Using population genomics to predict the epidemiology and evolution of R. solanacearum plant pathogen in the UK

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Plant pathogenic bacteria cause considerable economic losses globally due to damage to crops.Bacterial wilt, caused by the Gram-negative quarantine bacterium Ralstonia solanacearum, is one ofthe most important bacterial crop diseases. In the UK, R. solanacearum causes potato brown rot. UKoutbreaks have been associated with flooding or irrigation of potato crops from contaminated riverwater sources where it can persist by overwintering in the roots of its secondary host plant, WoodyNightshade. It is currently known that R. solanacearum densities peak in July-September when thewater temperatures are high and that the strains isolated from disease outbreaks are highly related tothe environmental strains isolated from water and alternative hosts upstream of the infested potatofields. While these findings suggest that environmental reservoirs play important roles in the diseaseoutbreaks, it is still unclear how the R. solanacearum population has dispersed, expanded and evolvedsince the first disease finding in 1992.This project will use population genomics and a collection of time sampled pathogen isolates tounderstand the epidemiology and genomic evolution of R. solanacearum in the UK river system. Thestudentship will address three research areas:1) Global pathogen dispersal: comparison of UK isolates with an existing sequence database of R.solanacearum genomes to determine whether the UK population is genetically unique and locallyadapted and to estimate the frequency of international dispersal.2) Evolutionary dynamics: to what extent has R. solanacearum changed during the UK diseaseoutbreaks since 1992? Can we identify quantitative traits that are important for pathogenic vs.environmental isolates by using genome-wide association approaches (GWAS)? Can we use genomedifference to infer something about pathogen ecology and adaptation in environmental reservoirs andis R. solanacearum still evolving in the UK?3) Spatial and temporal distribution of R. solanacearum genotypes: We will develop a genomicdatabase that will help in identifying novel outbreak strains, to infer the likely geographic source of their2origin and to match specific control management strategies against the given outbreak strain.The project combines next-generation genome sequencing, bioinformatics and evolutionary biology tounderstand the dynamics of concurrent plant pathogen outbreaks.