Genomics-driven surveillance of Brown Wheat Rust (Puccinia triticina)

Brown rust, also known as leaf rust, is caused by the obligate biotroph basidiomycete Puccinia triticina and is the most common rust disease of wheat worldwide. Whilst the genetic diversity of P. triticina has been monitored across the world through the use of Simple Sequence Repeat (SSR) and Random Amplified Polymorphism DNA (RAPD) markers, genomic data has only recently become available, opening up new avenues of research. A novel pathogen surveillance technique, termed ‘field pathogenomics’, has been developed for the closely related plant pathogen Puccinia striiformis, which allows rapid detection of pathogen variants directly from infected wheat samples taken from the field through transcriptomic sequencing of infected material. In this study, a genomic approach was used in combination with the field pathogenomics technique to characterise the European brown rust population and genetic diversity. This involved genomic sequencing of 32 UK brown rust isolates from the years 2006-2015 to characterise the UK brown rust population in the years prior to this project, accompanied by transcriptomic sequencing using the field pathogenomics technique of 73 European field isolates from the 2017 and 2018 growing seasons. Phylogenetic and population genetic analysis of 105 brown rust isolates illustrated that they are all closely related with very little genetic diversity. This study does not find separate populations of P. triticina, as have been previously categorised through the use of SSR markers, but demonstrates that the genetic information used to assign samples to population groups must be considered when looking at population genetics of a clonal, highly genetically similar, organism