Exotic Genetic Lineages Rapidly Replace Established Exserohilum turcicum Populations in the Swiss Rhine Valley

ABSTRACT Climate change and modern agricultural practices contribute to the global spread of plant pathogens, with severe consequences for local crop production. The fungal maize pathogen Exserohilum turcicum causes northern corn leaf blight (NCLB) and was introduced to Europe in the late 19th century, rapidly expanding thereafter. It now persists in four major clonal lineages and multiple physiological races, defined by their interactions with maize disease resistance genes. In a metagenomic survey of natural infections on the susceptible landrace Rheintaler Ribelmais in the Swiss Rhine Valley during 2016 and 2017, we found that one clonal lineage, the ‘Small clonal’ cluster, was dominant. We repeated the surveys in subsequent years and applied a novel pooling strategy by combining 10 infected leaves per sampling location to facilitate large‐scale sampling. This approach increased sample throughput while reducing sequencing costs. The new survey in 2021 and 2022 revealed a temporal shift in population structure: exotic genetic lineages from the tropical ‘Kenyan’ cluster have become predominant, suggesting a recent introduction and establishment of genetically diverse, tropical E. turcicum lineages into a temperate agricultural system. We also found that the microbial community composition of infected leaves varied across years but remained largely consistent between maize variety types (landrace vs. hybrid). Overall, metagenomic pool sequencing of infected leaves proves to be a cost‐effective, spatially resolved method for pathogen monitoring and provides insights into the evolving epidemiology of E. turcicum , with implications for developing durable resistance in maize breeding.