The effects of diurnal temperature fluctuation and the utility of degree days for modeling clubroot on canola (Brassica napus L.) caused by Plasmodiophora brassicae Woronin were assessed using microscopy and qPCR, and in field trials. Temperature fluctuation had little effect on pathogen development. The optimal temperature for root hair infection was 25° C. Air and soil degree days and rainfall were used as metrics for estimating clubroot development, with only limited success. Several cultivars of cabbage (Brassica oleracea L. var. capitata) with unknown clubroot resistance mechanism(s) were assessed using staining and microscopy, and qPCR. In field trials, ‘Bronco’ was susceptible to clubroot (100 DSI), ‘Kilaherb’ was resistant (0 DSI), and ‘B-2819’ was intermediate (53 DSI). Plasmodiophora brassicae was present in cortical tissue of all cultivars. A delayed disease phenotype in ‘B-2819’ may indicate a quantitative resistance genotype that could be exploited in research on resistance genes and breeding.

This thesis is an investigation of detecting and quantifying airborne inoculum of Sclerotinia sclerotiorum (Lib.) de Bary to improve the Sclerotinia rot of carrot (SRC) forecast model. A quantitative polymerase chain reaction (qPCR) assay was developed to specifically detect and quantify DNA from airborne ascospores of S. sclerotiorum. The qPCR assay was evaluated on air samples collected using a Burkard Sampler, and showed that ascospores of S. sclerotiorum were specifically detected among a pool of foreign DNA. The concentration of detected ascospores was related to the observed incidence of SRC to suggest a preliminary threshold of 2 to 4 ascospores m-3 of air for SRC development. Evaluation of an Andersen Sampler, the blue plate test (BPT) and the qPCR assay showed that the latter two methods were equally effective in detecting and quantifying ascospores of S. sclerotiorum and consistently detected greater numbers of ascospores than an Andersen Sampler. Three days are required to confirm the presence of S. sclerotiorum using the BPT, while results from the qPCR assay can potentially provide results within five hours of air sampling. The choice of detection method depends on the available resources and need for a quick result. Analysis of data from nine years of air sampling using the BPT indicated that a single air sampling site is sufficient to detect ascospores when counts are low, increasing to two sites during periods when ascospores are detected near threshold levels and crop and environmental conditions are conducive to disease. Chitosan and canopy trimming were evaluated to manage SRC under field conditions. Chitosan reduced area under the disease progress curve (AUDPC) by 55 and 42% in 2009 and 2011, respectively, which was comparable to a standard fungicide. Trimming enhanced chitosan efficacy, reducing AUDPC by 88 and 82% in 2009 and 2011, respectively. Trimming as a stand-alone treatment reduced AUDPC by 66% in 2011. Under controlled environmental conditions, chitosan inconsistently enhanced defense responses against S. sclerotinia. The results show that chitosan has potential to be integrated into SRC management systems, particularly when combined with foliar trimming in years with moderate to high disease risk. / National Research Council of Canada; University of Guelph; Department of Plant Agriculture; Ontario Ministry of Agriculture, Food and Rural Affairs

<p>  </p> <p>Emerging pathogenic fungi have become a topic of conservation concern due to declines seen in several host taxa. One newly emerging fungal pathogen, <em>Ophidiomyces ophiodiicola</em>, has been well documented as the causative agent of Snake Fungal Disease (SFD). SFD has been found in a variety of snake species across the United States, including the Eastern Massasauga (<em>Sistrurus catenatus</em>), a federally threatened rattlesnake species. Most work to date has involved detecting SFD for diagnosis of infection through direct sampling from snakes. Attempts to detect <em>O. ophiodiicola</em> in the environment to better understand its distribution, seasonality, and habitat associations are lacking. I collected topsoil and ground water samples from four macrohabitat types in northern Michigan at a site where SFD infection has been seen in Eastern Massasauga. I used a quantitative PCR (qPCR) assay targeting the internal transcribed spacer region (ITS) developed for diagnosis of SFD after extracting DNA from samples. <em>Ophidiomyces</em> DNA was successfully detected in topsoil, with minimal to no detection in groundwater samples. The frequency in which <em>Ophidiomyces</em> was detected in a sample did not differ between habitats, but samples grouped seasonally showed higher detection occurring during mid-summer. Investigation of the correlation of environmental parameters on <em>Ophidiomyces</em> occurrence recovered no relationships. Our data suggests that season has some effect on the presence of <em>Ophidiomyces</em>. Differences between habitats may exist but are likely more dependent on the time of sampling and currently uninvestigated soil parameters. These findings build on our understanding of <em>Ophidiomyces</em> ecology and epidemiology and inform where snakes like the Eastern Massasauga may be encountering the fungal pathogen. Furthermore, they assist with developing conservation practices aimed at reducing <em>O. ophiodiicola </em>exposure in imperiled snake species. </p>