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Browsing by Author "Gaines, Todd, advisor"

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    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.
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    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.
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    Integrated weed management: insights from a weed resistance survey and non-chemical weed seed control in the Central Great Plains
    (Colorado State University. Libraries, 2023) Simões Araujo, André Lucas, author; Gaines, Todd, advisor; Dayan, Franck, committee member; Fonte, Steven, committee member
    With the impending release of genetically engineered sugar beet varieties with resistance to glyphosate, dicamba, and glufosinate, significant changes are expected in weed management practices, particularly with regards to in-crop weed control. Glyphosate is used during fallow and in-crop periods, while dicamba is commonly employed in fallow applications, specifically targeting glyphosate-resistant weed species. This study provides insights into the resistance status and frequency of resistance in problematic weed species to the three active ingredients in sugar beet systems across Colorado, Nebraska, and Wyoming. While numerous studies have highlighted the widespread prevalence of glyphosate-resistant kochia and Palmer amaranth across the United States, there is limited research focusing on these species within the context of a sugar beet system. Additionally, our findings reveal the first occurrence of glyphosate-resistant and dicamba-resistant Palmer amaranth populations in Colorado, and dicamba-resistant kochia populations within a sugar beet system. Furthermore, we report that all dicamba-resistant kochia populations tested in Colorado lack a known target-site resistance mechanism, suggesting the involvement of a novel resistance mechanism. Surveys assessing glufosinate resistance in the sugar beet system have not been conducted until now, and we provide valuable baseline information on the resistance frequency for this herbicide prior to an anticipated increase in glufosinate use. To address the widespread issue of herbicide resistance in various crop systems, it is crucial to adopt alternative strategies that mitigate resistance evolution and maintain the long-term effectiveness of available herbicides. One promising approach is chaff lining, a harvest weed seed control method that has gained popularity in Australia due to its effectiveness in reducing populations of herbicide-resistant ryegrass, especially when combined with other weed control methods. However, the efficacy of chaff lining may be influenced by several factors, including crop and environmental factors, as reported in Australian literature. Scientific studies assessing the applicability and effectiveness of chaff lining in the United States are limited. Recognizing this research gap and aiming to explore the potential of chaff lining, our study investigated its applicability in field settings within the Central Great Plains region of the United States. Through our research, we provide insights into chaff lining efficacy of and highlight the potential inconsistencies that may arise in suppressing weed seeds using this method. Notably, we demonstrate that various factors, including location and environmental conditions, may be involved and impact the effectiveness of chaff lining as a weed management strategy. These findings underscore the importance of integrating chaff lining with other weed management methods to achieve effective and sustainable weed control. Chaff lining, like any other weed management strategy, should not be solely relied upon. Instead, it should be implemented as part of an integrated approach to ensure its long-term effectiveness.
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    Investigating fluroxypyr resistance in Bassia scoparia
    (Colorado State University. Libraries, 2021) Todd, Olivia, author; Gaines, Todd, advisor; Bedinger, Patricia, committee member; Argueso, Cristiana, committee member; Jahn, Courtney, committee member
    Synthetic auxin herbicides are designed to mimic indole-3-acetic acid (IAA), an integral plant hormone affecting cell growth, development, and tropism. Recent developments in synthetic auxin herbicide research have produced several new reports of synthetic auxin resistant weeds and novel resistance mechanisms, including resistance by cytochrome P450 metabolism to mutations in auxin co-receptors. In this document, we investigate specific genes in the auxin signaling pathway that may be involved in weed resistance to the synthetic auxin herbicide fluroxypyr, an economically important method of broadleaf weed control in wheat. The auxin signaling pathway is well characterized, but for many herbicides in the synthetic auxin group, the specific gene family members for receptors and co-receptors with which they interact in the auxin signaling pathway remain unknown. We characterized this Bassia scoparia line using greenhouse studies, dose responses, absorption/translocation and metabolism using 14C-fluroxypyr. To supplement these physiology studies, we conducted an RNA-sequencing experiment using the de novo transcriptome of Bassia scoparia to characterize gene expression in response to fluroxypyr using variant calling and differential expression in R. In addition to investigating this resistance case, this document also describes methodologies for creating crop resistance to pendimethalin via EMS mutagenesis. Through this experiment, many individuals have been found to reach full maturity in the northern Colorado region before the growing season ends. Backcrossing to the inbred parent Sorghum bicolor to begin genetic characterization is the next step following completion of the early maturing line characterization and genetic validation.
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    The genetics and genomics of herbicide resistant Kochia scoparia L.
    (Colorado State University. Libraries, 2018) Patterson, Eric L., author; Gaines, Todd, advisor; Saski, Chris, committee member; Sloan, Daniel, committee member; Pearce, Stephen, committee member
    Weed genomics resources lag behind other plant biology disciplines despite larger annual crop losses occurring due to weeds than to plant pathogens or invertebrate pests. To date only a handful of weed genomes are assembled, and what is available is generally incomplete, poorly annotated, or only useful to a small group of researchers. Recent advancements in sequencing and an increased interest in the genetic foundations of weedy traits have contributed to driving de novo genome assemblies for key weed species. The introduced weed species Kochia scoparia (kochia) is the most important weed species in Colorado and severely impacts yield in various crop systems including sugar beet, wheat, and corn. Additionally, kochia rapidly invades disturbed land including roadsides, drainage areas, rangelands, and pastures. Kochia spans a massive geographic distribution, from as far south as Mexico, as far north as Saskatoon, Canada, as far east as the Mississippi river, and as far west as Oregon. Locally, kochia populations are well adapted to various abiotic stresses including drought, cold, high salinity, and high wind. Recently, and most importantly, kochia has evolved resistance to several modes of herbicide action. Currently kochia populations exist that are resistant to acetolactate synthase (ALS) inhibitors, photosystem II (PSII) inhibitors, several synthetic auxin compounds, and the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) inhibitor, glyphosate. Individuals have even been identified that are resistant to all four modes of action (MOA) simultaneously. Each herbicide mode of action (MOA) resistance case is caused by different mutations or even different mutation types (target site SNPs, copy number variation, translocation changes, etc.). Selection pressure from herbicides is intense as not having the proper allele is lethal; therefore, resistance alleles are selected and go to fixation quickly. Kochia populations may be especially prone to herbicide resistance for a variety of physiological reasons, as kochia plants can produce thousands of seeds, are wind pollinated, are primarily outcrossing, and have tumbleweed seed dispersal in the windier environments like eastern Colorado and Kansas. Additionally, there may be genetic and genomic explanations for rapid herbicide resistance evolution such as rapid mutation rates or dynamic responses to environmental stress. Glyphosate resistance, in particular, has driven a significant amount of herbicide resistance research in this species. In this case, resistance is caused by copy number variation of the target gene, EPSPS. Over production of the EPSPS enzyme makes normally lethal doses of glyphosate inadequate for control. Many of the details underlying gene amplification are missing, such as what are its origins and what genes are included in the duplication event. Understanding mechanisms of gene duplication is fundamental to understanding the evolution of resistance, predicting future gene duplication events, and understanding the significance of fitness and inheritance studies.