Genetics and Genomics Commons^™

Snp Genotyping For Purity Assessment Of A Forage Oat (Avena Sativa L.) Variety From Colombia, Luis Fernando Campuzano-Duque, Diego Bejarano-Garavito, Javier Castillo-Sierra, Daniel Ricardo Torres-Cuesta, Andrés J. Cortés, Matthew Wohlgemuth Blair

Agricultural and Environmental Sciences Faculty Research

Single nucleotide polymorphism (SNP) markers have multiple applications in plant breeding of small grains. They are used for the selection of divergent parents, the identification of genetic variants and marker-assisted selection. However, the use of SNPs in varietal purity assessment is under-reported, especially for multi-line varieties from the public sector. In the case of variety evaluation, these genetic markers are tools for maintaining varietal distinctness, uniformity and stability needed for cultivar release of multi-line or pure-line varieties of inbred crops. The objective of this research was to evaluate the purity and relationships of one original (AV-25) and two multi-line sub-populations …

Coping With Environmental Constraints: Geographically Divergent Adaptive Evolution And Germination Plasticity In The Transcontinental Populus Tremuloides, Roos Goessen, Nathalie Isabel, Christian Wehenkel, Nathalie Pavy, Lisa Tischenko, Lyne Touchette, Isabelle Giguère, Marie-Claude Gros-Louis, Jérôme Laroche, Brian Boyle, Raju Soolanayakanahally, Karen E. Mock, Javier Hernández-Velasco, Sergio Leonel Simental-Rodriguez, Jean Bousquet, Ilga M. Porth

Aspen Bibliography

Societal Impact Statement

Syntheses clearly show that global warming is affecting ecosystems and biodiversity around the world. New methods and measures are needed to predict the climate resilience of plant species critical to ecosystem stability, to improve ecological management and to support habitat restoration and human well-being. Widespread keystone species such as aspen are important targets in the study of resilience to future climate conditions because they play a crucial role in maintaining various ecosystem functions and may contain genetic material with untapped adaptive potential. Here, we present a new framework in support of climate-resilient revegetation based on comprehensively understood …

Genetic Protocols For Dna Extraction From White-Tailed Deer Cast Antlers To Confirm Individuality, Zach Carter, Brian C. Peterson, Casey W. Schoenebeck, Kimberly A. Carlson

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

White-tailed deer (Odocoileus virginianus) are the most sought-after deer species in America. The antlers of mammals, such as deer, are one of the fastest regenerative tissues in the world and are grown and naturally cast every year. Research on cast antlers have been used for a variety of purposes including population comparisons and impacts of deer health due to climatic stressors. When investigating cast antlers, it is important to confirm individuality of match sets in addition to antlers of the same individual between years. Therefore, individuality must be confirmed genetically, and protocols must be developed and established to …

The Roles Of Epithelial–Mesenchymal Plasticity In Tumor Heterogeneity, Metastasis, And Patient Survival In Breast Cancer, Meredith Septer Brown

Dartmouth College Ph.D Dissertations

The Epithelial-to-Mesenchymal transition, a critical cellular process in development, is frequently co-opted by solid tumors to promote invasion and metastasis. In particular, the hybrid or intermediate EMT state, possessing both epithelial and mesenchymal characteristics, is associated with increased cancer stemness and plasticity. Similarly, intra-tumoral heterogeneity in solid tumors, in particular breast cancer, is associated with poor prognosis, tumor growth, proliferation, drug resistance, and metastasis. We sought to understand the link between the generation of intra-tumoral heterogeneity and the intermediate EMT state and their impact on tumor progression and patient prognosis. As part of my thesis work, I developed a model …

Population Genetics Of Cownose Rays, Rhinoptera Spp. In The Western Atlantic, Helen Weber

Master's Theses

Using molecular tools (e.g., the NADH subunit II mitochondrial gene), this study was the first to document the Brazilian cownose ray, Rhinoptera brasiliensis, within the northwestern Atlantic (NWA), and was the first study to examine population structure in R. brasiliensis within the NWA or northern Gulf of Mexico (GMX), revealing novel insights into the population biology of the animal and extending its range by nearly 1,500 km. This study also examined the sympatrically occurring American cownose ray, R. bonasus, and found population structure between the NWA and the GMX and the NWA and the southwestern Atlantic (SWA). High …

A Dual-Function Gene In Zea Mays That Encodes Two Β-Amylase Proteins With Different Cellular Locations And Functions, Kenan Ozcan

Masters Theses, 2020-current

A noncanonical β-amylase7 (BAM7) gene found in some basal angiosperms and some monocots, including corn, appears to encode two functionally distinct proteins. Phylogenetic evidence suggests that BAM7 originated from a fusion event that combined a BZR1-like DNA-binding domain to the 5’ end of BAM2 about 400 million years ago (mya). In Arabidopsis thaliana (At), AtBAM7 is a catalytically-inactive transcription factor found in the nucleus and AtBAM2 is a catalytically-active, tetrameric starch hydrolase found in the chloroplast. These proteins are encoded on different chromosomes. The corn (Zea mays, Zm) genome does not contain a BAM2 gene, however …

Bee Brains: Dissecting Pollinator Behavior And The Importance Of Plasticity In The Face Of Changing Environments, Rachel Brant

Dissertations

All organisms face environmental variability, and much of contemporary biological research aims to understand the mechanisms allowing organisms to adapt and survive in the face of change. Animals residing in urban habitats face particularly high levels of unpredictability and environmental fluctuation due to changes based upon human desire. Though urban areas are considered relatively novel habitats, numerous species have adapted to city life, mediated through behavioral and physiological plasticity. Native bee species show particularly high species richness and abundance in urban settings, but the mechanisms driving this pattern are poorly understood. In this dissertation, I explore how bees employ plasticity …

Vitamin And Mineral Supplementation And Rate Of Gain In Beef Heifers I: Effects On Dam Hormonal And Metabolic Status, Fetal Tissue And Organ Mass, And Concentration Of Glucose And Fructose In Fetal Fluids At D 83 Of Gestation, Ana Clara B. Menezes, Kacie L. Mccathy, Cierrah J. Kassetas, Friederike Baumgaertner, James D. Kirsch, Sheri T. Dorsam, Tammi L. Neville, Alison K. Ward, Pawel P. Borowicz, Lawrence P. Reynolds, Kevin K. Sedivec, J. Chris Forcherio, Ronald Scott, Joel S. Caton, Carl R. Dahlen

Department of Animal Science: Faculty Publications

Thirty-five crossbred Angus heifers (initial BW = 359.5 ± 7.1 kg) were randomly assigned to a 2 × 2 factorial design to evaluate effects of vitamin and mineral supplementation [VMSUP; supplemented (VTM) vs. unsupplemented (NoVTM)] and different rates of gain [GAIN; low gain (LG), 0.28 kg/d, vs. moderate gain (MG), 0.79 kg/d] during the first 83 d of gestation on dam hormone and metabolic status, fetal tissue and organ mass, and concentration of glucose and fructose in fetal fluids. The VMSUP was initiated 71 to 148 d before artificial insemination (AI), allowing time for mineral status of heifers to be …

Breeding Sustainable Beef Cows: Reducing Weight And Increasing Productivity, Warren M. Snelling, R. Mark Thallman, Matthew L. Spangler, Larry A. Kuehn

Department of Animal Science: Faculty Publications

Programs for sustainable beef production are established, but the specific role of beef cows in these systems is not well defined. This work characterized cows for two traits related to sustainability, cow weight (CW) and cumulative weight weaned (WtW). Cow weight indicates nutrient requirements and enteric methane emissions. Cumulative weight weaned reflects reproductive performance and avoidance of premature culling for characteristics related to animal health, welfare, and worker safety. Both traits were evaluated with random regression models with records from a crossbred population representing 18 breeds that conduct US national cattle evaluations. The genomic REML analyses included additive and dominance …

Insights Into The Speciation Process From Genomic And Phenotypic Analysis Of An Avian Hybrid Zone In Amazonia, Glaucia Christina Del-Rio

LSU Doctoral Dissertations

Understanding the outcome of secondary contact is essential to shed light on the mechanisms governing species formation and maintenance. In Amazonia, closely related bird taxa with limited dispersal abilities are often separated by rivers, which presumably act as dispersal barriers. However, at the headwaters, rivers cease to be dispersal barriers, and this generates opportunities for secondary contact. In my dissertation, I studied genomic mechanisms associated with phenotypic differences, mitochondrial DNA structure, and putative reproductive barriers between two hybridizing Amazonian bird species in the genus Rhegmatorhina, a group of antbirds that find their arthropod prey exclusively by following army-ant swarms. …

Heterogeneity Of Gene Trees, Jonathan Nenye Odumegwu Unm

Mathematics & Statistics ETDs

Multilocus phylogenetic studies often show a high degree of gene tree heterogeneity —gene trees that have different topologies from each other as well as from the species tree topology. In some cases, this can lead to studies with hundreds of loci having distinct gene tree topologies. The degree of heterogeneity is expected to increase when there is a high degree of incomplete lineage sorting due to short branches (as measured in coalescent units) in the species tree. Other potential sources of heterogeneity include other biological processes such as introgression, recombination within genes, ancestral population structure, gene duplication and loss, and …

Plastic And Evolved Responses In The Eastern Oyster, Crassostrea Virginica, To Environmental Variation In The Northern Gulf Of Mexico, Kyle Sirovy

LSU Doctoral Dissertations

Climate change and other anthropogenic impacts are causing rapid alterations to many of the world’s most productive coastal ecosystems and there is an urgent need to understand how species will respond to these environmental changes. Organisms may respond through plasticity, evolution, or the evolution of plasticity. In this dissertation, I evaluate the role of plastic and evolved responses in the eastern oyster, Crassostrea virginica, to environmental variation in the northern Gulf of Mexico. I use comparative transcriptomics, physiology, and morphology to examine the relative contribution of plastic and evolved responses for oysters exposed to low salinity and outplant sites …

Statistical Genetic Discoveries Using Restricted Maximum Likelihood Method, Erika Wu

2022 REYES Proceedings

In statistical genetics, genetic association and genomic prediction become more successful with a highly heritable trait. Identifying highly heritable components of a complex disease can thus advance scientific understanding of the disease and potentially lead to effective prevention and treatments. Using Matlab and existing large-scale genome datasets, we evaluate a restricted maximum likelihood approach to identify highly heritable components of a complex disease as a function of multiple clinical variables.

Diversity In Darkness: Shedding Light On Cryptic Species In The Cave Beetle Genus Darlingtonea Valentine Using 3rad Sequencing And Consequences Of Climate Change Based On Thermal Tolerance And Dehydration Resistance, Athanasios S. Apostolopoulos

Masters Theses & Specialist Projects

The relationship between geographic distribution and phylogeny is pronounced in patchy, discontinuous habitats that limit gene flow, such as cave ecosystems. The isolating nature and selective pressures of cave environments can result in relatively high levels of endemism and cryptic speciation in cave faunas. Cryptic speciation exhibited in cave faunas is poorly studied, though it is an integral aspect to consider when discussing conservation efforts.

Our study employed the 3RAD genomic sequencing technique and robust population sampling across the distribution of a monotypic genus of cave beetle, Darlingtonea Valentine, that inhabits karst systems in a nearly 200 square mile range …

Beta-Adrenergic Agonists Alter Oxidative Phosphorylation In Primary Myoblasts (Short Communication), Renae Sieck, Leah K. Treffer, Anna M. Fuller, Martonio Ponte Viana, Oleh Khalimonchuk, Ty B. Schmidt, Dustin T. Yates, Jessica Lynn Petersen

Department of Animal Science: Faculty Publications

Beta-adrenergic agonists (β-AAs) are widely used supplements in beef and pork production to improve feed efficiency and increase lean muscle mass, yet little is known about the molecular mechanism by which β-AAs achieve this outcome. Our objective was to identify the influence of ractopamine HCl and zilpaterol HCl on mitochondrial respiratory activity in muscle satellite cells isolated from crossbred beef steers (N = 5), crossbred barrows (N = 2), Yorkshire-cross gilts (N = 3), and commercial weather lambs (N = 5). Real-time measurements of oxygen con­sumption rates (OCRs) were recorded using extracellular …

Cas9/Nickase-Induced Allelic Conversion By Homologous Chromosome-Templated Repair In Drosophila Somatic Cells, Carissa Klanseck, Victor Lopez Del Amo, Ethan Bier, Annabel Guichard

Faculty, Staff and Student Publications

Repair of double-strand breaks (DSBs) in somatic cells is primarily accomplished by error-prone nonhomologous end joining and less frequently by precise homology-directed repair preferentially using the sister chromatid as a template. Here, a

Increasing The Resilience Of Plant Immunity To A Warming Climate, Jong Hum Kim, Christian Castroverde, Shuai Huang, Chao Li, Richard Hilleary, Adam Seroka, Reza Sohrabi, Diana Medina-Yerena, Bethany Huot, Jie Wang, Sharon Marr, Mary Wildermuth, Tao Chen, John Macmicking, Sheng Yang He

Biology Faculty Publications

Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone, is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism. Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B (phyB) and EARLY FLOWERING 3 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates (GDACs) …

Growing Space Management In Boreal Mixedwood Forests: 22 Year Results, Richard Kabzems, George Harper, Che Elkin

Aspen Bibliography

Boreal mixed forests of trembling aspen (Populus tremuloides) and white spruce (Picea glauca) can provide higher outputs of many ecosystem goods and services, combined with resilience for changing environmental conditions. In this study, we examine the growth of white spruce and aspen over a range of stand compositions created by spot and broadcast treatments of broadleaves using manual and chemical means, aspen spacing, and untreated control. Twenty-two growing seasons postharvest, treatment responses created a range of broadleaf densities and spatial arrangements, reflected in significant differences in heights and diameters of the spruce mixedwood component. At this …

Population Genomics Of The Giant Caribbean Sea Anemone Condylactis Gigantea (Anthozoa: Actiniidae) In Florida And Across The Caribbean, Nancy E. Sheridan

USF Tampa Graduate Theses and Dissertations

The giant Caribbean sea anemone Condylactis gigantea is a long-lived, conspicuous, and phenotypically diverse species native to the western Atlantic Ocean (from Bermuda to southeast Brazil), Caribbean Sea, and southeastern Gulf of Mexico. This sea anemone is an important benthic community member that provides habitat to numerous species, including cleaner shrimp. This relationship makes these animals desirable to aquarists for both enjoyment and the service provided by the shrimp for the overall health of an aquarium, and which is why they are sought.

The extraction of about 3.3 million C. gigantea individuals in Florida over a 23-year period for the …

Metaphylactic Antimicrobial Effects On Occurrences Of Antimicrobial Resistance In Salmonella Enterica, Escherichia Coli And Enterococcus Spp. Measured Longitudinally From Feedlot Arrival To Harvest In High-Risk Beef Cattle, Nathan S. Long, James E. Wells, Elaine D. Berry, Jerrad F. Legako, Dale R. Woerner, Guy H. Loneragan, Paul R. Broadway, Jeff A. Carroll, Nicole C. Burdick Sanchez, Samodha C. Fernando, Carley M. Bacon, Cory L. Helmuth, Taylor M. Smock, Jeff L. Manahan, Ashley A. Hoffman, Kristin E. Hales

Department of Animal Science: Faculty Publications

Aims: Our objective was to determine how injectable antimicrobials affected populations of Salmonella enterica, Escherichia coli and Enterococcus spp. in feedlot cattle.

Methods and Results: Two arrival date blocks of high-risk crossbred beef cattle (n = 249; mean BW = 244 kg) were randomly assigned one of four antimicrobial treatments administered on day 0: sterile saline control (CON), tulathromycin (TUL), ceftiofur (CEF) or florfenicol (FLR). Faecal samples were collected on days 0, 28, 56, 112, 182 and study end (day 252 for block 1 and day 242 for block 2). Hide swabs and subiliac …