Written by Joel Prince Dube from the University of Pretoria, South Africa. This is the report from a BSPP Grace Waterhouse Fellowship. Click here to read more/apply for one yourself.
Potato is ranked the fourth major food crop in the world, exceeded only by wheat, rice and maize. It is considered the most important dicotyledonous source of human food. In South Africa annual production is approximately 2.2 million tonnes, and production is spread over 16 different geographic areas with a wide range of soils and climatic conditions.
There are over 31 known pathogens of potato and the majority of these are soil-borne. These pathogens act by affecting either crop development or tuber quality, therefore detection and identification of these pathogens remains critical for control and management. In South Africa potato diseases of economic importance include early blight, late blight, common scab, powdery scab, soft rot, black leg, and of late, brown spot caused by Alternaria alternata.
Molecular methods provide a more accurate approach to detecting and identifying pathogens compared to traditional methods based on structural properties of pathogens; however, DNA extraction remains a major bottleneck in the process of analysing soil samples due to presence of inhibitors. Therefore robust DNA extraction methods, as well as sensitive, specific and rapid molecular diagnostic methods that can identify species are required for accurate diagnosis of soil borne pathogens.
My one month fellowship visit was hosted by Dr James Woodhall, a researcher at the Food and Environmental Research Agency (Fera) in York. The main objectives of the fellowship were to gain practical experience in DNA extraction methods from soil samples, as well as to get hands on experience with using and developing real time PCR (qPCR) and loop mediated isothermal amplification (LAMP) assays to diagnose some of the potato pathogens of interest to my studies in South Africa.
During my visit I learnt about designing new qPCR and LAMP assays. Whilst qPCR is an established tool in most plant pathology laboratories, LAMP is a rapid isothermal amplification technique which has the potential for use in field. LAMP is a somewhat novel molecular diagnostic tool and consequently relatively few assays have been developed for potato pathogens, therefore as part of my visit I learnt how to design LAMP assays and go through the validation process for new assays at Fera.
I also learnt about various DNA extraction methods, particularly for extracting high quality DNA from bulk soil samples. This method involves automated isolation of high quality DNA from soil, capturing DNA but also removing PCR-inhibiting compounds such as humic acid. For LAMP assays I learnt about a rapid DNA extraction method which is applicable in the field.
My visit to FERA has empowered me as a scientist as I have learnt new techniques and strengthened the ones I had, all which I can implement back home in South Africa. Working together with UK scientists and gaining knowledge in new and novel techniques has boosted my confidence and knowledge which will help me in any further research I am going to engage during my studies in South Africa.
Other than my proposed research at FERA, I was privileged to learn about next generation sequencing using the MiSeq, and even participated in an experiment from the library preparation to the actual run. I also had the opportunity to take part in a field trip to Driffield where we collected soil samples as well as infected plant material. I was also fortunate to attend the 2014 Fruit Focus event during which I was privileged to take a tour of the East Malling Research facilities and interact with other scientists while exchanging ideas.
Fera is situated in the magnificent city of York, which provided the perfect outdoor experience when not in the lab. It was truly a blessing to tour the city and experience all of the medieval history locked in it. I also had the opportunity to visit other towns such as Leeds, Manchester and London where I explored a great deal of British history.
I would like to thank everybody at Fera, particularly James Woodhall for his unwavering dedication and hospitality during my visit, Kate Perkins and Eder Samoza, for impeccable assistance in the lab.
Finally, I am grateful to the BSPP for granting me this rare opportunity to enhance my laboratory skills and keeping me up to date with recent technology, all of which will help me advance science in South Africa and help progress in my career.
Joel Prince Dube
University of Pretoria, South Africa