Theses and Dissertations at Montana State University (MSU)
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Item Elucidation of mechanisms of host plant resistance to wheat stem sawfly (Cephus cinctus Norton) in relation to antibiosis and the early stem solidness phenotype(Montana State University - Bozeman, College of Agriculture, 2023) Hager, Megan Sunshine; Chairperson, Graduate Committee: David K. Weaver; This is a manuscript style paper that includes co-authored chapters.In the North American Great Plains, wheat stem sawfly (WSS), Cephus cinctus Norton is a serious pest of cultivated cereals including common bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum L. var durum). The solid stem phenotype is usually the basis of an effective management strategy in preventing infestation and yield loss in areas which experience pressure from large and damaging WSS populations. However solid stem expression can be negatively influenced by environmental effects and fully solid stems decrease the effectiveness of biological control of WSS by endemic parasitoids, highlighting a need for new sources of resistance outside of the solid stem phenotype. Here, we use 'omics technologies to comprehensively examine potential mechanisms of resistance including antibiotic resistance in oat, as well as small molecules, transcripts, photosynthetic parameters and volatile organic compounds in spring and durum wheat which help to explain decreased levels of infestation and lower incidence of stem cutting observed with the early solid stem phenotype. Genes and metabolites related to cellular organization, lignin composition and stem tissue structure appear to be involved in the resistance observed in oat and are also related to the early stem solidness phenotype in spring and durum wheat. Additionally, metabolic differences in abundance of lipids and carbohydrates were observed between oat and wheat as well as in spring and durum wheat near isogenic lines. Collectively, this research provides insight into the impacts that plant metabolites and gene expression may have on plant resistance to WSS.Item Genetic dissection of malt quality in barley: an examination of hydration index and metabolite QTL(Montana State University - Bozeman, College of Agriculture, 2024) Jensen, Joseph Riley; Chairperson, Graduate Committee: Jamie Sherman; This is a manuscript style paper that includes co-authored chapters.Malting barley is a high value crop for American farmers. Through the malting process grain is turned into malt which is primarily used in brewing but can also be a flavor and nutritional additive for the food industry. During the malting process hydration of the endosperm is a rate limiting step resulting in increased time and water usage if a third water immersion is needed during steeping. To better understand the genetics of endosperm hydration we used a genome wide association (GWAS) population to map quantitative trait loci (QTL) for malt quality, hydration index (endosperm hydration), and seed morphology traits. We found six hydration index QTL with three related to seed size (qHYI1H, qHYI3H.a, and qHYI3H.b), two improving malt quality (qHYI2H and qHYI6H), and the last (qHYI7H) wasn't related to any other traits. We then wanted to see the relationship between hydration index and dormancy because dormancy is needed to prevent preharvest sprouting. Preharvest sprouting in malt barley results in extreme price reductions for producers however the dormancy genes needed to prevent this negatively impact malt quality. Using a biparental mapping population we were able to map two hydration index QTL and relate them to the dormancy gene SD2. Our results confirmed SD2 negatively impacts malt quality but when the positive alleles for hydration index are present, they negate dormancy's negative effects on quality. The results from these two studies show hydration index can benefit growers and maltsters with barley and malt production. Our third study looked at metabolite variation in the GWAS population to see if we could identify QTL related to malt flavor. This would help craft malt houses and breweries which are usually in search of unique flavors. We were able to identify 827 metabolite QTL however the most impactful to flavor were amino acid, saccharide, and maltol QTL which totaled 39. The three maltol QTL which are directly related to flavor all co-located with maltol precursors (amino acids and saccharides) showing these QTL would be good targets for marker assisted selection to create maltol variation.Item Consider the roots: examining barley belowground in the search for adaptation(Montana State University - Bozeman, College of Agriculture, 2024) Williams, Jessica Lynn; Chairperson, Graduate Committee: Jamie Sherman; This is a manuscript style paper that includes co-authored chapters.Barley is important for global food security and sustaining the economically valuable malt industry. Montana is a top barley producer in the United States, but terminal drought stress poses a significant threat to this production by negatively impacting yield and quality. New crop varieties with enhanced environmental adaptation and soil resource extraction would help address this and other issues facing modern agriculture. Stay-green is a trait that extends grain fill in cereals and can stabilize yield and quality under drought. However, this trait and its benefits can be inconsistent across environments and its successful incorporation into breeding strategies would benefit from expanded understanding of stay-green. Roots may play a role in stay-green physiology. Roots provide plants with the water and nutrients needed for growth and are important for crop performance in their own right. Different root system architectures provide adaptation to different environmental stressors, but studying these belowground structures is challenging. Adaptation is also impacted by soil properties and microbial communities. For this dissertation, roots were examined in greenhouse seedling assays and field trials in Montana. Agronomic performance was also assessed for malt barley and spring wheat cultivars varying for stay-green, a biparental barley population segregating for stay-green, and a diverse mapping population of barley lines from different breeding programs. Stay-green cultivars had a greater percentage of deep roots, more prolonged root growth during grain fill, and greater yield. Analysis of the biparental population identified genetic co-segregations of stay-green, root phenotypes, grain quality, and quality stability between environments, further supporting the benefit of stay-green in dry environments and its connection to roots. The diverse mapping population was used to find associations between the relative abundances of bacteria in the rhizosphere and barley genetic loci, that were mostly environment specific. Rhizospheric bacteria may be involved in local adaptation of plants. Finding plant genetic signal for these microbial characteristics supports the idea that it may be possible to breed crops with enhanced ability to recruit beneficial microbiomes if environmental influence and agronomic impact can be understood. Root examination remains a challenging but worthwhile avenue to pursue in crop adaptation research.Item Evaluating alfalfa weevil (Hypera postica) resistance to mode of action group 3A pyrethroid insecticides in the western United States(Montana State University - Bozeman, College of Agriculture, 2023) Rodbell, Erika Adriana; Chairperson, Graduate Committee: Kevin Wanner; This is a manuscript style paper that includes co-authored chapters.Alfalfa weevil (Hypera postica Gellenhal [Coleoptera: Curculionidae]) is an insect pest of forage alfalfa (Medicago sativa L. [Fabales: Fabaceae]) in the western United States. Over the last half-century, insecticides have been the primary control tactic used by alfalfa producers. However, in 2015 numerous reports of pyrethroid insecticide (mode of action (MoA) 3A) failure to control alfalfa weevil populations were made. In 2019, Montana producers were reporting the same failures in their production systems. Therefore, research efforts in the Wanner Lab commenced in 2020 with the exclusive research goal of identifying pyrethroid resistant alfalfa weevil populations in the western United States. The focus of the research is four-fold. The first was to identify alfalfa weevil lambda-cyhalothrin resistance and susceptibility in Montana. The second was to identify lambda-cyhalothrin resistance and susceptibility in Arizona, California, Montana, Oregon, Washington, and Wyoming. The third was to identify if resistance to lambdacyhalothrin resulted in the loss of efficacy of other MoA 3A active ingredients. The fourth was to develop a case study addressing integrated resistance management recommendations for alfalfa weevil pyrethroid resistance mitigation. We conducted our research through contact bioassays, molecular genomics, and field trials, to corroborate our results and to identify if alfalfa weevil strain was a factor influencing our documented pattern of resistance. Cumulatively, our results suggest that alfalfa weevil lambda-cyhalothrin resistance is present in Arizona, California, Montana, Oregon, Washington, and Wyoming, and that susceptible populations remain in the western region. Our data further illustrate that regardless of alfalfa weevil strain, alfalfa weevils resistant to lambda-cyhalothrin will be resistant to other type II pyrethroid active ingredients and permethrin. A pattern seen in three distinct alfalfa production zones in the western United States (i.e., Arizona, Montana, and Washington), determined by both contact bioassays and field trials. In conclusion, our results illustrate a challenge that forage alfalfa production faces in the western United States and provides strategies that western forage alfalfa producers can employ to mitigate pyrethroid resistance from developing.Item Characterization and assessing fungicide sensitivity of Fusarium spp. causing root rot and wilt in lentils in the northern Great Plains(Montana State University - Bozeman, College of Agriculture, 2022) Bugingo, Collins; Chairperson, Graduate Committee: Mary Burrows; This is a manuscript style paper that includes co-authored chapters.Fusarium root rot and wilt are yield limiting diseases caused by Fusarium spp. in lentils globally. Seedborne Fusarium species and races of Fusarium oxysporum f. sp. lentis (Fol) have not been characterized. The sensitivity of commonly used fungicides on prevalent species is not fully known. In 2019 and 2020 commercial lentil fields were surveyed and seed lots collected from infected patches and further isolation, morphological and molecular characterization was conducted in the laboratory. Additional isolates and lentil seed were received from Washington, Montana, Idaho, North Dakota, southern Canada, and Spain for fungicide, seedborne Fusarium spp. and race-characterization of Fol respectively. In addition to assessing presence of seedborne Fusarium pathogens on the seed coat, the cotyledon and embryo were assessed for the presence of Fusarium spp. Fungicide sensitivity was assessed using mycelial assays and an additional spore assay for pyraclostrobin. A total of 84 seed lots from the Northern Great Plains (NGP) were assayed where a total of 486 and 228 Fusarium isolates were isolated in 2019 and 2020, respectively and all the representative isolates were virulent with a 1.5-4.5 root rot severity rating. Most isolates were found in the seed coat (57- 75%), cotyledon (19-23%) and embryo (6-20%) for the 2019 and 2020 isolates, respectively. F. oxysporum and F. acuminatum were all either sensitive or intermediately sensitive to prothioconazole and ipconazole. A total of 51 isolates were race-typed and 9 races identified whereby race 7 and 1 were the predominant at 53% and 16%, respectively. This study underscores the importance of understanding Fusarium spp. composition in lentil production, role of seedborne inoculum, fungicide efficacy in root rot/wilt management and race composition upon developing effective Integrated Pest Management (IPM) strategies.Item Using genetic and genomic techniques to uncover cryptic diversity for improving aquatic invasive plant management(Montana State University - Bozeman, College of Agriculture, 2021) Chorak, Gregory Michael Thomas; Chairperson, Graduate Committee: Ryan Thum; This is a manuscript style paper that includes co-authored chapters.Genetic diversity can be important at many levels of invasive species management. And, for different questions, it matters at which level we measure diversity to understand its relevance. Some invaders may look similar to other species, so identifying the species to be managed may be difficult without genetic tools. Once the species has been identified, understanding the diversity in that species may be important to identify management units, invasive traits, and the possibility of spread. Finally, understanding how the alleles an individual possesses determine the traits expressed can give managers the tools to control for unwanted traits of an invasive species. In this body of work, I uncover diversity at the species/taxon level, the genotype/clone level, and finally at the gene level in invasive aquatic weed species. At the taxon level, I found that one invasion of aquatic weeds in the northeastern US was actually two or more separate invasions and taxa. At the genotype level, I found that the same genotype responds the same to a common herbicide management regardless of where it is found, and that different genotypes have varying responses to a common herbicide treatment. And, at the gene level, I found that different genotypes with different growth rates have different gene expression in the control and transcriptional response to a common herbicide treatment. At each of these levels, managers have questions and concerns about management decisions. Understanding that there were two unique taxa in what was considered one invasion informed managers that there may be variance in management relevant traits between the two. In the genotype level study, we learned that determining which clones are present in a lake slated for herbicide management may inform which herbicides to use. And, at the gene level, we are starting to understand the molecular process of management relevant phenotypes so that one day managers can screen for molecular markers that will reveal herbicide response of individuals slated for management.Item Taxonomic and phylogenetic studies of West Indian lycidae (Insecta, Coleoptera, Elateroidea)(Montana State University - Bozeman, College of Agriculture, 2021) Ferreira, Vinicius de Souza; Chairperson, Graduate Committee: Michael A. Ivie; This is a manuscript style paper that includes co-authored chapters.The Thonalmini and Leptolycini are two tribes of Net-winged beetles (Insecta, Coleoptera, Lycidae) endemic to the West Indies. Both tribes are characterized by their confusing taxonomic history and poorly known biology and evolutionary patterns, and the study of both groups is the topic of this dissertation. One of the chapters of this dissertation provides a taxonomic revision of the genus Thonalmus Bourgeois, 1883, the sole member of the tribe Thonalmini. In this study, I provide an updated taxonomic revision of the group, illustration of diagnostic characters, an identification key, distribution maps, updates in the nomenclature of the group and description of seven new species. I also provide the first species level phylogenetic hypotheses for Thonalmus (morphology, molecular based and total evidence), biogeographical dispersal patterns hypotheses, a time-calibrated phylogeny and character state reconstruction for the species of the genus. The other chapter of this dissertation investigates the different life- stages of the Leptolycini of the Puerto Rican bank. The morphology of the Leptolycini males conforms with other groups suspected to be paedomorphic, whilst the females are unknown and suspected to be completely larviform. In this chapter, I provided for the first time DNA barcoding life stages associations based on partial sequences of cytochrome c oxidase subunit 1 (COI) of adult males and their immature forms from Puerto Rico, altogether with collections- based associations of adult males, immatures and one extreme paedomorphic female from the Virgin Islands. In order to carry out these life-stage associations, I prepared an in-depth review of the Leptolycini fauna of the Puerto Rican bank (Puerto Rico and Virgin Islands), which is also presented in this chapter. This study provided the morphological diagnoses of the semaphoronts that were found in the region and several taxonomic and nomenclatural changes are proposed, including the descriptions of one new genus and seven new species and an updated key for all species and genera of the region.Item Aphanomyces euteiches spatial distribution, host studies, and characterization in Montana(Montana State University - Bozeman, College of Agriculture, 2022) Murphy, Carmen Yvette; Chairperson, Graduate Committee: Mary BurrowsGrowing pulse crops in Montana has been inhibited by biotic constraints to production, including a complex of pathogens causing root rot. Aphanomyces root rot, caused by the soilborne oomycete, Aphanomyces euteiches, causes plant stunting and yellowing, root browning and constriction, and reduces yield in dry pea and lentil in the state. Twelve fields with a history of pulse root rot were sampled in northeast Montana with three 100 m entrance transects and one 50 m transect at a low spot or problem area. Soil from each 10 m quadrat within transects was assessed for root rot using a greenhouse bioassay with a susceptible dry pea variety, and with PCR. Samples were also analyzed for soil properties and nutrients. Distribution of the pathogen was sporadic in most fields, except for fields that had been growing pulses in a consistent rotation, where root rot severity was high and consistent. Soil pH, organic matter, potassium, and sulfur concentration were correlated with Aphanomyces root rot, and isolates varied in their response to acidic pH in vitro. Using a highly virulent A. euteiches isolate, greenhouse trials were conducted to assess the pathogen load of inoculated soil after growing host and non-host plant species, measured with a bioassay. Greenhouse pots were inoculated with 500 oospores per gram prior to planting plant treatments. Growing host plants resulted in higher root rot severity on dry pea bait plants compared to non-host plant treatments. When five cycles of plants were grown in greenhouse pots inoculated with A. euteiches, using five 'rotation' treatments, one treatment with three consecutive rounds of non-host plants reduced the disease severity score in one trial repetition compared to treatments with less than three successive rounds growing a non-host. This research indicates that sampling strategies for Aphanomyces root rot requires multiple sampling locations within a field to enhance the probability of detection, and that crop rotation is an important tool for management of pathogen load in the soil.Item Leveraging a global spring, 2-row barley population to accelerate the development of superior forage barley varieties for Montana growers(Montana State University - Bozeman, College of Agriculture, 2021) Hoogland, Traci Janelle; Chairperson, Graduate Committee: Jamie ShermanAs more people around the globe escape poverty, they are eating more meat and dairy products. To support this increased demand for animal products there is an urgent need to develop more sustainable high-quality forage and hay crops for the livestock production industry. Barley (Hordeum vulgare spp. vulgare L.) is considered one of the most drought tolerant of the annual cereals and spring barley has been shown to out yield established perennial forages under drought conditions in central Montana (Cash, Surber, & Wichman, 2006). To accelerate the development of superior forage barley varieties for Montana, the following goals were identified 1) Utilize a genome wide association analysis to find genetic regions related to key forage and agronomic traits, 2) Use statistical modeling to a) examine the relationship between difficult to measure forage traits such as quality and yield, and easy to measure agronomic traits such as flowering time and plant height, b) identify agronomic traits that can be used as proxies for yield and quality in the earliest stages of the breeding program when genetic and phenotypic variability are at their greatest. Through these techniques the importance of variation in timing of plant maturity was identified. Statistical modeling showed that variability in forage yield and quality was observed to be closely related to variability in the timing of heading and soft-dough dates. Plant height was also determined to be of importance especially for biomass yield. Through genome-wide association analysis, novel QTL were discovered in relation to all studied traits. QTL were detected on all seven chromosomes and the majority of forage trait QTL co-located with QTL related to the timing and progression of plant development and maturity. This appeared to indicate that in a population of global barley accessions, the loci with the greatest impact on forage traits may be those containing genes regulating plant development and senescence. This further strengthened the evidence from the modeling study that a relationship exists between the two trait categories: traits for measuring the timing of plant development and forage traits.Item Improving genomic resources for the study of invasiveness in Eurasian watermilofil (Myriophyllum spicatum) and their hybrids(Montana State University - Bozeman, College of Agriculture, 2021) Pashnick, Jeffrey John; Chairperson, Graduate Committee: Ryan Thum; This is a manuscript style paper that includes co-authored chapters.Genomics has revolutionized the way biologists ask fundamental questions about evolution. The thousands to tens of thousands of molecular markers generated through modern genomics increase the likelihood of detecting traits associated with a phenotype of interest. While genomics provides ever increasing evidence detecting these traits, they must be developed in each new system. Myriophyllum spicatum L. (Eurasian watermilfoil, EWM) and their hybrids with native Myriophyllum sibiricum Komorov (northern watermilfoil, NWM) are heavily managed aquatic plants in the United States. Genotypes both within and across these taxa and their hybrids can differ in their growth and herbicide response, prompting interest in determining which specific genotypes and genes will respond best to specific control tactics. However, because genotypes are unable to be distinguished by morphology, distinguishing genotypes requires molecular markers. EWM, NWM, and their hybrid are hexaploid (2n=6x=42) and developing these molecular markers requires accurately genotyping in a hexaploid with unknown chromosomal inheritance. The first manuscript of this dissertation empirically tested the genotyping information obtained from three commonly used molecular marker types, AFLPs, microsatellites, and GBS data. We found that while GBS markers have the lowest error rate, all molecular marker types provide the same genotype information. In the second chapter we used a mapping population, GBS data, and likelihood models to determine if watermilfoil was an allohexaploid, autohexaploid, or a mix between them. We found overwhelming evidence that watermilfoil is an allohexaploid across the genome. Finally, using the characteristics of each molecular marker type, the third chapter developed a cost-effective and information dense panel of microhaplotypes to genotype in watermilfoil. Microhaplotyping data can be shared across laboratories and promotes collaboration with weed managers by informing management with genetic information. Together, the work in this dissertation provides diploidized molecular markers and polyploid mode of inheritance to begin to connect genotype to herbicide response traits in watermilfoil.