Written by Evren Bingol. This is the report from a 2020 BSPP Lockdown Bursary. Click here to read more/apply for one yourself.
Even though there was a COVID-19 pandemic going on, I felt very happy to be awarded a BSPP Lockdown Bursary. Phoma Stem Canker is a disease caused by two closely related fungal pathogens (Leptosphaeria maculans and L. biglobosa) causing significant crop and financial losses. The main aim of my project was to investigate the molecular events in the genome of L. maculans leading to the development of specific virulence against host resistance.
During this project, I was introduced to various bioinformatic tools and workflows on Galaxy software, which I used to identify and extract specific effector (Avr) genes from genome sequences of 34 L. maculans isolates. Then, multiple sequence comparisons were performed using Clustal Omega to identify specific mutations in different isolates causing virulence against resistant (R) genes. I had training on using databases such as NCBI and Ensembl Fungi. I have also performed mapping and quality checks on sequence reads obtained from Illumina sequencing.
I was fortunate enough to combine my remote work on bioinformatics with laboratory-based practical work. Following the work I have done in bioinformatics, I wanted to do some laboratory work (pictured) and learn new molecular techniques that my undergraduate degree does not cover. However, due to COVID-19 environment, I needed specific permission to access the laboratory. I was privileged to be given permission to work in the laboratory thanks to the Dean of School of Life and Medical Sciences, Dr Richard Southern. The laboratories here were set up with COVID-19 measures in place to keep everyone safe. I was provided my Personal Protective Equipment, and supply of reagents and equipment I would need during the project.
Over the 8-week period, I was introduced to many different laboratory techniques. I assessed oilseed rape yield components, such as number of pods per plant and thousand seed weight. I processed spore tapes from drums of spore samplers that were used in field trials, counted the ascospores on the tapes and extracted DNA from the spore tapes. I was taught how to do qPCR to quantify L. maculans and L. biglobosa DNA from samples I have extracted. I have also done RNA extraction from inoculated leaf samples and fungal mycelial samples. I was taught how to assess the concentration and quality of DNA/RNA samples and PCR products using Qubit and Nanodrop machines and agarose gel electrophoresis. In addition, I was also introduced to another fungal disease of oilseed rape, light leaf spot caused by Pyrenopeziza brassicae.
At the end of my project, I can say that this was an absolutely amazing experience. I have not only learnt many different molecular techniques, but also enjoyed every single day working on this project. I am inspired to do a PhD in molecular plant pathology. My particular interest is the interactions between pathogens L. maculans, L. biglobosa, and P. brassicae. I would like to thank the BSPP and my supervisor Dr Chinthani Karandeni-Dewage for supporting me for this amazing experience. I would also like to thank Dr Yongju Huang and PhD student James Fortune for their help, and fellow bursary student Amina Sultana for her support during the course of this project.
University of Hertfordshire