The ANSC Animal Genetics and Genomics Lab

the ANSC Animal Genetics and Genomics Lab members
Back row (L-R): IBRAHIM HUSSAIN, Renae Sieck, Anna Fuller, Alexa Barber, and Dr. Jessica Petersen,
Front row (L-R): Leah Treffer, Rachel reith, and Charlet Reebenaker

PEOPLE


Photo Jessica Petersen

Jessica Petersen, PhDCV

Current Lab Members

profile picture of Renae Sieck.

Renae Sieck

Renae Sieck BS Animal Science, UNL (2019); MS expected Animal Breeding and Genetics, UNL (2021)

Renae grew up near Crete, Nebraska where her family has a cow-calf operation. Showing cattle in 4-H and FFA sparked her interest in livestock animals. As a continuation of Renae’s undergraduate research she is looking at a gene in draft horses that plays a role in neural crest cell migration and coat color. Her current research focus is to determine the molecular mechanisms by which beta-agonists alter the efficiency of growth in skeletal muscle. She is evaluating cattle fed beta-agonists under heat stress. She is also studying how these feed additives affect mitochondrial function in bovine myoblasts.

profile image of Rachel Reith.

Rachel Reith

Rachel Reith BS Animal Science, Kansas State University (2019); MS expected Animal Breeding and Genetics, UNL (2021)

Rachel’s project is looking into the cellular effects of beta agonists and heat stress in cattle. She is interested in the changes of adipose transcription due to these stressors. Outside of school, Rachel enjoys playing video and board games, solving puzzles, and baking desserts.

Undergraduate Researchers

Leah Treffer

Leah Treffer- Junior Biology Major, Nebraska Wesleyan University

Leah is involved in Nebraska Wesleyan’s NSF-STEM program and is a first-year member of the NE-INBRE program. She runs cross country and track at Wesleyan and in her free time enjoys biking and relaxing in her hammock. Leah is focused on the relationship between yaks and cattle, specifically looking at mitochondria variations and their effect on mitochondrion efficiency using mtDNA sequence, ddPCR, and cell culture. She is also focused on understanding the linage of American yaks and their relationship to Bos indicus and Bos taurus cattle.

profile picture of Alexa Barber.

Alexa Barber- Senior Animal Science Major, UNL

Alexa developed a love for horses at an early age. Alexa was a working student at a horse barn in the suburbs of Chicago during her high school years. During high school, Alexa also discovered a passion for genetics. Alexa was recently awarded an ARD Undergraduate Research Grant to support her research on the genetic basis of white markings in Clydesdales. Alexa uses a standardized scale to determine phenotypes and performs DNA isolation from hair samples to genotype each horse. Using this data, Alexa is running association analysis studies to determine which genes influence roaning and white splotching in Clydesdales. When Alexa is not working in the lab, she enjoys horseback riding, painting, and spending time with her friends and family.

profile picture of Charlet Reebenaker.

Charlet Reebenaker- Senior Animal Science Major, UNL

Charlet is originally from southern New Jersey. She enjoys going kayaking and spending time with all animals. She worked with MS student Erin Duffy to examine the microbiome of lambs fed beta adrenergic agonists. She is currently working with MS students Rachel and Renee investigating the effects of heat stress and feed supplements on cattle.

Research Technologist/Laboratory Manager

profile picture of Anna Fuller.

Anna Fuller- BS Animal Science, UNL (2008); MS Reproductive Biology, University of Wyoming (2010)

During Anna’s undergraduate education at UNL she worked with Dr. Weber studying the effects of Bcl2L on sertoli cells in the testes, as well as with Dr. Cupp studying KDR-LacZ-expressing cells in vascular development. During graduate school she studied the neural basis for low-sexually-performing rams, as well as GRP and FSH expression in the pituitary gland. After graduate school Anna worked at Neogen GeneSeek in multiple divisions. She currently is managing the lab, investigating a genetic basis for Shivers in horses and helping students with various projects. In her free time she enjoys reading and playing board games.

Past Lab Members

Erin Duffy- BS Animal Science, University of Illinois (2016), MS Animal Breeding and Genetics, UNL (2019)

Erin identified alterations in the ruminant microbiome due to heat stress as well as diet supplementation and identified possible correlations with the transcriptome of the host.

Current Position: Research Technologist at the Medical College of Wisconsin

Shauna Tietze- BS Biology, Nebraska Wesleyan University (2013); MS Biology, Georgia Southern University (2016)

Shauna played a critical role in laboratory organization and management and leading the development of new assays.

Current Position: Sales Representative at Thermo Fisher Scientific

Isabel Grazian- BS Animal Science, UNL (2018)

Isabel worked with MS student, Rachel Kubik, to examine dysregulation of genes in the adrenergic pathway in the skeletal muscle of lambs fed beta adrenergic agonists.

Current Position: Veterinary student at Louisiana State University School of Veterinary Medicine

Morgan Parris- BS Animal Science, UNL (2018)

Morgan was awarded top poster in the junior class at the April, 2017, UNL Undergraduate Research Fair. Her poster was titled "Genomic Analysis of Dwarfism in Black Angus Cattle.” Morgan was involved in DNA isolation and candidate gene sequence for a variety of projects in the lab.

Current Position: Lab Technician I at Neogen Corporation

Rachel Kubik- BS Biology, Nebraska Wesleyan University (2016); MS Animal Breeding and Genetics, UNL (2018)

Rachel’s project focused on understanding how ruminant livestock respond, on a genomic level, to heat stress and beta adrenergic agonists. The mRNA and small RNA transcriptome from blood and muscle samples of cattle supplemented with beta agonists were evaluated. In a larger experiment, Rachel evaluated the transcriptome of sheep under acute and chronic heat stress.

Current Position: Research Technologist I at Nebraska Center for Virology

Taylor Barnes- BS Animal Science, UNL (2016); MS Animal Breeding and Genetics, UNL (2018)

Taylor (co-advised by Dr. Yates) worked to understand the physiology of skeletal muscle growth and metabolism in ruminant animals subject to heat stress and supplemented with beta-adrenergic agonists. Additionally, Taylor completed a project examining how students’ inherent strengths may contribute to their success in team-based projects in the classroom.

Current Position: PhD student at Texas A&M focused on teaching pedagogy in STEM courses.

Caleb Kemnitz- BS Animal Science (2017)

Caleb worked to identify altered methylation patterns in a gene involved in a myopathy of Quarter Horses and contributed to several other projects of the lab including the study of heat stress in market lambs.

Current Position: Veterinary student in the UNL/Iowa State University program.

Sara Nilson– BS in Animal Science, Oklahoma State University (2014); MS in Animal Science (UNL Animal Breeding and Genetics; 2016)

Sara's MS research focused upon identifying differential expression of transcripts in cattle with a persistent infection of bovine viral diarrhea virus (BVDV). To do so, Sara used RNA-sequencing of healthy animals and individuals infected with one of three strains of the virus to identify how gene expression changes as a result of infection.

Current Position: PhD Student at the University of Missouri

Maci Lienemann– BS Animal Sciences (2016)

Maci worked to identify genomic regions of selection associated with EPD values in beef cattle bulls.

Current Position: PhD Student at the University of California – Davis

Michele Gibbens– BS Animal Science (2014)

Michele worked to sequence a candidate gene for coat color patterning in yak.

Current Position: Michele is following her dream working with dogs at Nebraska Dog Trainers.

Ryan Hagenson– BS Biochemistry and Molecular Biology, Nebraska Wesleyan University (2015); MS Biomedical Informatics, UNO (2017)

Working in our lab over the summer of 2014, Ryan worked to write computer scripts to identify gene networks that have been targeted by selective breeding in seven breeds of beef cattle.

Current Position: Bioinformatics Scientist at Omaha’s Henry Doorly Zoo and Aquarium

LAB INTERESTS

The focus of the Animal Genetics and Genomics lab is to identify genetic variants that act to alter phenotypic traits and understand their mechanisms of function. Much of our work is focused upon understanding genetics of disease, but other works includes the study of traits such as muscle mass and coat color.

Our current focus is to understand the genetic architecture underlying disease and muscle phenotypes to apply this knowledge to advance animal health within each species, across species (cattle <-> horse), and to produce information that may also benefit human medicine.

Genetic studies of animals are exciting for several reasons. First, by learning more about how genetics influence individual traits, we can use this information to improve animal health and production. Second, because of the unique population structure of domestic species such as cattle and horses (breeds that represent nearly closed populations of animals all with very similar genetics, and with many highly related individuals), we have greater statistical power to map genes and mutations in domestic animals than we would studying diverse, outbred populations. Finally, the gene(s) that influence an animals' susceptibility to disease, their patterns of growth and metabolism, and things such as coat (hair) color, are often under similar genetic control to traits found in humans. Agricultural species such as cattle and horses are often overlooked as potential systems in which to study biology and genetics of human disease and traits.

The FAANG Project (Functional Annotation of ANimal Genomes)
An international effort was recently launched to build a comprehensive database of functional elements in animal genome. For more information on the goals of the consortium, see faang.org

Our lab is contributing to this effort in a collaborative project with UC Davis, funded by the Grayson-Jockey Club Research Foundation, Inc., to collect and analyze data from two Thoroughbred mares to being to create an atlas of gene regulation in the horse. Tissues from these horses were collected in 2016. In addition to representing a significant biobank of rigorously phenotyped, healthy adult mares, select tissues are currently being processed for RNA and ChIP-seq. In addition to the Grayson-Jockey Club funding, individual labs have contributed to "adopt-a-tissue" to move the effort forward more quickly.

Learn about our collaborators on this project:
Dr. Carrie Finno, DVM, Ph.D. http://www.vetmed.ucdavis.edu/faculty/results.cfm?fid=22055
Dr. Rebecca Bellone, Ph.D.

Overview of Research Topics

Functional Annotation of the Equine Genome

Regulation of the genome is complex and dynamic. This is clearly demonstrated by the fact that all cells of an individual contain the same DNA sequence but perform very different and specialized functions. The development of reference genome sequences for agricultural species in the early 2000s has significantly advanced discovery and the application of genetic and genomic tools to benefit animal health and production. It now, however, is clear that the next step in advancing genomics is to develop a more comprehensive understanding of genome regulation. Our laboratory is working to contribute to the Functional Annotation of ANimal Genomes (FAANG) initiative through the creation of an atlas of genome function for the adult Thoroughbred. To do so we are assaying genome transcription, chemical and structural modifications – noting which regions of the genome are active at various time points in an individual’s life and in specific tissues or cell lines. We believe a clear annotation of these regulatory regions in the reference assemblies of agricultural species will significantly accelerate the connection of genome to phenome, and provide data to inform the next-generation of tools for genomic selection. This project is supported by the USDA-NIFA and is in close collaboration with researchers at the University of California-Davis (Drs. Carrie Finno and Rebecca Bellone), the University of Kentucky (Dr. Ted Kalbfleisch), and the University of Pavia, Italy (Dr. Elena Giulotto). Previous work of this collaborative effort has resulted in the banking of material from two Thoroughbred mares and data on genome transcription and histone modification across a variety of tissues. The current work is expanding data collection to stallions and also focused on questions of centromere evolution.

Come work with us! We are recruiting a post-doctoral researcher for this effort. The successful candidate should have experience in analyzing next-generation sequence data and an interest in functional and/or evolutionary genetics. If you are interested, please contact Dr. Petersen.

Multistate Research - Impacts of Stress Factors on Performance, Health, and Well-Being of Farm Animals

Mitigating stress and ensuring animal well-being is of the utmost importance for the livestock industry. Significant evidence associates stress with decreased growth, performance, and carcass merit of beef cattle as well as increased mortality. In addition to mitigating stress, maximizing the efficiency of livestock growth is vital to meeting the world’s growing demand for animal protein while also minimizing resource utilization. Our work in this area revolves around the use of beta-adrenergic agonists (βAA) and the impact of heat stress on animal performance. The importance of each is outlined below. Heat Stress and Livestock Production: Heat stress costs the beef industry an estimated $300 million/year. This impact is not limited to the humid sub-tropic climate of the Southeast – heat stress in Nebraska has been blamed for loss of 6.7 kg per head per year and in the death of 1.5 of every 1,000 animals. Variation exists in tolerance to environmental stressors and performance within and among breeds. As producers are faced with new challenges of unpredictable environmental stress and heightened demand for production, and with the expertise of our research team, we have an opportunity to better understand the physiological means by which some animals tolerate heat stress with the possibility that once these coping mechanisms are understood, producers can exploit this information in management decisions.

Beta-adrenergic agonists: Supplementation with β-adrenergic agonists (βAA) prior to harvest has allowed cattle producers the ability to significantly increase the efficiency of growth. Although βAA supplementation is of significant economic benefit to production, other reports, largely anecdotal, have suggested these products induce unwanted stress on the animal. More troubling, an association between βAA supplementation and increased mortality was suggested although the data were correlative – no direct association was identified. Stimulating the adrenergic system, βAA supplementation, however, may have unwanted secondary effects when the animal is experiencing stress (such as heat). In a controlled environment, a recent study by members of our team indicated that βAAs did not negatively impact the immune, metabolic or endocrine response. The animals’ response to βAA supplementation, however, has not been fully evaluated in the presence of environmental stress (heat). Further, while βAA supplements are known to increase production efficiency, the specific molecular mechanisms through which this occurs are not understood. With the changing climate, a rising demand for beef, and a universal concern for animal well-being, it is critical to understanding the specific physiological and molecular processes altered by βAA and if these processes may further be influenced by stress.

The goals and objectives of the W3173 multistate project reflect the gap in our knowledge of stress management and mitigation in livestock and its importance to animal agriculture. The objective of our team is to produce rigorous scientific data to provide for the development of new management strategies to increase the efficiency of livestock production. Our current work is focused on refining our understanding of the molecular and physiological mechanisms by which livestock respond to heat stress and βAA supplementation, and how those responses and their interaction affect animal well-being and production.

This work is a collaborative effort within the Department of Animal Science at UNL (Drs. Dustin Yates and Ty Schmidt) as well as with University of Arizona researcher, Dr. Duarte Diaz, and Colorado State professor, Dr. Tim Holt.

Identification of variation underlying novel traits

Additional work in our lab is focused on understanding how variation in the genome alters various phenotypes from coat color in yak and horses to unwanted lethal traits in livestock. Examples of success in this area range from the identification of the genes altering coat and nose color in yak to a de novo mutation resulting in osteogenesis imperfecta in Red Angus calves. We work closely with UNL Veterinary Diagnostic Center pathologist, Dr. David Steffen, producers, and breed associations in cases where genetic mutations may be to blame for novel, often undesirable, phenotypes.