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 has contributed to this collaborative project to develop atlas of gene regulation in the horse. Primary collaborators include Drs. Carrie Finno and Rebecca Bellone at UC Davis, Dr. Ted Kalbfleisch at the University of Kentucky, and Dr. Elena Giulotto at the University of Pavia (Italy).
Studies of Population (Breed) Diversity
Most breeds of domestic species are closed populations – no new genetics are allowed into the breed through crossbreeding. Therefore, inbreeding (mating between relatives) is often unavoidable. Inbreeding at a high level can result in decreases in fitness; however, inbreeding also is a means to concentrate the genetic variation that results in desirable phenotypes while removing variation that may be unwanted. Although pedigree records help us to track changes in a population, the use of genomics is the best way to assess diversity of a breed. Genetic studies can also reveal historic changes in the population.
Ongoing work in collaboration with Drs. Ted Kalbfleisch and Ernie Bailey at the University of Kentucky Gluck Equine Research Center is focused on developing a catalog of diversity in the US Thoroughbred. With this information, we can then model how management decisions may alter the rate of change in diversity. The characterization of diversity of the US Thoroughbred will also allow for monitoring of diversity in the future.
Similar work was conducted in the Clydesdale, with a focus on how the Clydesdale horses in Scotland are related to those in North America. This work was included in the BBC Documentary, Clydesdale, Saving the Greatest Horse.
Ongoing work is examining changes in genetic diversity of the US Shire.
The impact of heat stress on animal welfare and productivity
Heat stress is a growing concern for livestock production. With collaborators in physiology (see Dr. Dustin Yates), meat science (see Dr. Ty Schmidt), and animal welfare/behavior (see Dr. Ruth Woiwode), we are working to understand the animal's response to heat stress. Our lab focuses on how the genome responds by studying changes in the transcriptome and in DNA methylation. By comparing data among animals and across breeds, we are learning about physiological pathways important for resilience to heat stress. Earlier work also investigated the interaction of β-agonist supplementation (common in finishing livestock) with heat stress. Anecdotal evidence suggested these supplements may negatively impact animal welfare when provided at a time of stress. Our data have provided evidence that these supplements may help mitigate some of the negative effects of stress and do not exacerbate the stress response.
Identification of de novo variation in cattle resulting in lethal or unwanted phenotypes
Multiple genomics approaches led to a custom genotyping array to uncover genetic sources associated with variation in age at puberty and sow fertility.
New mutations arise all the time. Most often they are not perpetuated. Occasionally, however, these mutations result in an unwanted, lethal, or unhealthy phenotype. Our lab works closely with Dr. David Steffen at the Veterinary Diagnostic Center to identify these novel variants. As a result of this work, breed associations and commercial genotyping facilities can offer genetic tests producers can use to avoid matings that could result in affected calves.
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.
Multi-state 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 multi-state 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 University of Nebraska-Lincoln (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 University of Nebraska-Lincoln 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.