Theses and Dissertations

Permanent URI for this collectionhttps://hdl.handle.net/10217/100349

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Open Access
Molecular mechanisms of herbicide resistance in rice and kochia
(Colorado State University. Libraries, 2024) Gupta, Srishti, author; Dayan, Franck E., advisor; Gaines, Todd A., advisor; Reddy, Anireddy, committee member; Kumar, Vipan, committee member
Herbicide stress is an important challenge in agriculture and understanding how plants respond to herbicide exposure is crucial for developing effective weed management strategies. Transcription factors (TFs) play a pivotal role in regulating gene expression and mediating plant responses to various environmental stimuli, including herbicide stress. This dissertation aimed to elucidate the role of TFs in herbicide tolerance and sensitivity across plant species. A brief introduction was provided in Chapter 1. Subsequently, by analyzing transcriptomic data from different studies, we identified key TFs involved in herbicide responses. Our findings in Chapter 2 revealed distinct TF signatures, including bZIP, NAC, WRKY, and ERF, that were consistently upregulated in herbicide-tolerant plants. associated with herbicide tolerance or sensitivity, suggesting potential regulatory mechanisms in metabolic pathways and downstream signaling. These results underscore the importance of complex interplay between herbicide class, treatment duration, and plant species on TF expression patterns. In Chapter 3, we focused on herbicide resistance in rice, a critical staple crop. Transcriptomic analysis revealed upregulation of key detoxification genes, including glutathione S-transferase (GST) and cytochrome P450 (CYP450), in the NTSR mutant, suggesting their involvement in herbicide metabolism. Functional characterization confirmed increased glutathione S-transferase activity in the NTSR genotype. Additionally, computational studies identified a novel transcription factor, ZOS-1-16, with a potential role in regulating herbicide response. We investigated a novel non-target site resistance (NTSR) mechanism conferred by a mutation in the transcription factor ZOS-1-16. Our findings demonstrated that ZOS-1-16 upregulates genes like GSTs and CYPs involved in herbicide detoxification, leading to increased resistance to the herbicide quizalofop-p-ethyl (QPE). This study highlights the potential of targeting TFs for developing herbicide-resistant rice varieties. Finally, Chapter 4 explored glyphosate resistance in the invasive species Bassia scoparia (kochia). We investigated the inheritance of glyphosate resistance in kochia populations and found that it is primarily due to an increase in the copy number of the EPSPS (5‐enolpyruvyl‐3‐shikimate phosphate synthase) gene. Additionally, we estimated the outcrossing rate of kochia under field conditions and found a high level of outcrossing, which contributes to the rapid spread of glyphosate-resistant biotypes. Overall, this dissertation provides valuable insights into the role of TFs in herbicide responses and highlights the potential for developing novel strategies to enhance herbicide tolerance and manage herbicide-resistant weeds.
Embargo
Herbicide resistance in kochia and wheat: the loss and gain of weed control tools for wheat production
(Colorado State University. Libraries, 2024) Montgomery, Jacob S., author; Gaines, Todd, advisor; Dayan, Franck, committee member; Pearce, Stephen, committee member; Mason, Richard, committee member
Weeds are one of the main causes of yield loss across agricultural systems worldwide. Currently, weed control in crop production systems relies heavily on the use of chemical herbicides. While these herbicides are largely effective and very efficient, they are prone to herbicide resistance evolution in weeds. Herbicide resistance evolution is the most pressing issue facing weed scientists, currently. As researchers scramble to develop new weed control technologies, herbicide resistance traits enable the use of herbicides in new cropping systems. While this is not the long-term answer to issues facing weed managers, herbicide resistance traits offer a short-term solution to systems that may be desperate for answers. Kochia is a tumble weed that was introduced to North America in the 1800's. Since its introduction, kochia has invaded many settings of the American West. Its abiotic stress tolerance, tumble seed dispersion mechanism, and ability to outcross allow it to invade new areas and maintain genetic diversity for selection to act on. In a study reported here, I identify the genetic basis of resistance to the herbicide dicamba in a population of kochia collected from Colorado. I use linkage mapping to identify a region of the genome associated with resistance. Within this locus, I find a transposable element insertion within an exon of an AUXIN/INDOLE-3-ACETIC ACID gene. This insertion causes differential splicing that changes the amino acid sequence near the degron domain in resistant plants. I apply dicamba to Arabidopsis plants expressing wildtype ii and mutant alleles of this gene to demonstrate that this mutation is sufficient in causing dicamba resistance. Protein modeling suggests that while several amino acids are affected, a specific glycine-to-threonine substitution is likely the most important in causing resistance. Finally, the mutant allele of this gene segregates with reduced plant height and biomass, suggesting this resistance mechanism has a pleotropic effect of a fitness cost. This study demonstrates the diverse ways that adaptive alleles can be generated in weedy species and describes the genetic and physiological basis of dicamba resistance in kochia. These findings may be used to design new auxinic herbicides that are not affected by this resistance mechanism. With the loss of herbicide efficacy in the face of herbicide resistance evolution, as described above, wheat producers could benefit from the availability of more weed control options. In another study presented here, I utilize gene editing and traditional mutagenesis approaches to generate wheat plants that are deficient in sulfolipids. In rice, eliminating these sulfolipids clearly results in resistance to the herbicide oxyfluorfen. Liquid chromatography coupled with mass spectrometry (LC/MS) experiments confirmed that the edits I made to the gene UTP- GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 3 indeed resulted in drastic reduction in sulfolipid content. Dose response experiments showed that mutant lines gained moderate resistance to oxyfluorfen, but not lactofen, a herbicide from the same chemical family. Finally, LC/MS experiments confirmed that mutant wheat plants accumulated less porphyrin following oxyfluorfen application. The wheat lines developed in this study provide germplasm for trait introgression or a framework to make similar edits in locally adapted varieties to reproduce this herbicide resistance trait. If stewarded correctly, the trait will extend the effective lifespan of currently used herbicides in wheat and improve weed control.
Open Access
Management strategies for Cytospora plurivora: the role of canopy sprays in western Colorado peach orchards
(Colorado State University. Libraries, 2024) Greenberger, Jilly Sal, author; Stewart, Jane E., advisor; Tonnessen, Bradley W., committee member; Charkowski, Amy, committee member; Uchanski, Mark, committee member
Cytospora spp. are globally distributed pathogens on more than 120 species of woody plants, in both agricultural and natural systems. In Colorado, Cytospora canker, primarily caused by the fungal pathogen Cytospora plurivora, is one of the most destructive diseases affecting peach trees (Prunus persica), a key specialty crop with significant economic and cultural importance. The resulting yield loss and financial strain on peach growers threaten the survival of the industry and options for management are limited. No resistant varieties have been identified and no fungicides are currently registered for use on Cytospora canker in Colorado. Chemical management focuses on prevention of new infections on wounded tissue: the infection court for C. plurivora. Fungicides applied directly to pruning wounds have proven effective but are impractical for many growers due to the extensive labor required. Additionally, these spot treatments have not been evaluated for efficacy on wounds on main scaffold branches or trunks, which are critical infection sites. Canopy sprays, facilitated by air-blast sprayers, could be a more cost-effective option for Cytospora canker control, with the potential to target entire tree scaffolds. Air blast sprayers are currently used by growers to manage other diseases and pests, as well as for nutrient applications; however, their efficacy on canker pathogens is not well understood. This study aims to explore the utility of canopy sprays with air blast sprayers for management of C. plurivora in organic and conventional peach orchards, and to determine best practices for achieving optimum coverage of bark on scaffold branches. Field trials were conducted in organic and conventional orchards, located at the CSU Agricultural Experiment stations in western Colorado, to assess both spray coverage and fungicide efficacy. Field trials to assess air-blast spray coverage were conducted in the spring and summer of 2023 to explore the effect of season of application and fan use on bark coverage. Water Sensitive Paper (WSP) cards were placed at three heights on each tree, sprayed with water, and analyzed with ImageJ software (Rasband, 1997) to determine the percent coverage of cards. Higher percent coverage was observed in the spring on bare trees, likely due to foliage blocking cards in summer trials. Fan use had variable effects on coverage within and between orchard planting blocks. Issues with uniformity in coverage were observed in all orchard blocks, with top cards receiving the lowest coverage in almost all cases. Fungicide field trials were conducted in the fall of 2023 and spring of 2024. An Organic Materials Review Institute (OMRI) listed fungicide, lime sulfur (Lime-Sulfur Solution™, NovaSource), was tested in the organic orchard and a conventional fungicide, captan (Captan 4L, Drexel Chemical Company, Memphis, TN), tested in the conventional orchards. Trees were wounded and inoculated with mycelial plugs of C. plurivora at the bottom of primary scaffold branches, on mid-scaffold branches, and on top branches. Resulting lesions were measured several months post-inoculation to assess disease development. Fungicide efficacy was evaluated by comparing lesion area (mm2) of treated and untreated trees. In fall fungicide trials, minimal lesion growth was observed overall, and treatments with lime sulfur and captan showed no efficacy in any orchard planting block. In the spring fungicide trials, treatment with lime sulfur significantly decreased lesion size in the organic orchard: on middle branches by 58% and top branches by 87%. Results of captan treatments were inconclusive but warrant future studies. No efficacy was observed in one planting block in the conventional orchard, but in the planting block with more mature trees, captan treatment was associated with a 147% decrease in lesion size. The results of this study suggest that air blast sprayers may be an effective tool for C. plurivora management, but future studies are needed to confirm the extent of their efficacy. Fall canopy sprays may not be effective or necessary, while summer sprays may have limited efficacy due to low coverage on foliated trees. Efficacy was observed with spring application of lime sulfur at 3%, supporting its use in canopy sprays. Efficacy of captan applications could not be confirmed or rejected due to inconsistency of results. The rate used in this study, 3.5 liters/hectare, may be insufficient, as had been found previously. Midrate applications (7 liters/hectare) of captan should be tested in future studies. Overall, efficacy was limited, highlighting the importance of integrated pest management strategies and the need for continued research on alternatives to chemical control.
Open Access
Assessing the impact of hop latent viroid (HLVD) on hemp (Cannabis sativa) and exploring mitigation strategies
(Colorado State University. Libraries, 2024) Deyle, Luke, author; Nachappa, Punya, advisor; Nalam, Vamsi, committee member; Prenni, Jessica, committee member; Uchanski, Mark, committee member
The emergence of hop latent viroid (HLVd) in the hemp (Cannabis sativa L. <0.3% THC) and marijuana (C. sativa >0.3% THC) industries poses a significant threat to agricultural production. Since its first identification in California in 2019, HLVd has spread across the U.S. and Canada, causing substantial yield losses due to its ability to severely disrupt crop development. Mechanically transmitted through propagation, pollen, seed, and water, HLVd is challenging to control; and its impact on emerging crops like hemp is of particular concern. The overarching goal of this thesis was to determine the impact of HLVd on hemp quality and yield and to apply new knowledge and practices to manage HLVd, reducing losses in the hemp and marijuana industries in the U.S. and worldwide. Two objectives achieved this goal: 1) assess the impact of HLVd on the growth and yield of two hemp cultivars, NWG 2463 (dual-purpose fiber grain) and Unicorn (CBD), and 2) determine the effect of chemical elicitors in reducing HLVd infection levels and symptom development. HLVd infection did not impact overall yield metrics—such as biomass, flower, or seed yield—in either the dual-purpose cultivar NWG 2463 or the CBD cultivar Unicorn under the conditions of this study. However, HLVd-symptomatic plants in the CBD Unicorn cultivar exhibited significant reductions in cannabinoid levels, specifically THCA and CBLA: CBCA. These findings highlight the critical risks that HLVd presents to producers relying on consistent cannabinoid profiles. RT-qPCR analysis indicated that specific chemical elicitors may reduce HLVd levels in the CBD Unicorn cultivar, with 1-Triacontanol (TRIA) showing a marginally significant reduction in viroid titers compared to its ethanol (EtOH) control (p = 0.07), and Kinetin demonstrating a trend toward significance against its potassium hydroxide (KOH) control (p = 0.08). Beyond potential viroid reduction, chemical elicitors such as salicylic acid (SA), brassinolides (BR), and 6-benzylaminopurine (BAP) significantly increased biomass and flower production in the CBD Unicorn cultivar infected with HLVd. However, SA, BR, TRIA, chlormequat chloride (CCC), and methyl jasmonate (MeJA) also reduced key cannabinoid levels, notably THC and CBD, highlighting the complexity of using chemical elicitors in viroid-infected plants. The observed trade-off between enhanced plant growth and reduced cannabinoid content suggests that, although chemical elicitors may offer potential as part of an integrated management strategy, their application must be carefully optimized to avoid unintended crop losses. This research provides critical insights into the broader agricultural implications of HLVd on hemp production and highlights the need for refined viroid management practices. The potential impact of HLVd on hemp emphasizes the urgency of developing targeted strategies that balance yield improvement with cannabinoid preservation, thereby safeguarding the financial viability of hemp cultivation in the face of viroid challenges.
Open Access
Unravelling the resistance mechanism to dicamba in Palmer amaranth (Amaranthus palmeri)
(Colorado State University. Libraries, 2024) Moreno Serrano, Dustin Abdiel, author; Dayan, Franck E., advisor; Gaines, Todd A., committee member; Schipanski, Meagan, committee member
Auxin-mimic herbicides (AMHs) have been widely used for more than 70 years, primarily for control of pernicious broadleaf weeds and a few grassy weeds. So far 87 weeds have evolved resistance to AMHs, and it is expected to continue to increase over time. Resistance mechanisms to AMHs are not well understood and most of the reported cases have not been investigated to determine each individual resistance mechanism. Herbicide resistance mechanisms are classified into two main branches. Target-site-resistance (TSR) is when a mutation in herbicide binding site prevents the herbicide from interacting with the enzyme or when overexpression of the herbicide target site results in more enzyme than what the herbicide can inhibit in the plant cell. Non-target-resistance (NTSR) include enhanced herbicide metabolism, reduced absorption, altered translocation, and sequestration. In this current research, resistance to dicamba in a population of Amaranthus palmeri (Palmer amaranth) was investigated. In 2020 a population of the troublesome weed Amaranthus palmeri (Palmer amaranth) from Lauderdale county in Tennessee, USA, with a 12-fold resistance to dicamba was identified. Metabolism of dicamba was evaluated and tested using inhibitors of important enzymes involved in herbicide detoxification (e.g., cytochrome P450 monooxygenase and glutathione S-transferases). There was no difference in dicamba metabolism between the resistant Lauderdale (R_PA) and susceptible Arizona (S_PA) populations. RNA-seq study was conducted to investigate potential mutations in AUX/IAAs, which are transcriptional repressors. They regulate transcription factors like Auxin Response Factors (ARFs), and are also co-receptors of auxin-mimic herbicides, and are involved in the regulation of auxin response genes. A mutation in co-receptors can lead to auxin-mimic herbicide resistance; however, there were no mutations in 18 AUX/IAAs and also in other important proteins such as Transport Inhibitor Response 1 (TIR1), Auxin Binding Protein (APB), and Auxin Signaling F-box (AFB). In addition, auxin-response genes responded similarly or differently to dicamba in treated biotypes. Nevertheless, it is noteworthy that the expression of some AUX/IAAs genes changed after dicamba treatment in sensitive plants but not in resistant plants, especially AUX/IAA29. The results suggest that a physiological response is not primarily involved in the resistance mechanism to dicamba because no significant differences in dicamba metabolism were identified, suggesting that dicamba is broken down to less active metabolite, but at the same rate in both R_PA and S_PA. Additionally, no epinasty was observed in resistant plants, a common response when TSR is involved as a primary mechanism. PIF3/4, which is a key transcription factor involved in regulating plant development and response to light, responded to dicamba treatment in sensitive plants, while not responding in resistant plants after dicamba application. Also, expression of AUX/IAA29 did not respond in resistant plants, which is directly involved in the activation of PIF3/4, a transcription factor involved in auxin perception. We hypothesize that PIF3/4 may be involved in the resistance mechanism to dicamba through auxin signaling and/or regulation. However, this hypothesis should be validated by molecular techniques to confirm it. This dicamba-resistant Palmer amaranth biotype has a novel resistance mechanism that remains to be fully elucidated.
Open Access
Investigating ecological factors involved in the incidence and severity of Puccinia punctiformis infection in Cirsium arvense
(Colorado State University. Libraries, 2024) Astete Farfan, Almendra, author; Norton, Andrew P., advisor; Stewart, Jane E., advisor; Davis, Thomas Seth, committee member
The rust fungus Puccinia punctiformis has been proposed as a biocontrol agent against the widespread and noxious weed Cirsium arvense due to its specificity and ability to systemically infect and eventually kill C. arvense. However, the incidence of P. punctiformis is low in naturally infected systems. The environmental conditions of temperature and humidity to which P. punctiformis teliospores are exposed after production and until germination could affect their viability, and consequently, compromise the occurrence of infections. The first chapter of this thesis investigated teliospore viability for germination after exposure to different relative humidity (5 %, 22 %, 62 %, 90 % RH) and temperature levels (-20 °C, 6 °C, 23 °C) over the course of a year. Results showed that teliospore germinability decreases significantly faster when exposed to 23 °C and 62 % RH, or 90 % RH, followed by -20 °C and 5 % RH, compared to all other conditions. Teliospore priming is a stimulation process prior to germination that has been associated with increased germination in some rust fungi (Morin et al., 1992; Bruckart & Eskandari, 2002; Fisher et al., 2009). The second chapter examined how priming P. punctiformis teliospores, either in water or in a 250 µl/L solution of the germination stimulator dodecyl-NCS dissolved in water, influences their germinability, as well as the incidence and severity of systemic infection in C. arvense plants inoculated with the primed teliospores. Results showed that priming teliospores in water, without a germination stimulator, results in significantly higher germination rates compared to priming them in the 250 µl/L dodecyl-NCS solution. Furthermore, both priming treatments enable significantly greater germination proportions compared to not priming the teliospores. Statistically, the incidence and severity of the systemic infections caused by water-primed teliospores were not significantly different from those caused by teliospores primed in the 250 µl/L dodecyl-NCS solution. Ultimately, our findings suggest that environmental factors such as warm-humid and cold-dry conditions, reduce teliospore germinability. Consequently, these conditions can also limit P. punctiformis infection in C. arvense. For biocontrol purposes, we recommend to collect and store teliospores avoiding these adverse conditions to maximize their viability. Furthermore, we propose using water-primed teliospores for P. punctiformis inoculations on C. arvense, as they exhibited increased germination rates and may facilitate systemic infections in both axillar and new shoots.
Open Access
The impacts of high temperature on bacterial blight resistance genes in rice
(Colorado State University. Libraries, 2024) Shipp, Jennifer, author; Leach, Jan E., advisor; Argueso, Cristiana, committee member; Reddy, Anireddy, committee member
Rice is cultivated around the world and serves as a primary source of income and calories for many people. However, rice yield is threatened by the bacteria Xanthomonas oryzae pv. oryzae (Xoo), and outbreaks can be devastating to global communities. Xoo is the causal agent of bacterial blight (BB) in rice, and it proliferates in rice-growing climates. As climate change progresses, the trend of increasing BB severity may result in increased losses for growers. Disease severity, quantified through lesion lengths, increases at high temperature in rice. Previous studies indicated this pattern of increased disease phenotypes occurs even when a resistance (R) gene is present, except for one, Xa7. Our rationale for these experiments is to determine if the classification of an R gene can predict its performance against BB outbreaks. The classification of R genes in rice is a recent addition to the scope of our knowledge of plant pathology and has been the result of studies on nucleotide polymorphisms, genetic mapping, and fluorescent imaging of protein localization. Grouping the underlying mechanisms of action of individual R genes, such as the executor genes Xa7 and Xa10, allow for comparative studies to further elucidate details of their assigned classes. Not all R genes have been classified, but establishing a trend that some R genes maintain efficacy under higher temperatures would provide breeders with more tools to develop climate-friendly rice lines. This study indicates that R genes that remain effective at high temperature may be classified into the same category of executor R genes. More research is needed to determine if R gene classification predicts durability under heat stress. This study explores BB lesion lengths and Xoo colony counts at high and low temperatures. We find that at high temperature relative to low temperature, disease lesions were more severe in IR24, containing no active R gene, and in plants containing the R genes Xa21, xa5, and Xa3. Lesions were shorter in plants with Xa7 and Xa10. Additionally, under the same treatments, bacterial numbers increased to higher levels in IR24, Xa21, xa5, and Xa3. Numbers in Xa7 were reduced while numbers in Xa10 were low early in infection, but eventually increased beyond those measured at low temperature. Degree of lesion restriction did not always correspond to degree of restricted bacterial numbers, suggesting that severity of lesions may not always be a predictor of bacterial multiplication in the plant. Xa7 and Xa10 are classified as executor R genes. The mechanism of action in these genes may play a role in their durability at high temperatures. We hypothesize that the success of executor R genes may be a result of protein accumulation in the nucleus. This mechanism might be analogous to instances of temperature sensitive pathogen defense related protein accumulation, as seen in Arabidopsis. This mechanism may be induced or enhanced by the presence of reactive oxygen species (ROS) or other heat-stress related markers. More research is needed to explore the signaling between heat-stress pathways and R genes.
Embargo
Buffering the effects of a changing climate: Salsola tragus as a potential source of stress tolerance genes
(Colorado State University. Libraries, 2024) Lemas, John M., author; Gaines, Todd, advisor; Brown, Cynthia, committee member; Henriksen, James, committee member
The tumbleweed Salsola tragus is an allotetraploid C4 weedy member of the Salsola polyploid complex. Commonly referred to as Russian thistle, it develops a thorny habit during inflorescence, and commonly separates at an abscission layer near the soil to form a tumbleweed. This species is economically important to all land use types and is especially impactful in the Northwestern United States where it affects spring cereal production. The International Weeds Genomics Consortium recently completed a fully annotated reference genome assembly for each of the sub genomes in the somatic cells of this allotetraploid. Polyploids, in general, are overrepresented in the most troublesome weeds globally, and Salsola tragus is no exception. Recurrent formation of polyploids, increased activity of transposable elements, and increased mutation rates that follow genome duplication may lead to the de novo formation and selection of novel highly adapted alleles over time. We utilized the reference genome assembly for this species to align a stress-response transcriptome to investigate how this species responded to two selected abiotic stressors. Many expected response pathways are represented, including response to stress phytohormones, sodium-proton antiporters, calcium exchangers, and cold-responsive binding factors. In addition, several uncharacterized proteins were differentially overexpressed in the shoot and root tissues of this species. Identified genes from this species may present novel alleles for osmotic and temperature stress tolerance. Uncharacterized genes may represent novel stress response genes and can be used to improve the provided reference annotation for this species. These genes of interest may provide the scientific community with additional genomic resources to bolster crop production in this era of climate change.
Open Access
Fire-associated shifts in the soil microbiome in western conifer forests: implications for Armillaria root disease biocontrol and management
(Colorado State University. Libraries, 2024) Fitz Axen, Ada J., author; Stewart, Jane E., advisor; Kim, Mee-Sook, committee member; Charkowski, Amy O., committee member; Abdo, Zaid, committee member
The research presented in this thesis integrates the current understanding of environmental disturbances, plant associated microbiomes, and microbial biological control of fungal forest pathogens to contribute to improved disease management. In Chapter 2, I examined how fire disturbances affect soil microbial communities in areas where Armillaria root disease, caused by the pathogen Armillaria solidipes, is prevalent by documenting changes to bacterial and fungal community diversity and composition following three distinct levels of burn severity (high, low, and unburned) in a conifer forest in northern Idaho, United States. Expected reductions in bacterial community alpha diversity were observed when comparing burned communities with unburned communities; however, fungal communities showed a lack of significant change in alpha diversity in response to burn severity at the sampling time of 15-months post-fire. However, in both bacterial and fungal soil communities, compositional changes corresponding to burn severity levels were observed. Further examinations characterized similarities and differences between burn severity-associated communities and Armillaria species-associated communities to determine how these microbial changes might influence Armillaria root disease. At high-severity burn sites, colonization by A. solidipes and the associated microbial community was prevalent when compared with low-severity burn and unburned sites. In contrast, the presence and abundance of the weakly pathogenic species A. altimontana and its associated microbial community, including beneficial ectomycorrhizal fungi, appeared to be negatively impacted by high-severity burns. Further research is needed to determine which microbial taxa are critical for promoting or suppressing A. solidipes activity, yet the results from this study suggest that high-severity burns may create environments hospitable to this pathogen and thus monitoring for increased disease pressure following severe burns may be warranted. Chapter 3 focuses specifically on beneficial members of the native soil microbial community that exhibit antagonistic activity against A. solidipes. Because these native species are adapted to the environmental conditions and community interactions, they are more likely than foreign microbial species to successfully establish a stable population required for effective biological control. I isolated putative native biological control agents from soil samples collected under different burn severity conditions and tested their in vitro capabilities to inhibit the growth of A. solidipes with dual culture confrontation tests. Effective in vitro pathogen inhibition was observed with 10 microbial isolates, including five bacterial isolates from the genera Bacillus and Caballeronia and five fungal isolates from the genera Trichoderma and Mortierella. Further examination of the sites these microbes and communities originated from and their compositional changes documented in Chapter 2 revealed that the presence or abundance of our effective biological control organisms did not differ based on burn severity. Importantly, this suggests that fire disturbances may not directly influence the use of these species in management methods for Armillaria root disease in similar conifer forests. However, considering the increased presence of A. solidipes observed following a high-severity burn, there may be additional biotic or abiotic influences apart from biological control agents that are influencing the activity of A. solidipes after fire. These studies enhance our understanding of how abiotic and biotic influences interact to affect the presence of virulent soilborne forest pathogens and associated soil microbes. Considering the effects of these interactions is critical for the development of sustainable long-term management strategies that will help to preserve these ecosystems facing increasing environmental and pathogen-related stressors. The overall goals of this research are to build upon the growing body of research examining how the soil microbiome contributes to disease development and to provide tangible results that can be incorporated by forest managers to help reduce damage caused by Armillaria root disease in fire-prone conifer forests.
Embargo
Species distribution models for and policy approaches to invasive plant ecology and management
(Colorado State University. Libraries, 2024) Teich, Nathan Benjamin, author; Brown, Cynthia S., advisor; Jarnevich, Catherine, committee member; Pearse, Ian, committee member; Evangelista, Paul, committee member
The ability of abundance-based Species Distribution Models (SDMs) to predict where invasive plants can be abundant, and to what degree, is a powerful research and management tool. Often, invasive plant abundance-based SDMs are created using similar inputs and approaches as occurrence SDMs. However, invasive plant ecology literature suggests that the factors found to control invasive plant abundance are more diverse and contextual, and therefore not entirely interchangeable with factors that control invasive plant occurrence. To ensure invasive plant abundance-based SDMs are leveraging the robust body of knowledge, this paper aims to highlight and summarize the ecological factors underpinning invasive plant abundance and reviews how those factors can be represented within abundance-based SDMs. I find that while the inclusion of invasive plant abundance governing factors often improves abundance-based SDM performance, certain governing factors are ubiquitously represented while others are less commonly accounted for in model creation despite their ecological importance. Barriers to incorporating invasive plant abundance governing factors into abundance-based SDMs often include data limitations or methodological uncertainty. Finally, we provide future research directions that would help address certain barriers and improve our ability to integrate abundance governing factors into SDMs. Invasive plants, when they become dominant components of a plant community, threaten native species and ecosystem processes. Abundance-based SDMs are gaining traction as a geospatial tool to predict where invasive plants can become abundant and have negative impacts. Biotic interactions influence invasive plant abundance locally but are often not included within the abundance-based SDM creation process. At present, it is unknown to what degree local-scale biotic interactions with other plant species determine locations where invasive plant species can become abundant. Using data from large-scale abundance observations of the invasive plant cheatgrass (Bromus tectorum) paired with data from plant communities in the western United States, we quantified the degree to which biotic interactions explain where cheatgrass is abundant beyond what would be anticipated from an abundance-based SDM created with abiotic and landscape context predictors alone. To this end, we fit Generalized Linear Models (GLMs) for different categories of cheatgrass abundance and used the predicted suitability SDM outputs alongside biotic variables, representing known competitive and facilitative interactions, to determine if including biotic interactions improved a model's explanatory power. The addition of biotic variables marginally improved GLMs for low (5-25%) and medium (25+-50%) cheatgrass abundance but displayed greater improved performance for high (50+%) cheatgrass abundance. Most notable amongst the specific biotic variables was the cover of perennial graminoid cover, representing known competitors of cheatgrass, which interacted with SDM environmental suitability to strongly reduce the probability of high cheatgrass abundance. These findings suggest that considering biotic interactions alongside SDM predicted suitability may indeed improve our ability to predict abundance locations of invasive plant species, but potentially only in specific contexts such as where that species can already achieve high abundance. Invasive plants cost the US billions of dollars each year due to ecological and economic impacts as well as management costs. One of the most common pathways of introduction and spread of invasive plants is through ornamental plant sales. While solutions such as regulations and voluntary self-bans have been implemented in some instances to mitigate this problem, widespread adoption has not occurred. As such, new alternatives should be explored. Opt-in labeling programs are commonly used throughout the agricultural industry to better inform customers about the products they are purchasing. An opt-in labeling program that consists of a partnership between retailers and governments or non-profit organizations could help reduce the spread of invasive plants by influencing customer behavior. This approach would be less costly to retailers than regulations, create new invasive plant prevention opportunities for governments and non-profits, and better inform consumers about specific invasive plant species.
Embargo
Candidate gene identification for glyphosate resistance and rapid cell death in Ambrosia trifida
(Colorado State University. Libraries, 2024) Sparks, Crystal Devona, author; Gaines, Todd, advisor; Dayan, Franck, committee member; Beffa, Roland, committee member; Nishimura, Marc, committee member; Westra, Phil, committee member
Glyphosate is one of the most widely used herbicides worldwide due to favorable chemical characteristics and availability of compatible transgenic biotechnology in crops. Resistance to glyphosate has evolved in many weed species capable of significant yield reduction in top production systems globally. One such species is Ambrosia trifida (giant ragweed), a monoecious broadleaf with imperfect flowers native to North America where it is highly competitive in corn, soybean, and cotton production. Some glyphosate resistant populations of A. trifida also display a rapid response with cell death in the mature leaves within 24-48 hours after treatment with glyphosate. Transcriptomic analysis revealed differential expression of multiple gene families associated with known glyphosate resistance mechanisms such as ATP-binding cassette (ABC) transporters and aldo-keto reductases. Gene ontology analysis showed an enrichment of many genes related to phytohormone response to biotic and abiotic stress in the differentially expressed genes. This could be related to a novel glyphosate resistance mechanism or a signaling cascade involved in the rapid cell death response. The A. trifida genome contains two loci of the glyphosate target site gene 5-enolpyruvylshikimate-3-phosphate-synthase (EPSPS), with a previously reported Pro106Ser mutation in EPSPS2. This locus showed up-regulation by three hours after treatment. Trait mapping revealed three genomic regions associated with glyphosate resistance and a single interval associated with the rapid response. Along with phenotypic segregation ratios, this indicates that resistance and rapid response traits are genetically independent and multiple genes likely contribute to resistance.
Open Access
Community structure and pathogenomics of Pinaceae-infecting Fusarium spp.
(Colorado State University. Libraries, 2024) Dobbs, John, author; Stewart, Jane E., advisor; Kim, Mee-Sook, committee member; Sloan, Daniel B., committee member; Heuberger, Adam L., committee member
Due to a warming climate, the need for nursery grown conifer seedlings is continually increasing. However, several Fusarium spp. that cause pre- and post-emergent damping-off and root disease can hinder production of conifer seedlings. These soil or seed-borne Fusarium pathogens of conifers infect seedlings through the developing roots, and their similar effects on conifer hosts suggests that these pathogens may share a common evolutionary history. The shared ecological function of these Fusarium pathogens is likely associated with lineage-specific (LS) chromosomes or virulence gene(s) that are shared among these species. Identifying these potentially shared chromosomes or gene(s) and their functionality is best approached through the use of multiple 'omics technologies. Taken together, genomics, transcriptomics, proteomics, and metabolomics provide a comprehensive overview of the plant-microbial interactions at the time of Fusarium infection. This research accentuates how a combination of these technologies, such as genomics and transcriptomics, can be used to elucidate the biology of Fusarium pathogens and identify the presence of virulence-associated LS chromosomes or virulence gene(s) that facilitate the development of tools to rapidly identify and track these important pathogens. Chapter two, published in Frontiers in Plant Science, presents the observed regional effect on community structure of Fusarioid fungi collected from conifer seedlings among nurseries across the contiguous USA. The need for a global consensus to establish and maintain databases based on Fusarioid species type strains as references due to the continuing taxonomic disputes about the appropriate classification of Fusarium spp. designations was also discussed. For this reason, phylogenetic placement of the isolates was used for species identification; however, it is recognized that more research, such as whole genome sequencing, is needed to further validate the taxonomic identify of the isolates used in this study. Chapter three presents the whole genome comparisons of 17 Fusarium spp. isolates collected from conifer seedlings. Based on phylogenetic analyses of 16 conserved loci and composition of predicted genes, species were shown similar within and among Fusarium species complexes. Putative profiles of pathogenicity/virulence genes, including secreted in xylem (SIX) genes 2, 3, 9, and 14, and secondary metabolites, including the mycotoxins fumonisin and deoxynivelanol, were identified among the species complexes, but validation of expression of these genes is needed to demonstrate their functionality. Chapter four explores the mechanisms of pathogenicity and/or virulence of two understudied Fusarium spp., F. commune and F. annulatum, on conifer and non-conifer hosts and the differential gene expression in a susceptible conifer species. Further, the putative secretome profiles of Fusarium spp. within species complexes were identified, containing secreted carbohydrate-active enzymes, major facilitator supergroup transporters, apoplastic effectors, and gene products involved in secondary metabolite biosynthesis such as prolipyrone B/gibepyrone D, aurofusarin, and deoxinivelanol. Results from this study showed F. annulatum and F. commune caused disease on young conifer and non-conifer seedlings and identified putative genes associated with broad pathogenicity, and possibly indicating age-related resistance within the conifer host to certain upregulated pathogenicity genes. Due to the threat of spreading fungal pathogens from nurseries to field sites through latent infected seedlings and seed, this research highlights the need for robust early detection methods, while also providing insight into the biology of 17 Fusarium spp. that are potentially pathogenic to conifer seedlings. This research will help further develop technologies that aid managers for controlling Fusarium damping-off and root disease and mitigating the spread of novel haplotypes across regions.
Open Access
Investigating the resistance status to permethrin and temephos in Aedes aegypti (the yellow fever mosquito)
(Colorado State University. Libraries, 2024) Arthur, Nicholas Wynne, author; Norton, Andrew, advisor; Camper, Matt, committee member; Kading, Rebekah, committee member; Saavedra-Rodriguez, Karla, committee member
Aedes aegypti (Ae. aegypti) is the principle urban vector of several viruses of high medical significance which carry a disease burden on a global scale. Ae. aegypti is anthropophilic and lives in close association with humans. This places nearly half of the global population at risk of becoming infected with an arboviral pathogen every year. Therefore, emphasis must be placed on investigating methods for controlling this vector to combat and reduce the spread of human disease. This is especially true in areas where socioeconomic factors promote sustained transmission cycles. While vector control programs use a variety of strategies, the primary method of reducing vector populations is through insecticide use. Widespread use of insecticides has placed intense selection pressures on Ae. aegypti populations and resistance mechanisms have developed. Target site modifications and the expression of detoxifying enzymes are the most significant resistance mechanisms to date. Several single nucleotide polymorphisms resulting in amino acid changes within the voltage-gated sodium channel (VGSC) have been shown to reduce binding site sensitivity and confer resistance to pyrethroids. Specifically, mutations at the knockdown-resistant (kdr) 410, 1,016, and 1,534 sites have been associated with a reduction in pyrethroid sensitivity. I investigated the resistance status to permethrin and temephos at five locations in Hidalgo County, Texas. I determined the presence of permethrin resistance using a well-characterized susceptible colony as a reference for insecticide sensitivity. The resistant allele C1,534 reached fixation at all sites and L410 and I1,016 were found at high frequencies. The permethrin resistance was over 40-fold when compared to the reference colony. The sites were less resistant to temephos at approximately 6-fold to 12-fold, which I attributed to cessation of this insecticide in the continental United States since 2016. In the absence of selection pressures mosquito populations trend towards susceptibility, which suggests that there are potential fitness costs associated with insecticide resistance. Studying these associations is important to public health as they may support different strategies to reduce vector populations. I used two collections from Tapachula, Mexico, that were free of pyrethroid exposure since 2013, to determine the presence of two previously described fitness cost metrics: wing length and egg production. I found that the average wing length of V410L and V1,016I homozygous resistant individuals were significantly smaller compared to homozygous susceptible individuals. The interaction between wing length and genotype had no effect on egg production. Wing length had no significant effect on egg production. Most notably, L410 and I1,016 resistant alleles had no effect on egg production.
Open Access
Factors contributing to herbicide response in CoAXium wheat
(Colorado State University. Libraries, 2024) Pelon, Amber L., author; Dayan, Franck, advisor; Gaines, Todd, committee member; Schipanski, Meagan, committee member
Compared to other pests, weed competition has the most significant negative impact on wheat grain yield. Understanding the contribution of metabolism in overall tolerance to herbicides can lead to new methods for controlling weeds in wheat. Glutathione S-transferase's (GSTs) role in the detoxification of herbicides has been studied since 1970. Previous literature reported increased resistance to herbicides with higher GST activity in black grass (Alopecurus myosuroides) and Asia minor bluegrass (Polypogon fugax). Resistance could be reversed by inhibiting GST activity. This research assesses the role of Phase 2 plant cell metabolism by testing (GST) inhibition to see if it influences the metabolism of quizalofop P-ethyl (QPE) in winter wheat (Triticum aestivum). We hypothesized that the addition of a safener would make the wheat more tolerant to the herbicide while the addition of a GST inhibitor would make the wheat more sensitive to QPE. Experiments were conducted analyzing the QPE effect on whole-plant biomass and an LC-MS/MS analysis of the amount of quizalofop acid (QZA) found in plant extracts. Safeners enhanced herbicide metabolism which increased CoAXium wheat tolerance to QPE. GST inhibitors, conversely, decreased herbicide metabolism causing CoAXium wheat to be more sensitive to QPE. Understanding the contribution of metabolism in overall resistance to herbicides can lead to breeding improvements for more herbicide-tolerant wheat varieties and new methods for controlling weeds in wheat.
Open Access
A microbiome approach to cultivation and management of sugar beet
(Colorado State University. Libraries, 2024) Gaylord, Margaret, author; Trivedi, Pankaj, advisor; Charkowski, Amy, committee member; Wallenstein, Matthew, committee member
The world's population is projected to reach 9.8 billion by 2050, while the urgent threat of climate change is expected to impact crop physiology and pest dynamics. Understanding, preserving and leveraging the plant-associated microbiome can result in enhanced agroecosystem functioning and disease resistance for agricultural crops, thus improving food security. Sugar beet, an economically important sugar producer in the northern hemisphere, offers insights into plant-microbiome dynamics due to its susceptibility to pathogenic microbes and its association with disease suppressive soils. Cultural and chemical management practices of sugar beet are a persistent debate due to the potential negative effects on the essential microbiome and the emergence of resistant populations. To investigate the impact of weed control strategies on the soil microbiome, we conducted a long-term field study at two locations. Using next-generation sequencing and in vitro assays, we assessed the effects of glyphosate, a mix of selective herbicides and tillage treatments on the structure and function of the soil microbiome. Furthermore, we isolated 136 bacteria from the sugar beet agroecosystem and evaluated their antagonistic abilities against key diseases of sugar beet. Through in vitro and greenhouse assays, we identified effective microbial consortia for disease reduction. Additionally, we investigated the interactions between a single antagonistic isolate and an important fungal disease of sugar beet using transcriptomic analysis to reveal underlying mechanisms for biological control and pathogen response. This comprehensive understanding of the impact of various management strategies on the microbiome provides crucial insights for future crop management and highlights the potential for exploiting beneficial microbes to enhance disease control.
Open Access
Exploring the hemp virome and assessing hemp germplasm for resistance to emerging pathogens
(Colorado State University. Libraries, 2024) Hackenberg, Laine, author; Nachappa, Punya, advisor; Roberts, Robyn, committee member; Stenglein, Mark, committee member
Hemp (Cannabis sativa L.), commonly grown for its seeds, fiber, and non-psychoactive cannabinoids, has been experiencing a resurgence in the United States with its recent legalization. While farmers across the nation have readily adopted this crop, resources for pest management are still lacking, particularly regarding the diversity and distribution of pathogens. As production increases and the crop diversifies, the emergence and spread of these pathogens are certain. To circumvent loss due to disease, research is needed understand the threats and to identify sustainable management options. The goal of this study is to describe the diversity and distribution of viruses/viroids infecting hemp in Colorado and to determine if there is genetic resistance to pathogens in hemp. The objectives of this study are to 1) characterize the virome of different hemp cultivars throughout the growing season across different locations and 2) screen a panel of genetically unique genotypes of hemp for resistance to emerging viruses/viroids of hemp. Throughout 2021 and 2022, the hemp virome was examined in four major hemp producing regions of Colorado. In total, nine fields were sampled, and each field was visited during three phenological stages (early vegetative, late vegetative, and mature flowering) in order to characterize the virome throughout the growing season. Leaf tissue samples were collected from two cultivars of hemp from each field site. These tissue samples were submitted for High Throughput Sequencing (HTS) and upon bioinformatic analysis, candidate virus/viroid sequences were validated. Across both years, a total of seven viruses were identified: Alfalfa mosaic virus (AMV), Beet curly top virus (BCTV), Cannabis cryptic virus (CanCV), Cannabis sativa mitovirus (CasaMV1), Grapevine line pattern virus (GLPV), Opuntia umbra-like virus (OULV), and Tomato bushy stunt virus (TBSV). All viruses identified had >97% nucleotide identity to the nearest GenBank accession. Between individual cultivars isolated from the same field, both similar and unique viromes were observed. Viral diversity and incidence increased as the growing season progressed for both years. The three viruses that were most commonly found across all regions were CasaMV1, GLPV, and BCTV. Dominating the virome in viral load were CasaMV1 and GLPV. Given the prevalence of BCTV in the virome, in addition to its prevalence in hemp across the western United States, 13 genotypes of hemp were screened for resistance to this pathogen. These genotypes of hemp are genetically diverse, which will aide in the discovery of candidate genes involved with resistance. BCTV is the causal agent of curly top disease which can have drastic symptomology in hemp plants, causing malformed growth, stunted plants, and crop loss up to 100%. Varying BCTV copy number was observed across the hemp genotypes. Additionally, percent disease index (PDI) was analyzed to determine the frequency of infection of individual genotypes. Two of the genotypes were observed to have a lower PDI than the others, 4587 and 4710. Hop latent viroid (HLVd) has been emerging as a threat to the cannabis industry. It has been described across North America but is believed to be worldwide due to its global distribution in hops. HLVd has been documented to cause drastic reduction in cannabinoid content in mature inflorescences and therefore has the potential for substantial economic losses. Although not identified within the 2021 or 2022 virome, HLVd was determined to be an important threat facing hemp production therefore it was included in the screening. Similarly to BCTV, a panel of 14 genetically unique genotypes of hemp were analyzed for resistance to HLVd. Resistance was identified in a single genotype, 517, which had a lower frequency of infection than the others. However, no varying viroidal loads were observed between genotypes. Throughout this study, viruses associated with hemp were described as well as the identification of genetic resistance to emerging pathogens. This work will help to further integrated pest management strategies and promote sustainable agriculture.
Embargo
The need for new inhibitors of photosynthesis in agricultural settings, and the novel herbicidal compound AS9057
(Colorado State University. Libraries, 2024) Twitty, Alyssa, author; Dayan, Franck, advisor; Abdel-Ghany, Salah, committee member; Phillip, Yael, committee member
Due to increased food demand, the need for use of herbicides is both necessary and on the rise. Several herbicide classes target photosynthetic electron transport: HRAC Groups 5, 6, and 22. These herbicides are used in large amounts in many different cropping systems to control several species of broadleaf and grass weeds. The first chapter provides a comprehensive review of what these photosynthesis inhibitors are, how they are used and their mode of action. Presently, commercial herbicides only inhibit electron flow at two different sites (PSII and PSI). Those which inhibit electron flow at PSII block the movement of electrons down the electron transport chain, while those which inhibit at PSI accept electrons. Necrosis developing on the leaves of plants treated with PSII and PSI inhibitors is due to the accumulation of reactive oxygen species. Evolution of resistance, toxicity concerns, and other limitations of these herbicides call for the exploration of new chemistries that can be used to target this pathway. One of these new chemistries has been identified as AS9057. AS9057 is a natural product identified as a novel herbicide with a potentially new mode of action using AI4AI, an AI platform for herbicide discovery developed by Agrematch. Greenhouse trials demonstrated that the herbicidal activity of AS9057 was light-dependent. The rapid burndown symptoms-developing on treated plants, combined with its chemical structure, suggested that AS9057 may target photosystem II. Measurements of photosynthetic electron transport rates in treated plants alongside data from oxygen evolution assays did not support this hypothesis. Further experiments suggested the AS9057 may instead act as an electron diverter. Oxygen consumption assays in isolated thylakoid membranes using a variety of electron transport inhibitors revealed that AS9057 likely acts on photosystem I in a similar manner to paraquat, but at a potentially new step between P700 and NADP+. This is consistent with other reports that AS9057 can act as an electron acceptor for flavoproteins. Ferredoxin-NAPD+ reductase is a flavoprotein with a redox potential similar to that of AS9057. Thus, it is currently hypothesized that AS9057 acts as an electron acceptor at or near the ferredoxin to form a radical and generate reactive oxygen species which causes the light-dependent herbicidal effect which is observed in treated plants from greenhouse trials.
Open Access
Population genetics prior to biological control: Ceutorhynchus weevils proposed for managing garlic mustard
(Colorado State University. Libraries, 2009) Rauth, Steven J., author; Hufbauer, Ruth, advisor
I studied the population genetic structure of three weevil species, Ceutorhynchus alliariae, C. roberti, and C. scrobicollis, being considered for the biological control of garlic mustard, Alliaria petiolata, in North America. My first objective was to develop a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay which could be used to identify the morphologically indistinguishable larvae. This assay was developed for use in the analysis of population genetic structure of the three species and to aid scientists in evaluating host-specificity test results where larval development was incomplete or adults failed to emerge. The resulting assay provides a fast and inexpensive means of identifying otherwise indistinguishable larvae. My second objective was to study the population genetic structure of C. scrobicollis, to evaluate whether the areas where individuals were being collected for host-specificity testing consisted of one or more populations, to estimate the numbers of individuals needed during host-specificity testing and later introduction to adequately represent the diversity of the population, and to evaluate dispersal potential. Results suggest that C. scrobicollis in the area of Berlin, Germany constitute a network of subpopulations with low but significant differentiation among sites and movement of individuals between sites. I estimated that the number of individuals that would need to be sampled to capture 90% or 99% of the genetic diversity in the Berlin area was 10 and 27, respectively. The estimated average dispersal distance based on assignment tests for C. scrobicollis was 28 km. My third objective was to compare the differences in population genetic structure between C. alliariae and C. roberti to determine whether differences in genetic diversity or dispersal potential might aid in prioritizing one species over the other. These two species have similar life histories, distributions, and effects on garlic mustard. Results showed that, over a comparable region in central Europe, total gene diversity was significantly higher in C. roberti, though the difference between the two species was relatively small. Assignment tests suggest there is substantial gene flow among sites for both species. Overall, the results were similar for both species, and I recommend prioritizing based on biological or methodological attributes.
Open Access
Molecular genetics of glyphosate resistance in Palmer amaranth (Amaranthus palmeri L.)
(Colorado State University. Libraries, 2009) Gaines, Todd A., author; Westra, Philip, advisor; Leach, Jan, advisor
Glyphosate resistant Palmer amaranth populations were identified in Georgia in 2004. Studies were undertaken to characterize inheritance, the molecular basis of resistance, and the potential for gene transfer to related Amaranthus species. Dose response results support rejecting a monogenic inheritance hypothesis in favor of an alternative polygenic, additive inheritance model. Apomixis in genetic populations used for inheritance studies is probably occurring and makes interpretation of inheritance difficult. Glyphosate resistance in Palmer amaranth appears to be incompletely dominant and may be polygenic. No target site mutations known to confer resistance were identified in resistant alleles of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, the target of glyphosate. Estimation of gene copy numbers of EPSPS relative to acetolactate synthase (ALS) in gDNA by quantitative PCR (qPCR) suggested that resistant plant genomes contain 64 to 128 times more copies of EPSPS than susceptible plants. qPCR on cDNA revealed that EPSPS was expressed approximately 35 times higher in resistant plants. Elevated EPSPS copy number is heritable and correlates with expression level and resistance in F2 populations. The molecular basis of resistance is likely due to increased production of EPSPS due to gene amplification. This is the first documented occurrence of EPSPS gene amplification in a weed population under glyphosate selection pressure. The risk of resistance gene transfer was measured with field studies and hand crosses with A. hybridus, A. retroflexus, A. powellii, A. spinosus, and A. tuberculatus. Glyphosate application (0.4 kg ha-1) was used to screen for resistant progeny from the crosses. Hybridization with A. spinosus occurred in both years of the field study and in hand crosses, with average frequency ranging from <0.01% to 1.4%. Hybrids with A. spinosus were either monoecious or dioecious. Monoecious plants produced seed through self-pollination, and the F2 progeny were segregating for resistance. Hybridization occurred in the 2007 field study with A. hybridus (<0.01%) and A. tuberculatus (0.08% and 0.19% for two accessions), all of the hybrid plants were dioecious, and none produced seed. The highest risk for glyphosate resistance gene transfer from A. palmeri is to A. spinosus.
Open Access
Iris yellow spot virus in Colorado onions: a survey of its spatial distribution and techniques to manage the pest
(Colorado State University. Libraries, 2007) Fichtner, Scott M., author; Schwartz, Howard F., advisor; Hill, Joe, advisor
The Iris yellow spot virus (IYSV) is a new, and at times devastating pathogen of alliums throughout the U.S. as well as many other countries. Since its discovery in Colorado in 2001, IYSV has been identified in nearly all of the major onion producing regions within the state. The severity of this virus disease appears to fluctuate from one year to the next but incidence continues to increase with newly infested fields identified each year. With the number of outbreaks on the rise and the inadequacy of current control strategies, new management techniques as well as novel chemistry pesticides have become a major focus for the management of this virus disease and its thrips vector. Our trials demonstrated the use of reflective materials such as straw or silver reflective mulch can result in a reduction in thrips populations by as much as 69% on onions and a reduction of nearly 9% in IYSV disease incidence. Additionally, Entrust (Spinosad) and Aza-Direct (Neem extract) were found to work as well as or better than conventional materials such as Warrior (Pyrethroid) and Lannate (Carbamate). To better understand the epidemiology of the IYSV pathogen, we also conducted an extensive survey at several locations along the Colorado Front Range and Western Slope. In our surveys, we collected information including thrips populations and incidence of IYSV using 0.2 ha grids developed using mapping software (MapInfo) creating several randomly chosen plots in each field. With data collected on several sampling dates, we attempted to identify a spatial correlation of within field spread of the virus during the growing season. The levels of positive spatial autocorrelation from our survey locations were minimal, this leads us to believe that secondary outbreaks of the disease are occurring in a random fashion across the field.