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.


Epidemiology and control of Dickeya on Scottish potatoes

This work encompasses three linked projects which started 01/04/2008 and are due to complete 30/06/2013.

Project collaborators: Fera, York, UK; James Hutton Institute, Dundee, UK; SASA

Funding from: Potato Council and the Contract Research Fund of the Scottish Government’s Directorate for Rural & Environment Research and Analysis

This work focuses on improving the understanding of the epidemiology of Dickeya dianthicola and ‘D. solani’ and identifying the risk of both these  pathogens establishing and spreading within the potato industry in Great Britain, with specific focus on Scotland’s seed potato industry. 

The projects will determine the spread of the pathogen from infected potato plants under controlled conditions and in commercial production, the role alternative hosts and irrigation may play and the survival of the pathogen in soil and in store.

Further details can be obtained from Gerry Saddler on 0131 244 8925 or by email.


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.


Potato Brown Rot

Ralstonia solanacearum contamination of Scottish rivers: Identifying the risks to high-grade seed production

Project start and end dates:  01/11/2003 – 31/10/2006

Project collaborators: Fera, York, UK; James Hutton Institute, Dundee, UK; SASA

Funding from: The Flexible Fund (now Contract Research Fund) of the Scottish Government’s Directorate for Rural & Environment Research and Analysis

Potato brown rot, caused by the bacterium Ralstonia solanacearum, has never been found in Scottish potatoes, however it was found in the Tay river system in 2000 in an area of high grade potato seed production. Restrictions were placed on potato production in this area to prevent its spread and a programme completed in 2004 to eradicate the bacterium from this watercourse.

This project was born out of this finding and its objectives were to determine the likelihood that further Scottish rivers may become contaminated in future with R. solanacearum, paying particular attention to river characteristics, the diversity of the aquatic secondary host (Solanum dulcamara) and the pathogen itself. These data were then used to determine whether such contamination could pose a significant risk to the health of potato crops in Scotland.

In summary, it was found that Scotland’s one case of river contamination with R. solanacearum occurred as a single or limited event. Surveys indicated that very few rivers in Scotland mimic the profile of this previously infested water course and as a consequence the risk of additional infestations was judged to be low in future years. However, as a precaution, all rivers which share key characteristics with the infested river are now included in Scotland’s annual river survey for R. solanacearum. Further work demonstrated that R. solanacearum is capable of colonising potatoes under Scottish conditions and all popular varieties are susceptible to the disease. It is of concern that should brown rot ever be introduced into Scotland, symptoms are unlikely to be evident in the growing plant or harvested tubers as it is likely that potatoes will become infected with low levels of inoculum and field conditions will seldom reach the elevated temperatures required for rapid progression of infection and symptom expression.  This finding reaffirms the continuing requirement to conduct post-harvest tuber testing.

Further details can be obtained from Gerry Saddler on 0131 244 8925 or by email.

Potato Ring Rot

Identification and reduction of risks posed by potato ring rot disease to the Scottish potato industry

Project start and end date: 05/12/2005 – 31/03/2009

Project collaborators: Fera, York, UK; James Hutton Institute, Dundee, UK; SASA

Funding from: Scottish Government’s Flexible Fund (now called Contract Research Fund)

Clavibacter michiganensis subsp. sepedonicus (Cms), potato ring rot has never been detected in Scottish potatoes. This project focused on identifying risks to Scotland’s potato industry should the pathogen ever be introduced.

A postal survey of all Scottish potato growers revealed that although infrequent, some growers exercised poor or inadequate cleaning of harvesters, graders, etc. and re-used bags and boxes returned to their farms without adequate cleaning and disinfection. All such practices were judged to be risky and could facilitate the spread of ring rot within Scotland should it ever be introduced at some future date. Controlled greenhouse experiments have shown that the most commonly grown cultivars in Scotland can be infected by Cms even at low inoculum levels but some varieties, such as cv. Desiree, show limited if any symptoms. This highlights the need to test for ring rot by laboratory testing as field symptoms are unlikely to be observed in all varieties currently grown in Scotland.

Materials commonly used in the potato trade that represent surfaces that could come into contact with Cms were collected. The persistence of the ring rot organism on these trade materials has been monitored as was the efficacy of washing and disinfecting these surfaces.  It is clear that some substrates currently in use by Scottish growers are ineffective at killing Cms and also that care must be taken to ensure a reasonable contact time with effective disinfectants to ensure an effective kill.

Optimisation of sampling strategies has been evaluated and a statistical model developed which will be applied to develop a sampling strategy during an outbreak situation.

This project was instrumental in shaping Scotland’s contingency plan for a future ring rot outbreak. 

Further details can be obtained from Gerry Saddler on 0131 244 8925 or by email.

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)