Browsing by Subject "Genetics"

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Assessing Function Efficiency of AtWUS Through Genetic Modifications
(2020-06) Badey, Nikil, B
This research aims to optimize developmental transporter, AtWUS by removing the dimerization domain found in exon 2 of the protein. By removing the dimerization domain, we were able to achieve a more sustainable and efficient system of growth unlike previous model comparisons of AtWUS.
Association Mapping for Net Blotch Resistance in Barley and a Study of Barley/Cereal Yellow Dwarf Virus in Minnesota
(2017-08) Adhikari, Anil
Genome wide association studies (GWAS) were conducted to identify net blotch (net form: caused by Pyrenophora teres f. teres) resistance loci in Ethiopia and Eritrea (EEBC) barley landraces and the elite germplasm of the Barley Coordinated Agricultural Project (Barley CAP). Two quantitative trait loci (chromosomes 5H and 6H) were identified in the EEBC. Resistance QTL were found in chromosomes 4H and 6H in the two-row panel, chromosomes 3H and 6H in the six-row panel and in chromosomes 3H, 4H, 6H and at an unmapped location in the combined Barley CAP germplasm. The distribution of Barley yellow dwarf (BYD), caused by Barley/cereal yellow dwarf virus (B/CYDV) in the Luteovirus family, in Minnesota was studied using 243 cereals and grass samples collected from 2013 to 2015. Reverse transcription polymerase chain reaction using virus strain specific primers revealed that BYDV-PAV was the most prevalent strain of B/CYDV.
Characterization Of TM9SF2 And WAC As Novel Colorectal Cancer Driver Genes
(2018-10) Clark, Christopher
The studies performed in this dissertation focused on the characterization of two candidate cancer genes, TM9SF2 and WAC, and their role in colorectal cancer (CRC). Interest in these two genes stems from their discovery as frequently mutated genes in a mouse-based CRC mutagenesis screen. The first chapter will discuss CRC and provide an historical overview of the methods used to discover novel CRC driver genes. The chapter will also cover modern strategies to identify exciting new CRC driver genes before it ends with a thorough overview of the transposon based forward mutagenesis screen used for CRC gene discovery. The second chapter describes my work demonstrating that the transmembrane protein TM9SF2 is a novel CRC oncogene. Here, we have shown that TM9SF2 is a significant driver gene in murine CRC tumors and, with multiple approaches, that TM9SF2 is overexpressed in approximately one-third of human CRC samples. We provide functional data demonstrating that shRNA-mediated reduction of TM9SF2 or complete knockout by CRISPR/Cas9 drastically reduces tumor fitness in human CRC cell lines. Finally, we provide evidence that high TM9SF2 expression is correlated with poor patient prognosis. The third chapter focuses on the WAC gene and its potential tumor suppressor activity in CRC. We have shown that WAC is frequently mutated in murine CRC mutagenesis screens and that reduction in WAC expression reduces cell growth. This chapter also discusses our finding that loss of WAC is detrimental to mouse embryonic development. The final chapter in this dissertation provides a discussion of the significance of these findings and how these results will impact the CRC research community.
Characterizing specific henetic and environmental influences on alcohol use
(2012-09) Irons, Daniel Edward
Although both genetic and environmental influences, as well as the interplay between them, are clearly important to the development of alcohol use and related psychopathology, the effects of many of the particular genetic variants and environmental risk factors responsible have not yet been confirmed. We conducted three studies with the goal of moving beyond abstract estimates of genetic and environmental variance to the assessment of whether specified risk factors were causally implicated in the development of alcohol-related behaviors and problems. First, in a longitudinally assessed sample of 356 adopted adolescents and young adults of East Asian descent, we examined the progression over time of the relationship between a functional polymorphism in the alcohol metabolism gene aldehyde dehydrogenase 2 (ALDH2) and multiple measures of drinking behavior. We found that the protective effect of the less-functional ALDH2 variant increased between mid-adolescence and early adulthood, and that non-biological parental alcohol use, but not sibling alcohol use, nor deviant peer affiliation, moderated the effect of the gene. In a second study, using a community-based sample of 7224 individuals assessed in early and middle adulthood, we employed multiple methods to conduct a comprehensive examination of the effects of markers in GABA system genes on measures of alcohol use and related symptomatology. We tested not only the potential effects of individual markers, but also their effects in aggregate, and at the whole-gene and system-wide levels. None of these methods produced results indicative of an effect of GABA system variants on measures of alcohol use or misuse. We conducted a third study with a sample of 1512 twins, longitudinally assessed from early adolescence into adulthood, to determine whether adult alcohol use and misuse, as well as other adult outcomes, could be attributed to the causal effect of alcohol exposures in early adolescence. We used two separate techniques to adjust for potentially confounding factors. First, we used a propensity score design to adjust for the potentially confounding effects of a number of measured background covariates. Second, we used the cotwin control design to adjust for confounding due to unmeasured factors (including genetic influences) shared between twins in pairs discordant for early alcohol exposure. The results of both methods applied in this third study were generally consistent with there being a causal effect of early alcohol exposures on the later development of adult alcohol problems and other related adult outcomes, but contrasting the two methods indicated that exposure effect estimates from the propensity score application were likely to be biased by unmeasured confounding variables. In summary, we have first substantially elaborated upon the effects of a genetic variant known to influence alcohol-related behaviors (in the ALDH2 gene); next, despite thorough investigation, we have found no evidence for the effects of a second set of purported genetic influences (GABA system genes); and finally, we provided evidence that early alcohol exposure likely exerts a genuinely causal influence on later alcohol-related problems and other adult outcomes.
Context-Driven Prior Distributions in Genome–Wide Association Studies, Medical Device Adaptive Clinical Trials, and Genetic Fine-Mapping
(2021-02) Kaplan , Adam
Present research has gravitated towards making inferences from high-dimensional data, the scenario when we have considerably more variables than the number of observations we have to estimate their effects on a given outcome, and standard statistical methodology cannot be used here. Models assuming that a majority of these variables do not associate with the outcome, or shrinkage models, have been used for such situations. However, most standard shrinkage models tend to ignore the natural dependencies within high-dimensional data. For instance, geneticists have well understood that rare mutations along the chromosome are correlated, and this correlation decreases as the spatial distance between the mutations increases. As a result, treating these variants as independent from one another misses supplementing the estimation of their relationships with the outcome, with this contextual information. In this dissertation, instead, we present models assuming that the variables’ effects are dependent on each other which appends the shortage in observations. Specifically, we introduce this version of shrinkage models in the contexts of a clinical trial for optimizing a medical device for one patient and detecting genetic variants that are associated with a disease.
Development of genetic tools in environmental Pseudomonas species
(2022-12) Kalb, Madison
Plant growth-promoting rhizobacteria possess many beneficial traits that make them desirable in agricultural applications. Several Pseudomonas spp. have developed a close association with plants and perform nutrient exchange as well as protect the plant from pathogens. Limited research has been done in genetically manipulating these organisms, which could further enhance the agricultural utility of these strains, providing a far less destructive alternative than the chemical fertilizers and pesticides used today. In this work I aimed to build a genetics system in several species of environmental Pseudomonas as the basis for future manipulation and research within these strains. I first investigated growth dynamics and transformation strategies to later introduce phage-derived recombinases for directed chromosomal mutation of the rpoB gene while providing direct comparison of these criteria between different strains of Pseudomonas. I also highlight some of the unique behavior within these Pseudomonas spp. that further emphasizes the individuality between strains and difficulty in creating a “one-size fits all” protocol, while identifying key components to consider when adapting an environmental bacterium to life in the lab.
Did You Give the Government Your Baby’s DNA? Rethinking Consent in Newborn Screening
(Minnesota Journal of Law, Science and Technology, 2014-05) Suter, Sonia
Newborn screening (NBS) has long offered the possibility of identifying rare conditions, which can be lethal or debilitating if not detected and treated quickly in the newborn period. These screening programs, usually mandatory, have been well established in every state since the 1960s. In the last decade, the number of conditions screened for has risen exponentially to include more than fifty inborn errors of metabolism, blood disorders, genetic, or other conditions. Not surprisingly, newborn screening programs have been widely accepted for their potential to save the lives of countless children. Despite their valuable public health benefits, however, old approaches to, and more recent expansions of, NBS raise important privacy and policy concerns. NBS samples are collected in most states without affirmative, or sometimes any, consent from parents. NBS programs now screen for an ever-broadening range of diseases—sometimes without careful assessment of the risks and benefits—including conditions for which there is no treatment. NBS samples are retained for long periods or indefinitely. And finally, few, if any, limits prevent potentially invasive uses of these samples by the government or third parties. Indeed, evidence suggests that a great deal of research is being conducted on these stored blood spots, the collection and storage of which many parents are simply unaware. Only a few lawsuits and legislatures have addressed the legality of these practices. With recent expansions in the scope of NBS and increased interest in these samples for research, it is time to take a fresh look at this long-standing public-health system and to reexamine some of the underlying philosophies and practices associated with it. While NBS offers important public health benefits, it also threatens some of the civil liberties of the parents and children involved. This piece argues for the need to strike a careful balance between the public goods and private interests, and describes a methodology that allows these competing values to be recognized in policymaking. It concludes by suggesting ways to balance the important values of maximizing the well-being of newborns and promoting research, while also protecting autonomy and privacy as much as possible.
An epidemiologic and genetic exploration of the etiology of Type 2 diabetes in the Atherosclerosis Risk in Communities (ARIC) and Epidemiology of Hearing Loss (EHLS)/Beaver Dam Offspring (BOSS) Studies.
(2011-10) Raynor, Laura A.
Type 2 diabetes is a major contributor to mortality and morbidity in the United States. The etiology of this disease is complex and our knowledge of it is incomplete. These analyses sought to increase our understanding of the etiology of type 2 diabetes and to distinguish newly identified risk factors that could someday be useful in clinical risk prediction models. The first paper examined the contributions of novel risk factors to the prediction of type 2 diabetes in the Atherosclerosis Risk in Communities (ARIC) study. There was only modest reclassification of risk with the addition of forced expiratory volume in 1 second (FEV1) to the risk model and a small improvement in the integrated discrimination index (IDI) with the addition of white blood cell count, activated partial thromboplastin time (aPTT), albumin, factor VIII, magnesium, hip circumference, heart rate, and a genetic risk score in the total cohort. In the case-cohort analysis there was no significant reclassification of risk, but the addition of adiponectin, leptin, gamma-glutamyl transpeptidase (GGT), ferritin, inter-cellular adhesion molecule 1 (ICAM-1), and complement C3 to models modestly improved the IDI. A second paper examined the association between sets of genome-wide association (GWA) derived type 2 diabetes score alleles with both incident type 2 diabetes and prostate cancer in the ARIC cohort. We found that these score sets derived from men were not significantly associated with type 2 diabetes in an independent target dataset of women, nor were they associated with prostate cancer in men. Secondarily, we conducted a pathway analysis of our GWA analyses of type 2 diabetes and prostate cancer. We failed to identify pathways significantly associated with both diseases; however, we did identify a pathway statistically significantly associated with type 2 diabetes, the growth hormone signaling pathway. A third paper looked for associations between genetic variants in the Wnt pathway and hemoglobin A1C (HbA1c) levels in the Epidemiology of Hearing Loss (EHLS) and Beaver Dam Offspring Study (BOSS) studies. No Wnt variants were significantly associated with HbA1c. Nor were we able to replicate the associations between three SNPS and HbA1c recently identified in a meta-analysis. This dissertation contributes to our understanding of type 2 diabetes risk prediction by showing that few novel risk factors contribute meaningfully to existing risk prediction and expands our understanding of the etiology of type 2 diabetes by identifying a genetic pathway significantly associated with this disease and its related quantitative traits.
Evaluating the Utility and Causative Genetics of Soybean Mutants
(2016-03) Campbell, Benjamin
Soybean (Glycine max (L.) Merr.) is the second most widely planted crop in the United States by acreage, but yet its genetic resources, mapping methodologies, and breeding improvements lag behind those of other major crop species. In the 20th century, soybean researchers gathered a wealth of natural soybean genetic diversity in the forms of soybean’s wild relative G. soja, soybean landraces, soybean elite lines, and spontaneous mutants. Starting in that same century, researchers began inducing soybean mutations through chemical or irradiation mutagenesis to generate new phenotypes. In the 21st century, these mutagenesis efforts have expanded and have been coupled with new genomics tools to enhance soybean functional genomics. These new mutagenesis efforts and genomics tools will be discussed in chapter one. One of the challenges facing soybean is the difficulties in gene mapping, cloning, and validation. A major focus of this dissertation is the adaptation of new genomics tools and mapping methodologies to soybean in order to facilitate the identification of causative mutants in soybean. Chapter two demonstrates a more classical approach to gene mapping and soybean whole plant transformation to identify the causative loci for three spontaneous chlorophyll deficient mutants. In contrast, chapter three utilizes a combination of new genomics approaches to map and clone a fast neutron induced mutant and validates the result using both a second mutant allele from a historic soybean mutant and transformation of an Arabidopsis mutant. Chapter four builds off of the results of chapter three in leveraging the genomic mapping approach to clone a spontaneous canopy architecture mutant. Several unexpected results and conclusions are reported in the following chapters. Chapter two provides evidence to challenge the widely held idea of gene redundancy in soybean provides an effective buffer against mutations. Additionally, to our knowledge, the research of chapter two reports the first instance of identical mutations affecting two different paralogs resulting in nearly identical phenotypes. Chapter three demonstrates that array comparative genomic hybridization technology and whole genome sequencing of mutant and wild-type bulks can be effectively combined to map and clone a fast neutron mutant from a small F2 population. The chapter also provides an example of the high complexity of mutations that can result from fast neutron irradiation. Chapter four describes the mapping and characterizing a short petiole mutant. The research identifies that the short petiole trait (lps1) is due to a three base-pair in frame insertion in an uncharacterized gene. It was found that the mutation decreases petiole length primarily by decreased cell length and that the short petiole trait could be agronomically beneficial through improved harvest index. The results from chapter four suggest that there is the capacity to improve soybean’s productivity and agronomics through modifications to canopy architecture, as has been demonstrated in other major crop species. The fifth and final chapter discusses potential future directions for soybean genomics research. New population designs with improved efficiency are described. Additionally, suggestions are made for how to utilize current technologies to improve next generation population designs.
Evaluation of phenotypic and physiologic characteristics of selected sources of white spruce, Picea glauca (Moench) Voss
(2013-12) Pike, Carolyn C.
White spruce is highly valued for its wood pulp in commercial forestry in Minnesota. Seed orchards have been developed using genotypes selected for increased volume production. I conducted three different experiments to study the variation of ecophysiologic traits among genotypes selected from the Minnesota Tree Improvement Cooperative's program to better characterize the phenotype of selected genotypes. In chapter 1, I analyzed wood specific gravity, tree volume, and leaf traits on 25-year old trees in a white spruce progeny test. Wood specific gravity was negatively correlated with tree volume. Needle traits, primarily specific leaf area (SLA), leaf area ratio (LAR) and leaf mass ratio (LMR), were positively correlated with wood volume. In chapter 2, I planted seedlings from four genotypes selected for superior volume growth and two wild sources in a common garden. I harvested ten trees from each genotype, each year for three years. I examined biomass allocation, tree allometry and assessed genetic correlations among allocation of biomass to major organs. The largest differences in biomass were found between the two wild sources that represented two different seed zones in Minnesota. Selected sources more closely resembled the southern, than the northern, wild source. The northern wild sources had slightly higher allocation to roots but otherwise no significant differences in allometry were found. In chapter 3, I set up an outdoor experiment by planting five selected- and two wild- seed sources into 1-gallon containers to test the effects of mid-winter warming on phenology and growth of white spruce. Bud-break time was delayed in plots that were warmed in February, and advanced in those warmed in March. Overall controls had the highest height growth and intermediate bud-break time. Climatic warming that takes place during winter months may delay or advance bud-break depending on the timing. Growth of white spruce is expected to decline with increased episodes of winter warming. Selected sources should be favored in reforestation across Minnesota because of the higher productivity and adaptability to local conditions.
Evolution and the climatic niche: Using genomics and niche modeling to explore how climate impacts evolutionary processes
(2022-02) Weaver, Samuel
Climate shapes the distributions of and interactions among species and thus influences many evolutionary processes related to the generation and maintenance of biodiversity. Oscillations in climatic regimes have played an important role in shaping the patterns of diversity by driving speciation events when previously connected populations become allopatrically isolated in different environments. Changing climates also are associated with extinction events when populations are unable to track their climatic niche or adapt to novel conditions. The rapid climate change caused by human activity emphasizes the need to understand the role climate plays in mediating species interactions and distributions. This work combines the use of climatic and genomic data across a variety of vertebrate systems to explore how climate has shaped the processes of speciation and evolution, and how climate may threaten the continued persistence of both recognized and unrecognized diversity. The evolution of a species’ climatic niche, or the climatic conditions under which a species occurs, plays a central role in generating diversity and adaptation to new environmental conditions. Faster rates of climatic niche evolution are associated with increased diversification rates, suggesting that the exploration of novel climate space can facilitate isolation and subsequent diversification. The evolution of traits that may increase or decrease rates of climate niche evolution, then, may play an important role in the colonization of novel environments and the formation of species. In my first chapter, I show that the evolution of a short aquatic larval stage in Desmognathus salamanders led to an increase in the rate of climatic niche evolution, which may have played a central role in the adaptive radiation of this group. Changes in climate have the potential to bring long-isolated species into contact with one another. Oftentimes, these species can produce viable offspring with one another and form hybrid zones. These hybrid zones often form along ecological gradients, with hybrids occurring in habitats intermediate to the climatic conditions occupied by the pure parental populations. In the Southern Appalachian Mountains, Plethodon shermani and Plethodon teyahalee hybridize extensively along an elevational gradient. P. shermani occurs on different mountaintop isolates, and P. teyahalee is distributed in between them at lower elevations. In my second chapter, I explore the genomic evidence for hybridization between these two species and whether climatic variation associated with elevation maintains species boundaries in this system. All surveyed parental P. shermani populations have experienced some degree of introgression from P. teyahalee, and multiple lines of evidence suggest that selection for P. teyahalee alleles drives asummetric introgression from P. teyahalee into P. shermani. We identify no intrinsic genetic barriers to gene flow, suggesting that these hybrid zones are regulated by ecological, rather than intrinsic factors. These findings suggest that all P. shermani populations are in danger of swamping by P. teyahalee as conditions in the Appalachians become warmer and drier. Genomics and niche modeling are powerful tools for identifying cryptic lineages of conservation concern within widespread species. In addition to identifying lineages, these approaches can inform managing agencies about threats to population persistence such as climate change-induced habitat loss and inbreeding. In my final chapter, I assess patterns of genomic and environmental differentiation among populations of Kinosternon hirtipes. Within this group, we identified multiple evolutionarily distinct lineages, many of which correspond to described subspecies. Genetic and ecological differentiation among these lineages appears to be due to vicariance associated with the Trans-Mexican Volcanic Belt. Northern populations exhibit low genetic diversity, high levels of inbreeding, and may lose over 85% of climatically suitable habitat to climate change, raising concern over their long-term viability.
From eugenics to public health genetics in mid-twentieth century Minnesota.
(2011-05) Holtan, Neal Ross
In the twentieth century, people in Minnesota experienced four developmental phases of human genetics in distinct organizational manifestations: the Minnesota Eugenics Society (organized in 1926), the Dight Institute for Human Genetics at the University of Minnesota (established in 1941), the Minnesota Human Genetics League (incorporated in 1945), and the Human Genetics Unit at the Minnesota Department of Health (authorized in 1959 and created in 1960). The first three phases are tied to the last, the unprecedented establishment of public health genetics that made Minnesota the first state to organize a public human genetics program. I examine the intellectual, scientific, and social roots of public health genetics and its relationship to the rest of public health practice before reaching the conclusion that the promise of public health genetics appeared to have been high for its proponents in the beginning, but because of the socio-cultural shifts of values in the 1970s and a poor fit with public health's traditional array of strategies, it did not thrive over time.
Genetic analysis and characterization of variegation in hybrid grape populations (Vitis spp.)
(2020-09) Olson, Jack
Variegation is a plant trait defined by “plants which develop patches of different colors in the vegetative parts”, although variegation can express in reproductive parts of plants as well (Kirk and Tilney-Bassett, 1978). Variegation is a common trait found among a wide variety of plant species and has been reported in V. vinifera, sport mutations, and segregating in hybrid grape populations (Reisch and Watson, 1984; Filler et al., 1994; personal observation). Variegation is highly desirable in ornamental plant breeding for its showy colors and patterns, but in grape seedlings, it has been observed to have deleterious effects in the form of shorter and less vigorous plants than their wild-type siblings. Mapping the locus or loci associated with variegation would allow for the development of markers to identify parents that may carry the recessive allele for the trait, allowing for more informative decisions on population size and parental combinations when making crosses (Chapter 2). Three different mapping approaches - bulked segregant analysis (BSA), Genome-wide association study (GWAS), and genetic mapping - were utilized to detect and validate associated loci. A total of 9 hybrid grape populations were utilized in mapping, of which all 9 were used in BSA, 3 (GE1642, GE1703, GE1895) were used in GWAS and 2 (GE1642, GE1703) were used in QTL genetic mapping. BSA detected four highly significant SNP markers on chromosome 14 between the physical positions of 21,425,721 to 21,425,734 Mbp. GWAS identified 24 significantly associated markers on chromosome 14 from 27.1 to 30.1 Mbp in GE1642 and GE1895; however, 9 markers on chromosome 11 from 12.1 to 18.4 Mbp were significantly associated with variegation in GE1703. Genetic mapping of GE1642 and GE1703 mapped the variegation the same regions, which validated the region identified in GWAS. Thus, two major loci on chromosomes 11 and 14 were associated with variegation in separate hybrid grape populations. Candidate genes for variegation were identified in the two locus regions for future studies. The effects of variegation on hybrid grape were examined in a variety of experiments in which it was discovered that variegation resulted in a reduction in photosystem II efficiency; reduced leaf chlorophyll and carotenoid concentration; altered leaf palisade mesophyll structure; and had significant reductions in plant growth-related traits (Chapter 3).
Genetic Analysis Of Whole-Plant Leaf Area, Leaf Shape, And Leaf Venation Branching In Soybean
(2020-04) McCoy, Erik
Increasing soybean production to meet growing demand requires closing the current yield gap, and approaching the yield potential through genetic improvement and optimization of cultivars for specific growth conditions. Leaf traits are important targets for improvement and play key roles in the capture and usage and storage of the resources needed for yield production. Leaf area has been shown to be associated with yield through its effect on transpiration and interception of photosynthetically active radiation (PAR). Leaf shape has similar effects on transpiration through boundary layer effects, and also controls the amount of intercepted PAR by altering the canopy structure and the amount of light that penetrates through the canopy. Leaf venation determines the rate of water flow through the plant, and the geometry of vein topology likely has a significant effect on this rate, and therefore the total water transpired by the plant as a whole. Vein branching angles are thought to play a role in hydraulic conductance, and may also act as a structural constraint to leaf area development. While leaf shape in soybean is known to be controlled by the Ln locus, which in addition pleiotropically affects seed size and number, the genetic basis of whole-plant leaf area and venation topology traits are yet to be discovered. Leaf area, shape, and venation topology are closely linked during leaf development, so an understanding of their genetic basis and relationship to one another is critical to the optimization of leaf type for a target environment. The goals of this study are to identify QTL for whole-plant leaf area, leaf shape, and vein branching angle, as well as to quantify and compare the relationships between these traits. A bi-parental SoyNAM population (IA3023 x LG94-1906) consisting of 136 genotypes was grown twice over two years and measurements were taken for whole-plant leaf area, whole-plant dry mass, specific leaf area, leaflet length, leaflet width, leaflet shape, vein branching angle, and leaflet area. QTL mapping and correlation analyses were performed for all of these leaf traits. Novel QTL were identified for whole-plant leaf area and vein branching angle that co-localized with the Ln locus. QTL identified for leaflet length, leaflet width, and leaflet shape also co-localized with the Ln locus as expected, however a second, novel QTL was identified for leaflet length. These results suggest that the Ln locus may contribute to leaf area and vein branching angle determination in addition to leaf shape and seed size/number. Further investigation into the genetic basis of these traits and their interactions will help in developing cultivars with ideal leaf types. A negative correlation between vein branching angle and whole-plant leaf area was found, supporting the hypothesis that larger branching angles constrain leaf area development. Additional study on this relationship in soybean and other crops may prove this connection spans across species, and can be a useful target in breeding for ideal leaf types.
Genetic and Genomic Analysis of Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon
(2016-08) Della Coletta, Rafael
Wheat stem rust, caused by the fungus Puccinia graminis f.sp. tritici (Pgt), is a devastating disease that has been under control for decades. However, new races of this pathogen have emerged that overcome many important wheat stem rust resistance genes, and their spread toward important areas of wheat production threatens global wheat production. Nonhost resistance in plants, which provides durable and broad-spectrum resistance to non-adapted pathogens, may hold great potential to help in the control of wheat stem rust, but the genetic and molecular basis of nonhost resistance is poorly understood. This research project employed the model plant Brachypodium distachyon (Brachypodium), a nonhost of Pgt, for genetic analysis to map loci associated with nonhost wheat stem rust resistance. Using bulked segregant analysis, next-generation sequencing, and bioinformatics approaches, seven quantitative trait loci were found to contribute to nonhost stem rust resistance in a recombinant inbred population derived from a cross between two Brachypodium genotypes with differing levels of resistance. In a second study, analysis of a Brachypodium recombinant inbred population segregating for an induced mutation that confers susceptibility to wheat stem rust led to the identification of a one base pair deletion in a gene that may be the cause of the mutant’s susceptibility. The gene is a homolog of the Arabidopsis gene TIME FOR COFFEE (TIC), which plays a role both in circadian clock regulation and jasmonate signaling. Collectively, the findings of this research project advance our understanding of the genetic basis of nonhost resistance to wheat stem rust, and will guide future research aiming to identify genes essential to the nonhost resistance response, as well as their mechanisms of action.
The genetic dissection of fruit texture traits in the apple cultivar honeycrisp.
(2010-12) McKay, Steven John
The commercially successful cultivar Honeycrisp, released by the University of Minnesota in 1991, is known for its high degrees of crispness and juiciness. This cultivar has been incorporated into numerous breeding programs in an effort to duplicate its desirable texture traits in conjunction with such other traits as disease resistance and improved tree vigor. This study characterizes several apple fruit texture traits within a large breeding population over several years, combining the established protocols of incomplete block design, sensory evaluation panels, and best linear unbiased prediction. Five full-sib families, all of which share `Honeycrisp' as a common parent, were assayed using a variety of molecular markers, and genetic maps were constructed for each of the five families. The five genetic maps were aligned to produce a consensus genetic map for `Honeycrisp'. Predicted genotype values from each of the five families were coupled with the corresponding molecular data and the genetic maps to identify quantitative trait loci (QTLs) for each family-by-year combination, which were compared relative to the consensus genetic map. Several intervals were identified within the map over which QTLs for multiple families and multiple years were collocated, reflecting consistent and robust QTLs. Results are largely in accordance with previous studies of other apple cultivars with notable exceptions, which are discussed in the context of the recently published apple genome sequence
Genetic understanding of resistance to foliar phylloxera, Daktulosphaira vitifoliae Fitch, in cold-hardy hybrid grapes
(2020-06) Yin, Lu
Phylloxera is an important pest infesting foliage of North American native Vitis species and cold-hardy hybrids between V. vinifera and V. riparia. Currently, chemical control is the only commonly used management method. There is a need to development integrated pest management strategies including the use of resistant varieties (Chapter 1). The effects of foliar phylloxera infestations on four grape varieties were a numeric reduction in unit yield of cluster weight, photosynthesis rate, and photosystem II efficiency. This reduction in cluster weight can be economically important to growers (Chapter 2). Most genetic studies in grape for resistance to phylloxera limited to the root. A previous study using a population, GE1025 (N=~125), detected the first quantitative trait locus (QTL), a ~15-cM region, for foliar resistance on chromosome 14. To fine map the QTL, a larger population, GE1783 (N=~1023), was created and genotyped with the rhAmpSeq technology with conserved haplotype markers across Vitis species. Through selective phenotyping using a 0-7 severity rating scale among other phylloxera severity traits on 188 potential recombinants of GE1783, we fine mapped the QTL to 2.1-4.9 Mbp on chromosome 14. A most probable candidate resistance gene plays a role in gallic acid formation (Chapter 3). To investigate antixenosis as a possible resistance mechanism, leaf trichome density was mapped in GE1025 with genotype-by-sequencing and phenotypic scores collected using a 0-6 trichome density scale at several leaf positions. Evaluations were done on forced dormant cuttings in two years and on field-grown leaves in one year. There was a ~ -0.2 correlation (r) between trichome density and phylloxera resistance. Two regions on chromosomes 1 and 10 were repeatedly detected for multiple trichome density traits. We fine mapped the chromosome 1 QTL to a 140-kb region using selective phenotyping in GE1783. We found insertion/deletion variations of the parents of the population in one candidate pseudogene in this region and three other candidate genes proposed previously (Chapter 4). In all, we identified closely linked markers that can be used for marker-assisted breeding for foliar phylloxera resistance to improve the cold-hardy hybrid grape germplasm and potential candidate resistance genes for future investigations.
Identification and Characterization of Important Quantitative Trait Loci for Soluble Solids and Titratable Acidity for Germplasm in the University of Minnesota Apple Breeding Program
(2020-12) Miller, Baylee
Apple fruit acidity and sweetness are two of the major trait components involved in apple seedling sensory evaluation. Published studies have alluded to some of the genetic components of apple fruit acidity and sweetness, but few have included an array of germplasm relevant to the University of Minnesota apple breeding program. With the release and subsequent frequent use of ‘Honeycrisp’ and ‘Minneiska’ apple cultivars as parents at the University of Minnesota, the germplasm set deviates from other breeding programs. In order to increase breeding efficiency and increase overall quality of apple seedlings, this study describes the genetic components of apple fruit acidity and sweetness and provides breeding insights to negate the creation of undesirable apple seedlings. This study uses data from 2010 to 2018 to characterize a wide but relevant array of germplasm, using six major families, three of which have ‘Honeycrisp’ as a parent, and three of which have ‘Minneiska’ as a parent. Three major loci associated with variation in titratable acidity content on linkage groups 1, 8, and 16, and two loci associated with variation in soluble solids content on linkage groups 1 and 13 were identified, and haplotypes were characterized for each locus. The conclusions from this study provide insights for designing crosses that create seedlings with desirable ranges of acidity and sweetness characteristics.
Identification of novel genes involved in prostate and Schwann cell malignancies utilizing a sleeping beauty transposon somatic cell mutagenesis screen
(2011-06) Rahrmann, Eric Patrick
The focus of this thesis was identification of new genes and genetic pathways altered in prostate cancer and malignant peripheral nerve sheath tumor formation utilizing a Sleeping Beauty somatic mutagenesis forward genetic screen. Mutagenesis of prostate epithelial cells gave rise to proliferative cell lesions that resembled early stages of prostate cancer. From these lesions, Pde4d, Klhl13, Braf, and Nras were identified as CISs. Moreover, Pde4d was shown to be a pro-proliferative factor in human prostate cancer cell lines and to be overexpressed in human prostate cancers. SB mutagenesis in Schwann cells gave rise to all stages of Schwann cell tumorigenesis including benign neurofibromas, plexiform neurofibromas, and aggressive MPNSTs. From these tumors, hundreds of CISs were identified including known tumor suppressors Nf1, Pten, and Cav1. Experiments with loss of Cav1 demonstrated cooperativity with EGFR overexpression in vivo for Schwann cell tumorigenesis.
Investigating invasive population genetics of rainbow smelt (Osmerus mordax) in the Laurentian Great Lakes Region
(2018-08) Dobosenski, Jamie
Increasing our understanding of aquatic invasive species is important because of the negative influence they can have on the economies and ecosystems of invaded regions by negatively affecting ecotourism as well as commercial and recreational fisheries. There is growing interest in how environmental variability (e.g. temperature) and stochastic invasion events (e.g. founder effect) affect the genetic composition of populations of invasive species. Rainbow smelt (Osmerus mordax) are a cold-water, planktivorous fish that spread into the Great Lakes basin in the early 1900s. We performed genetic analyses using microsatellites to determine if a temperature induced mortality event affected the genetic structure of a population of invasive rainbow smelt and to also investigate the influence stochastic invasion events have had on the genetic composition of invasive rainbow smelt populations across broad geographic ranges. Overall, there was no genetic difference in rainbow smelt collected before, during, or after the temperature induced mortality event. To investigate the influence stochastic invasion events have on populations of invasive rainbow smelt, we conducted population genetics analyses on rainbow smelt specimens from Lake Ontario, Lake Michigan, Lake Superior, and four inland lakes in Northern Wisconsin. Most population pairs had pairwise Fst values significantly different than zero except two comparisons. Based on clustering analysis and PCoA analysis, four distinct population clusters were identified. Overall, this study provides evidence that founder effects have more of an impact on invasive rainbow smelt population diversity than extreme population reductions.

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