Pest & Pathogen Diagnostics

Accurate and timely identification of plant diseases is important for many aspects of agriculture from correct diagnosis of field symptoms to their study as part of research programmes. Molecular methods are being increasingly utilised in the detection and study of plant pathogens, with the advent of real-time PCR further enhancing this area allowing faster, more sensitive and quantitative detection. With these advances has come an increase in the adoption of such technology in support of crop management decisions. 

Recent/current research projects include:

Additional information on a number of other pests and pathogens can be found using the links below.


Diagnosis of six Armillaria species

Armillaria (also known as the honey fungus) is a common pathogen/saprophytic fungi found in broad-leaved woodland and mature gardens. Six species (A. borealis, A. Cepistipes, A. gallica, A. mellea, A. ostoyae and A. tabescens) commonly occur in the UK but of these only two (A. mellea and A. ostoyae) are considered to be pathogens that can infect and kill healthy trees. Identification of the separate species using traditional techniques is very difficult and even the use of modern DNA based methodologies has not lead to the development of a rapid, cost effective assay. This leads to trees often being removed as a precautionary measure on the assumption that the two pathogen species that is present.

SASA in association with Forest Research have developed a PCR array assay which for the first time provides a rapid and reliably test which can separate all six species found in the UK.


Soil-borne viruses of potato - Potato mop-top virus (PMTV) and Tobacco rattle virus (TRV)

Both Potato mop-top virus (PMTV) and Tobacco rattle virus (TRV) cause spraing symptoms (necrotic arcs or lines) in the flesh of infected tubers. Such symptoms severely affect the marketability of tubers for the export, processing and packing markets. TRV-induced spraing is indistinguishable from PMTV-induced spraing, highlighting the importance of diagnostic testing in determining the cause of infection.

Both viruses are soil-borne and have different modes of transmission: PMTV is spread by the powdery scab pathogen Spongospora subterranea; TRV is transmitted by free-living nematodes (Paratrichodorus and Trichodorus spp).

Left to Right: Spraing symptoms in the flesh of a tubers, symptoms of PMTV infection on the leaves of a potato plant; vectors of PMTV and TRV: zoospore of Spongospora subterranea (© and Trichodorus spp. (©Broom’s Barn Research Centre) respectively.

Left to Right: Spraing symptoms in the flesh of a tubers, symptoms of PMTV infection on the leaves of a potato plant; vectors of PMTV and TRV: zoospore of Spongospora subterranea (© and Trichodorus spp. (©Broom’s Barn Research Centre) respectively.


Studies at SASA are focussing on maintaining the high health of seed potatoes grown for export. Soil-borne inoculum of PMTV has been shown to be more important then seed-borne inoculum in causing economic outbreaks of disease (view poster). A soil bioassay has been developed to monitor seed growing areas of Scotland. This could prove to be an effective tool in the formulation of advice to growers on both site and cultivar selection.


  • Diagnostics for PMTV and TRV in growing crops and tubers;
  • Studies on the relative importance of PMTV and TRV infection in spraing development in seed potatoes.


Potato Cyst Nematode

Potato Cyst Nematodes: New Legislation, New Technology

New Legislation

Potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis are serious pests of potato world wide, causing an estimated 12% crop yield loss. On 1 July 2010 a new EU PCN Directive came into force and increased sampling rates required by this new legislation mean that the number of soil samples SASA has to evaluate has risen from 6,000 to 18,000 per annum. SASA will not be able to fulfil its obligation using traditional methods of manually operated cyst extraction and visual examination of float material isolated from soil samples.

New Technology

  • An automated cyst extraction carousel is used to produce float material from soil samples.
  • An automated DNA extraction method is used to extract total DNA from these floats.
  • A new multiplex real-time PCR assay is used to detect PCN DNA from single cysts in a float. PCR set-up is carried out using a liquid handling robot. 
  • Using these new methods SASA can identify any PCN species present in up to 400 samples per day.

These new developments enable SASA to process up to 25,000 soil samples over a 6 month period, meeting our statutory obligations and maintaining the high health of Scottish seed potatoes.


Development and use of serological (ELISA-based) and molecular (Real-time PCR based) assays for the simultaneous detection of different virus species.

See the following pages for more information: