SASA is strategically placed to conduct applied R&D on Scottish crops and the pest and pathogens which affect them. Research is conducted either in-house or, more usually in collaboration with colleagues at James Hutton Institute, Dundee, Fera, York or other institutes across the UK, Europe and beyond. Most of its research activities are dependent on the use of molecular biology techniques, such as nucleic acid sequencing, fingerprinting and real-time PCR; exploiting the technology available in its state-of-the-art laboratories.

A major area for work is the use of molecular genotyping for the recognition of potato and barley varieties. SASA has also been developing and introducing into its routine work novel diagnostics for a whole range of pests and pathogens. More recently it has developed expertise in pathogen population dynamics, using a range of sequencing- and fingerprinting-based technologies.

Epidemiology & Population Dynamics

An important factor in the understanding of a disease’s development and its potential threat to plant health is the inherent diversity of the pathogen concerned. Such knowledge may allow the origin of an outbreak to be established, or better diagnostic tools to be developed. Study of changes in the pathogen population over time may highlight the potential for new, more aggressive strains to become established or that control measures such as plant resistance are likely to breakdown.


Control of soil-borne potato diseases using Brassica spp. Mediated Biofumigation

With increasing amounts of pressure put on to growers to cut their use of potential environmental hazardous pesticides and fumigants, a considerable amount of interest is being shown within alternative methods of pathogen and pest control.  One such method has been termed Biofumigation.  It is a method that exploits toxic compounds that are already naturally released via glucosinolate hydrolysis which occurs during the breakdown of Brassica plant tissues. 

Although it is known that the compounds are released during mastication of the Brassica cells, many gaps still exist in our understanding of these, and whether such effects are transferable to a field scale.  This study will uncover a greater in-depth knowledge of biofumigation, which will aid understanding of the complex processes involved and it’s potential to be used as part of an integrated disease management programme. 

TOP: Potato tuber with external symptoms of black scurf.  BOTTOM: Black dot microsclerotia on potato tubers This project will concentrate upon using biofumigation to suppress soil-borne pathogens that infect potatoes, of which there are a significant number of, such as – black dot (Colletotrichum coccodes), silver scurf (Helminthosporium solani), common scab (Steptomyces scabies), stem canker and black scurf (Rhizoctonia solani) and skin spot (Polyscytalum pustulans).  Such diseases are known to cause reduced development of the plant, lower tuber quality and produce unsightly blemishes, which all in turn lead to reduced marketable yield. 

The project will investigate many aspects of the pathogen: biofumigation interaction, initially determining, through the use of in vitro assays, if a proposed system will work within it’s most controllable form.  This data will provide a basic understanding of the processes involved and interpretation of effects observed under a controlled soil environment.  Ultimately to provide scientific robust evidence on the potential role of biofumigation in an integrated control programme.


Phytophthora ramorum and Phytophthora kernoviae are two pathogens which in Scotland so far affect mainly hardy ornamental plants like Rhododendron, Viburnum or Magnolia in nurseries and gardens.

Both pathogens have also the potential to cause serious damage to our natural wood- and heathland and are therefore subject of official control and eradication measures. SASA is collaborator in a multidisciplinary research project funded by the Scottish Government combining field studies of selected outbreak sites, modelling of expected disease progress and molecular characterisation of pathogen strains. The aim is to increase our knowledge about disease establishment, spread, risks and impact under Scottish climate and conditions to support official disease management.

Left to right: Simultaneous infection of Rhododendron with Phytophthora ramorum and Phytophthora kernoviae; Oospore of Phytophthora kernoviae; Soil sampling at Phytophthora kernoviae outbreak site.


Virus Biodiversity and Epidemiology

Molecular diversity and Epidemiology of Potato virus Y (PVY)

PhD studentship (SASA-University of Nottingham-Potato Council Ltd) 
The Scottish seed potato industry accounts for 75% of all UK production and is worth an estimated £80 million. Potato virus Y is widely distributed in the potato growing areas worldwide. PVY is transmitted non-persistently by non-colonizing aphid vectors, resulting in rapid acquisition and transmission of the virus. There are three commonly described PVY strains: ordinary or common strain (PVYO), stipple streak strain (PVYC) and the veinal necrosis strain (PVYN). Surveys of PVY populations worldwide have identified a drift in the PVY population towards recombinant PVYN strains, where so-called PVYNTN(N-Tuber Necrosis) recombinant strains are causing tuber ringspot necrosis. The emergence and spread of PVYNTN strains has led to large economic losses and highlighted the need for accurate discrimination between PVY variants and better understanding of their pathogenicity and epidemiology.

The purpose of our Potato Council funded PhD project is to understand the mechanisms that drive PVY molecular diversity and epidemiology. See also the poster, Biodiversity and Epidemiology of Potato Virus Y. The key aims are:

  • Characterisation of the population structure of PVY field isolates
  • Biological and molecular characterization of major PVY isolates: mapping  genetic determinants responsible of vein necrosis and tuber ringspot necrosis
  • To gain a better understanding of PVY epidemiology
  • To further improve molecular diagnostic methods of viruses
  • Advice on the potential risk effect of PVY (and other viruses) on seed potato production

Left to right: Aphid vector of PVY, vein necrosis and tuber ringspot necrosis on potato caused by variants of PVY strain NTN. Electron micrograph of PVY virions (VIDE Plant Virus database, University of Idaho, USA)

Left to right: Aphid vector of PVY, vein necrosis and tuber ringspot necrosis on potato caused by variants of PVY strain NTN. Electron micrograph of PVY virions (VIDE Plant Virus database, University of Idaho, USA).

Aphids and virus transmission in seed potato crop

Potato Council Ltd, Project R428, Consortium SCRI-SASA-SA-SAC-FERA

The aim of this project is to improve control strategies by understanding interactions between virus source, virus trains, aphid species and aphicide effects.

Virus Characterisation

SASA uses molecular biology techniques in its research on viruses – this research includes topics such as identification, detection and variability of viral species. Such research is usually conducted in collaboration with other scientists with specialisms such as virology and antibody production. We participate in molecular characterisation studies of Scottish potato viruses isolated during crop surveillance (e.g. Browning et al., 2004). Mortensen et al. (2010) characterised potato viruses (PVA, PVS, PVV and PVX) found in potatoes originating from Shetland and compared them to viruses from Scottish mainland crops. These studies inform the assay design process which is vital in the production of robust molecular methods such as PCR. 

We collaborate on the molecular characterisation of potato Carlaviruses of quarantine interest, such as Potato Latent Virus (Brattey et al., 2002), Potato Rough Dwarf Virus and Potato Virus P (Nisbet et al., 2006). Related to this is work on identification of viroid isolates from various plants (James et al., 2007). Viroids are unusual plant pathogens, consisting of a naked circle of RNA; they are a great concern in the commercial production of many plant species.

See details of SASA publications on Virus Characterisation mentioned on this page.


Relationship between Carlavirus coat proteins (from Nisbet et al., 2006)

Relationship between Carlavirus coat proteins (from Nisbet et al., 2006)

Molecular Genotyping

Traditionally the identification of cultivars has been based on the visual assessment of a number of specific traits such as leaf shape and size, growth habit and flower colour. The advent of molecular techniques provides an opportunity to generate specific genome marker systems for the identification and study of cultivars. Whilst current work has mainly been centred around the use of random genomic markers such as microsatellites (SSR) the development of single nucleotide polymorphisms (SNP’s) which can be associated with specific genes, provides an opportunity to predict specific characteristics of a cultivar on the basis of a laboratory assay.

Barley Genotyping

Single nucleotide polymorphisms (SNPs) are the smallest unit of genetic variation and are abundant in animal and plant genomes. They are an excellent choice for studies on plant genetics and breeding. Many SNPs have been discovered in the barley genome and it is hoped that shortly SNPs will be identified that are directly linked to key traits measured during the DUS testing of varieties. At SASA we are using the relatively new method of temperature switch PCR (TSP) to differentiate barley varieties on the basis of their SNPs. If successful this method can be used by other laboratories that do not have access to hi-tech equipment such as DNA sequencers or real-time PCR machines as the TSP products can be separated by simple agarose gel electrophoresis. Preliminary results are encouraging and all of the varieties tested can be differentiated using 25 markers.

Dendogram constructed from the TSP SNP profiles for 12 barley varieties Dendogram constructed from the TSP SNP profiles for 12 barley varieties


Bere Barley Genotyping

Bere barley (Hordeum vulgare) is a traditional Scottish barley landrace that is still grown using a traditional system by growers mainly in the islands. It is probably the oldest cereal ‘variety’ grown commercially in Europe and possibly the world. Bere barley has adapted to enable it to grow in the poorer acidic soils found on in Northern Scotland and there is renewed interest in its use in breeding programs.

Bere barley samples from the Scottish islands were collected and analysed using 29 microsatellite markers.

Scottish islands where Bere barley samples were collected

Scottish islands where Bere barley samples were collected

Tree showing molecular relationships amongst Bere barley samples from the islands

Tree showing molecular relationships amongst Bere barley samples from the islands


Significant genetic variance was observed between the 3 island groups, possibly explainable by their geographical isolation.

No accounts of seed exchange between island groups, only within island groups which would support the suggestion of isolated populations.

The oral and genetic data suggests that the bere barley from each island group has been separated for some time.

Western Isles demonstrated the highest level of genetic diversity of the 3 island groups (also the most diverse ecological environment).

Potato Genotyping

The European Union Common Catalogue (EUCC) for potato contains over 1,000 varieties. Each year member states add varieties to the list after they have undergone Distinctness, Uniformity and Stability (DUS) testing according to international guidelines. Identification of cultivars by morphological characteristics is a highly skilled and time-consuming task. For these reasons a rapid and robust method for variety identification to aid the management and maintenance of existing variety collections and for the screening of new candidate varieties would therefore be a highly useful tool for DUS testing stations. SASA has developed a rapid and robust identification system using 12 microsatellite markers.


Microsatellite profiles for 3 varieties with marker SSR1

Microsatellite profiles for 3 varieties with marker SSR1.


Over 1,300 varieties have been analysed using the system and virtually all varieties can clearly be differentiated by their unique molecular profiles. The only exceptions are somaclonal variants e.g. King Edward and Red King Edward.

Differentiation of some popular potato varieties grown in Scotland (scale % similarity)

Differentiation of some popular potato varieties grown in Scotland (scale % similarity).


The fingerprinting method is fast with only 1 to 2 days required and any part of the plant can be used for identification. It is also possible to type some food products (e.g. potato crisps). SASA now offers DNA fingerprinting of potato varieties as a service. For information contact Helen Ventisei or Alex Reid (dnafingerprinting@sasa.gov.scot).

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 (©www.spongospora.ethz.ch/sss.htm) 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 (©www.spongospora.ethz.ch/sss.htm) 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