College of Agriculture & Natural Resources

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The collections in this community comprise faculty research works, as well as graduate theses and dissertations.

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    MEDIATION OF CORTICOSTERONE-INDUCED GROWTH HORMONE GENE EXPRESSION IN CHICKEN EMBRYONIC PITUITARY CELLS: IDENTIFICATION OF TRANS-ACTING FACTORS AND A NOVEL PITUITARY CELL TYPE
    (2024) Liu, Kuan Ling; Porter, Tom E.; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Growth hormone (GH) is responsible for up to 30% of growth in broiler chickens. Somatotrophs, or GH secreting cells, begin to differentiate around embryonic day (e)14, in conjunction with an increase in the primary plasma glucocorticoid (GC) corticosterone (CORT). CORT treatment of e11 chicken embryonic pituitary (CEP) cells induces premature GH secretion. This GC-induced process involves trans-acting factors because the GH gene lacks a canonical GC response element (GRE). In addition to the binding of ETS1 and the GC receptor (GR) to the GC-responsive region (GCRR; 1045/ 964), we hypothesize that there are other regulatory factors necessary for CORT responsiveness. By modifying the pGL3_-1742/+25 GH-luciferase reporter, we have constructed various other GH-luciferase reporters and analyzed them for promoter activity in response to CORT treatment. We identified a putative distal (d) ETS-Like 1 (ELK1) binding site that is necessary. The proximal (p)PIT1 site and pTATA box were also identified to be critical for CORT induction of the GH gene. Interestingly, cloning multiple copies of the extended GCRR (eGCRR; -1067/-900) further increased promoter activity in an additive manner under both basal and CORT treated conditions. Through single-cell RNA sequencing (scRNAseq), 8 members of the ETS family of transcription factors were identified in > 5% of the somatotroph population. Commercial antibodies were validated, and human (h)ETV1, hELF2, hELK3, and hETV6 antibodies were confirmed to recognize their recombinant chicken ortholog and to identify their corresponding protein in e11 CEP cells. Results from chromatin immunoprecipitation quantitative PCR suggest that multiple ETS members are involved in CORT induction of the GH gene with more evidence pointing towards ELF2 and ELK3. Identifying trans-acting factors for the GH gene inducible by CORT allows for better understanding of endogenous GH regulation in chickens. Further analysis of the scRNAseq data from e11 CEP cells revealed a cluster of cells expressing genes for more than one hormone-producing cell type (“premature nebulous” cluster). Within the premature nebulous cluster, a large population (~30%) was co-expressing proopiomelanocortin (POMC) and growth hormone (GH). We named this novel cell population the cortico-somatotrophs. Through RNA fluorescent in-situ hybridization (RNA-FISH) and dual label immunofluorescence, we verified the existence of the cortico-somatotrophs at both the mRNA and protein level, respectively. Cortico-somatotrophs were also shown to share genes for receptors normally specific to both corticotrophs (CRH-R1) and somatotrophs (GHRHR). Additionally, in response to CORT treatment, the cortico somatotrophs showed an increase in GH as well as a decrease in POMC mRNA levels. The discovery of the cortico-somatotrophs suggests a modification to the current dogma on pituitary cell lineages, where corticotrophs and somatotrophs may have overlapping developmental pathways. In conclusion, our discovery of the cortico somatotrophs has furthered our understanding of CEP development and opened the door for further exploration of the cell lineages during pituitary development.
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    Phenotypic and Genetic Analysis of Reasons for Disposal in Dairy Cattle
    (2024) Iqbal, Victoria Audrey; Ma, Li; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Reasons for disposal are defined as why a cow has left the herd during lactation and are documented as termination codes. Dairy cattle termination codes were collected by Dairy Records Processing Centers and stored in the National Cooperator Database maintained by the Council on Dairy Cattle Breeding for analysis. The list of possible termination codes is as follows: code 0 is cow lactation that ended typically without an abortion, code 1 is locomotion problems, code 2 is female transferred or sold, code 3 is low milk yield, code 4 is reproductive problems, code 5 is unspecified reasons, code 6 is death, code 7 is the presence of mastitis, code 8 is abortion, code 9 is udder problems, code A is an unfavorable phenotype, and lastly code B is undesirable temperament. Understanding termination codes is the key to understanding and improving farm management. Unfortunately, the secondary termination codes are not utilized, despite studies saying one reason is too limited. Heifer termination codes should be more utilized, and studies show that this could improve heifer management. The four processing centers' principal termination codes deviated a little from year to year, but processing center D had the most variation in principal termination codes. There were few records with termination codes 9, A, and B. There was low lameness found for Jersey cattle but more fluctuations for their termination codes 6, 7, and 8. Jersey's main reason for disposal was sold and low milk yield. As for Holstein, the main reasons for disposal were low milk production and death. Recommendations include removing termination code 5 (other reasons) and enforcing a secondary termination code for code 2 (sold). Also, including the percentage of animal records used in traits developed at the CDCB was recommended to encourage farmers to add more records to improve breeding selections. Overall, the top main reasons for disposal were low milk yield, death, and reproduction across breeds from 2011 to 2022. To determine whether health traits correlate to termination codes and how health traits change the probability of survival, a multinomial logistic regression was developed, where twelve health traits, breeds, and other factors were used as an independent variable for the termination code, the dependent variable. The output is a regression coefficient list that conveys the effect of each health trait for each termination code. The results show the apparent impacts of animal breeds on different termination codes, such as dairy crossbreeds negatively affecting termination due to reproductive advantages that follow the literature. Lastly, using termination codes as phenotype, this study focuses on developing a genome-wide association study (GWAS) using the Weighted single-step Genomic Best Linear unbiased prediction (WssGBLUP) model to find significant SNPs related to survival in Holstein cows. In summary, this study provided an understanding of reasons for disposal trends, modeled the reasons for disposal, determined the likelihood of termination post-incidence, and found the heritability and important SNPs of each termination code.
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    INTEGRATING FORWARD AND REVERSE GENETIC TOOLS FOR FAST FORWARDING WHEAT IMPROVEMENT
    (2024) Schoen, Adam William; Tiwari, Vijay K; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Bread wheat (Triticum aestivum) provides roughly 20% of the human daily caloric intake and is an important crop for global food security. Changing climatic conditions as well as biotic and abiotic stresses are threatening wheat production worldwide. Sustainable and continuous improvement of wheat using novel genes and alleles is critical to tackle wheat’s imminent challenges. Recent advances in wheat genomics have allowed researchers now to fast-track gene discovery pipelines by implementing strategies first developed in less complex model species. This thesis explores the use of forward and reverse genetic approaches to efficiently discover, map, and validate genes controlling important agronomic traits in bread wheat as well as describes a robust protocol to reduce the generation time in winter wheat. Speed breeding is an important tool that utilizes an increased photoperiod and growing temperature to increase vegetative growth and reduce the time from sowing to harvest. Chapter 1 of this thesis outlines a reproducible method to significantly reduce the generation time in winter wheat from over 120 days based on what has been previously reported to 93 days regardless of vernalization requirements or photoperiod sensitivity and provide a useful tool to increase the pace of the genetic gains in the winter wheat breeding programs. Tillering in wheat directly influences the major yield-related trait, spikes per unit area. Using the forward genetics approach, chapter 2 of thesis reports the identification of a novel tiller inhibition gene (tin6) to a small physical region of 2.1 Mb region on chromosome 2DS. This was the first example of using a genome coming from the pan-genome of wheat to perform MutMap. Using reverse genetics also has the potential to improve the end-use properties of wheat by knocking out genes which result in an increase of the nutritional value of the flour. Chapter 3 of this thesis, TILLING was used to identify knockouts in all three homeologous copies of the starch synthase gene SSIIa, which has been shown to increase the amount resistant starch in the endosperm of wheat which is known to have health benefits in humans. The grains coming from triple knockouts of SSIIa contained 118% higher resistant starch, and though they showed a decrease in thousand kernel weight, they did not have a shriveled phenotype which had been seen in other ssiia mutants. Chapter 4 of the thesis demonstrate reference genome enabled positional cloning of a tiller inhibition gene (tin3) in diploid wheat species Triticum monococcum. A MutMap population generated from a cross between tin3 and wildtype T. monococcum resulted in the identification of a single candidate gene, encoding a BLADE-ON-PETIOLE-Like protein, containing a splice-variant mutation. To show the power of using a diploid species for translational research in hexaploid wheat, the reverse genetics approach TILLING (Targeting Induced Local Lesions IN Genomes) was used to identify mutations in all three homeologous copies of tin3 in the Jagger mutant population. The full null mutant for the tin3 locus in wheat showed significantly reduced tillering in comparison to wildtype providing concrete evidence that genetic discoveries that are found in diploid wheat can be effectively translated to hexaploid wheat. There are some genes and QTLs have been identified that increase spike length, spikelets per spike, and grain size, very few studies have focused on increasing the number of grains per floret. Chapter 5 of the thesis was focused on positional cloning of the Mov-1 locus which is the underlying gene responsible for the multiovary (MOV) phenotype. The Mov-1 locus dominantly expresses as three ovaries per wheat floret, each of which develop into a grain. Using high resolution genetic mapping with the MOV-reference genome and gene expression data, we identified a single candidate gene that was localized to a small 144kb region on the Mov-1 physical region. To validate the role of the Mov-1 candidate gene in the MOV phenotype, ethyl methanesulfonate (EMS) and gamma radiation mutagenesis was performed to create deleterious point and deletions mutations, respectively. Using 5 independent TILLING and 5 deletion mutants this study demonstrate that Mov-1 candidate gene is required for the MOV phenotype in wheat. It is an exciting time to work in wheat research as the growing wheat genomic toolbox allows for researchers to efficiently identify and validate genes that have potential to improve wheat performance. The methods and findings in this body of work provide a breadth of knowledge that can be implemented in additional genetic studies in wheat in order to fast-track gene and trait discovery for the benefit of wheat geneticists and breeders alike.
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    A WIDE SCALE INVESTIGATION INTO LNCRNA IN BOS TAURUS
    (2023) Marceau, Alexis; Ma, Li; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Although the history of genetic research has focused on genes and gene products, there is an interesting emerging subclass of genetic elements: long noncoding RNAs (lncRNAs). These are portions of the genome that are longer than 200 base pairs in length and are transcribed from DNA to RNA but do not yield a protein. The function of lncRNA is wide reaching and difficult to define; however, they are predominantly linked to the regulation of gene expression. This is done via transcriptional control, translation control, pre- and post- transcriptional and translational control, epigenetic modifications, RNA processing,as well as other methods. In this dissertation, multiple Bos taurus tissues across various life conditions were investigated in order to identify lncRNA and to begin making predictions about the role and function of identified transcripts. First, lncRNA were identified and analyzed in Bos taurus rumen tissue in pre-weaning and post-weaning cattle. lncRNA were implicated in the weaning process and demonstrated enrichment in complex traits, indicating the continued impact rumen-associated lncRNA have on dairy cattle. Following this study, mammary tissues from dry and lactating cattle were used for lncRNA analysis, in relation to the lacta-tion processes. This study revealed both the presence and impact of mammary lncRNA, and identified lncRNA associated with genes and biological processes that are strongly linked to lactation and mammary tissue function. Subsequently, immune system related tissues were analyzed for lncRNA and their roles. This investigation demonstrated lncRNA to be present in all investigated tissues, including transcripts being repeatedly present. Further analysis into identified lncRNA associated transcripts with genes and functions that are crucial to immune response. Finally, a tutorial was created to make lncRNA identification research more easily accessible to future researchers. The findings and creations of this dissertation increase the knowledge base of lncRNA and their role, allowing for further research endeavors and improvements in Bos taurus husbandry.
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    TO WHAT EXTENT DO MODE OF REPRODUCTION, LEVELS OF GENOTYPIC DIVERSITY, AND CONNECTIVITY IN Vallisneria americana MICHX. CONFER RESILIENCE TO A CHANGING CLIMATE?
    (2023) Perkins, Carrie; Neel, Maile C.; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The macrophyte Vallisneria americana Michx. (Hydrocharitaceae) is a foundational submersed aquatic vegetation (SAV) species that provides valuable ecosystem services, such as nutrition for waterfowl and shelter for fish. When healthy, V. americana can absorb excess nutrients from the water and stabilize sediments, but many of its meadows, which span freshwater to oligohaline environments in eastern North America, have been declining since European settlers cleared the land. Declines only intensified in the 1950s due to chronic environmental stressors and major storm events. To determine the extent to which remaining populations can adapt through natural selection or acclimate to novel environmental conditions, I combined observational field data, greenhouse experiments, and spatial modeling to quantify V. americana reproduction at local to regional scales, evaluate evidence of local adaptation and acclimation to environmental stress, and assess the extent to which high levels of connectivity in a V. americana-dominated landscape can absorb environmental stress.I quantified reproduction at 15 sites in the Chesapeake Bay and 14 sites in the Hudson River, with sites in each geographic region spanning the portion of the salinity gradient in which V. americana grows (0-12 ppt). Numbers of inflorescences, sex ratios, and distances among male and female inflorescences varied greatly across latitude and along salinity gradients. Hudson V. americana had fewer inflorescences across two sampling seasons than Chesapeake Bay V. americana but delayed phenology, skewed sex ratios, and large distances among males and females relative to the Chesapeake Bay were more pronounced in 2018. In 2018, warmer spring and summer water temperatures in the Chesapeake coincided with our findings of higher flowering, fruiting, and potential for pollination at the three Chesapeake sites that served as means of comparison to the Hudson. By contrast, in 2020 Hudson plants were larger and produced more inflorescences in July than Chesapeake plants produced in June, indicating that the regional difference in phenology may be smaller than our hypothesis of approximately 23 days, although it is difficult to estimate how much smaller. We attribute this result to sites in the Hudson – mainly those in the tidal-fresh zone of the river – being highly responsive to unusually warm 2020 spring water temperatures. But not all sites experienced this warmth. The tidal-saline zone of the Hudson and the non-tidal zone of the Chesapeake had the fewest flowers and fruits of either region, likely due to the synergistic effects of cold temperatures and high salinity and turbidity in the former and fast currents in the latter inhibiting growth and reproduction. Through greenhouse experiments evaluating growth and reproduction of Chesapeake and Hudson V. americana grown in different salinity conditions, we found evidence of one-way local adaptation in plants sourced from brackish waters of both the Chesapeake and Hudson. In the first experiment (parental-generation), brackish-source plants demonstrated phenotypic buffering, a stress-induced version of phenotypic plasticity. When exposed to three salinity treatments (0 ppt, 6 ppt, and 12 ppt) applied after plants had sprouted, brackish-source plants buffered the effects of salt stress via increased vegetative growth in the form of many ramets and turions at the cost of small stature. By contrast, plants sourced from fresh waters of both regions grew tall in fresh water, but photosynthetic leaf material declined from the time of salt application (June) to the end of the experiment (September). The most severe salinity treatment, 18 ppt, was lethal to most individuals regardless of source habitat. Unfortunately, neither phenotypic buffering nor phenotypic plasticity sensu stricto was carried over via transgenerational plasticity (TGP), when turions were exposed to 12 ppt immediately upon planting (offspring generation). This early-development salt exposure proved lethal for some individuals and sublethal (had a negative effect on growth but did not result in mortality) for others, with turions either failing to sprout or growing a single shoot that was minuscule in stature. Parental-generation salt exposure only exacerbated these offspring effects, producing a non-adaptive TGP effect, resulting in even lower chance of sprouting, higher chance of mortality, and smaller stature. Evidence of local adaptation and acclimation to salinity only when exposure begins later in development suggests that populations have potential for resilience to saltwater intrusion (movement of saline water into fresh water) only if salinities do not remain elevated during the time of early plant development (spring/early summer) and across multiple seasons. In the event of prolonged salinity stress, much habitat (~10,000 hectares) that is currently mesohaline (5-12 ppt) but within the range of tolerance for V. americana will become unsuitable. In our spatial model of SAV persistence in the V. americana-dominated Upper Chesapeake Bay, high connectivity and high probability of SAV presence were found not only in the freshwater head of the Bay, but also in mesohaline (5-12 ppt) and oligohaline (0.5-5 ppt) waters near Middle River. Persistence of predominantly freshwater aquatic macrophytes in Middle River suggests that either 1) plants are locally adapted to brackish waters or 2) existing connectivity buffers the stress of low-quality habitat. Excess nitrogen, an anthropogenic environmental stressor that remains at high levels in Baltimore Harbor and other tributaries, was correlated with a decreased probability of SAV presence in the southern portion of our study area. As expected, low nitrogen, low salinity, and high landscape connectivity at the head of the Bay coincided with the highest predicted probabilities of SAV presence, particularly in the core of the one of the largest SAV beds in the entire Chesapeake Bay, the Susquehanna Flats.
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    The Genetic Architecture of Complex Traits and Diseases in Dairy Cattle
    (2022) Freebern, Ellen; Ma, Li; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Genetic architecture refers to the number and locations of genes that affect a trait, as well as the magnitude and the relative contributions of their effects. A better understanding of the genetic architecture of complex traits and diseases will be beneficial for analyzing genetic contributions to disease risk and for estimating genetic values of agricultural importance. In particular, genetic and genomic selection in dairy cattle populations has been well established and exploited through genome-wide association studies, sequencing studies, and functional studies. The objective of this dissertation is to understand the genetic architecture of complex traits and apply the understanding to investigate the biological relationship between genetics and diseases in dairy cattle. First, we performed GWAS and fine-mapping analyses on livability and six health traits in Holstein-Friesian cattle. From our analyses, we reported significant associations and candidate genes relevant to cattle health. Second, we evaluated genome-wide diversity in cattle over a period of time by running GWAS and proposed a gene dropping simulation program. From this study, we identified candidate variants under selection that are associated with biological and economically important traits in cattle. Also, we demonstrated that gene dropping is an applicable method to investigate changes in the cattle genome over time. Third, we investigated the effect of maternal age and temperature on recombination rate in cattle. We provided novel results regarding the plasticity of meiotic recombination in cattle. Additionally, we found a positive correlation between environmental temperature at conception and recombination rate in Holstein-Friesian cows. Collectively, these studies advance our understanding of the genetic architecture and the biological relationship between complex traits and diseases in dairy cattle.
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    MRP5 AND MRP9 PLAY A CONCERTED ROLE IN MALE REPRODUCTION AND MITOCHONDRIAL FUNCTION
    (2021) Chambers, Ian George; Hamza, Iqbal; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Heme is an essential iron-containing cofactor in proteins that perform diverse functions in biology. Free heme is not only hydrophobic but also generates cytotoxic peroxide radicals. In eukaryotes, heme synthesis occurs in the mitochondria but must be transported to different intracellular organelles to be utilized by hemoproteins, a process that remains poorly understood. In Caenorhabditis elegans, MRP5/ABCC5 is an essential heme exporter as mrp-5 knockout worms are unviable due to their inability to export nutritional heme from the intestine to extra-intestinal tissues. Heme supplementation restores viability of these mutants but fails to restore male reproductive deficits. By contrast, MRP5 in mammals regulates heme levels in the secretory pathway but shows no reproductive phenotypes. Phylogenetically, the closest homolog of MRP5 in vertebrates is MRP9/ABCC12, which is absent in C. elegans raising the possibility that MRP9 may genetically compensate for MRP5 lossin vertebrates. Here, we show that MRP5 and MRP9 double knockout (DKO) mice are viable but reveal significant male reproductive deficits, reminiscent of mrp-5 worms. Although MRP9 is highly expressed in sperm, MRP9 knockout mice show reproductive phenotypes only when MRP5 is absent. Unlike other ABCC transporters, these proteins localize to mitochondrial-associated membranes (MAMs), dynamic scaffolds that associate the mitochondria and endoplasmic reticulum. Consequently, combined loss of both transporters results in abnormal sperm mitochondria and reduced fertilization rates in DKO mice. Untargeted metabolomics show striking differences in metabolite profiles in the DKO testes, consistent with the localization of these transporters to MAMs where inter-organellar metabolite exchange occurs. RNA-seq results show significant alterations in genes related to mitochondria function and energy production, EIF2 signaling, and retinoic acid metabolism. Targeted functional metabolomics reveal retinoic acid levels are significantly lower in the DKO testes. These findings establish a model in which MRP5 and MRP9 play a concerted role in regulating normal male reproductive functions and mitochondrial sufficiency.
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    MODULATING KEY GENES INVOLVED IN PANCREAS FORMATION AND INSULIN SIGNALING USING CRISPR/CAS9 IN THE PIG
    (2019) Sheets, Timothy P; Telugu, Bhanu P; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Among the metabolic diseases, diabetes remains a “pressing problem” as recognized by World Health Organization, not only due to the impact on individuals’ lives, but also because of the rapid increase in newly diagnosed patients. To better understand the mechanisms of diabetes, this dissertation investigates the role of NGN3 in pancreas development using CRISPR/Cas9 gene targeting in the pig model. NGN3 was selected for study because of its critical role in endocrine pancreas formation. Our research demonstrates that the targeted ablation of NGN3 blocks development of the endocrine pancreas, a finding supported through gene expression analysis. Furthermore, follow-up studies show that clonal piglets derived from NGN3-ablated animals lack the major endocrine islet cell types and subsequent expression of key endocrine hormones. This porcine model provides valuable insights into the study of type 1 diabetes in early post-natal life and future applications of human-to-pig chimeric organ development for transplant surgery. Expanding upon this porcine model for diabetes, we sought to apply this approach to the study of type 2 diabetes using a novel pig model, thus bridging the gap between mouse and human. For this endeavor, we identified GRB10 as a potential critical mediator in insulin signaling, development, and growth potential following an extensive literature review. The potential for dual applications in both agriculture and medicine was also identified as an objective. Analysis of qPCR data from in vitro overexpression studies supports that GRB10 modulates insulin signaling through the canonical insulin pathway. Additional data from two in vivo gene editing trials targeting the GRB10 locus in both Ossabaw and domestic pig breeds show a supportive qualitative trend towards growth regulation in the Ossabaw pig breed. Further evidence is required to determine whether GRB10 plays the same role in the domestic pig, as a limited cohort size of mutants precluded an extensive analysis of phenotypes. Together, our assessment of NGN3 and GRB10 offer significant potential for modeling of both type 1 and type 2 diabetes as well as modeling of growth traits in the pig through application of advanced genome engineering technology.
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    INITIATION AND PROGRESSION OF BRAF/NRAS WILDTYPE MELANOMA IN UV-INDUCED MOUSE MODELS OF CUTANEOUS MELANOMA
    (2018) Michael, Helen Thompson; Samal, Siba; Merlino, Glenn; Veterinary Medical Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Melanoma is the deadliest skin cancer and is responsible for nearly 60,000 deaths worldwide each year. At least some melanomas are believed to arise from stepwise progression from normal melanocytes through a benign nevus stage to malignant melanoma and finally metastatic disease. Approximately 20-50% of melanomas have evidence of a pre-existing nevus, indicating that progression is an important route of melanomagenesis. Ultraviolet radiation exposure is believed to play an important role in nevus and melanoma formation, although the mechanisms of this remain unclear. Childhood sunburn and intermittent sun exposure are epidemiologically linked to increased melanoma risk. While most melanomas have activation of the mitogen activated protein kinase pathway, often due to mutations in BRAF or RAS genes, nearly 15% of cutaneous melanomas do not have an identified strong driver. Despite targeted therapies and immunotherapy, the death rate from melanoma has remained nearly static for several decades, so there is a need to identify additional genes and pathways to provide novel therapeutic targets. We hypothesized that progression of melanocytic lesions from benign to malignant is associated with the acquisition of additional genomic mutations. Unlike wildtype mice, hepatocyte growth factor (HGF) transgenic mice have “humanized” distribution of melanocytes along the dermal-epidermal junction. Following a single dose of UV at 3 days of age, HGF mice develop melanocytic nevi and melanomas. In this project, two HGF models were used to generate melanocytic lesions. The first model, on an albino FVB background had a tumor incidence of only 10% and used melanocyte-specific green fluorescent protein expression to identify early nevi and melanomas. The second model, on a C57BL/6 had a high tumor incidence (80%), and 60% of tumor-bearing mice have metastatic lesions. Sequencing of melanocytic lesions at different stages revealed a variety of driver mutations, including Nf1, Gnaq, and Gna11, as well as genes and pathways with less established roles in melanoma development. Our data provide a broad overview of genes and pathways involved in progression of non-BRAF, non-NRAS melanoma. Additionally, we present the first potential germline variants that may increase metastatic susceptibility for melanoma patients. These genes suggest potential biomarkers for progression of melanocytic lesions.
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    Genetic Architecture of Complex Traits and Accuracy of Genomic Selection in Dairy Cattle
    (2018) Jiang, Jicai; Ma, Li; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Genomic selection has emerged as an effective approach in dairy cattle breeding, in which the key is prediction of genetic merit using dense SNP genotypes, i.e., genomic prediction. To improve the accuracy of genomic prediction, we need better understanding of the genetic architecture of complex traits and more sophisticated statistical modeling. In this dissertation, I developed several computing tools and performed a series of studies to investigate the genetic architecture of complex traits in dairy cattle and to improve genomic prediction models. First, we dissected additive, dominance, and imprinting effects for production, reproduction and health traits in dairy cattle. We found that non-additive effects contributed a non-negligible amount (more for reproduction traits) to the total genetic variance of complex traits in cattle. We also identified a dominant quantitative trait locus (QTL) for milk yield, revealing that detection of QTLs with non-additive effect is possible in genome-wide association studies (GWAS) using a large dataset. Second, we developed a powerful Bayesian method and a fast software tool (BFMAP) for SNP-set association and fine-mapping. We demonstrated that BFMAP achieves a power similar to or higher than existing software tools but is at least a few times faster for association tests. We also showed that BFMAP performs well for fine-mapping and can efficiently integrate fine-mapping with functional enrichment analysis. Third, we performed large-scale GWAS and fine-mapped 35 production, reproduction, and body conformation traits to single-gene resolution. We identified many novel association signals and many promising candidate genes. We also characterized causal effect enrichment patterns for a few functional annotations in dairy cattle genome and showed that our fine-mapping result can be readily used for future functional studies. Fourth, we developed an efficient Bayesian method and a fast computing tool (SSGP) for using functional annotations in genomic prediction. We demonstrated that the method and software have great potential to increase accuracy in genomic prediction and the capability to handle very large data. Collectively, these studies advance our understanding of the genetic architecture of complex traits in dairy cattle and provide fast computing tools for analyzing complex traits and improving genomic prediction.