Nanopore technologies for Septoria Surveillance

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Septoria tritici blotch (STB) of wheat is the most economically important disease affecting wheat production in Northern Europe. STB is controlled using a combination of agronomy, genetic resistance and fungicides however, selection and subsequent adaptation of the underlying pathogen populations can lead to breakdowns in host resistance and resistance to chemical controls. As the pathogen adapts we will need to understand the composition of the pest population (or pathotypes) to be able to describe specific differences between members of the same species and how these differences affect the range of wheat varieties affected by STB. An effective and cost-efficient solution for STB will directly depend on our understanding of the underlying pathogen (Zymoseptoria tritici). The use of advanced sequencing technologies has the potential to quickly and efficiently screen many individual pathogen isolates, providing a wealth of information at a low cost. This type of approach has already been demonstrated to be a powerful tool in yellow rust of wheat. However, the cost of purchasing machinery required to conduct sequencing is often prohibitive and runs can take between 24-48 hours to complete. There are also requirements for high-powered computing facilities and experienced operators to conduct the relevant analyses to arrange sequencing data in to a practical format. NanoPath will employ the MinION sequencer from Oxford Nanopore Technologies as a surveillance tool to improve the speed and ease at which researchers can identify and survey new pests in the field. This will first assess the utility of the MinION and help to develop a model and computational platform to apply nanopore sequencing to a wider range of crop pathogens. The MinION device is portable and able to generate sequencing data following a relatively easy-to-use process. We also propose to implement a data analysis pipeline that will make use of a number of open-source primary data software tools optimised for the discovery and characterisation of genetic variants this crop pathogen.