This is the report from a BSPP Lockdown Bursary.
Even though time has moved on, and a lot of the restrictions across the UK are being lifted as I write, the impacts of COVID-19 is still felt throughout our communities. In my case the pandemic meant that I effectively lost half of my second and half of my third year of work. Right before the pandemic, I had only just managed to get all my methods working and was about to start experiments that would produce meaningful results. I was also due to start field trials on the Isle of Wight, with my industrial partner, to collect the main set of data for my work. All these experimental plans had to be cancelled. Which meant that during lockdown I was still at a stage in my PhD where I did not have any results to write up or any work that could have been done from home. Even though I attempted to make the best of the situation, my research was restricted, and I was falling behind in my PhD. The BSPP Covid-19 support fund gave me the security to be able to capitalise on my research and realise its full potential.
My PhD focuses on early detection of tomato powdery mildew (TPM), also known as Pseudoidium neolycopersici, in greenhouses. TPM is the main reason why tomato growers spray fungicide according to the 2019 Fera report on edible protected crops. Therefore, it is vital to be able to detect TPM as early as possible to prevent disease establishment by warning growers. An alert should be raised as soon as possible to allow growers to react accordingly to the disease. My project aims to work with volumetric spore-trapping equipment, such as the 7-day Burkard spore trap, and couple it with molecular techniques, such as a qPCR or LAMP assays, to detect and alert growers to TPM before visible symptoms appear in the greenhouse. The technology could also be used to monitor the levels of disease throughout the season if necessary.
Due to the lack of knowledge of the TPM fungus, the project needed a lot of development before it could progress. This included obtaining the sequences of target genes to successfully design a LAMP or qPCR assay that would be species specific and sensitive enough to be compatible with spore-trapping equipment. Filling in an information gap on the performance of spore traps in commercial greenhouses. And to generate a library of isolates of TPM and successfully cultivate them. These questions have now been addressed within the scope of this PhD.
Primarily, the funded extension gave me the time for an extra fieldwork season. Even though my PhD was 4 years long, the first year that I was supposed to collect data was plagued by a tomato brown rugose fruit virus pandemic that had broken out in the tomato industry worldwide. My second year was then plagued by Covid-19. This meant I only had one year, my third year, for data collection. However, a minimum of two years of field data is required to consolidate the results. This has been realised by the funded extension and will mean that I will be able to publish my findings.
The BSPP Covid-19 support fund has enabled me to address the basic questions mentioned above and further develop that knowledge. For example, I have sequenced several genes, that are known to cause resistance to several target fungicides, as part of developing a qPCR assay. Genetic resistance in P. neolycopersici has not been studied to date which will enable me to report on these findings in the future. A further example has been my ability to fully analyse the dataset collected in the 2021 field season in commercial greenhouses. Visual disease assessments that were taken over a specific time series have been modelled using the kriging method. This has helped me to understand more about the spread of the disease and how it behaves in a greenhouse environment. However, kriging was not a skill I was familiar with and has required additional time to learn from scratch.
This three-month extension has put me in a better position to focus fully on my research and execute it to the best of my ability without the need to compromise on its quality by chasing funds to complete it. For that I am forever grateful to the BSPP.
Anastasia Sokolidi
The fungal pathogen of Pseudoidium neolycopersici
A 7-day volumetric spore trap
