Theses and Dissertations at Montana State University (MSU)
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Item An exploration of whole-genome comparative genomic strategies for polyploid crop genomes(Montana State University - Bozeman, The Graduate School, 2022) Reynolds, Gillian Lucy; Co-chairs, Graduate Committee: Brendan Mumey and Jennifer A. LachowiecGenome comparison for large and complex polyploid crop genomes is a highly complex venture, yet it is critical. Given a rising demand for food coupled with yield-impacting resource limitations and rapidly changing global climates it has never been more important to characterise the underlying genetic variation which underpins traits of agronomic interest. In this work, the problem of polyploidy genome comparison is explored at three levels. The first chapter characterizes the sequence relationships that exist between, and within, polyploidy genomes. This is achieved by hijacking a metagenomic strategy for rapid, and efficient, genome sequence classification. The second chapter then utilizes the identified subgenome- specific k-mer profiles for recruitment of assembled contigs and scaffolds previously only recruitable via more resource intensive optical mapping strategies. This makes a greater proportion of the assembled data usable for downstream variant analysis. The third chapter then zooms into the problem of how to identify variants from large -scale sequencing data while minimizing bias and computational costs. A critical assessment of modern variant calling for crop genomes is performed and an algorithm to further extend a new, resource efficient, approach for large scale comparative genomics is presented and critically evaluated. In all, the work presented herein takes a top-down journey from genome- and subgenome- level comparative genomics all the way to identifying base-pair resolution strategies that are capable of revealing the underlying sequences responsible for keeping the world fed.Item Role of crop fertility and seed treatments in managing fusarium root rot of lentil (Lens culinaris Medikus) in the northern Great Plains(Montana State University - Bozeman, College of Agriculture, 2021) Atencio, Sydney Christine; Chairperson, Graduate Committee: Perry Miller and Mary Burrows (co-chair)Lentil is a relatively new but economically important crop for the state of Montana, along with surrounding states in the northern Great Plains. Comparatively little is known about the basic fertility of lentil, and importance of inoculant type on lentil. Additionally, the rise of pulse crop acres in the northern Great Plains, has given rise to root rot pathogens, such as Fusarium root rot. Fusarium root rot of pulses, has a wide host range, limiting the efficacy of rotation in its management. This research is comprised of two main studies. Field trials occurred at sites in Bozeman, Havre, Moccasin, and Sidney in 2019 and 2020. The objective of chapter two was to evaluate the effect of rhizobial inoculant formulations (granular vs. seed-coat/peat-powder) and nutrient additions (potassium, sulfur, and a micronutrient fertilizer), on lentil establishment, growth, seed protein, and yield. For chapter two, in six of eight site-years there was no yield difference between inoculant types. Applications of sulfur (S) fertilizer increased yield at three of eight site-years by an average of 303 kg ha-1 (17%) compared to treatments without S. Results from this study further suggest the importance of S fertilization for lentil. The objective for chapter three was to evaluate seed treatments' ability to control Fusarium root rot on lentil establishment, growth, disease severity and yield. In three of eight site-years, the inoculated control had a relatively high disease severity compared to other seed treatments. In general, treatment responses varied across site-year due to low disease pressure. Additionally, F. graminearum and F. oxysporum were isolated at a high frequency from control plots at sites in 2019. Data from 2020 is pending.Item Improving malt barley agronomics via allelic selection of senescence and flowering time controlling genes(Montana State University - Bozeman, College of Agriculture, 2020) Alptekin, Burcu; Chairperson, Graduate Committee: Andreas M. Fischer; Dylan Mangel, Duke Pauli, Tom Blake, Jennifer Lachowiec, Traci Hoogland, Andreas Fischer and Jamie Sherman were co-authors of the article, 'Combined effects of glycine-rich RNA binding protein and a NAC transcription factor extend grain fill duration and improve malt barley agronomic performance' submitted to the journal 'Theoretical and applied genetics' which is contained within this thesis.; Dylan Mangel, Duke Pauli, Tom Blake, Jennifer Lachowiec, Jamie Sherman and Andreas Fischer were co-authors of the article, 'Dissecting the effects of senescence-regulating HvNAM1 and HvNAM2 transcription factors on malt barley agronomics' submitted to the journal 'Molecular breeding' which is contained within this thesis.; Dylan Mangel, Duke Pauli, Tom Blake, Hannah Turner, Jennifer Lachowiec, Jamie Sherman and Andreas Fischer were co-authors of the article, 'Allelic selection of senescence and flowering time controlling genes confers malt extract stability' submitted to the journal 'Journal of the American Society of Brewing Chemists' which is contained within this thesis.Malt barley (Hordeum vulgare L.) is a high-profit crop for farmers; yet, its production raises challenges that need to be addressed. The standards for grain quality in malt barley are stringent, and the rejection of non-qualified grains by maltsters is the leading cause of revenue loss for malt barley producers. Rejection is mainly due to high grain protein content and low kernel plumpness which both cause significant problems in the malting process. While proper growing practices can improve malt quality, the industry requires genotypes that have more stable malt quality. Therefore, understanding the molecular mechanisms associated with grain quality can be applied to improve selection of superior malt varieties. A considerable volume of literature has suggested that regulation of whole-plant senescence and flowering processes in cereals have direct influences on grain yield and quality parameters. The central question in this dissertation examined whether malt barley agronomic and end use quality can be improved by the selection of varying alleles for genes associated with plant development. With this purpose, two whole-plant senescence-regulating NAM, ATAF and CUC (NAC) transcription factors, HvNAM1 and HvNAM2, and a flowering-time controlling Glycine-Rich RNA Binding Protein (HvGR-RBP1) were studied. Molecular markers for selection of alleles from varieties 'Karl' (with consistently low grain protein) and 'Lewis' were developed, and an advanced-generation malt barley breeding population was genotyped. Statistical analysis of growth parameters from this population showed that selection of HvNAM1 'Karl', HvNAM2 'Karl' and HvGR-RBP1 'Lewis' alleles ensures a longer grain filling period in malt barley. Plants with prolonged grain filling also exhibited increased kernel plumpness and test weight. Additionally, selection of 'Karl' alleles for both NAC genes decreased grain protein content ensuring grain quality for malting. The improvement of grain characteristics correlated with improved malt phenotypes, for example a ~2% increase in malt extract, and improvement in other malt characteristics such as beta-glucan content and alpha-amylase activity was observed. Overall, these data show that molecular genetics and allelic selection for genes controlling plant development is promising for advancing malt quality. Research performed here has a direct potential for improving the profits for malt barley producers.Item Screening field pea (Pisum sativum L.) for tolerance to high salinity conditions(Montana State University - Bozeman, College of Agriculture, 2020) Tracy, Jacob D.; Chairperson, Graduate Committee: Kevin McPheeField pea (Pisum sativum L.) is an important salt-sensitive crop utilized in rotation with cereals in semi-arid cropping systems in the Northern Great Plains (NGP). Saline soils (EC > 4 dS m -1) negatively impact over 10.8 million acres in Montana, the second largest producer of field pea in the US. Despite its global importance, few studies have explored field pea response to high salinity conditions outside of germination testing and even fewer have looked at tolerance to sodium sulfate (Na 2SO 4), the dominant salt affecting plant growth in the NGP. In this study, 311 accessions comprising the genetically diverse USDA Pisum single plant (PSP) core collection were screened under high Na 2SO 4 conditions in germination and seedling experiments. Germination screening was conducted in petri dishes within a dark growth chamber. Accessions received H 2O (control) or 16 dS m -1 Na 2SO 4 (highly saline) solution for 8 days. The mean percent germination compared to the control was used as the indicator for tolerance. A preliminary greenhouse concentration series experiment using 7 levels of Na 2SO 4 (0, 3, 6, 9, 12, 15, and 18 dS m -1), supported screening seedlings at 9 dS m -1 Na 2SO 4. Greenhouse screening was conducted in plastic pots of coarse sand media. Accessions received a nutrient solution (control) or 9 dS m -1 Na 2SO 4 and nutrient solution daily. Salinity symptom scores were assessed on days 21, 28, 35, and 38 post-sowing using a visual growth response scale of 1-9 (healthy-dead). Phenotypic measurements and the Area Under the Injury Curve (AUIC) were used as indicators for tolerance. A Genome Wide Association Study (GWAS) was conducted using the phenotypic data collected and a large dataset of 68,222 Single Nucleotide Polymorphisms developed from the USDA PSP plus core collection. Potential candidate breeding germplasm conferring high salinity tolerance at the germination and seedling growth stages was identified. Significant marker-trait associations were discovered for all traits measured, providing potential Marker-Assisted Selection (MAS) opportunities.Item The characterization of fungicide resistance, population structure, and aggressiveness of fungal species associated with ascochyta blight of pulse crops in Montana(Montana State University - Bozeman, College of Agriculture, 2019) Owati, Ayodeji Stephen; Chairperson, Graduate Committee: Mary Burrows and Bright Agindotan (co-chair); Bright Agindotan, Julie Pasche and Mary Burrows were co-authors of the article, 'The detection and characterization of QOI-resistant Didymella rabiei causing ascochyta blight of chickpea in Montana' in the journal 'Frontiers in plant science' which is contained within this dissertation.; Bright Agindotan and Mary Burrows were co-authors of the article, 'First microsatellite markers developed and applied for the genetic diversity study and population structure of Didymella pisi associated with ascochyta blight of dry pea in Montana' in the journal 'Fungal biology' which is contained within this dissertation.; Bright Agindotan and Mary Burrows were co-authors of the article, 'Characterization and detection of fungal species associated with ascochyta blight of dry pea in Montana' submitted to the journal 'Plant disease' which is contained within this dissertation.; Bright Agindotan and Mary Burrows were co-authors of the article, 'The development and application of real-time and convention SSR-PCR assays for rapid and sensitive detection of Didymella pisi associated with ascochyta blight of dry pea' submitted to the journal 'Plant disease' which is contained within this dissertation.Ascochyta blight (AB) of pulse crops causes yield loss in Montana, where 1.24 million acres were planted to pulses in 2018. Pyraclostrobin and azoxystrobin, quinone outside inhibitor (QoI) fungicides, have been the choice of farmers for the management of AB in pulses. QoI-fungicide-resistant Didymella rabiei isolates were found in one chickpea seed lot each received from Daniels, McCone and Valley Counties, MT, from seed produced in 2015 and 2016. Multiple alignment analysis of amino acid sequences showed a mutation that replaced the codon for amino acid 143 from GGT to GCT, introducing an amino acid change from glycine to alanine (G143A), which is reported to be associated with QoI resistance. Under greenhouse conditions, disease severity was significantly higher on pyraclostrobin-treated chickpea plants inoculated with QoI-resistant isolates of D. rabiei (QoI-R) than sensitive isolates (QoI-S) (p-value = 0.001). D. rabiei-specific PCR primer pair and probes were developed to discriminate QoI-R and QoI-S isolates. In North America, AB of dry pea is caused by a complex of fungal pathogens (Didymella pisi, Peyronellaea pinodes, and Peyronellaea pinodella). D. pisi is the predominant causal pathogen of AB of dry pea in Montana resulting in yield losses. Thirty-three microsatellite markers (SSR) were developed and used to analyze the genetic diversity and population structure of 205 D. pisi isolates from four geographical regions of Montana. Unweighted Neighbor-joining, principal coordinate, and population structure analyses grouped these 205 isolates into two major sub-groups. The clusters did not match the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 15% among populations. There was moderate genetic variation in the total populations (PhiPT = 0.153). Recently, a shift in pathogen composition has been observed in Montana from D. pisi to P. pinodes and P. pinodella. Also, a Phoma sp. was found associated with AB contaminated dry pea seeds and included in this study. Mycelial growth and sporulation were evaluated at different temperatures. Also, the pathogenicity of Phoma sp. and the difference in aggressiveness among the fungal pathogens was evaluated. At all temperatures, Phoma sp. had the highest growth rate (p-value = < 0.001) and produced more spores than the other species (p-value = < 0.001). P. pinodes caused greater disease severity than the other species when inoculated on pea plants (cv. Carousel, p-value < or = 0.001). The Phoma sp. was not pathogenic. Peameal agar was used to visually discriminate between fungal species. Diagnosis of AB of dry pea is challenging because of the complex of pathogens involved. Also, they have slow growth rate and different morphotypes. Currently, there are no PCR-based assays developed for D. pisi or any of the fungal pathogens associated with the AB complex of dry pea. D. pisi specific SYBR green SSR-qPCR and conventional SSR-PCR assays were developed for rapid detection and quantification of D. pisi both in-planta and in-vitro.Item Extending cool season production of vegetables in the high tunnel: balancing heat and light(Montana State University - Bozeman, College of Agriculture, 2019) Baumbauer, David Alan; Chairperson, Graduate Committee: Mac Burgess; Macdonald H. Burgess was a co-author of the article, 'The Montana high tunnel growers survey - identifying grower practices and concerns' submitted to the journal 'HortTechnology' which is contained within this thesis.; Macdonald H. Burgess was a co-author of the article, 'Row cover influences light transmisson, air and soil temperatures in the high tunnel during Spring and Fall' submitted to the journal 'Journal of agricultural and forest meteorology' which is contained within this thesis.; Macdonald H. Burgess was a co-author of the article, 'Season, sowing date, and row cover influence the production of cool season vegetables in the moveable high tunnel' submitted to the journal 'Canadian journal of plant science' which is contained within this thesis.; Colleen B. Schmidt and Macdonald H. Burgess were co-authors of the article, 'The influence of low daily light integral on the growth of baby kale, lettuce and spinach' submitted to the journal 'HortScience' which is contained within this thesis.Montana high tunnel growers face challenges associated with being at a northern latitude and high elevation. The wide seasonal fluctuation in photosynthetically active radiation coupled with wide diurnal temperature swings produces a dynamic growing environment within the high tunnel. This dissertation is comprised of four studies investigating the management of light and temperature and their influences on high tunnel grown crops. Chapter one is an introduction to high tunnels and production strategies. Chapter two discusses the results of the Montana High Tunnel Growers Survey, in which respondents reported that managing the high tunnel environment was their number one challenge. Two thirds of respondents produced crops during the shoulder seasons of spring and fall, a period of time when the climatic conditions are especially dynamic. Chapter three presents the findings on the influences various types of season extension have on light and temperature levels and the impacts they have on the accumulation of growing degree hours, soil degree hours, and daily light integral. While each layer retains heat, moderating the effect of low night air temperatures, it comes at the cost of lower light energy at the crop level. Heat retention performance of high tunnel plus row cover improves as outside air temperature decreases, maintaining crop level air temperature at -3°C despite an outside air temperature of -22°C. Chapter four presents the results of seeding date and row cover effects on the yield and days to harvest of six cool season crops. Row cover within the high tunnel only improved crop yields when outside air temperatures were well below the historical average. The early seeding date in the fall resulted in higher yields and fewer days to harvest, indicating that the two weeks difference between August 15th and August 30th has a large impact on production. Chapter five reports on the influence of low daily light integral has on the production of kale, lettuce, and spinach. While all three responded to increasing light, lettuce had the largest response with a 200% increase in dry weight when the daily light integral increased from 8 to 14 mol m -2 d -1.Item The impact of farm-level variables on federal crop insurance coverage level selection(Montana State University - Bozeman, College of Agriculture, 2019) Boyd, Mark Weiderspon; Chairperson, Graduate Committee: Eric BelascoThis thesis evaluates the significance of farm-level variables related to cash flow on coverage level selections as a potential explanation for the well-documented behavioral anomaly in producers' federal crop insurance coverage level selection choices. The current crop insurance literature appears to lack a clear explanation of why producers choose to insure at lower or less than economically optimal coverage levels. To inform this question, the relationship between liquidity factors and insurance coverage level selection are estimated empirically using linear and fixed effects models with data from the Agricultural Resource Management Survey, Risk Management Agency Summary of Business, and the Risk Management Agency Actuarial Data Master. Specifically, this research endeavors to evaluate the associations between variables related to cash flow and coverage level selection, as well as isolate the effect of premium rates on coverage selection, in order to provide evidence that constrained cash flow may be the reason for the appearance of nonutility maximization in coverage level selection. The results indicate that variables directly related to cash flow such as higher costs are associated with significant differences in coverage level selection, though the direction of the association is dependent on the type of costs, whether fixed or variable, while higher revenue higher acreage farms insure at higher coverage levels. In addition, higher premium costs are associated with lower coverage level selection, despite subsidy incentives indicating expected cash flow plays a significant role in coverage level decisions.Item Weed and crop discrimination with hyperspectral imaging and machine learning(Montana State University - Bozeman, College of Engineering, 2019) Scherrer, Bryan Joseph; Chairperson, Graduate Committee: Joseph A. ShawHerbicide-resistant weed biotypes are spreading across crop fields nationally and internationally and mapping them with traditional crop science methods - cloning plants and testing their resistance levels in a lab - are costly and time consuming. A segment of the field of precision agriculture is being developed to accurately and quickly map the location of herbicide-resistant and herbicide-susceptible weeds using advanced optics and computer algorithms. In our study, we collected hundreds of thousands of spectra of herbicide-resistant and herbicide-susceptible biotypes of the weeds kochia, mare's tail and lamb's quarter and of crops including barley, corn, dry pea, garbanzo, lentils, pinto bean, safflower, sugar beet at the Southern Agricultural Research Center in Huntley, Montana using a hyperspectral imager. Plants were imaged in a controlled greenhouse setting as well as in crop fields using ground-based and drone-based imaging platforms. The spectra were differentiated from one another using a feedforward neural network machine learning algorithm. Classification accuracies depended on what plants were imaged, the age of the plants and lighting conditions of the experiment. They ranged from 77% to 99% for spectra acquired on our ground-based imaging platform and from 25% to 79% on our drone- based platform.Item Effect of spectral band selection and bandwidth on weed detection in agricultural fields using hyperspectral remote sensing(Montana State University - Bozeman, College of Agriculture, 2017) Tittle, Samuel Bryant; Chairperson, Graduate Committee: Rick L. LawrencePresence of weeds in agricultural fields affects farmers' economic returns by increasing herbicide input. Application of herbicides traditionally consists of uniform application across fields, even though weed locations can be spatially variable within a field. The concept of spot spraying seeks to reduce farmers' costs and chemical inputs to the environment by only applying herbicides to infested areas. Current spot spraying technology relies on broad spectral bands with limited ability to differentiate weed species from crops. Hyperspectral remote sensing (many narrow, contiguous spectral bands) has been shown in previous research to successfully distinguish weeds from other vegetation. Hyperspectral sensor technology, however, might not currently be practical for on-tractor applications. The research objectives were to determine (1) the utility of using a limited number of narrow spectral bands as compared to a full set of hyperspectral bands and (2) the relative accuracy of narrow spectral bands compared to wider spectral bands. Answers to these objectives have the potential for improving on-tractor weed detection sensors. Reference data was provided by field observations of 224 weed infested and 304 uninfested locations within two winter wheat fields in Gallatin County, Montana, USA. Airborne hyperspectral data collected concurrently with the reference data provided 6-nm spectral bands that were used in varying combinations and artificially widened to address the research objectives. Band selection was compared using Euclidean, divergence, transformed divergence, and Jefferies-Matusita signature separability measures. Certain three and four narrow band combinations produced accuracies with no statistical difference from the full set of hyperspectral bands (based on kappa statistic analysis, alpha = 0.05). Bands that were artificially widened to 96 nm also showed no statistically significant difference from the use of 6-nm bands for both all bands and select band combinations. Results indicate the potential for bands that can differentiate weed species from crops and that the narrowest spectral bands available might not be necessary for accurate classification. Further research is needed to determine the robustness of this analysis, including whether a single set of spectral bands can be used effectively across multiple crop/weed systems, or whether band selection is site or system specific.Item Impacts of copula modeling and parametric variation on revenue policy premium rates in multiple peril crop insurance(Montana State University - Bozeman, College of Agriculture, 2015) Simonds, Seth Neil; Chairperson, Graduate Committee: Vincent H. Smith; Joseph Atwood (co-chair)Federally subsidized multiple peril crop insurance is the primary mechanism by which U.S. farmers receive public income. This study investigates the role of copula modeling in developing revenue product premium rates for multiple peril crop insurance. Simulation and empirical experiments are used to examine the viability of a ratemaking practice that relies on an assumed Normal copula. This study shows that the assumption of a copula cannot be statistically justified and that premium rates generated within copulas and between alternative copulas can diverge as a function of the marginal price and yield distributions, their relationship and the level of protection a producer elects. The current ratemaking practice does not account for the imprecision of premium rates implicit to a copula based approach. A copula selection method is proposed and examined in order to reduce premium rate imprecision resulting from copula misspecification. A non-copula based ratemaking method may better meet the overt policy objectives of multiple peril crop insurance.
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