Southern Blight (SB), caused by the fungus Athelia rolfsii, has increasingly impacted Mississippi soybean production with estimated economic losses in recent years rising from $181,616 in 2016 to $9,508,412 in 2021. Currently, there are no recommended fungicides and no known commercially available cultivar resistance. Eleven cultivars were evaluated for their response to the presence of Athelia rolfsii in the 2021 field trial. An in vitro fungicide assay was conducted to evaluate the efficacy of five fungicides to determine the respective EC50. These fungicides were then evaluated in combination with three cultivars, one mild, one moderate, and one severe in the 2022 field trial and in the growth chamber trial. A rapid and quantitative method was developed to evaluate the response of these commercially available soybean cultivars in combination with fungicides to SB. Determining effective management options has the potential to decrease disease losses for Mississippi Soybean growers.

Early planting of indeterminate soybean varieties has increased yield potential in Mississippi. Narrow row patterns have effectively alleviated canopy closure problems and maximized light interception. Stresses related to inadequate drainage persist. Field experiments were conducted in 2006 and 2007 to evaluate productivity and profitability of bedding systems to minimize stresses related to poor drainage. Soybean planted on a conventional 100 cm bedding system provided a higher degree of growth and development and higher seed yields than flat plantings when border irrigated both years. Raised 100 cm-wide beds offered 23 to 45% greater net returns above input costs relative to flat plantings in 2006 and 2007 respectively. Under simulated flood irrigation, soybean planted on 200 cm-wide beds produced yields similar to conventional beds in 2006; however in 2007 200 cm-wide beds produced higher yields than flat planted plots but lower than 100 cm-wide beds.

Macrophoma rot is a general term for fruit rots of Vitis spp. caused by the fungus Neofusicoccum ribis (syn. Botryosphaeria ribis) or closely related or renamed taxa, including Botryosphaeria dothidea. While mainly observed as a fruit pathogen of muscadine grape, the disease has recently been observed on bunch grapes in Virginia. Isolates (N = 835) were collected from Petit Manseng fruit clusters from seven Virginia vineyards in 2018 and 2019. A subset of these isolates was sequenced using three primer sets (ITS, RPB2, and EF). The preliminary result showed a single taxonomic strain of N. ribis. A controlled inoculation study of Petit Manseng clusters verified that infection could occur anytime between bloom and 2 weeks post-veraison; however, both the mean cluster incidence and the severity of Macrophoma rot did not differ from each other at any growth stage during the season. A season-long cluster exposure experiment showed that any amount of sun exposure significantly increased Macrophoma rot severity compared to shaded clusters, and that full sun exposure was associated with greatest rot severity. This finding contravenes current management recommendations for Macrophoma rot, and it raises yet unanswered questions as to why exposed clusters are more susceptible to Macrophoma rot than are shaded clusters. An in vitro fungicide assay study using nine fungicides identified captan, thiophanate-methyl, and tetraconazole as potential candidates for management of Macrophoma rot which need to be investigated further. / Master of Science in Life Sciences / Macrophoma rot is a general term for fruit rots of grapes caused by the pathogenic fungi in the family Botryosphaeriaceae. The rot is mainly observed on Muscadine grapes, but recently more cases were found on a wine grape cultivar Petit Manseng in Virginia. Macrophoma rot symptoms begin as dark brown, circular lesions on the surface of the berry and look similar to sunburn and other fruit rots. As the disease progresses, the lesion envelopes the entire berry and black fruiting bodies develop. Severe cases may lead to crop loss. The same group of pathogens is also associated with rots on other crops including apple, pear, olive, and kiwis. Very little is known about the disease cycle and the control of Macrophoma rot, therefore, an investigation into this fungal pathogen was needed. Multiple studies with the wine grape variety Petit Manseng were conducted during the 2018-2019 growing seasons, including a survey, leaf removal trial, and an inoculation study. Results showed that a species called Neofusicoccum ribis was found in vineyards across northern and central Virginia based on the genetic identification of fungal isolates collected at seven vineyards in those areas. Macrophoma symptoms were observed to be more prevalent and severe in more exposed clusters based on a leaf removal experiment. An artificial inoculation experiment revealed that grape clusters are susceptible to Neofusicoccum ribis at any time during the season. Based on the screening of nine fungicides, three chemicals (captan, thiophanate-methyl, and tetraconazole) showed promising results as possible management tools for Macrophoma rot. The knowledge collected will lead to an increase in understanding of this fungal pathogen and to further studies to manage Macrophoma rot.

Gaeumannomyces tritici is a soil-borne, highly destructive, wheat root pathogen, causing take-all disease. Some modern, elite, winter wheat cultivars possess a genetic trait promoting low take-all inoculum build-up (LowTAB). This leads to reduced disease if wheat is grown in the same field the next year. This PhD aimed to test if genetics (LowTAB) and chemistry will individually or synergistically influence take-all fungal inoculum build-up in first wheats as methods to control second wheat take-all disease. The underlying mechanism, epidemiology, agronomy and genetics of the TAB (take-all build-up) trait in eight first wheat field trials was investigated. This identified two minor QTLs conferring the LowTAB trait, in a doubled haploid mapping population. This PhD also confirms the highly complex cultivar-year-field interactions that underpin this trait. Root phenotyping experiments in the field and laboratory highlight that the TAB trait is not likely to be the result of root system architecture variation. Future field trials are planned to confirm the QTLs identified and to test for links between TAB and root-soil-microbial interactions. The effect of foliar applied chemistry (fungicide: Amistar, active ingredient: azoxystrobin and plant growth regulator: Moddus, a.i. trinexapac-ethyl) combined with genetics (TAB) on first wheat take-all inoculum build-up and second wheat disease was investigated. To complement this, laboratory screens were performed checking for common target site mutations to the azoxystrobin fungicide, in new and historic G. tritici isolates. For the first time, legacy effects of first wheat foliar chemistry on second wheat disease were identified, however no synergy with genetics were found. Early first wheat Amistar sprays reduced second wheat take-all disease, whilst later sprays and plant growth regulator, Moddus; had no effect. However, first wheat inoculum reduction by Amistar, could not be directly linked to the second wheat disease outbreaks observed. No evidence of fungicide resistance was found in 40 UK isolates, thus the varied efficacy of Amistar is linked to soil dose rate at the different application times. The collective PhD findings of the effect of first wheat chemistry and genetics make a significant contribution to the control of take-all disease in commercial second wheat crops.

Botrytis bunch rot, caused by Botrytis cinerea, is a fungal disease that primarily affects the fruit of wine grapes. Infection of fruit consequently results in reduced yields and wine quality. These factors lead to significant economic losses for growers which prompts the implementation of management practices to control the disease. One objective of this study was to evaluate the level of resistance that populations of B. cinerea in the Central Coast region showed to various chemicals. A fungicide assay was conducted to determine resistant phenotypes to six fungicide active ingredients (pyrimethanil, iprodione, fenhexamid, fludioxonil, trifloxystrobin, boscalid). Thirty-five (2020) and 88 (2021) B. cinerea isolates were collected from Santa Maria, Cambria, Paso Robles, and Edna Valley in California and screened for resistance. The frequencies of populations (2020, 2021) showing resistance to each active ingredient were: pyrimethanil (94.3%, 81.8%), trifloxystrobin (97.1%, 100%), boscalid (77.1%, 77.3%), fenhexamid (8.6%, 25%). The majority of isolates were sensitive to iprodione (100%, 100%), fludioxonil (100%, 100%), fenhexamid (88.6%, 75%), and boscalid (22.9%, 22.7%). These results documented the accumulation of resistance in B. cinerea to various fungicides commonly used for Botrytis bunch rot management in California’s Central Coast. Another objective of this study was to determine the effective concentration of the six fungicides that reduces mycelial growth of the fungus by 50% (EC50). Seven B. cinerea isolates in 2020 and ten isolates in 2021 were selected and subjected to a sensitivity screening with serial dilutions of the different fungicide active ingredients. The fungicides found to have the highest EC50 values indicating reduced efficacy for inhibiting B. cinerea growth were Scala® (FRAC 9), Flint® (FRAC 11), and Endura® (FRAC 7). The fungicides found to have the lowest EC50 values indicating higher efficacy for inhibiting B. cinerea growth were Scholar® (FRAC 12) and Rovral® (FRAC 2). The results from this study provided information regarding the accumulated resistance of B. cinerea populations to certain chemical groups and therefore the efficacy of different fungicide active ingredients. This information can be utilized by growers as a tool to enhance and develop fungicide spray programs that effectively manage Botrytis bunch rot in Central Coast vineyards.

<p>  </p> <p>Tar spot is a new foliar disease of corn in the United States. Tar spot was first detected in 2015 and is now among the most important corn diseases in the Midwest. Tar spot is caused by the obligate biotrophic fungus, <em>Phyllachora maydis</em> Maubl, from the genus, <em>Phyllachora </em>which consist of over 1,200 species of host-specific fungi. Due to the recent emergence, studies relating to <em>P. maydis</em> population dynamics in the U.S. are limited. How much genetic diversity, variation, and level of gene flow are occurring within and among these populations? Knowledge of the population dynamics is imperative for understanding the pathogen’s biology, ecology, epidemiology, and management. Currently, no corn hybrid is fully resistant to tar spot. Foliar fungicides are currently the most effective option for disease management, but best practices for fungicide management remain unknown. Better information is needed on fungicide efficacy and fungicide application timing to reduce tar spot severity, protect yield, and increase profitability for Indiana corn growers. </p> <p>This research dissertation presents four chapters to answers those questions and bridge the gaps between the knowns and unknows of this novel corn-<em>Phyllachora maydis</em> pathosystem. <strong>Chapter 1</strong> presents a literature review on tar spot of corn, its economic impact, the causal pathogen, its host, lifecycle, distribution, and known management strategies as a resource for understanding the pathosystem in the U.S. <strong>Chapter 2</strong> examines the genetic population structure, diversity, geneflow and mode of reproduction in Midwest U.S. by employing microsatellite (SSR) markers. <strong>Chapter 3</strong> presents results from multi-year, multi-location, small-plot field trials on the net return of foliar fungicides and fungicide timing on tar spot management in Indiana. Lastly, <strong>Chapter 4</strong> concludes by evaluating of an integrated management strategy for tar spot by examining the integration of tillage, corn hybrids and fungicide application in reducing tar spot severity while protecting yields.</p> <p>Results provided in this research dissertation will be used to guide future studies and provide stakeholders such as researchers, corn growers, extension personnel in academia and industry with valuable information needed to guide effective disease management decisions. </p>

<p>  </p> <p>Over the past two decades, emerging fungal pathogens have been reported in numerous groups ranging from mammals to key crop species across the globe. To combat the rise of these fungal pathogens in industrial agriculture, fungicides have been developed and subsequently applied en masse. Despite their growing usage, research examining the effects of these anthropogenic contaminants on natural systems is severely limited compared to other major classes of pesticides. Of particular concern are their impacts on aquatic systems, which can be especially at risk due to their proximity to agriculture. Herein I used a tiered approach to assess the impacts of this class of pesticides on aquatic ecosystems using amphibians as model system. In the first chapter, I assessed the acute toxicity of two widely applied fungicides, pyraclostrobin and chlorothalonil, to six different species of amphibians commonly found in the Midwest. My results showed that these fungicides are very acutely toxic to several species of amphibians at levels within the expected environmental concentration (EEC). In the second chapter, I examined the impacts of long-term low-dose exposure of pyraclostrobin on the growth, development, and activity levels of three species of amphibians. Despite the acute toxicity of pyraclostrobin, sublethal effects of the fungicide were rather limited with only minor effect on growth and activity. In the third chapter, I investigated the effects of fungicide exposure on host-parasite interactions using trematodes and American Bullfrog tadpoles. I found that in all treatments pyraclostrobin increased parasite loads from ~3 to 8 times compared to control tadpoles. Additionally, parasite loads were approximately 2 times higher in tadpoles with the continued fungicide exposures compared to those tadpoles that were moved to fresh water following initial fungicide exposure. Finally, my fourth chapter investigated the impact of pyraclostrobin and chlorothalonil application regime on community-level interactions under semi-natural conditions. While chlorothalonil had limited effects on the community, I found that pyraclostrobin was acutely toxic to Gray Treefrogs at environmentally relevant concentrations and these effects were stronger with more frequent applications. Collectively, my research has demonstrated that fungicides can be acutely toxic to amphibians at EECs under laboratory and semi-natural conditions. Additionally, they have the potential to alter disease dynamics by increasing infection risk. Given our increasing usage of fungicides to control emerging fungal pathogens, a greater emphasis on understanding the environmental implications of this management strategy is needed to inform ecological risk assessments. </p>

Master of Science / Department of Plant Pathology / Erick D. DeWolf / Stripe rust, caused by Puccinia striiformis f. sp. tritici, historically has been a minor problem in the Great Plains. However, Kansas had significant losses due to stripe rust in 2001, 2003, and 2005. Recent research on the population of P. striiformis suggests changes in the fungal population may have been responsible for these epidemics. The objectives of this research were to determine conditions that are favorable for the infection of P. striiformis f. sp. tritici isolates from the current population and develop models to predict infection events. Two week old potted seedlings were inoculated with an isolate of P. striiformis and exposed to ambient weather conditions for 16 hours. Results of this bioassay were used to develop logistic regression models of infection. Models using hours at relative humidity >87%, leaf wetness, and mean relative humidity predicted infection with 93%, 80%, and 76% accuracy. Future research will use these results to determine weather patterns that influence the probability of stripe rust epidemics and to facilitate the development of regional prediction models for stripe rust. Foliar diseases of wheat result in an average yield loss of 7.8% in Kansas. Although it is possible to reduce these losses with foliar fungicides, the yield increases resulting from these applications may not justify the additional costs. The objective of this research was to develop models that help producers identify factors associated with disease-related yield loss and the profitable use of foliar fungicides. Data were collected for two years at three locations in central Kansas to determine yield response to fungicide application on eight varieties with varying degrees of resistance. Logistic regression was used to model the probability of a yield response >4 bushels per acre based on disease resistance of a variety, historical disease risk, and in-season disease risk. The accuracy of the resulting prediction models ranged from 84% to 71%. A model combining in-season disease risk and variety resistance was most accurate. The prediction accuracy of the model was 79% when tested with an independent validation dataset. In the future, these models will serve as educational tools to help producers maximize profit and productivity.

Thesis (MScAgric)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Please refer to full text for abstract / AFRIKAANSE OPSOMMING: Sien volteks vir opsomming

Azoxystrobin (AZY), a systemic broad-spectrum fungicide, is applied on crops to control soil-borne pathogenic fungi. This study aimed to determine the effects of AZY on non-target plant species and Glomus intraradices Schenck & Smith, an arbuscular mycorrhizal fungus (AMF) associated with plants' roots. We hypothesized that AZY negatively affects AMF viability; and that, if the plants were dependent on this symbiosis, AZY exerts an indirect detrimental effect on plant growth. To test this, three mycotrophic (Phalaris arundinacea L., Solidago canadense L., Geum canadense Jacq.) and one non-mycotrophic (Chenopodium album L.) native plant species were subjected to five AZY doses with or without AMF. Plants were grown for 60 days in a greenhouse, in individual pots, (4 plants X 2 AMF X 5 AZY X 6 replicates), and mesocosms (1 mes. X 2 AMF X 5 AZY X 6 replicates), and harvested 30 days after spraying, and dry mass was taken. Fresh root samples were used for microscopic assessment of AMF colonization. The results from the individual pot experiment show that the effects of AZY on biomass varied across plant species. AZY led to a significant increase in shoot and root mass of P. arundinacea, and a decrease in shoot mass of AMF inoculated G. canadense. The presence of AMF resulted in a significant increase in root and shoot mass of P. arundinacea, and an increase in root mass of S. canadense and shoot mass of C. album. In the mesocosm experiment AZY did not have a significant effect on the measured parameters, although the presence of AMF significantly increased root, shoot, and total dry mass of G. canadense and P. arundinacea. Conversely, AMF significantly decreased shoot and total dry mass of S. canadense. The results suggest that both direct and indirect effects should be taken into account when assessing the impact of pesticides on non-target plant species.