By David Jones, Broad Acre Agronomist

This week I’m looking at soil borne cereal diseases, some of which affect more than just cereals. I have seen four of the diseases already in Kenya, in cereal crops in Timau, Nakuru and Naivasha.

Take All

  • This is a soil borne fungus that affects continuous cereals. The tell-tale sign is blackened roots, that even when washed off and sliced with a scalpel blade are black to the centre. Affected tillers have white, unfilled heads too. A 12-month break is usually required to eliminate the pathogen.
  • Where cereals are grown continuously the affect is lessened – after three or four cereal crops the yield penalty is far lower as antagonistic fungi build up in the soil and reduce the fungus in the soil.
  • Yield losses are greatest when planting into wet soil that dries out as the crop matures; this is because the initial infection is very rapid causing maximum root damage, resulting in the crop suffering from moisture stress later in the season during grain fill.
  • Loose, puffy seedbeds can worsen the effects. Areas of lighter soil are worst affected as is why the disease often occurs in large patches, rather than uniformly across a field.
  • Following a broadleaved crop that had poor grassweed control – it is important to control all volunteer cereals to prevent disease carryover.
  • Specific Take-all seed dressings are the most effective treatment and provide a very good response in most countries.
  • Get your nutrition in early before the roots give up.


Patch affected by Rhizoctonia

  • Very patchy in nature, usually visible as circles up to a few metres in diameter in the crop from an early stage.
  • The fungus grows out of residue particularly in wet conditions, through a mass of fungal hyphae in the soil (hence the circular patches of infected crops).
  • Importantly rotations do NOT help control Rhizoctonia due to the wide range of hosts
  • Rhizoctonia is susceptible to soil movement so cultivations can help. In no-till situations, extended points on the planter to disturb the soil below the seed can help significantly.
  • Always worse when soil fertility is low (particular P and Zn).
  • Seed dressings are available in other countries, but not yet in Kenya. There is evidence the Sulfonylurea herbicide can exacerbate Rhizoctonia, so avoid these herbicides in badly affected shambas.

  • Most active between 10-15 C. In the warmer conditions that we have, root damage is most likely to be visible on the Crown roots, as the Seminal roots grow quickly enough to get through the initial infection.
  • There is evidence that increasing organic matter and biological activity in the fallow can reduce the disease by supporting populations of fungi that are antagonistic to the Rhizoctonia. The GRDC in Australia have also found that high levels of nitrogen can ‘switch off’ this suppressive activity. Both these points have implications – both good and bad – for cover cropping.

Cereal Cyst Nematode

  • Patchy stunting and yellowing of the crop across the shamba
  • Twisted roots with excessive knotting and characteristic cysts 1-2mm diameter at flowering
  • Nematodes hatch in moist and cool soils (below 15C) so it is very unlikely to be encountered in all but the highest areas of Kenya.
  • Survives in soil for only 2 years so very unlikely to be seen where a proper rotation is in place and where cereal volunteers are well controlled in the fallow to prevent cyst carryover.

Crown Rot 

  • Whiteheads in crop at early grainfill, and knock 10-20% off yield.
  • Tends to be worse in low rainfall years though not always. Continuous cereals, especially with stubble/residue retention is worst.
  • Browning of the stem base, which when peeled back sometimes reveals the pink fungus
  • Barley is susceptible than wheat, but be aware that it actually increases the disease inoculum for the following crop.
  • Needs a two year break from cereals to get maximum benefit. Oats are almost a break crop as they have a very low carryover. Canola and peas are better breaks because it will allow you to get rid of any grass host-species such as Setaria or Eleusine.
  • Above ground the symptoms looks similar to Take-all, but Crown Rot results in golden-brown roots rather than black.

Root Lesion Nematode

  • These can affect quite a few crops, so it is really important to check with a lab what species you have when they are identified in the field. Some species will not colonise peas for example, while other cannot survive in Faba beans. This is invaluable when you are planning the rotation, which at present is the only way of preventing the problem in field crops.
  • Lupins and cover crops of Fenugreek are very resistant to most nematode species, so try and plan a two year break.
  • Unlike Cereal Cyst Nematode there is no root knotting or Cysts visible – just a lack of small lateral roots as the photo shows from CropPro.
  • Resistant varieties are commonly used in other countries, but not in Kenya yet.
  • Nematodes don’t spread very far without human assistance! Cleaning machinery after infected fields goes a long way to containing the problem

Fusarium Foot Rots (Seedling Blight)

  • Brown staining of the stem bases and white heads at ear emergence.
  • This affects all cereals and is usually caused by Fusarium.
  • Successive cereals are most at risk, particularly in cool, wet seedbeds where there is plenty of disease in the soil, but NOT always – various fungi cause similar symptoms in warm conditions.
  • Untreated seed increases the risk – don’t be tempted to cut corners.
  • Causes seedling death in small plants, and restricted growth in larger plants such as the one in the photo found at Timau.


Pulse diseases

As a general rule, leave at least 4 years between pulse crops, and ideally 6 or 7 years for peas. This can be shortened to two years at a push if you are growing Soyabeans and are not seeing Sudden Death Syndrome or Soyabean Cyst Nematode.

But what if you have several pulses in the rotation, or are looking to introduce nitrogen fixing cover crops or clover/Lucerne for forage? Many diseases of pulses are common to all widely grown legumes, however some are specific to one or a small number species.

For example, growing Vetch won’t make your Ascochyta any worse in Faba beans. Or if you are suffering from Aphanomyces Foot Rot in peas every four years, try alternating Beans or Chickpeas so that there is an 8 year gap in the rotation between pea crops.

Rhizoctonia on the other hand affects Peas and Lupins badly, so if it’s in your wheat and pea crops, think hard before introducing lupins to the rotation even to replace peas.

S = susceptible MS = moderately susceptible MR = moderately resistant R = resistant


My final thought for the week ahead is ‘Relay Cropping’. I have a couple of friends in France experimenting with this technique on their farms and I’m puzzled and intrigued at the same time. A very different and complex approach to getting more than one crop out of one season, but the point is that this is highly thought provoking; if you are going through the crop weeding, planting on wide rows anyway, or finding yourself with a full bank of moisture and looking to make use of it…

Both crops will yield less than they would planted conventionally, at the normal times of year. But in aggregate the combined yield of the two crops is far greater than one crop.

Till next time!


About David


David Jones is the Broad Acre Specialist at Crop Nutrition Laboratory Services Ltd. (CROPNUTS). David has a keen interest in soils and no till farming systems where he has undertaken work looking into weed levels and changes in soil structure, and has extensive experience in field trials and in the development of precision farming techniques. In his spare time he enjoys playing rugby.