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Plant-Pest Epidemiology

Work Package 2.1 - Crop and grassland production and disease control

Research Deliverable 
2.1.4 Plant pest epidemiology
Leading Ideas 
Plant and Animal Health


Endemic and new or emerging pests and diseases are a risk to Scottish crop production. The level of risk is increased as a result of climate change, adaptations in the organisms and changes to agrochemical regulations and product availability. The development of appropriate control strategies relies on improving understanding of the epidemiology of these native and non-native threats. This focuses on: (i) monitoring of pest and pathogen populations, (ii) characterisation of their response to environmental change and management practices, (iii) derivation of key parameters defining risk of infection and spread and (iv) development of models for forecasting the risk of disease outbreaks. The benefits will include new scientific evidence to support policy decisions, the development of practical disease control solutions, and the creation of tools to support decision-making in the agricultural industry.

Some key endemic threats being investigated include: Fusarium species (causing Fusarium head blight on a range of cereals), Phytophthora infestans (potato late blight), Pectobacterium atrosepticum (potato blackleg), and Globodera pallida (potato cyst nematode). Some important emerging threats being investigated include: Drosophila suzuki (spotted wing drosophila), Ericaphis scammeli­ (blueberry aphid), Myzus persicae (potato-peach aphid), Ramularia collo-cygni (Ramularia leaf spot in barley), Rhynchosporium commune (barley leaf blotch), and Pyrenophora tritici-repentis (wheat tan spot).

Aim of Research

Improved risk management and control of plant diseases: to be achieved through an understanding of key epidemiological parameters and optimal ways of manipulating them. These parameters underpin the development of epidemiological models that can be used to predict the effect of management strategies, including crop protection and host resistance. This work aims to define the parameters for problematic and economically important diseases of crops of particular importance to Scotland in order to deliver practical disease control solutions.


2021 / 2022
2021 / 2022

Epidemiological modelling: A standalone desktop app (autoMLfast) was developed for use by non-modellers that fully automates the machine learning workflow from data upload to generation of the best predictive model. The new app is freely available for download. Early-in-season aphid catches at different suction trap sites in the RIS/SASA network were examined as potential predictors of arrivals at other locations, and a report submitted to SASA. Bioeconomic models were developed to describe the response of growers to disease threats in forestry (Dothistroma), horticulture (Xylella) and agriculture (PCN). Papers are in preparation for the forestry and holticulture analyses. An R package was developed containing mechanistic models to inform control of PCN. A Plant Pathology paper was published, and the code is available for download.

Inoculum sources: Controlled experiments showed that direct drilling of crops leads to increased risk of Fusarium head blight, as transmission occurred more easily when debris was on the surface of the soil. Strawberry plants grown in numerous locations across Scotland were collected from farm shops and supermarkets and tested for symptoms of Erwinia pyrifoliae, a new bacterial disease of strawberry that recently appeared in mainland Europe. All samples tested negative (as in the previous year) and a report was made to SASA. A protocol for use of a microfluidics system for counting spores has been produced and is available from

Pathogen populations: A range of DNA-based molecular methods were applied to better understand populations of Phytophthora infestans and promoted to the benefit of plant disease management throughout the year via social media, conference presentations, press releases, Agricultural press, and a podcast. DNA from strains in the core Pectobacterium collection at Hutton and from commercial samples were used to test if a single target sequence metabarcoding method for strain discrimination could be improved via use of multiple metabarcoding sequences. A potential future approach for improvement involving accessory genomes was identified and will be investigated in the SRP 2022-2027. The role of Pectobacterium flagella in colonisation and adhesion to potato roots was investigated, and results showed that the ability of the bacteria to swim and not necessarily the presence of flagella affects its adherence to the potato plant. The results have fed into an ongoing BBSRC project on blackleg. Twelve primers to assess the virulence status of Globodera pallida were developed and tested with 11/12 of these primers working successfully across a range of field populations. These primers will form the basis for future work in this area. A paper was published in Frontiers in Plant Science.

2020 / 2021
2020 / 2021

Potato pests and pathogens. Potato late blight populations are predominantly clonal in the UK, but there is accumulating evidence of sexually reproducing populations in crops in northeast Scotland. To examine the relative threats and management implications posed by this region of high genetic diversity, samples were taken and tested for aggressiveness and virulence. Results were compared to the clonal lineages that dominate elsewhere in the UK and Europe and provided valuable best-practice advice for Scottish growers.

A desk study to investigate the scope for improvement of risk models for late blight found that estimating available inoculum at crop emergence is worthwhile and this work is being developed further.  

Potato Cyst Nematode is an economically important pest of potatoes in Scotland which is difficult to eradicate once an infestation occurs and is therefore best managed using host resistance. Potato breeding lines that incorporate different sources of resistance to Globodera pallida (the white potato cyst nematode), were challenged with a panel of nematode populations selected for their virulence characteristics. Several breeding lines with very high levels of resistance were identified and will inform breeding activities that aim to improve levels of host resistance to this important pest.

Potato blackleg is the most significant bacterial disease affecting potato production in Scotland, yet little is understood about the pathogenesis of the disease. Fundamental research to determine the precise mechanism by which the bacterium (Pectbacterium atrospeticum) colonises the potato plant was conducted and will continue in year 6.

Fruit pests and pathogens. Analyses of six species of aphid count data collected by the UK-wide suction trap monitoring program over the period 1970-2017 were conducted focusing on modelling seasonal arrival times, modelling seasonal abundances, and initial development of an early warning model for arrivals based on data from more southerly sites. A report on the findings was written and made available to SASA. Spotted wing drosophila was monitored at two Scottish locations as part of the UK Monitoring Programme allowing a better understanding of pest distribution and spread in the UK, habitat preferences and pest biology.

Cereal pests and pathogens. Data mining techniques were used to identify the key environmental parameters that drive Ramularia leaf spot (caused by Ramularia collo-cygni) epidemics in winter barley crops. Analysis indicated that warmer and wetter springs created conditions which seemed to promote fungal colonisation of the host plant and lead to higher disease levels in the crops in the late season. Samples of emerging cereal pathogens (e.g., Pyrenophora trictici, Bipolaris sorokinia) were collected from field trials and their sensitivity to commercial fungicides was tested.

Climate change research. The desktop app futureCROP was developed to enable users with no modelling experience to perform climate change risk assessments for crop pests and pathogens using state-of-the-art machine learning techniques. It is freely available for download.


Output from RD2.1.4. was used to leverage £2.2M of Scottish Government funding over 5 years to tackle potato cyst nematode and safeguard Scotland’s bulb and potato sector. Project title: Delivering a sustainable potato industry for Scotland through management of Potato cyst nematode.

Machine learning techniques developed in RD2.1.4. to help understand and predict SWD population dynamics were used to leverage additional funding: (i) £243k (Innovate UK) to develop a generic machine-learning based decision support system “Machine-Cast: a scalable machine learning framework for forecasting risk of crop pests and pathogens”; (ii) £50k (Plant Health Centre)  “Modelling the spread of PCN in Scotland to identify the key factors responsible and the most appropriate management options for future mitigation”; and (iii) £31k (AHDB) to develop the results for SWD into a decision support tool that will be made freely available online for use by the soft fruit industry.

A suite of three desktop apps for performing climate change risk assessments are now freely available for download. They can be used to fit a wide variety of models to your own pest/pathogen/crop data, including state-of-the-art machine learning algorithms, and make spatial projections in real national-scale crop distributions under a range of future climates.

2019 / 2020
2019 / 2020

Potato pests and pathogens. Further data for development and evaluation of risk models for late blight of potatoes were obtained, allowing quantification of the impact of many risk factors on crop infection. Potato late blight outbreaks were sampled intensively with industry support, those in NE Scotland were genetically highly diverse. Analysis of virulence traits provided valuable information for future blight breeding strategies. Genomic analysis of sequenced isolates of Pectobacterium atrosepticum and subsequent pathogenicity testing provided valuable information for the development and use of diagnostics and biocontrol methods for potato blackleg. A candidate gene that can differentiate the more virulent potato cyst nematode populations from other populations has been discovered, enabling field population changes to be monitored to ensure that the host resistance currently being developed by scientists is durable and broad-spectrum. The findings have been used to leverage a PhD studentship via USDA funding. Results were widely communicated to the Scottish potato industry and scientific community.

Fruit pests and pathogens. Monitoring of Spotted Wing Drosophila (SWD) at commercial grower sites and testing of fruits was carried out. Machine learning was applied to these data to develop models for predicting many epidemiologically important aspects of infestation: SWD abundance and flight activity, the first peak of summer morph flies, the male:female sex ratio, and female spring activity and fecundity. The findings were widely disseminated to growers’ groups, industry and policy stakeholders. Models for the abundance and timing of aphid flights were refined and spatial patterns in aphid catches analysed, providing further insight into aphid activity in and around crops. Blueberry plants and strawberries, sampled at the Hutton and on a selection of growers’ sites, tested negative for the potential new disease threats of Blueberry scorch virus and Erwinia pyrifoliae respectively.

Cereal pests and pathogens. Work is ongoing to understand the influence of environmental factors and varieties in Ramularia leaf spot epidemics in barley in order to develop a robust forecasting scheme. The effect of inoculum sources on tan spot epidemics in barley was investigated using field trials and spore trapping and meteorological data was used to relate spore trapping results to field trial disease levels.

Climate change research. A desktop app that enables users with no modelling experience to perform climate change risk assessments for crop pests and pathogens was extended with new functionality and developed for improved ease of use: with a single click it can now create risk models that are a function of multiple climate variables, and it includes the latest UKCP18 climate projection data. It is freely available for download.

Disease management. The effect of land managers' attitudes to risk on management choices was used to compare the optimal response of farmers and foresters to a range of disease threats, using real-world forestry and agricultural case studies.


Research on Pectobacterium atrosepticum, specifically the identification of sub-groups through genomic analysis of sequenced isolates and differences in their pathogenicity, provided valuable information for the development and use of improved diagnostics. This knowledge is now being used to develop biocontrol agents in an Innovate UK phage project and has leveraged a £2.2M grant (UKRI Strategic Priorities Fund- Bacterial Plant Diseases).

Using the data collected from ongoing pest monitoring, machine learning was used to develop models for predicting epidemiologically important aspects of infestation by Spotted Wing Drosophila. The findings were widely disseminated to growers’ groups, industry and policy stakeholders. The SWD modelling was used to leverage additional AHDB funding to develop useful tools for deployment to industry.

A dataset collected over 3 years allowed the impact of previously understudied factors, e.g. size of inoculum source, wind direction and rating for cultivar resistance to foliar blight on the risk of potato crop infection by Phytophthora infestans to be studied. The potential implications of various late blight risk factors was widely communicated to the Scottish potato industry, e.g. SAC Association of Potato Producers, Crop Protection in Northern Britain.

2018 / 2019
2018 / 2019

Potato pests and pathogens. Several field trials and small-scale experiments have provided modellers with the data they need to develop risk models for potato diseases such as Altenaria, Sclerotinia and late blight. Work is ongoing to develop markers for potato cyst nematode virulence, so that field population changes can be monitored. This will ensure that the host resistance currently being developed by scientists is durable and broad-spectrum. Analysis of five years of Phytophthora infestans samples from the NE of Scotland is complete and is shedding light on the origins and spread of this pathogen at local and national scales. The background prevalence of Pectobacterium has been characterised through whole genome sequencing of historical and environmental samples. The results establish a new baseline for population studies of Pectobacterium.

Fruit pests and pathogens. Work continues to monitor populations of Spotted Winged Drosophila. Trap data is providing an early alert to growers and useful information on the influence of biotic and abiotic factors on population density that is being used to develop predictive models. Blueberry leaves collected from grower sites tested negative for Blueberry Scorch Virus, a threat to fruit production. A new aphid arrival prediction model and a new mid-season aphid abundance model was developed and tested against trap data for numerous different aphid species.

Cereal pests and pathogens. An improved diagnostic method was utilised to investigate the link between Fusarium species in wheat and mycotoxin levels in seed. Winter barley grain samples have been delivered and will be tested for the presence of emerging diseases of barley, such as tan spot (Pyrenophora tritici-repentis). These data will be used to identify inoculum sources and understand the influence of the environment on spore dispersal.

Climate change research. A desktop app for performing climate change risk assessments for crop pests and pathogens was extended with a unique functionality for projecting future dispersal of pests and pathogens among GB crop locations.

Disease management. Data was used to create a conceptual model to compare how different farmer attitudes to risk and the decision time frame affect management choices for disease control.


  • “A Scottish Update on Spotted Wing Drosophila in 2018” was presented at the Scottish Society for Crop Research soft fruit winter meeting, held at the James Hutton Institute. This was attended by over 90 delegates from the soft fruit industry.
  • “Mycotoxin Levels in Seed Samples from Scottish Crops” was presented at SRUC winter roadshows in January 2019.
  • Updated bacterial classification software (PYANI) was made available for download and use at:
2017 / 2018
2017 / 2018

Potato pests and pathogens. Recent field isolates of potato cyst nematode were compared to historical collections, and no major differences in multiplication rates were found, although populations in England were found to be more virulent. More than 7000 samples of Phytophthora infestans from across Europe were examined in relation to potato crop data and key epidemiological traits to inform models of blight development and spread. 50 isolates of Pectobacterium atrosepticum were obtained from Aberdeenshire and analysis revealed greater genome variation than found in similar studies on international populations.

Fruit pests and pathogens. Numbers of Spotted wing drosophila caught in the monitoring sites have increased and exceeded the levels caught in the previous two years. Blueberry leaves were collected from grower sites and tested negative for Blueberry scorch virus. Aphid count data from suction traps was used to compare different modelling approaches for predicting aphid arrival and mid-season abundance. Further genotyping of Scottish and English trap samples of aphids (Myzus persicae, Sitobion avenae) revealed no neonicotinoid (insecticide) resistance in the UK population.

Cereal pests and pathogens. Samples of Ramularia collo-cygni from 2016 Scottish barley crops infected with leaf spot were characterised using molecular techniques (SSR markers) and tested for fungicide sensitivity. Trials designed to show the effects of mixing different barley varieties on the level and spatial distribution of Rhynchosporium revealed a dominant role of nutrition in the mixtures efficacy.

Disease management. A pilot survey of land managers behavioural choices was completed and used to design a larger survey, the results of which will be used to create a conceptual model of how farmer attitudes to risk and the decision time frame affect management choices for disease control.


  • Software (4C model) for performing climate change risk assessments for crop pests and pathogens was made available for download and use at: This software was featured as a SEFARI case study.
  • A new Ramularia leaf spot topic sheet and guidelines for scoring disease was published by AHDB:
  • Results from the research to characterise UK potato cyst nematode populations for resistance evaluation, and on Ramularia control were presented at the Crop Protection in Northern Britain conference in 2018.
2016 / 2017
2016 / 2017

Potato pests and pathogens. Data for >2000 GB Phytophthora infestans samples were analysed . Results indicated a series of dominant clones and some diverse sexually recombining populations. The diverse populations in northeast Scotland indicates a local source of soil-borne inoculum but the isolates are not genetically distinct from those in the rest of Britain or mainland Europe.

Fruit pests and pathogens. Sampling for Spotted wing drosophila took place across four sites in Scotland, and an additional two sites were added; trap counts were low compared to English catches. Samples of aphids (Myzus persicae, Sitobion avenae) collected in 2016 from Scottish traps were genotyped and analysed, with no neonicotinoid (insecticide) resistance detected. Similar levels of pyrethroid resistance to 2015 samples were found in S. avenae.

Climate change research. A desktop app for performing climate change risk assessments for crop pests and pathogens in real GB crop locations was designed and coded.

Disease management. A prototype modelling framework for decision making by land managers in response to perceived and actual disease risk was conceptualised, and choice experiments designed.


  • The genome sequence of the barley pathogen Ramularia collo-cygni has been annotated offering insights into the biology and infection strategy of the fungus
  • Climate change risk assessments for a diverse array of pests and pathogens in Scottish agriculture were performed using the desktop app and ultimately published in peer-review journals and policy briefs for the Scottish Government.
  • New information on changes to the European population of Phytophthora infestans was presented at the EAPR Pathology & Pests Section Meeting in Dundee.

Future Activities

Work will continue to gain insight into the epidemiology of endemic and emerging threats to cereal, potato and fruit crops, as these are the most economically important crop production sectors in Scottish agriculture. Potato cyst nematode (PCN) is the most important pest of potatoes in the UK and tests that can anticipate breakdown of resistance to PCN in potato varieties will be developed in order to provide an early warning, allowing the development of alternative management strategies. We will also investigate the effectiveness of combining resistance genes to G. pallida populations. The virulence and aggressiveness of the constantly evolving Phytophthora infestans (potato late blight) population will be characterised and used to tailor best-practice management advice to growers. Pectobacterium (potato blackleg) is the most serious bacterial disease of crops in the country, and work will be undertaken to develop diagnostic tests that can distinguish pathogenic strains of Pectobacterium from non-pathogenic strains, to aid in decision-making on the likelihood of disease development.

In terms of emerging threats, several cereal diseases have been increasing in recent years and research is planned to establish the sensitivity of these emerging diseases to currently available fungicides. Further sampling of Ramularia leaf spot is planned in order to develop a robust forecasting scheme.

Selected Outputs

Crop connectivity under climate change: future environmental and geographic risks of potato late blight in Scotland

Blight 2016 Population dynamics: What does it mean for agronomists?

Tracking populations of Phytophthora infestans from field to continent via the Euroblight database. 

Assessment of the spread of pyrethroid resistant grain aphid (Sitobion avenae) and an update on changes in the population structure of peach potato aphid (Myzus persicae) in Scotland

Compendium of Raspberry and Blackberry Diseases and Pests

Ramularia leaf spot in barley.

Forecasting the spread of aerially transmitted crop diseases with a binary classifier for inoculum survival.

Potential impacts of climate change on the threat of potato cyst nematode species in Great Britain.

4C Model: Crop Connectivity under Climate Change. Software made available at:

Updated bacterial classification software is available for download and use at:

First evidence of retained sexual capacity and survival in the pyrethroid resistant Sitobion avenae (F.) (Hemiptera: Aphididae) SA3 super-clone following exposure to a pyrethroid at current field-rate,

Evidence for selection pressure from resistant potato genotypes but not from fungicide application within a clonal Phytophthora infestans population.

Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs.

Threat of establishment of non-indigenous potato blackleg and tuber soft rot pathogens in Great Britain under climate change.

Fungal, Oomycete and Plasmodiophorid Diseases of Potato. In: The potato crop.

AGROFIT. Acesso: 02.08.2019.

Susceptibility of potato varieties to populations of Globodera pallida selected for increased virulence.

Ramularia collo‐cygni – An Enemy in Waiting.

Population dynamics of the potato cyst nematode, Globodera pallida, in relation to temperature, potato cultivar and nematicide application.

Variable ITS-copy number at different developmental stages of Meloidogyne hapla and M. chitwoodi.

Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs.

The ENHANCED MAGNAPORTHE RESISTANCE 1 locus affects Ramularia leaf spot development in barley.

Expansin-like Exl1 from Pectobacterium is a virulence factor required for host infection, and induces a defence plant response involving ROS, and jasmonate, ethylene and salicylic acid signalling pathways in Arabidopsis thaliana.

Genotyping of Phytophthora infestans in Eastern Africa Reveals a Dominating Invasive European Lineage.

Rhynchosporium leaf scald disease incidence: seed source and spatial pattern.

Forecasting Risk of Crop Disease with Anomaly Detection Algorithms

Integrated potato late blight management in response to an evolving pathogen population.

Reducing Pesticide Use while Preserving Potato Productivity and Profitability

Drought has negative consequences on aphid fitness and plant vigor: Insights from a meta-analysis


Plant Diseases Caused by Dickeya and Pectobacterium Species

Pectobacterium and Dickeya: Taxonomy and Evolution

The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida

Resisting Potato Cyst Nematodes With Resistance

Development of a Strategic DST for PCN

R Package for modelling PCN

A process-based, stage-structured model of potato cyst nematode population dynamics: Effects of temperature and resistance

More accurate measurement of temperature in potato drills increases predicted potato cyst nematode population growth

Control of barley disease

Cooke DEL, Sullivan L, Lynott J, Lees AK 2022.  Late blight: 2021 population change, fungicide sensitivity and IPM implications. Scottish Agronomy: Potato Technology Transfer Event presentations 1-2 Feb 2022, Perth, UK

Cooke DEL, Brierley J, Toth IK, Randall E, Humphris S, Jones J, Cock PJ. 2022. Applications of DNA metabarcoding for plant pathogen tracking and diagnostics. Crop Production in Northern Britain Conference. Online 1-2 March 2022.

Cooke DEL, Lees AK 2021 ‘Late Blight IPM @CSC: informing decision making’ IPM/CSC talk at stakeholders online meeting 7 June 2021 IPM@Hutton/Centre Sustainable Cropping stakeholder workshop, Monday 7th June, 10-12 am, Online meeting.

Cooke DEL 2021. Blight studies reveal evolution of potato disease in Europe and Asia. April 28 2021. Press release on James Hutton Institute web site.

Clarke A, Cooke DEL 2021. Why emerging blight strains are a concern and how they will be tackled. Farmers Weekly. July 2021. After interview with D Cooke

Cooke DEL, Porter C, Goddard P. 2021 Blight management podcast for BASF Fri 24 June 2021. Online at

Annual policy report on incidence of Erwinia pyrifoliae sent to SASA

autoMLfast: A standalone desktop app that automates the machine learning workflow to generate the best predictive model for your data.

A protocol for use of the microfluidics system for counting spores has been produced and is available from

Gartner, U., Hein, I., Brown, L.H., Chen, X., Mantelin, S., Sharma, S.K., Dandurand, L-M., Kuhl, J.C., Jones, J.T., Bryan, G.J. & Blok, V.C. (2021).  Resisting potato cyst nematodes with resistance. Frontiers in Plant Science 12, 483.

James Price, Vanessa Young, Drummond Todd, Katharine Preedy & Vivian Blok (2021).  Assessing durability of potato breeding lines to Globodera pallida populations.  AAB improving global and local IPM conference, Grantham, 2021.