stands, reduces the spread of the disease to other plants.

Diseases occurring mainly on crowns and roots

Fungal diseases

Fusarium wilt
(Fusarium oxysporum f. sp. medicaginis)

The first signs of the disease are wilted shoots. In the early stages of the disease the leaves may wilt during the day but recover at night. Yellowing of the leaves and stems follows, and the leaves become reddish.

At first only one side of the plant may be affected but after some months the whole plant may die off. Dark or reddish brown streaks appear in the central cylinder of the taproot. In cross-section these look like small partial or complete circles. In the advanced stage of the disease, the outer ring of the central cylinder or the whole cylinder is discoloured.

Fusarium wilt can be distinguished from bacterial wilt by the dark or reddish brown discolouration of the central cylinder as opposed to the pale or yellow-brown discolouration associated with bacterial wilt. The discoloured tissue is also more defined in Fusarium wilt – the cortex and bark remain uninfected.


Because the fungus can survive for years in the soil, the only practical method of control is to use resistant cultivars.

Phytophthora root-rot
(Phytophthora megasperma f. sp. medicaginis and P. dreshsleri)

In wet soil under cool conditions, seedlings may become infected with Phytophthorawilt. The seedling wilts or may be dwarfed with small dark green cotyledons which die within a couple of days.

If the soil moisture and humidity are high and the temperature moderate, the seedling may survive an infected taproot by forming secondary roots above the lesion. Older infected plants wilt and the leaves, especially the lower leaves, become yellow or reddish brown.

The taproot and secondary roots rot from the point where the plants die or are seriously dwarfed. Lesions occur where side roots branch from the tap root. At first the lesions are pale brown with vague margins; later they become black.

The yellow discolouration of the tissue which spreads from the cortex into the xylem tissue is a clear characteristic of Phytophthora. Taproots can be infected at any depth, but generally they begin to rot at the point where drainage is poor, either as a result of cultivation methods which cause ploughsole, or of a subsoil which is not well drained.

This causes obvious dead patches in the land, later invaded by grass. In waterlogged soil the disease can cause serious losses in the stand.

It occurs in the Western Cape, Eastern Cape, Free State, Gauteng and Mpumalanga.


Soil and water control is the most important control measure. Deep soil cultivation which breaks up ploughsole improves drainage and reduces the length of time water stands in the lands. The land may also be leveled.

This reduces the time allowed for flood irrigation. By controlling the time of irrigation, the disease can also be controlled in irrigated areas. Resistant cultivars, in combina- tion with correct management, are highly successful in the control of Phytophthora root rot. Resistance is not operative in seedlings, however, and metalaxyl may be used as a seed treatment to protect seedlings.

Crown rot and root rot complexes
(Colletotrichum, Fusarium, Pythium, Rhizoctonia, Phoma, Phytophthora, Sclerotinia, Stagonospora and Ditylenchus)

Crown and root rot are chronic diseases in lucerne all over the world.

It may be caused by individual pathogens as described elsewhere, or it may be the result of a complex of pathogens and other agents. The complex may consist of various combinations of genera and species of fungi, bacteria and nematodes.

Although the symptoms of crown and root rot are characteristic, they are not specific to any one of the organisms comprising the complex. The disease complex can be recognised by the brown, necrotic areas in the crown and root cortex.

Sometimes the crown becomes black, rotten and, if cut through lengthwise, is found to be hollow, or there are obvious black necroses on the roots. In advanced stages both the cortex and the vascular tissue are infected.

The vigour of the plants is more and more reduced the more the roots decay. Plants in advanced stages of the disease become dwarfed, wilted and eventually die. Crown rot sometimes causes plants to grow crooked as a result of axillary buds dying in the infected area of the crown.

New side roots that develop from the crown may keep the plant alive temporarily if the tap root has died. Straw-coloured, dead shoots occur on the land (just as in anthracnose). The disease becomes a problem when plants are under stress, for instance by poor fertilisation, excessive cutting, drought, etc. It occurs country-wide.


Good management practices will prevent losses. Plant resistant cultivars. Adopt a good cutting/harvesting schedule and prevent the crown being shaded. Provide sufficient soil nutrients, especially potassium. Control insects.

Diseases caused by nematodes

Root knot nematode
(Meloidogyne spp.)

Plants infected with root knot nematodes are dwarfed. Infected roots branch excessively and have galls. Some galls may be small and can be missed unless looked for carefully.


Resistant cultivars are the best existing method of control as the use of chemicals is uneconomical. Rotation is not effective because the nematode can reproduce on the majority of non-grasses.