Genetics and Genomics Commons^™

Interview With Orca Winner John Hibbing, Political Science; How Political Attitudes Correlate With Physiological Traits, Mark A. Griep, John Hibbing

UNL ORCA Interview Series

Dr. John Hibbing was awarded the ORCA in 1993. John was born in 1953 in Paullina, Iowa. He earned a bachelor's in secondary education from Dana College in Blair, Nebraska, but then realized that teaching high school wasn't for him. Instead, he attended the University of Iowa, where he earned a master's and doctorate in political science. In 1981, he joined the University of Nebraska-Lincoln as an assistant professor of political science and rose quickly through the ranks. Initially, he studied the reasons that members of the U.S. Congress retire. This led to a longer-term collaboration with Kevin Smith and …

Improving Genomic Prediction For Feed Efficiency Traits In Beef Cattle Using Microbiome As An Intermediate Omics, Egodage Bhagya Sewwandi Samarakoon

Department of Animal Science: Dissertations, Theses, and Student Research

Feed efficiency traits, including feed conversion ratio (FCR), average daily gain (ADG), and average daily dry matter intake (ADDMI), are economically important in beef cattle production. Emerging evidence suggests that host genetics influences feed efficiency traits through the microbiome. This study evaluates the integration of microbiome data as an intermediate layer in the Neural Network Mixed Model (NNMM), which hierarchically models genotype–microbiome–phenotype relationships as a unified regulatory network to improve genomic prediction accuracy. To reduce the computational burden of NNMM, microbiome features dimension were reduced using principal component analysis (PCA) and direct feature selection of top-ranked open reading frames (ORFs) …

Population Structure And Connectivity Of Atlantic Nurse Sharks (Ginglymostoma Cirratum) In The Bahamas And Outlying Areas, Baylie A. Fadool

School of Natural Resources: Dissertations, Theses, and Student Research

Understanding animal ecosystem dynamics and behavior at the individual and population levels is essential for identifying life-history patterns and important areas for management and conservation. Marine fish species often face minimal geographic barriers to movement, but environmental (temperature, salinity, current) or intrinsic barriers (philopatry, site fidelity) can dictate gene flow. Atlantic nurse sharks (Ginglymostoma cirratum) are an International Union for Conservation of Nature (IUCN) listed ‘vulnerable’ species and present a unique opportunity to investigate patterns of population structure and connectivity in large-bodied sharks. They are benthic and display reproductive philopatry, with recent work suggesting they have the capacity …

Characterization Of Mitochondrial Dna Repair Components And Repair Choices At Targeted Double-Strand Breaks In Arabidopsis Thaliana, Moira Rodriguez

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Plant mitochondrial genomes are complex when compared to most other eukaryotic mitochondrial genomes. They are large and variable in size, expand and rearrange frequently, abundant in non-tandem repeats, but maintain a very low synonymous substitution rate in the remaining coding regions. Many of these complexities can be explained by the increased use of double-strand break repair for DNA damage. To advance the understanding of mitochondrial genome dynamics as it relates to double-strand break repair, we performed a forward genetics screen to identify proteins involved in DNA repair in plant mitochondrial genomes. Through this screen, we identified an RNA/DNA helicase, Suv3, …

Functional Genomics Of Phosphatidylcholine Biosynthesis In Saccharomyces Cerevisiae, Amanda Marie Maliva

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Phosphatidylcholine (PtdCho) is a prominent structural building block of cell and organelle membranes in animal, plant, and fungal cells and some bacteria. Due to its abundant nature in the plasma membrane and intracellular organelle membranes in eukaryotes, the biosynthesis of PtdCho must remain regulated to preserve the correct membrane lipid composition. Dysregulations in PtdCho metabolism can lead to mitochondrial dysfunction, cell death, and the development of diseases including cancer, atherosclerosis, and hepatic diseases. Knowledge of PtdCho has remained limited to the genes involved in its three biosynthetic pathways (Kennedy (K), methylation (M), and acyltransferase (A)), despite the growing realization of …

Associations Of Variation In Mtdna With Feed Efficiency In Beef Cattle And The Evaluation Of Transcriptomic Changes In Fetal Kidney Due To Hydrallantois, Lauren Elizabeth Seier

Department of Animal Science: Dissertations, Theses, and Student Research

Project 1 focused on the central role that mitochondria play in ATP production, highlighting that variation within the mtDNA may influence feed efficiency. Variation in the mitochondrial genome was uncovered, and associations with feed efficiency in beef cattle were identified. Growth and feed intake phenotypes, as well as low-pass sequencing, were collected on beef steers across two populations. Protein coding variants were identified and used to classify animals into mitochondrial haplotypes. A linear mixed model was employed, which detected a significant association between mitochondrial haplotype and DMI. A significant haplotype with a variant in Complex I was associated with reduced …

Update To: Advancing Butterfly Systematics Through Genomic Analysis, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick Grishin

The Taxonomic Report of the International Lepidoptera Survey

In this update, we propose (type species or type localities in parentheses): Lochris Grishin, nom. nov. (Lasaia oileus Godman, 1903; Lepidoptera: Riodinidae) as a new substitute name for Locris Grishin, 2025 preoccupied by Locris Stål, 1866 (Cercopis rubra Fabricius, 1794; Hemiptera: Cercopidae), 5 new species, and 5 new subspecies: Emesis (Mandania) mandarina Grishin, sp. n. (Brazil: Santa Catarina) and Emesis (Mandania) mandela Grishin, sp. n. (Venezuela, Carabobo) in Riodinidae Grote, 1895 (1827); others in Hesperiidae Latreille, 1809: Telegonus (Rhabdoides) flavifimbro Grishin, sp. n. (Colombia), Urbanus (Urbanoides) dolus Grishin, sp. n. (Colombia: …

Cazyme Gene Cluster Diversity In Human Gut Microbiome, Yi Xing

Department of Food Science and Technology: Dissertations, Theses, and Student Research

In gut microbiome research, carbohydrate-active enzyme gene clusters (CGCs) have emerged as key functional units for understanding microbial glycan degradation. Unlike taxonomic or broad pathway annotations, CGCs offer gene-cluster-level resolution and capture substrate-specific microbial functions. However, their diversity and distribution in relation to host metabolic phenotypes, such as obesity, remain poorly characterized. This study tests the hypothesis that the composition and abundance of fiber-targeting CGCs vary between obese and healthy human gut microbiomes, reflecting distinct microbial carbohydrate utilization strategies. To examine this, we constructed a high-quality reference CGC dataset comprising 94,019 clusters from the Unified Human Gastrointestinal Genome and profiled …

Implications Of Type Iv Pilus Retraction For Dna Uptake By Acinetobacter Baumannii, Yafan Yu

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Horizontal gene transfer (HGT) via natural competence allows bacteria to incorporate extracellular DNA (eDNA) into their genomes, facilitating genetic diversity and adaptation. In Acinetobacter species, natural competence depends on DNA binding and uptake mediated by type IV pili (T4P). T4P are dynamic extracellular filaments composed primarily of the major pilin subunit PilA, along with a few minor subunits. T4P drive a range of cellular functions including twitching motility, biofilm formation, and DNA uptake, with some functions dependent on pilus retraction and others not. However, how Acinetobacter T4P bind DNA and how T4P/eDNA interactions impact biofilm formation remain unclear. Here, I …

Integrating Genomic And Phenomic Breeding Tools For Wheat Stem Sawfly Resistance In Hard Winter Wheat, Sydney E. Graham

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The wheat stem sawfly (WSS; Cephus cinctus) is an insect pest that affects wheat (Triticum aestivum) in the Northern Great Plains. This pest causes stem cutting that makes the plants susceptible to lodging and results in up to 30% yield loss. The primary management strategy for producers is utilizing host plant resistance, for which the main trait is stem solidness. This trait increases the pith thickness and provides resistance to the WSS by increasing larval mortality and reducing stem cutting. While stem solidness is largely controlled by a known major gene (SSt1), the phenotypic expression is also …

Consumer Acceptance Of Gene-Edited Food: The Role Of Knowledge, Trust, And Information, Anubrata Deka, Syed Imran Ali Meerza, Amalia Yiannaka

Cornhusker Economics

The research aims to assess consumer preferences and attitudes toward CRISPR applications in the food sector and estimate consumer willingness to pay for a food product developed using CRISPR technology to enhance food safety and confer health benefits. Additionally, the research assesses the impact of information provision on perceptions, attitudes and willingness to pay. Specifically, we consider the potential effect of both the nature of information provided (i.e., whether it emphasizes the differences between GM and CRISPR technology or not) and the delivery format (i.e., text versus video) used to present content-equivalent information. In this context, we also assess consumer …

Graduate Student Literature Review From "The Development Of The Brouwer Equation To Estimate Heat Production: Past, Present, And Future Perspectives" In Journal Of Dairy Science (2025), Addison L. Carroll, Paul J. Kononoff, Tami M. Brown-Brandl

Department of Animal Science: Faculty Publications

Appendix 1, supplemental to "The development of the Brouwer equation to estimate heat production: Past, present, and future perspectives," Journal of Dairy Science (2025).

Derivation Of The Maintenance Energy Requirements In Growing Jersey Heifers: Supplementary Table S1, Addison L. Carroll, Michael J. Vandehaar, Paul J. Kononoff

Department of Animal Science: Faculty Publications

Supplemental table for Addison L. Carroll, Michael J. VandeHaar, and Paul J. Kononoff. Derivation of the maintenance energy requirements in growing Jersey heifers. Journal of Dairy Science (2025).

Identification Of Benzothiophene-Derived Inhibitors Of Flaviviruses By Targeting Rna-Dependent Rna Polymerase, Leah Liu Wang, Shazeed-Ul Karim, Aidan Hand, Ryan Brunkhorst, Mackenna Petersen, Sarah Altam, Yi Liu, Luwen Zhang, Fengwei Bai, Shi-Hua Xiang

School of Biological Sciences: Faculty Publications

Flaviviruses such as Dengue, West Nile, and Zika viruses are mosquito-borne RNA viruses that can cause serious diseases in humans. To develop effective drugs for treating these viruses’ infections, we create a new approach for developing common or shared drugs that may work for several different viral species of flaviviruses. It is based on the conserved RNA-dependent RNA polymerase (RdRp), which is the key enzyme for viral replication. We built up a common structure of RdRps (POLcon) from their consensus sequence. A conserved Triple-D structural motif was identified at the active site of POLcon that has been used for virtual …

Relationship Between Host Genomics And Microbiomics In Beef Cattle, Andrew D. Lakamp

Department of Animal Science: Dissertations, Theses, and Student Research

As sequencing technology becomes more affordable and throughput increases, microbiome information is becoming more readily available. For beef cattle selection, microbial information has a variety of uses including being a target for genetic prediction or used as a means to explicitly describe additional phenotypic variability in other traits.

Infectious bovine keratoconjunctivitis (IBK), commonly known as pinkeye, is a disease that infects the ocular surface and surrounding tissue which is an animal health and producer economic concern. Vaccinations have shown to have variable effectiveness, while limited genetics studies have suggested that direct genetic selection for resistance would be slow. Therefore, an …

Porcine Peritoneal Macrophages Are Susceptible To Porcine Reproductive And Respiratory Syndrome Virus Infection, Kassandra Durazo-Martinez, Jayeshbhai Chaudhari, Sushmita Kumari, Hiep Vu

Department of Animal Science: Faculty Publications

Previous studies have suggested that porcine peritoneal macrophages (PPMs) are resistant to PRRSV infection, whereas porcine alveolar macrophages (PAMs) are highly susceptible. This contrast is intriguing, as both cell types belong to the same monocyte/macrophage family. The current study aimed to investigate the host factors contributing to the differing susceptibility of PPMs and PAMs to PRRSV infection. We found that PPMs exhibit a higher frequency of CD14+ cells compared to PAMs, suggesting a more immature macrophage phenotype in PPMs. Importantly, PPMs expressed both CD163 and CD169, the key receptors for PRRSV entry, although the frequency and intensity of CD163 and …

Protracted Maternal Malnutrition Induces Aberrant Changes In Maternal Uterine Artery Hemodynamics And The Metabolic Profiles Of The Dam And Neonate, Jennifer F. Thorson, Ligia D. Prezotto

Department of Animal Science: Faculty Publications

Malnutritional stress during gestation is a well-established driver of metabolic disfunction in offspring. Extended exposure to malnutrition requires metabolic plasticity as the animal shifts toward a catabolic state. In this paper we demonstrate the influence of malnutrition throughout gestation on uterine artery hemodynamics and the metabolism of the dam and neonate. We hypothesized that gestational malnutrition reduces blood flow of the maternal uterine artery and regulates the metabolic profile of the dam and offspring. Further, the combination of these factors consequently influences the concentration of metabolites in the cerebrospinal fluid of the neonate at birth. To test our hypotheses, pregnant …

Adding Gastrointestinal Parasite Resistance To The Breeding Objective In Hair Sheep: Initial Step, Robert M. Forbes, Thomas W. Murphy, Joan M. Burke, David R. Notter, Matthew L. Spangler, Michael D. Macneil, Ronald M. Lewis

Department of Animal Science: Faculty Publications

The U.S. Maternal Hair Index was designed by the National Sheep Improvement Program (NSIP) to increase total weight of lamb weaned per ewe lambing (TW). Producers are interested in adding gastrointestinal nematode (GIN) resistance to this breeding objective since parasitism causes substantial economic losses. The NSIP provides producers with estimated breeding values (EBV) for postweaning fecal egg count (PFEC), an indicator of GIN resistance. Our objective was to gauge the effects of including PFEC as another selection criterion and goal trait. Selection index theory was used to construct 11 indexes. …

Analyses Of Whole-Genome Sequences From 185 North American Thoroughbred Horses, Spanning 5 Generations, Ernie Bailey, Carrie J. Finno, Jonah N. Cullen, Ted Kalbfleisch, Jessica Lynn Petersen

Department of Animal Science: Faculty Publications

Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5–5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Individual coefficients of inbreeding, estimated from ROH, averaged 0.266 (Group 1) and …

Complete Genome Sequence Of An Indian Outbreak Strain Of Chikungunya Virus, Eshna Laha, Deepak Jena, Viplov K. Biswas, Sharad Singh, Sunil K. Raghav, Asit K. Pattnaik, Soma Chattopadhyay

Nebraska Center for Virology: Faculty Publications

Here, we report the complete genome sequence of an Indian strain of chikungunya virus isolated from an infected patient from Hyderabad, Andhra Pradesh, India, during a massive outbreak in 2005–2006. The genome length spans 11,811 nucleotides and has a poly(A) tail of 29 residues at the 3′ end.

Technical Note: Assessing Gps Sensor Accuracy Using Real-Time Kinematic Device For Livestock Tracking, Biquan Zhao, Rebecca Mcdermott, Galen E. Erickson, Yijie Xiong

Department of Animal Science: Faculty Publications

The technical aspects of global positioning system (GPS) sensors have been improved substantially over the years, making them valuable and popular tools for livestock tracking. Using GPS sensors allows producers and researchers to locate grazing livestock, monitor their behavior and distribution, and gather referencing information about the health status of the animals and pastures. However, interpreting the behavior of grazing livestock, such as cattle, from GPS data can be difficult due to positioning inaccuracies. Without knowing the positioning accuracy range of GPS sensors, achieving high-level confidence in determining grazing densities and identifying abnormal livestock movement patterns is challenging. …

Knockdown Of Gonadotropin-Releasing Hormone Ii Receptor Impairs Ovulation Rate, Corpus Luteum Development, And Progesterone Production In Gilts, Amy T. Desaulniers, Rebecca Cederberg, Clay A. Lents, Brett White

Department of Animal Science: Faculty Publications

Reproduction is classically controlled by gonadotropin-releasing hormone (GnRH-I) and its receptor (GnRHR-I) within the brain. In pigs, a second form (GnRH-II) and its specific receptor (GnRHR-II) are also produced, with greater abundance in peripheral vs. central reproductive tissues. The binding of GnRH-II to GnRHR-II has been implicated in the autocrine/paracrine regulation of gonadal steroidogenesis rather than gonadotropin secretion. Blood samples were collected from transgenic gilts, with the ubiquitous knockdown of GnRHR-II (GnRHR-II KD; n = 8) and littermate controls (n = 7) at the onset of estrus (follicular) and 10 days later (luteal); serum concentrations of 16 steroid hormones …

Impact Of Partial Oil Removal On Energy Content Of Distillers Grains Plus Solubles For Finishing Cattle, Jordan E. Burhoop, J. L. Sperber, Curt J. Bittner, F. Henry Hilscher, J. C. Macdonald, Galen E. Erickson

Department of Animal Science: Faculty Publications

Two experiments evaluated the impact of the reduction in the percentage of corn oil remaining in distillers grains plus solubles (DGS) after the ethanol plant de-oiling process or by adding corn oil back to DGS following de-oiling on finishing cattle performance and nutrient digestion. Experiment 1 utilized 320 yearling steers (initial BW = 413 kg; SD = 25 kg) fed in 32 pens (10 steers/pen) and assigned to one of four treatments (n = 8 pens/treatment). The four treatments consisted of a blended DRC:HMC corn control diet (CON), de-oiled modified distillers grains plus solubles included at 40% of diet DM …

Identifying Genes Linked To Variation In Metabolic And Whole Plant Phenotypes Using Data From Genome Resequencing, Transcriptomics, And Metabolic Profiling Of A Field-Grown Maize Diversity Panel, Ramesh Kanna Mathivanan

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Maize metabolism is highly complex and influenced by genetic variation, yet the specific genes contributing to this variation and their links to non-metabolic traits remain less understood. To address this knowledge gap, we identified genes involved in maize metabolic variation and linked them to non-metabolic traits. We utilized a quadruplicate dataset of whole genome resequencing, transcriptomic, metabolic, and whole plant phenotype data from a single common field experiment of 660 diverse maize inbred lines. Leaf samples were collected shortly before flowering and analyzed using GC-MS for 26 metabolites. A Resampling Model Inclusion Probability Genome-Wide Association Study (RMIPGWAS) of approximately 2.6 …

Investigating Associations Between Activity And Performance Traits Across Three Breeds Of Swine Using NuTrack, Dalton R. Obermier

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Feed costs are the largest contributor towards the variable costs of pork production. To decrease feed cost while not sacrificing output requires an improvement in feed efficiency (FE). A potential approach to expand available phenotypes associated with FE is with activity tracking, yet the relationship between activity and performance is not well defined in swine. Therefore, the objective of this study was to quantify associations between activity and feed intake traits. Average daily feed intake (ADFI) was collected on 1,766 purebred boars of three genetic lines (Duroc, Landrace, and Yorkshire) using FIRE (Osborne Industries, Inc., Osborne, Kansas) at a testing …

Developing A Comprehensive Genome-Scale Metabolic Model For The Arabidopsis Thaliana Root System, Lohani Esterhuizen

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Arabidopsis thaliana (Arabidopsis) is the most well-established model plant to date. Being the first plant to have its genome mapped, studies on Arabidopsis have provided insurmountable insights into the physiological and biochemical nature of plants. Methods that allow us to computationally study the metabolism of organisms include the use of genome-scale metabolic models (GEMs). Despite its popularity, no GEM currently maps the metabolic activity in the root system of Arabidopsis, which is the first organ to face and respond to stress conditions in the soil. This work aims to develop and implement a comprehensive GEM of the Arabidopsis root system …

Assessment Of Genetic Diversity And Population Structure Of U.S. Polypay Sheep From Breed Origins To Future Genomic Selection, Carrie S. Wilson, Jessica Lynn Petersen, Luiz F. Brito, Brad A. Freking, Sara M. Nilson, J. Bret Taylor, Thomas W. Murphy, Ronald M. Lewis

Department of Animal Science: Faculty Publications

Knowledge of past and present genetic diversity within a breed is critical for the design and optimization of breeding programs as well as the development of strategies for the conservation of genetic resources. The Polypay sheep breed was developed at the U.S. Sheep Experiment Station (USSES) in 1968 with the goal of improving productivity in Western U.S. range flocks. It has since flourished in the more intensively managed production systems throughout the U.S. The genetic diversity of the breed has yet to be documented. Therefore, the primary objective of this study was to perform a comprehensive evaluation of the genetic …

Evaluation Of The Capacity And Effective Angle Of Thalamic Damage For 2 Commercially Available Captive Bolt Tool Types On Cadaver Heads From Sows >200 Kg Body Weight, Karly N. Anderson, Ruth Woiwode, Ashlynn A. Kirk, Jennifer Berger, Arquimides A. Reyes, Perle E. Zhitnitskiy, Kurt D. Vogel

Department of Animal Science: Faculty Publications

This study evaluated the ability of 2 penetrating captive bolt (PCB) types (PISTOL, INLINE) to reach and disrupt the thalamus when applied in 2 placements (FRONTAL, BEHIND EAR) to chilled cadaver heads (N = 60) from sows >200 kg. Heads were randomly distributed across 6 treatments (n = 10): FRONTAL-INLINE, FRONTAL-PISTOL, FRONTAL-NO SHOT, BEHIND EAR-INLINE, BEHIND EAR-PISTOL, and BEHIND EAR-NO SHOT. The FRONTAL shot was placed 3.5 cm superior to the optic orbits at the midline; the BEHIND EAR shot was placed directly caudal to the pinna of the ear on the same plane as the eyes and targeting the …

Hybridization Between The Rare Gray-Headed Chickadee And The Abundant Boreal Chickadee In The Midst Of Shifting Climate, Matthew R. Armstrong

School of Natural Resources: Dissertations, Theses, and Student Research

As species respond to changing climate, distributions and abundances may shift and alter species interactions. Hybridization, a relatively widespread phenomenon becoming more common with climate change, can have beneficial and detrimental effects on population growth rates and genetic integrity. Beneficial effects due to the introduction of advantageous alleles and increased genetic diversity may result from hybridization. Species may also accrue fitness costs associated with changing climates if mismatches occur between environmental variables and phenotypes. The gray-headed chickadee, Poecile cinctus lathami, is an extremely rare songbird that has experienced marked declines in recent decades within its restricted distribution in Alaska …

Heat Stress Changes The Bovine Methylome And Transcriptome And Investigation Of Two Novel Genetic Defects In Cattle, Rachel Renae Reith

Department of Animal Science: Dissertations, Theses, and Student Research

Heat stress is a major concern for livestock producers due to its negative impact on animal health and productivity. Heat stress does so by altering expression of genes through different regulatory mechanisms such as DNA methylation. Understanding how heat stress alters gene expression will help elucidate the genetic basis of physiological changes as well as identify targets for possible heat stress mitigation. The purpose of the first study was to understand how heat stress alters the adipose and skeletal muscle transcriptomes in zilpaterol-fed Brahman, as zilpaterol improves muscle growth and may mitigate the effects of heat stress. Differential expression and …