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Abstract
This dissertation explores several research topics and aspects, including molecular assay design, genomic analysis, and biological experimental design in two pathosystems. Dollar spot is the costliest turfgrass pathogen worldwide and rapidly causes damage that affects turfgrass quality and value. Clarireedia jacksonii and C. monteithiana are the two most common species that cause dollar spot in the United States, and rapid pathogen detection is required for management. This research included designing, testing, and optimizing two novel dollar spot detection assays. In three hours, a co-dominant cleaved amplified polymorphic sequences (CAPS) assay can detect and differentiate the two species, C. jacksonii and C. monteithiana. A portable colorimetric probe-based loop-mediated isothermal amplification (LAMP) assay can detect both U.S. species found in grass samples within 1.2 hours. These tools allow for faster, more precise dollar spot detection and will help turfgrass managers make better decisions. Switching from pathogen detection to disease protection, Trichoderma is a biological control fungus that forms protective symbiotic rhizosphere relationships. The Trichoderma strain T22 has been used for decades, but little research has been performed to understand its genomic background. This research included sequencing the protoplast fusion participants, T12 and T95, and comparing those genomes to the resulting T22 genome. This study found that T22 does not have genomic contributions from T95 supported by single nucleotide polymorphisms or structural variants. Additionally, the genetic differences between T12 and T22 were examined and detailed to aid future research in enhancing Trichoderma biocontrol. Continuing to evaluate plant and ecosystem protection, this research also investigated using Trichoderma T22 to manage the nitrous oxide (N2O) emissions of the fungal pathogen Fusarium verticillioides (Fv). N2O is a potent greenhouse gas released by fungi during agricultural use that contributes to global warming and systemic nitrogen loss. Results found that T22 produces N2O in some specific conditions and can mitigate Fv N2O emissions in others. Additionally, both strains produced small amounts of N2O in the soil settings tested. These results show that T22 has promise as an N2O mitigator but requires more research and potential genetic modification to remove N2O production potential.