Browsing by Author "Gaines, Todd, committee member"
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Item Open Access Artificial intelligence powered personalized agriculture(Colorado State University. Libraries, 2023) Tetala, Satya Surya Dattatreya Reddy, author; Simske, Steven, advisor; Conrad, Steve, committee member; Gaines, Todd, committee member; Nalam, Vamsi, committee memberThe integration of Artificial Intelligence (AI) in agriculture has shown the potential to improve crop selection and enhance sustainability practices. In this study, we aim to investigate the benefits and feasibility of using AI-powered personalized recommendations for crop selection and sustainability practices in the context of agroecology. We propose to lay the foundation for an agricultural recommendation engine that considers several parameters that influence yield and presents the best crop(s) to sow based on the model's output. We aim to examine this recommendation engine's impact on agriculture's sustainability and to evaluate its effectiveness and accuracy. Our ultimate goal is to provide a comprehensive understanding of the potential benefits and challenges of using AI-powered recommendations in agriculture and to lay the foundation for the development of a practical, effective, and user-friendly recommendation engine that can help farmers make informed decisions about their crops and improve the long-term sustainability of agriculture.Item Open Access Characterization of Sorghum bicolor genotypes under varying water regimes(Colorado State University. Libraries, 2019) Person, Taylor, author; Jahn, Courtney E., advisor; Byrne, Pat, committee member; Gaines, Todd, committee memberAgriculture is the largest consumer of fresh water, accounting for 70% of use globally. The availability of water is expected to decrease in future climate models. It is imperative to develop crop varieties with improved performance under targeted limited water environments. One approach to address this aim is capitalizing on inherent variability for drought tolerance traits in crops. Depending on the nature of water stress and other environmental factors, specific root morphology, shoot morphology, and the harvest index are selectable traits that can distinguish performance of different genotypes in crops. These aforementioned parameters discriminate relative water-stressed performance in many studied crop species. Among these is sorghum (Sorghum bicolor), a grain crop adapted to many different environments, particularly where limited rainfall is an agricultural constraint. The specific objectives of the following thesis were to 1) characterize the morphology of a sorghum recombinant inbred line (RIL) population (n = 430) of Sorghum bicolor for response to varying moisture regimes and 2) evaluate 10 selected genotypes for below-ground morphology in the greenhouse and field for response to varying moisture regimes. This population expresses a wide range of phenotypes in response to varying moisture regimes in panicle weight, shoot weight, harvest index, plant height, stem diameter, tillering and days to flowering. Ten selected RILs, including the two population parents, BTx623 and IS3620C, represent the population distribution and respond uniquely to different moisture environments. When subjected to drought stress and subsequent recovery when re-watered in the greenhouse, root system response varied at both time points. Root system and stem size are indicators of this response and vascular tissue variation may play a role in these varied responses. In the field, the root system of these ten RILs, as quantified by crown root angle, had a tendency to grow more vertically than horizontally under dryland conditions while high moisture environments showed no association with root system orientation. Taken together, this study provides foundational knowledge on above and below-ground responses of RIL population BTx623 X IS3620C to varying moisture environments.Item 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 memberCompared 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.Item Open Access Indaziflam: a new cellulose biosynthesis inhibiting herbicide provides long-term control of invasive winter annual grasses(Colorado State University. Libraries, 2017) Sebastian, Derek James, author; Nissen, Scott, advisor; Beck, George, committee member; Meiman, Paul, committee member; Gaines, Todd, committee memberInvasive winter annual grasses such as downy brome (Bromus tectorum L.) are a threat to native ecosystems throughout the US. These invasive grasses exploit moisture and nutrients throughout the fall and early spring before native plants break dormancy. This results in decreased native species abundance and development of monotypic stands. Short-term downy brome management has been shown to be effective; however, the soil seed reserve has often been overlooked although it's the mechanism responsible for rapid re-establishment. While glyphosate, imazapic, and rimsulfuron are herbicides commonly recommended to control invasive, annual grasses, their performance is inconsistent, and they can injure desirable perennial grasses. Indaziflam is a recently registered cellulose-biosynthesis inhibiting herbicide, providing broad spectrum control of annual grass and broadleaf weeds. Indaziflam (Esplanade®, Bayer CropScience) is a cellulose biosynthesis inhibiting (CBI) herbicide that is a unique mode of action for resistance management and has broad spectrum activity at low application rates. At three sites, glyphosate and rimsulfuron provided less downy brome control than indaziflam one year after treatment (YAT). Percent downy brome control with imazapic decreased significantly 2 YAT (45-64%), and 3 YAT (10-32%). Across all sites and application timings, indaziflam provided the greatest downy brome control 2 YAT (89-100%) and 3 YAT (83-100%). At two additional sites evaluating five application timings, indaziflam treatments resulted in superior invasive winter annual grass control 2 YAT (84% ± 5.1 to 99% ± 0.5) compared to imazapic (36% ± 1.2). Indaziflam treatments significantly increased biomass and species richness of co-occurring species, 2 YAT. In a greenhouse bioassay, indaziflam was significantly more active on downy brome, feral rye (Secale cereale L.), jointed goatgrass (Aegilops cylindrica L.), Japanese brome (Bromus japonicus Thunb.), medusahead (Taeniatherum caput-medusae [L.] Nevski), and ventenata (Ventenata dubia (Leers) Coss) compared to imazapic, with the exception of jointed goatgrass. Comparing all species, the GR50 values for imazapic were on average 12 times higher than indaziflam. Indaziflam's increased activity on monocots could provide a new alternative management strategy for long-term control of multiple invasive winter annual grasses that invade >23 million ha of US rangeland. Indaziflam could potentially be used to eliminate the soil seed bank of these invasive grasses (< 5 years), decrease fine fuel accumulation, and ultimately increase the competitiveness of perennial co-occurring species.Item Open Access Investigating resistance and the rapid response to glyphosate in giant ragweed (Ambrosia trifida L.)(Colorado State University. Libraries, 2016) Van Horn, Christopher R., author; Westra, Phil, advisor; Reddy, Anireddy, advisor; Argueso, Cris, committee member; Gaines, Todd, committee member; Leach, Jan, committee memberThe introduction of glyphosate-resistant crops along with widespread multiple in-season applications of glyphosate as part of weed management strategies that fail to address long-term weed control have provided the perfect scenario to foster the recent boom in glyphosate-resistant weeds. In order to implement best strategies to manage glyphosate-resistant weeds, it is important to understand the mechanism of resistance. Glyphosate targets and inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which prevents the synthesis of aromatic amino acids. We have investigated the mechanism of glyphosate resistance using several geographically diverse giant ragweed populations. From these populations we have characterized three phenotypic responses to glyphosate treatment: susceptible (GS), resistant slow response (GR slow), and resistant rapid response (GR rapid). Glyphosate resistance in giant ragweed (Ambrosia trifida L.) was first discovered in 2004 and the rapid response biotype was first identified in 2008. The molecular basis for resistance and the rapid response remains unknown. Our objective is to analyze glyphosate resistance and the rapid response in giant ragweed using physiological and molecular techniques. In whole-plant dose-response experiments conducted under greenhouse conditions, the glyphosate ED50 values (the effective dose that reduced shoot mass 50% relative to non-treated plants) of GR rapid biotypes were 4.2- and 2.3-fold greater than the ED50 values of GS biotypes and GR slow biotypes were 3.3- and 3.6-fold greater than the ED50 values of GS biotypes. The effective concentration that increased shikimate accumulation 50% relative to non-treated leaf tissue (EC50) was 4.1- and 3.9-fold higher (P < 0.05) for GR rapid and GR slow biotypes, respectively, than GS biotypes based on values averaged across accessions of the same biotype. However, at high glyphosate concentrations (1,000 to 2,000 μM), shikimate accumulation in the GR biotypes was similar to or greater than the GS biotypes. EPSPS sequence analysis showed no nucleotide mutation at a position where mutations are known to confer resistance in multiple species. Genomic copy number analysis found no evidence of target gene amplification. Whole plant physiology experiments suggest the rapid response is carbon dependent and both Phenylalanine and Tyrosine play a role in the stimulation of the rapid response. Excised leaf discs show H2O2 accumulation in mature leaf tissue of the GR rapid response biotype within 30 minutes after glyphosate application. Transcriptomic analysis of GR rapid and GS giant ragweed has identified significant differentially expressed genes that may be linked to glyphosate resistance and/or the rapid response. RNA-seq data was validated through qRT-PCR analysis. Six candidate genes were analyzed using qRT-PCR, two of which were selected for further expression analysis in an F2 population segregating for resistance. The final two candidate genes, osmotin 34 and S-adenosylmethionine synthetase 3, did not show a similar segregation pattern as seen in the F2 individuals. The large amount of RNA-seq data collected will continue to be used to determine key marker genes that could provide further insight into the glyphosate resistance mechanism present in this species. These initial results provide a framework for the future of giant ragweed glyphosate resistance research, which becomes increasingly important as the use of glyphosate-resistant crops develops world-wide. With this research, we can continue to work toward sustainable forms of herbicide weed management.Item Open Access Mapping Rhizoctonia root and crown rot resistance from sugar beet germplasm FC709-2 using new genomic resources(Colorado State University. Libraries, 2024) Metz, Nicholas, author; Mason, Esten, advisor; Dorn, Kevin, committee member; Richards, Christopher, committee member; Gaines, Todd, committee memberSugar beet (Beta vulgaris subsp. Vulgaris) provides about 35% of the refined sugar globally, and over half of the domestic production in the United States. Sugar beet are primarily grown in temperate climates from plantings in late spring and harvest in the fall. In the United States sugar beets are grown in four diverse regions: the upper Midwest (Minnesota and North Dakota), the far west (California, Idaho, Oregon, and Washington, the Great Plains (Colorado, Nebraska, Montana, and Wyoming), and the Great Lakes (Michigan). Multiple pests and pathogens continue to threaten tonnage and recoverable sugar yields. These are controlled through planting genetically resistant cultivars, agronomic cultural practices and chemical applications throughout the growing season. With a shrinking set of chemical and cultural control options to manage these production threats, the need for continued improvement upon host plant resistance is important. Decades of global breeding efforts to improved disease tolerance in sugar beet has been effective, but molecular and genomic guided breeding and disease resistance characterization in sugar beet is only now emerging. The most important root pathogen in sugar beet is Rhizoctonia Root and Crown Rot (RRCR) caused by the fungal pathogen Rhizoctonia solani. This disease is estimated to cause up to 50% localized losses, and regularly causes 57 million dollars in economic losses per year despite the use of tolerant varieties, chemical control, and cultural practices. Public sugar beet pre-breeding has developed hundreds of widely utilized lines with novel traits and combinations of traits, including for RRCR resistance. One such line, FC709-2, displayed exceptional tolerance to Rhizoctonia solani released from the United States Department of Agriculture sugar beet breeding program in Fort Collins, Colorado. This germplasm line is base for many RRCR resistant cultivars used by growers around the world. In this study, new germplasm, genetic, and genomic resources revolving around FC709-2 were developed. These resources include a new germplasm line derived from the purification of FC709-2. By using stricter selection pressure and single seed decent a more homogenous seed lot was created to be used by other breeding programs. A new reference genome created from a single highly RRCR resistant plant using the most recent sequencings and bioinformatic technologies will be used to discover genes that are responsible for a wide array of plant interactions. Last, novel QTLs associated with RRCR resistance were discovered using a bi-parental mapping population and bulk segregate analysis. Collectively, these results show that discovering novel RRCR resistance genes in a highly resistant germplasm line using a purpose-built reference genome is a streamlined and accurate method. With these new resources in place researchers around the world can use them to discover the genes responsible for RRCR resistance, create markers for more accurate selections, and follow the methods described to be implemented in other plant breeding programs.Item Open Access Physiological and biochemical mechanisms behind the fast action of glufosinate(Colorado State University. Libraries, 2019) Kagueyama Takano, Hudson, author; Dayan, Franck E., advisor; Westra, Philip, advisor; Reddy, Anireddy, committee member; Preston, Christopher, committee member; Gaines, Todd, committee memberGlufosinate is one of the few herbicides that are still effective for controlling herbicide resistant weeds, but its performance is often inconsistent and affected by environmental conditions. It inhibits glutamine synthetase (GS) by competing with glutamate for the active binding site. Unlike other amino acid biosynthesis inhibitors, glufosinate is a fast-acting herbicide and susceptible plants develop visual symptoms within a few hours after treatment. Inhibition of GS leads to ammonia accumulation and photosynthesis inhibition, which have traditionally been proposed as the causes of the rapid phytotoxicity. This dissertation presents a new understanding of the mechanism(s) of action of glufosinate and a biochemical approach to improve its herbicidal efficacy. Glufosinate uptake is inhibited by glutamine levels in the plant, and translocation is not affected by the rapid phytotoxicity. Glufosinate translocates primarily through the apoplast (xylem) rather than the symplast (phloem) probably due to its physicochemical properties and the absence of an effective membrane transporter. Glufosinate efficacy is proportional to the herbicide concentration in leaf tissues. Neither ammonia accumulation nor carbon assimilation inhibition are directly associated with the fast action of glufosinate. Instead, rapid phytotoxicity results from a massive light-dependent accumulation of reactive oxygen species (ROS). Inhibition of GS blocks the photorespiration pathway leading to a massive photooxidation damage. Under full sunlight, the excess of electrons is accepted by molecular oxygen leading to ROS generation. These free radicals cause lipid peroxidation, which ultimately leads to rapid cell death. The addition of protoporphyrinogen oxidase (PPO) inhibitors to glufosinate enhances ROS accumulation and herbicidal activity. This enhanced activity results from protoporphyrin formation at high levels due to a transient accumulation of glutamate, the precursor for chlorophyll biosynthesis. The herbicide combination also showed enhanced activity in the field and may help to overcome the lack of glufosinate efficacy under certain environmental conditions.Item Open Access Protoporphyrinogen oxidase: origins, functions, and importance as an herbicide target site(Colorado State University. Libraries, 2021) Barker, Abigail, author; Dayan, Franck, advisor; Snow, Christopher, committee member; Pilon, Marinus, committee member; Gaines, Todd, committee memberProtoporphyrinogen IX oxidase (PPO)-inhibiting herbicides are effective tools to control a broad spectrum of weeds, including those that have evolved resistance to glyphosate. Their utility is being threatened by the appearance of biotypes that are resistant to PPO inhibitors. While the chloroplastic PPO1 isoform is thought to be the primary target of PPO herbicides, evolved resistance mechanisms elucidated to date are associated with changes to the mitochondrial PPO2 isoform, suggesting that the importance of PPO2 has been underestimated. Our investigation of the evolutionary and structural biology of plant PPOs provides some insight into the potential reasons why PPO2 is the preferred target for evolution of resistance. The most common target-site mutation imparting resistance involved the deletion of a key glycine codon. The genetic environment that facilitates this deletion is apparently only present in the gene encoding PPO2 in a few species. Additionally, both species with this mutation (Amaranthus tuberculatus and Amaranthus palmeri) have dual targeting of PPO2 to both the chloroplast and the mitochondria, which might be a prerequisite to impart herbicide resistance. The most recent target-site mutations have substituted a key arginine residue involved in stabilizing the substrate in the catalytic domain of PPO2. This arginine is highly conserved across all plant PPOs, suggesting that its substitution could be equally likely on PPO1 and PPO2, yet it has only occurred on PPO2, underscoring the importance of this isoform for the evolution of herbicide resistance. As glyphosate resistance becomes widespread, weed control turns to older mechanisms of action with less resistance. Protoporphyrinogen oxidase (PPO) inhibitors are a versatile class of herbicides that have been used since the 1960's, with active ingredients that work in pre-emergent and post-emergent applications. Differential efficacy of PPO inhibitors applied pre-emergent, early post-emergent and late post-emergent has been observed in multiple species and settings. Understanding the cause of higher efficacy in younger plants could preserve these important weed control tools. To understand the differing efficacies elements that affect the mechanism of action of PPO inhibitors were analyzed over the course of plant growth including target site transcript levels and protein levels, herbicide uptake, antioxidant capacity, and indicators of flux through the pathway. Data show levels of PPO do not explain differential efficacy. Increases of glutamate, the pathway precursor, do increase damage due to PPO inhibitor treatment, but increased levels are not observed in younger plants. Differential efficacy is likely due to a combination of increase in antioxidant capacity and a decrease in herbicide uptake. Other possible factors such as metabolism will need to be measured in future work. Protoporphyrinogen oxidase (PPO) is a critical enzyme across life as the last common step in the synthesis of many metalloporphyrins. The reaction mechanism of PPO was assessed in silico and the unstructured loop near the binding pocket was investigated. The substrate, intermediates, and product were docked in the catalytic domain of PPO using a modified Autodock method, introducing flexibility in the macrocycles. Sixteen PPO protein sequences across phyla were aligned and analyzed with Phyre2 and ProteinPredict to study the unstructured loop from residue 204–210 in the H. sapiens structure. Docking of the substrate, intermediates, and product all resulted in negative binding energies, though the substrate had a lower energy than the others by 40%. The α-H of C10 was found to be 1.4 angstroms closer to FAD than the β-H, explaining previous reports of the reaction occurring on the meso face of the substrate. A lack of homology in sequence or length in the unstructured loop indicates a lack of function for the protein reaction. This docking study supports a reaction mechanism proposed previously whereby all hydride abstractions occur on the C10 of the tetrapyrrole followed by tautomeric rearrangement to prepare the intermediate for the next reaction. Weed control is essential in modern agriculture, though it becomes more difficult with increasing resistance levels to current herbicides and a slow process to register a new mechanisms of action because of safety concerns and current methods. Agrematch provides a new method to identify possible herbicide candidates using an artificial intelligence algorithm that takes into effect biological parameters with the goal of reducing R&D time on new herbicides. Herein we describe the discovery of 4-chloro-2-pentenamides as novel inhibitors of protoporphyrinogen oxidase, a known herbicide target site, by the Agrematch AI. The herbicidal activity is confirmed in greenhouse assays, with the highest performing AGR001 showing good activity pre-emergent at 150 g/ha and post emergent as low as 50 g/ha on the troublesome weed palmer amaranth (Amaranthus palmeri). A lack of activity is shown on PPO resistant palmer amaranth carrying the ΔG210 deletion mutation. The mechanism of action is confirmed by the herbicide dependent accumulation of protoporphyrin IX, subsequent light dependent loss of membrane integrity, and direct inhibition of protoporphyrinogen oxidase in an in vitro assay. Modeling of the docking of these inhibitors in the active site of protoporphyrinogen oxidase confirms the target.