This dissertation explores various aspects of the pathogen D. humulicola. The research tested multiple fungicide products to determine effective management strategies for the disease. Additionally, a qPCR tool was developed for the detection of D. humulicola in different plant materials. Lastly, a genome was produced, and a population genetics study was conducted using D. humulciola isolates from the eastern United States and Canada. The first research objective of this dissertation was to determine if fungicides could be used for the treatment of halo blight. For three years field trials were conducted using 10 fungicides registered for use hop to determine their efficacy against halo blight. To validate field results, the EC50 value was determined for some of the active ingredient including flutriafol, tebuconazole + fluopyram, cyflufenamid, and trifloxystrobin + salicylhydroxamic acid (SHAM). A discriminatory dose was used to test the sensitivity of 206 D. humulicola isolates in a poison agar assay. Results showed that tebuconazole + fluopyram decreased the incidence and severity of halo blight in the field. Also, this product had EC50 values of 2.26 x 10-1 ppm and significantly reduced the growth of most of the isolates tested. Trifloxystrobin + SHAM decreased the presence of halo blight in the field, but some isolates were not inhibited by the discriminatory dose concentration. The second research objective was to develop a diagnostic tool for D. humulicola. A quantitative polymerase chain reaction (qPCR) assay based on the translation elongation factor 1-alpha gene was developed. We assessed this assay for direct detection of D. humulicola in plant tissue and investigated aspects of the disease cycle through three distinct experiments: 1) detection of D. humulicola in hop rhizomes to determine the colonization range of the pathogen, 2) determining how quickly can D. humulicola be detected in hop leaves post inoculation, and 3) monitoring the presence of D. humulicola in cones in a hop yard and comparing isolation methods and the assay. The limit of detection for the assay was 100 fg of DNA. The assay showed no cross-reactivity with other hop pathogens or endophytes, nor with other Diaporthe species tested. Detection of D. humulicola occurred one day after inoculation. The assay detected D. humulicola in both apparently healthy and diseased rhizome tissue. The assay successfully detected the pathogen in individual hop cones and inflorescences throughout the season, surpassing the culture-based method in positive identification rates. The third objective was to produce and annotate a genome for D. humulicola. The draft genome for D. humulicola, was assembled with both long and short read sequencing. The draft genome consists of 49.82 MB assembled into 180 contigs, with a GC content of 51.2%. The genome was annotated, and 11,773 genes were predicted, including 2,752 genes with common names. Finally, the genome was used to conduct a population genetics experiment using 64 different D. humulicola isolates from Michigan, New York, Minnesota, and Canada. Single nucleotide polymorphisms (SNPs) were discovered and filtered using GATK. Population Structure was determined using STRUCTURE v.2.3.4 and using the Evanno method the populations cluster into 4 or 6 different populations. Using Fst Minnesota isolates appear to have high levels of population differentiation when compared to the different populations. Mating types were determined for each isolate where Mat-1-2-1 were the larger part of the population with 59 percent of the isolates having this locus. This dissertation also includes an extension fact sheet for halo blight, and disease notes for different occurrences of halo blight in the United States and Canada.
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