Transcriptome-Derived Amplicon Sequencing Markers Elucidate the U.S. <i>Podosphaera macularis</i> Population Structure Across Feral and Commercial Plantings of <i>Humulus lupulus</i>

Obligately biotrophic plant pathogens pose challenges in population genetic studies due to their genomic complexities and elaborate culturing requirements with limited biomass. Hop powdery mildew (Podosphaera macularis) is an obligately ascomycete that threatens sustainable hop production. P. macularis populations of the Pacific Northwest (PNW) United States differ from those Midwest Northeastern States, lacking one two mating types needed for sexual recombination harboring strains are differentially aggressive on cultivar Cascade able overcome Humulus lupulus R-gene R6 (V6), respectively. To develop a high-throughput marker platform tracking flow genotypes across internationally, we used existing transcriptome diverse isolates design multiplex 54 amplicon sequencing markers, validated panel 391 U.S. samples 123 international samples. The results suggest commercial yards form closely related Kingdom, while feral locations grouped Eastern Europe. Included this was successfully tracked V6-virulence 65 66 confirmed V6-phenotype. A new qPCR assay genotyping type generated highest resolution distribution map date. Together, these strategies enable inexpensive pathogen spread among geographical regions single-colony provide roadmap markers other obligate biotrophs.