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.

Euphresco PHYLIB I

Below are links to presentations from the Euphresco PHYLIB I meeting, held in Tenerife, 20-21 February 2013.

View presentations from the Euphresco PHYLIB I end of project meeting, 1-2 October 2014

Euphresco PHYLIB I End of Project Meeting

1-2 October 2014 at SASA, Edinburgh, UK

Download the Euphresco PHYLIB I End of Project Meeting report.


Delegates at the Phylib End of Project Meeting, held at SASA, Edinburgh, October 2014



  1. EU PHYLIB project. Welcome to Scotland. John Speirs, Scottish Government (policy), UK.
  2. An introduction to SASA.  Kevin O'Donnell, Scottish Government (SASA), UK.
  3. Occurrence of 'Ca. Liberibacter solanacearum' in Finland; what do we know so far. Anne Nissinen MTT, Agrifood Research, Finland.
  4. Genome sequencing of 'Ca. Liberibacter solanacearum infecting carrots in Finland'. Minna Pirrhonen, University of Helsinki.
  5. Transmission tests of 'Ca Liberibacter solanacearum' by carrot seeds. Marianne Loiseau, ANSES, Lab. de la Santé des Vegetaux, Angers, France.
  6. Current situation of 'Ca. Liberibacter solanacearum' in Spain. Mariano Cambra, IVIA, Valencia, Spain.
  7. Ca. Liberibacter solanacearum': a carrot seedborne bacterium. Gabi Teresani, IVIA, Valencia, Spain.
  8. Experimental transmission of  'Ca. Liberibacter solanacearum' by Bactericera trigonica. Estrella Hernández, ICIA, Tenerife, Spain.
  9. Overview. Activities of NVWA-NRC, NL Molecular test methods for 'Ca. Liberibacter solanacearum'. Tjou-Tam Sin (Leon), NPPO, The Netherlands. 
  10. Liberibacter research in Belgium, an update. Kris De Jonghe, Institute for Agricultural and Fisheries Research, Plant Science Unit-ILVO, Belgium.
  11. Psyllid survey in GB carrot and potato crops and EPG feeding behaviour  study. Larisa Collins, Fera, UK.
  12. The survey for 'Ca. Liberibacter solanacearum' and psyllids in Scotland. Fiona Highet, Scottish Government (SASA), UK. 
  13. 'Ca. Liberibacter solanacearum detection in potato microplants. Wendy Monger, Scottish Government (SASA), UK. 
  14. Research progress on potato zebra chip disease in Canada. (Sean) Xiang Li, CFIA, Canada. Presented by Colin Jeffries.
  15. Phytoplasma Survey Results of ZMMAE. Anyur Karahan, Plant Protection Central Research Institute, Turkey.
  16. Microarrays for discrimination of phytoplasmas. Proof of principle. Catherine Harrison, Fera, UK.
  17. Reliability of testing potato microplants for infection with phytoplasmas. Monika Krol, Scottish Government (SASA), UK. 
  18. Proficiency test results, for the testing of potato infecting phytoplasmas. Carolyn Nisbet, Scottish Government (SASA), UK. 
  19. Potato Phytoplasma research in Belgium, an update. Kris De Jonghe, Institute for Agricultural and Fisheries Research, Plant Science Unit-ILVO, Belgium
  20. Contribution to the PHYLIB project. Activities in Hungary in 2012-2013-2014. Maria Kolber. Presented by Colin Jeffries
  21. ‘Ca Phytoplasma asteris’. First find in commercial carrot crop in the UK. Carolyn Nisbet, Scottish Government (SASA), UK
  22. EUPHRESCO. Where to next. David Kenyon and Mariano Cambra, respectively Scottish Government (SASA), UK and IVIA, Valencia, Spain.

View presentations from the Euphresco PHYLIB I meeting, held in Tenerife, 20-21 February 2013

See also Euphresco PHYLIB II page.

Euphresco PHYLIB II

The biology and epidemiology of ‘Candidatus Liberibacter solanacearum and potato phytoplasmas and their contribution to risk management in potato and other crops

Project start date: March 2016

Project duration: 3 years

Project coordinators: Jennifer Sjölund and Colin Jeffries

PHYLIB II is a Euphresco Project involving 17 research partners from 14 different countries. It is coordinated under the Euphresco Network which supports phytosanitary policy and operations, as well as improving European phytosanitary science capability. PHYLIB II is a follow on project from PHYLIB: Epidemiology and diagnosis of potato Phytoplasmas and ‘Candidatus Liberibacter solanacearum’ and their contribution to risk management  (2012-2014); See also the PHYLIB I End of Project Meeting page.


Presentations from the first PhyLibII meeting, held at the University of Bologna, Italy, 27-28 April 2017

A. Bertaccini. Welcome Address. University of Bologna (UniBo), Italy

M.J. Sjolund, C. Jeffries, M. Carnegie, A.F.C. Greenslade, D. Ouvrard, F. Highet, D.M. Kenyon, J.R. Bell. EUPHRESCO & PhyLibII and the detection of vectors in Scotland. Science and Advice for Scottish Agriculture (SASA), UK

K. De Jonghe. Investigation of the presence of phytoplasmas and ‘Candidatus Liberibacter solanacearum’ in potato and carrot in Belgium and tracking their (potential) vectors. Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Belgium

N. Tjou-Tam-Sin, M. Bergsma-Vlami, J. van de Bilt, P. Gorkink, M. Westenberg, B. van de Vossenberg. The Netherlands’ CLso* survey up to 2016 and Next Generation Sequencing (NGS) in carrot survey. Netherlands Food and Consumer Product Safety Authority (NVWA), Netherlands

R.A. Gottsberger & C. Lethmayer. Austrian activities on the ‘Candidatus Liberibacter solanacearum’ outbreak: host plant and vector monitoring around Innsbruck (Tyrol). Austrian Agency for Health and Food Safety (AGES), Austria

M. Pirhonen. Present situation with `Ca. Liberibacter solanacearum´ in Finland. University of Helsinki, (UHE) Finland

E. Satta, S. Paltrinieri, A. Bertaccini. Methods to distinguish phytoplasmas and haplotypes of ‘Candidatus Liberibacter solanacearum’. University of Bologna (UniBo), Italy

M. Loiseau, A.-C. Le Roux, I. Renaudin. The project to study the epidemiology of ‘Candidatus Liberibacter solanacearum’ in susceptible crops in France. French Agency for Food, Environmental and Occupational Health & Safety (ANSES) & Fédération Nationale des Producteurs de Plants de Pommes de Terre (FN3PT), France

E. Back, A. Philip, M.J. Sjölund, C. Jeffries, D.M. Kenyon. Transmission of CaLsol from seed to seedlings. Science and Advice for Scottish Agriculture (SASA), UK

V. Ilardi, V. Lumia, E. Di Nicola, M. Tavazza. ‘Candidatus Liberibacter solanacearum’ in Carrot, Parsley and Celery seeds sold in Italy. Plant Pathology Research Centre in Rome (CREA), Italy

Y. Shneyder. Methods of diagnostic of ‘Ca. Liberibacter solanacearum’ used in Russia and future plans. All-Russian Plant Quarantine Center (VNIIKR), Russia

T. Dreo. dPCR as a tool for quantification of target sequences for diagnostic and research purposes. National Institute of Biology (NIB), Slovenia



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.


POnTE Pest Organisms Threatening Europe

POnTE websiteSASA is pleased to announce that it is a partner in a 4 year EU  Horizon 2020 project (POnTE) to investigate 4 major plant pests threatening Europe 

Horizon 2020 is the EUs Framework Programme for Research and Innovation and  POnTE’s 25 partners  will receive € 6.8 million over 4 years to develop early detection and surveillance tools, and produce new knowledge with practical solutions on how to control these pests: Xylella fastidiosa in olive, grapevine, citrus, stone fruit, ornamentals and landscape trees of high socio-economic importance; ‘Candidatus Liberibacter solanacearum’ in crops such as potato, tomato and carrot and Hymenoscyphus fraxineus (anomorph. Chalara fraxinea) and Phytophtora spp affecting broadleaf and conifer species in forest ecosystems.  For more information visit the POnTE website.

SASA’s main roles are to: develop molecular assays for the detection and identification of psyllid species in Europe (and elsewhere) that are potential vectors of ’Ca Liberibacter solanacearum’; and to evaluate suction traps as a tool for monitoring vector migration. 

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:

Validation of Next Generation Sequencing

          British Council-Peru


SASA is pleased to announce that they have been awarded:  a Science and Innovation Programme grant from the British Council-Peru  to “Validate next generation sequencing: a revolutionary method for testing nuclear potato stocks for virus freedom and safeguarding plant health in the international exchange of potato germplasm”

The Initial Institutional Collaborations programme  (Part of the Science and Innovation Programme) encourages the development of joint research projects between Peruvian and British institutions. For this 4 month project a multi-discipline consortium of SASA, the International potato Centre (CIP), The Agricultural University (UNALM) and the Peruvian Plant Heath Service (SENASA) has been formed,  bringing together regulatory plant virologists, researchers and potato specialists to validate and progress the use of next generation sequencing (NGS) into routine use for detecting potato viruses. NGS has the potential to detect all viruses (known, and as yet undiscovered) in a single assay, thus improving the detection of pests in potato nuclear stocks and germplasm exchanged internationally both pre-export and in post-entry quarantine. The collaboration will also strengthen information exchange to answer emerging questions linked to plant-virus and vector-virus trophic relationships, virus epidemiology and to the biological significance of newly identified viruses.  View the press release