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Sclerotinia stem and root rot of soybeans16 July 2013

Nico Barnard, Research Agronomist

Fig 1. The stems of affected plants are covered in a dense white fungal growth with black sclerotia development on the inside and outside of the stem

Soybeans are our most important rotation crop and the second largest grain crop in South Africa. Besides drought, Sclerotinia is the biggest limiting factor of successful soybean production.

In practice, farmers adapt their soybean production systems to maximise yield. Growing soybeans for high yield potential favours the development of Sclerotinia. Prolonged, wet, humid and cool weather conditions (18 to 24°C) just before or during flowering are conducive for infection. Just a few sclerotia on the soil surface can have devastating consequences if favourable conditions occur during flowering. The disease is very common in areas or lands where moisture collects due to persistent mist, dew or irrigation. Temperatures higher than 32°C suppress the disease.


Infected soybean plants suddenly begin to wilt and the leaves and stem turn a pale light brown. Dead plants are clearly visible between healthy plants as the leaves don’t fall off immediately (Fig 4). The dead plant is usually visible two to three weeks after the first flowers appeared. The stems of infected plants are covered in a dense white fungal growth which later develops into the hard black survival structures (sclerotia) that may develop on the inside and outside of the stems and pods (Fig. 1). The black sclerotia are reminiscent of rat droppings. The severity of damage is determined by the number of plants that are infected and the timing thereof. Plants that are infected late in the growing season can still contribute towards overall yield.

The disease cycle

The visible black sclerotia serve as the survival structures. During the harvesting process the sclerotia are spread across the soil surface. If the sclerotia are worked into the soil the survival capacity of the sclerotia is extended up to seven years. Sclerotia on top of the soil or up to 5 cm below the soil surface can germinate under favourable conditions. They can form mycelia that infect the plant directly or a mushroom-like flesh-coloured structure called an apothecium (Fig. 3). The apothecia produce large amounts of spores that are spread by wind or splattering raindrops. These spores germinate in a wet environment in the presence of a good food source. Dead soybean flowers are the ideal source of nutrition for the germinating Sclerotinia spores and the majority of infections occur in the leaf axil, where the spikelets are attached (Fig. 2). The growing fungus breaks down the dead tissue of the flower and releases oxalic acid and enzymes that kill the living plant tissue. Sclerotinia has several alternative broadleaf hosts including many weeds.

Sclerotinia management practices

No single practice can control the disease. However, when the first symptoms are observed, it is often too late and very little can be done to prevent the disease. Controlling or minimising the impact of the disease can be obtained with a combination of practices. 

  1. Prevent the establishment of the disease on the field. Sclerotia are present in soybean stover and can be transferred from one land to another by combine harvesters. Harvest infected lands last and thoroughly clean the combine afterwards. If contractors are used, the combine must be thoroughly cleaned before harvesting commences. Plant high quality seed that has been properly processed to prevent sclerotia establishment. According to research by the University of Illinois and Iowa in the USA, Sclerotinia can survive on the soybean seed coat even if it is not visible to the naked eye; avoid any seed produced on lands infected by Sclerotinia.

  2. Extending crop rotation intervals can reduce the virulence of the disease. Maize (and other grass-like species) are not Sclerotinia hosts and are good rotation crops. Lands that appear to be severely infected should be planted to maize for more than two years. If at all possible, planting winter grain such as wheat or oats will create a favourable microclimate where many of the spores can be released in the absence of a host upon which the fungus can survive. Crop rotation with any other broadleaf crop should be avoided.

  3. Effective weed control is necessary. It is particularly important during the production of a rotational crop so that the disease does not survive on weeds.

  4. Row widths and plant population have an effect on the incidence of Sclerotinia. Wider rows and lower plant populations can create a drier microclimate that may theoretically reduce the incidence of the disease. Please bear in mind that wide rows and lower plant populations are detrimental to the yield potential. If the general climatic conditions are favourable for the outbreak of the disease, wide rows may also be severely infected. Rows wider than 0.91 m may also serve as pathways within which the wind can spread spores over vast distances.

  5. There are fungicides available that can control Sclerotinia to a certain extent. There are two major limitations in the use of fungicides. Firstly, the coverage obtained with standard spray equipment is not adequate because the location of infestation is beneath the canopy, namely the flower. Secondly, the flowers that develop after treatment are not protected at all.

  6. Tillage may affect Sclerotinia in various ways. Sclerotia can survive in the soil for up to seven years, only the sclerotia in the top 5 cm can germinate and release spores. By ploughing the spores deep into the soil the germination of the sclerotia can be reduced, but subsequent tillage may bring it to the top again. In a crop rotation system, deep tillage before planting maize, followed by shallow tillage before the subsequent soybean planting can reduce the incidence of Sclerotinia.

  7. In a long-term no-till system where soybeans are rotated with maize, the number of viable sclerotia in the soil is reduced because less mixing of the soil occurs.

  8. Nitrogen fertilisation increases and accelerates the formation of the leaf canopy that creates a favourable microclimate for the spread of Sclerotinia. The same occurs when beef, pork or chicken manure is used as fertiliser. 

The impact of the disease will only be reduced by a holistic management approach. All role-players in agriculture must pool resources to find solutions to the problem. Through our PANAGRI programme PANNAR is committed to finding practical on-farm solutions to this dilemma. 

Fig 2. Infected spikelet, Fig 3. The mushroom-like apothecia

Fig 4. Soybean land that is severely infected

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