This project investigated the spread and economic impact of potato cyst nematodes (PCN) in the county of Angus in Scotland. Two species (Globodera rostochiensis and Globodera pallida) co-evolved with the potato in South America and have since been introduced into other areas of the world such as the UK. When PCN are present in soil, they damage the roots of potato plants, inhibiting growth and reducing yield. Once cysts are present in soil, they are almost impossible to eradicate and can survive for 30 years in the absence of a host.
The project was jointly supervised by Professor Adam Kleczkowski from the University of Strathclyde and Dr Jon Pickup from SASA (Scottish Government). Prof. Kleczkowski’s main areas of research lie in mathematical modelling and statistical analysis of epidemiological systems whereas Dr Pickup is the Head of Virology and Zoology at SASA specialising in potato pests and diseases.
Based on the SPUDS data set made available by SASA, the area and proportions of area testing positive for both species of PCN were examined, and graphs were created in Excel for each year of testing. The geographical spread throughout Angus was mapped using the leaflet package in R. The Shiny package in R was utilised to create a web application, animating the annual area testing positive for G. pallida in Angus over the period 2010-2018. R was also used to create an exponential model of the pests’ area of infestation and economic impact on the farming industry in Angus.
The analysis conveyed that the area testing positive for G. pallida is growing rapidly compared to G. rostochiensis. Between 2010 and 2018 the number of parishes infected with PCN rose significantly along with the levels of infestation. This is thought to be a result of an increased planting of potatoes which are resistant to G. rostochiensis but susceptible to G. pallida.
The exponential model was constructed based on the data and this estimated that the annual area found infested with G. pallida in 1995 was 43.9 hectares with a standard error of 1.2. The growth rate was estimated to be 0.098 with a standard error of 0.01, producing a doubling time of 7 years. The model conveys a substantial increase in the area infested with G. pallida in the future, predicting that the annual area infested with G. pallida in 2030 will have increased to 1300 hectares (fig 1). The cumulative area was expected to reach approximately 13,700 hectares by the same year. Assuming that there will be a 100% loss in seed potato yield, the initial annual loss of profit from seed potatoes was estimated to be £281k in 1995. The economic model predicted that the value lost due to G. pallida in 2030 will be over £6 million yearly in the Angus region only.
During my research I struggled particularly with the coding of the interactive map on Shiny. I previously had only used R for statistical analysis so creating a web application was a new challenge for me. However, I found various helpful forums online to assist with this.
It is proving increasingly challenging to find PCN-free land in the UK thus breeding programmes are being developed to produce varieties of potato resistant to PCN, particularly the increasingly prevalent G. pallida. My analysis emphasises how crucial such programmes are. Furthermore, the financial loss from the disease may highlight to farmers in the area the importance of being cautious where the spread of PCN is concerned.
This period of research has helped me gain many new skills beyond the scope of my university course. I gained knowledge on how to code mathematical models using R and learned to use a web application package which will be useful in my future career. I had many opportunities to use my initiative by steering the areas of work towards my own interests and suggesting further areas of investigation to be carried out.
University of Strathclyde
Plot of new areas of infestation by G. pallida in Angus each year with exponential model and 95% prediction intervals