Developing new tools for interrogating cereal invaders

Emerging and re-emerging diseases of humans, animals and plants pose a significant hazard to public health and food security. With recent advances in DNA and RNA sequencing, bacteriologists and virologists are capitalizing on these technological advances by integrating high-resolution genotypic data into pathogen surveillance activities. However, the application of genomics to emerging filamentous plant pathogens has lagged. Filamentous plant pathogens tend to have large genomes and are often obligate parasites that cannot be axenically cultured in the laboratory. To address these limitations, we developed a robust and rapid “field pathogenomics” strategy. We applied this method in 2013 to the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST), using transcriptome sequencing of PST-infected wheat leaves to gain insight into the population structure of an emerging pathogen. Our analysis uncovered a dramatic shift in the PST population in the UK and supports the hypothesis that recent introduction of a diverse set of exotic PST lineages may have displaced the previous PST populations. Whilst effectively capturing pathogen diversity, transcriptome sequencing of infected host tissue can also be leveraged to assess the genotype of the host. In the future, this will provide a rapid means of confirming whether previously resistant wheat varieties have indeed been broken by virulent races of the pathogen, using samples submitted directly to national pathology surveys. Our field pathogenomics approach circumvents the difficulties associated with less-tractable filamentous plant pathogens and can be applied to other emerging populations of pathogens.