Small grain diseases affect production by reducing the yield and impairing the quality. To maximize profits, producers need to understand the influences that diseases may have on the crop potential. A single fungal pathogen may attack a range of small grains, while other small grain pathogens may be confined only to infecting a specific host. Additionally, cultivars may vary in their susceptibility to different diseases. Here, some of the most important diseases of small grains in South Africa are discussed.




Leaf and Stem diseases


The rusts are widespread and important diseases of small grains, but it also infect many other wild and cultivated grasses. In South Africa, asexual urediniospores are the major source of inoculum for all rust diseases. In the non-crop season, rust pathogens survive on volunteer plants and the wind-dispersed urediniospores formed on these plants then become an inoculum source for infection of the next season’s crop. Small grain crops of the following season are then infected and first symptoms are typical urediniospore pustules. Later in the season, another kind of dark coloured spores known as teliospores, develop within lesions and the lesions start to appear black in colour. In other countries, teliospores play an important role in the sexual disease cycle but the alternate host plants, that these spores infect, do not occur within the small grain production areas in South Africa and thus teliospores are not of importance in our cultivation systems.

All the rust diseases can affect grain yield and quality, although the extent to which a cultivar will be affected will depend on the level of susceptibility of that cultivar and environmental conditions that favour the proliferation of the disease. In general, stem rust is more destructive than leaf rust or stripe rust, but as mentioned, the cultivar and area under production should also be considered. Devastating crop losses, and even total crop losses have been experienced as a result of rust diseases and it remains one of the biggest challenges to the successful cultivation of small grains. Breeding and planting cultivars that are resistant to rust is one of the most important ways of controlling the disease. Several research groups in South Africa are dedicated to the development of rust resistant cultivars. However, the process of breeding resistant lines takes time and it usually takes a number of years before a new resistant cultivar becomes commercially available. Moreover, rust diseases may overcome the host resistance, so the use of fungicides forms an important part of the control of these diseases on susceptible cultivars. In South Africa, the application of fungicides for the control of rust is widely practiced. Foliar fungicides are generally applied at an early stage, around the seven-leaf stage and again later at the flag leaf stage in order to control rust diseases.

Stem rust

Puccinia graminis f.sp. tritici- wheat, barley, triticale
Puccinia graminis f.sp. avenae- oats
Puccinia graminis f.sp. secalis- rye

Stem rust, also known as black rust because of the formation of black teliospores in pustules late in the season, is a widespread and economically important disease of a number of cereal grains. Disease symptoms occur on leaf sheaths (Fig. 1), leaf blades, stems (Fig. 2.) and spikes (Fig. 3.). The epidermis is ruptured by elongated oval shaped pustules (uredia), which contain masses of red-brown coloured urediniospores. These pustules may converge so that big parts of the stem appear red-brown in colour. 





Fig. 1. Stem rust pustules on a susceptible wheat leaf Fig 2. Stem rust pustules on a susceptible wheat stem Fig. 3. Stem rust pustules on a susceptible wheat ear


Leaf rust

Puccinia triticina f.sp. tritici- wheat, triticale
Puccinia hordei- barley

Leaf rust (Fig. 4 & 5), also known as brown rust because of the discolouration of infected leaves, occurs commonly in areas where wheat and barley are grown. Orange brown elliptical pustules are found scattered at random on the leaves. The pustules may be surrounded by a yellow halo. Under high disease pressure, pustules appear on the ears of the grain as well.  



Fig. 4. Leaf rust pustules on a susceptible wheat leaf Fig 5. Leaf rust infection on a susceptible wheat plant in the field


Stripe rust

Puccinia striiformis f.sp tritici- wheat, barley
Puccinia striiformis f.sp hordei- barley

Stripe rust (Fig. 6 & 7), also known as yellow rust because of the distinct yellow colour of the pustules, occurs throughout the small grain production areas of South Africa, but is found more frequently in the Free State. Typical stripe rust symptoms consist of yellow to orange coloured pustules that develop in narrow stripes on the leaf sheaths and on the inner surfaces of glumes and lemmas of the heads.




Fig. 6. Yellow rust pustules on a susceptible wheat leaf Fig. 7. Yellow rust infection of susceptible wheat plants in the field


Crown rust

Puccinia coronata f.sp. avenae- oats

Crown rust (Fig. 8.), is a widespread and damaging disease of oats. On susceptible cultivars, bright orange to yellow couloured elongated oval pustules occur mainly on leaves, but can also occur on the sheaths and floral structures. The yield and quality of oats are affected by this disease and the groat mass can be reduced. In addition to planting resistant cultivars and spraying foliar fungicides, the chances of suffering high levels of infection can be circumvented by adjusting planting dates. Earlier seeded oats tend not to suffer as much damage as later seeded oats. The application of fungicides can be highly effective for controlling crown rust, but it is often, especially when oats are grown for animal feed, not economically justified.



Fig. 8. Crown rust pustules on a susceptible oat leaf


Powdery mildew
Erysphe [Blumeria] graminis f.sp tritici- wheat
Erysphe [Blumeria] graminis f.sp hordei- barley
Erysphe [Blumeria] graminis f.sp avenae- oats
Erysphe [Blumeria] graminis f.sp secalis- rye

Powdery mildew is a very common disease of cereals worldwide (Fig. 9.). Symptoms are most often seen on leaves and include fluffy white pustules that become grey as they age. These pustules can be scraped off the surface of the leaf, as the infection on the leaf surface is very superficial. Later in the season, black dots may be found embedded in the white pustules. These dots are the fruiting bodies of the fungus. The fungus survives non-crop seasons as dormant mycelium on host debris or in volunteer crops. Later spores called conidia, which are mainly produced on volunteer plants serve as a source of inoculum. The disease is more prevalent in densely planted fields that are over-fertilized. In the United Kingdom, up to 25% loss in yield has been recorded; however yield losses in South Africa have not been measured. Small grain producers should take note that powdery mildew can cause losses if not controlled. The foliar application of fungicides is a reliable method of controlling the disease and it is widely practiced.



Fig. 9. White fungal growth of the powdery mildew fungus on a susceptible barley leaf


Septoria diseases

Several species of Septoria are pathogens of small grains. In many wheat-growing areas, these diseases are of significant economic importance. Septoria diseases occur more frequently in areas where crops are planted densely and receive great amounts of fertilizer. Different Septoria diseases may occur in combinations within fields and on individual plants. The diseases are difficult to differentiate from each other without careful microscopic examination of the fruiting bodies and spore morphologies. The Septoria complex is believed to destroy two percent of the world’s wheat annually. It reduces seed set, impairs seed filling and shriveled grain is lost with the chaff at harvest time. Greatest losses are incurred when significant disease infections occur before heading. The pathogens are weakly virulent on barley, rye, triticale and other wild grasses, but lesions are small and sporulation of the fungi are restricted. Stagonospora nodorum (previously known as Septoria nodorum) only infects the leaves of rye plants and not the heads.

Septoria leaf blotch

Septoria tritici- wheat, triticale

Septoria leaf blotch and glume blotch
Stagonospora nodorum (ex Septoria nodorum )- wheat, barley, triticale, rye

Septoria leaf blotch is a common disease of especially wheat in areas where wet and windy conditions prevail during the growing season. Two different pathogenic organisms can cause Septoria leaf blotch and the symptoms vary slightly. When the plant is infected by Septoria tritici, leaf lesions first appear as small brown spots, which develop in a longitudinal direction along with the veins of the leaf and later form elongated ovals. These lesions develop grey water soaked areas in the centre in which black pycnidia (Fig. 10.), the fruiting bodies of the fungus, are formed. Lesions may merge gradually as the season progresses and can affect the majority of the leaf area and cause severe necrosis.

Similarly, when the plant is infected with Stagonospora nodorum, oval lesions that coalesce to form larger areas of necrotic tissue form on the leaf. However, the distinctive black pycnidia, or fruiting bodies, that form on the inside of the lesion when it is infected with Septoria tritici cannot be seen and these lesions are often surrounded by a clearly visible yellow chlorotic halo (Fig. 11.). During prolonged wet weather, masses of pink spores are exuded by the pycnidia of Stagonospora nodorum. Septoria leaf blotch lesions first appear on the lower leaves and dependant on favourable environmental conditions, spread to the upper leaves. These pathogens survive the non-crop season on cereal stubble and debris and on volunteer plants.

Septoria leaf blotch can lead to devastating crop losses. As the crop matures the Stagonospora nodorum pathogen becomes more aggressive and nodes and glumes are also infected. The glume blotch infection starts at the tips of the glumes and lemas as grey discolouration across the glume with a brown lower border. The disease develops in a downward direction and the lower brown border is replaced by grey discolouration. Pycnidia, the fruiting bodies of the fungus, can form within these lesions. An important measure for control of the disease is disposal of contaminated crop debris by burning it or ploughing it into the soil. Genetic resistance is an important measure for control of the disease, however many South African cultivars are susceptible to Septoria diseases. Appropriate crop rotation can significantly reduce the disease inoculum. The correct application of foliar fungicides to control of the Septoria diseases can be highly effective as a measure of disease control.



Fig. 10. Septoria leaf blotch symptoms caused by Septoria tritici showing black fruiting bodies visible within the brown necrotic lesions on a susceptible wheat leaf

Fig. 11. Septoria leaf blotch caused by Stagonospora nodorum, showing brown necrotic patches over the surface of a susceptible wheat leaf


Ear and grain diseases

Bunts and smuts

Smuts and bunts infect small grain cereals and several species of grass. These fungi produce masses of black spores that partially or completely replace the heads, spikelets and kernels. In South Africa, these diseases are controlled by the routine application of seed treatments by seed distributing companies. Farmers who retain seed to plant as animal feed must use seed dressings against bunts and smuts. Failure to treat seed, in order to save on input costs, leads to the increased incidence of these diseases.

Loose smut

Ustilago tritici- wheat
Ustilago nuda- barley
Ustilago avenae- oats

Loose smut (Fig. 12) is a common small grain disease that occurs widely in areas where wheat, oats and barley are grown. Symptoms are not apparent until ear emergence. Infected ears emerge earlier, have a darker colour and are slightly longer than those of healthy plants. Infected spikelets are transformed into powdery masses of dark brown teliospores. Within a few days, the spores are blown away and only the rachis remains. When a spore lands on a flower of a small grain plant in the surrounding area, it germinates and infects the reproductive tissues of the grain so that the embryos of developing seeds are also infected. The fungus then survives as dormant hyphae in infected seed. After seed germination, the fungus forms a systemic infection in the plant and later, as the plant approaches heading, the fungus penetrates the head tissues and converts it to a brown powdery mass of teliospores. Yield losses are roughly equal to the percentage of infected ears. In contrast to stinking smut (Tilletia spp.), the quality of the harvested grain is not affected. This disease is effectively managed by the application of seed treatments, although some seed treatments may impede seed germination. The use of high quality, disease free seed is also an effective way of controlling the disease, as the only source of inoculum is infected seed.



Fig. 12. Loose smut infection in a susceptible wheat ear


Covered smut

Ustilago hordei - barley, oats, rye

Covered smut (Fig. 13) is a common disease of mainly oats and barley, but it also infects rye and other wild grasses. Symptoms are not obvious until after ear emergence. Smutted heads emerge later than healthy heads and may become trapped in the flag leaf sheath and fail to emerge. With severe infections plants become dwarfed. Parts of the infected ear or the whole ear are transformed into powdery masses of dark brown teliospores, which are covered by a persistent membrane from where they are released at harvest, when this membrane is disrupted. The covered smut fungus survives in soil and on the surface of seed. The fungus infects the germinating seed through the coleoptile. After seed germination, the fungus forms a systemic infection in the plant and later, as the plant approaches heading, it penetrates the head tissues and converts it to the brown powdery masses of teliospores. The dark powder from the teliospores discolours the grain and it affects grain quality and marketability. Covered smut is of economical importance in areas where seed treatments are not routinely used. Several seed treatments are registered for the control of covered smut in South Africa.



Fig. 13. Covered smut infection in a susceptible barley ear


Karnal Bunt

Tilletia indica- wheat, triticale

Historically, Karnal bunt did not occur in South Africa. It was identified for the first time in December 2000 from the Douglas irrigation area. Currently several measures are in place to limit the spread of this disease throughout the country. These measures include testing of registered seed units and commercial grains for the presence of teliospores (Fig. 14.) and quarantine regulations on the transport and entry of grains to mills and other delivery points. Since Karnal bunt is regarded as a quarantine disease according to South African regulations, all occurrences of this disease should be reported to the National Department of Agriculture (NDA). It is also important to implement phytosanitary measures in quarantine areas to prevent movement of the pathogen out of the infested area. In this respect, all farming equipment and machinery should be washed with pressurized water before leaving a Karnal bunt zone.

Karnal bunt infected kernels appear blackened, eroded and emit a foul ‘fishy’ odour. In infected spikes, the glumes may also appear flared and expose bunted kernels. Spikes of infected plants are generally reduced in length and in number of spikelets. However, only a few florets per spike might be affected and it may be difficult to identify the disease in the field, as the whole ear does not necessarily become infested. Microscopic examination of the seed to detect the presence of the teliospores is a more reliable method of identification. The primary inoculum source is soil or seed contaminated with teliospores. These teliospores germinate and generate another kind of spore, known as basidiospores. One teliospore can produce up to 200 basidiospores that germinate and infect the head tissues of the plant. The infection is localised and not systemic as with loose smut and covered smut. Individual fungal cells within the kernel are converted to teliospores and parts of, or the whole of the diseased kernel is completely displaced by masses of teliospores as the kernel matures. Karnal bunt is of economical importance mainly due to the reduction in flour quality of grain infected with the disease. The flour will have a disagreeable odour and depending on the percentage infection, be darkened by the teliospores. This disease does not lead to yield losses as such. Karnal bunt is difficult to control. A first measure of protecting plants is preventing the entry of the pathogen to a certain area. Therefore, it is of utmost importance to adhere to quarantine regulations and to plant seed that has been certified to be disease free. Some fungicides applied at ear emergence may reduce the incidence of the disease but it is unlikely that they will prevent infection.



Fig. 14. A micrograph of the teliospores of Tilletia indica


Stem base and root diseases


Gaeumannomyces graminis var. graminis- wheat, barley, rye, triticale
Gaeymannomyces graminis var. tritici- wheat, barley, rye
Gaeumannomyces graminis var. avenae- oats

Take-all (Fig. 15) occurs widely throughout the small grain producing areas in South Africa. This disease affects the roots, crown and basal stem of small grains, wheat in particular and wild grasses. It is an important disease in areas where wheat is cultured intensively, the soil pH is neutral or alkaline, moisture is abundant and soils are deficient in manganese and/or nitrogen. Mildly infected plants appear to have no symptoms of the disease, while more severely infected plants ripen prematurely and are stunted. Take-all symptoms are more apparent during heading, as infected plants are uneven in height, die prematurely and whole plants discolour to the colour of ripe plants. A typical take-all infestation is characterised by the appearance of patches of white heads amongst areas with healthy green plants before ripening (Fig. 16). The heads that ripen prematurely tend to be sterile or to contain shriveled grain. Diseased plants pull up easily. Roots appear blackened and brittle and crowns may take on a black colour, which is indicative of the disease. The pathogen persists in infected host residues from where the ascospores can act as sources of inoculum. Roots growing near infected residues become infected and early infections may progress to the crown. The disease is favoured by poorly drained soils, high seedling densities and high organic matter content in the soil. As the pathogen is favoured by wet conditions, the disease is more prominent in wet years or in irrigated fields. If conditions become dry, the pathogen becomes less active. The best way to control take-all is by crop rotation. A one-year break from barley or wheat using oats can be sufficient to control the disease. Volunteer plants, grassy weeds and crop residues, that may harbour the pathogen, should be destroyed. Take-all can also be controlled to a certain extent by ensuring that the wheat plants have sufficient nutrients to promote healthy root growth.



Fig. 15. The blackened crowns of a susceptible wheat plant with take-all infection




Fig. 16. White ears of take-all infected wheat plants among healthy green plants in the field


Eyespot, Strawbreaker

Helgardia herpotrichoides- wheat, barley, oats, triticale
Helgardia acuformis- wheat, barley, rye

Eyespot (Fig. 17) is a disease that affects the base of the small grain plant. Wheat is more susceptible than other small grains and wheat grown in the winter rainfall areas of the Western Cape are more often affected than the wheat cultivated in other areas. The disease is more prevalent in early sown, over fertilized crops and in areas with moisture retentive soils. After infection, the symptoms may not be visible for up to a few months. Early symptoms on young plants are indistinct honey brown lesions on the base of the stem. The characteristic eye-or lens-shaped eye spot lesion only appears on mature wheat. This light brown lesion generally appears below the first node. Grey mycelium of the fungus can also be found inside the stem cavity. The disease does not kill plants as such, but weakens the individual tillers so that the tillers lodge and complicates harvesting of the fallen heads. Lodging of the plants is a result of a breakage in the stem at the point of the lesion. Kernel size and number is also reduced. Severe eyespot may lead to premature ripening of the ears. Eyespot inoculum (asexual spores), arises from cereal stubble and debris and is dispersed by the splashing of raindrops. The spores infect coleoptiles and leaf sheaths and secondary conidiospores form within four to 12 weeks. The secondary conidiospores do not contribute to the epidemic, but rather serves as a source of inoculum for the following season’s crop. Control of eyespot includes the ploughing or burning of small grain cereal crop residues. Crop rotation, away from a host for 2 years will lead in a decline of the inoculum present on residues. Eyespot can successfully be controlled by the application of fungicides. In South Africa, resistant cultivars are not commercially available.



Fig. 17. Typical eye shaped lesions of the eyespot disease of wheat on the crowns of a susceptible wheat plant

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