Abstract
Sheep are a globally important species raised for meat, milk, and fiber. Research in livestock genomics, including sheep, is important to increasing disease resilience and production of animal products while decreasing environmental impact of raising animals. Sheep have adapted to many different environments across the world, which has led to specialized traits including heat tolerance, disease resilience, and increased growth and meat quality. The first study presented in this dissertation found that sheep selected to fit production systems across the world are genetically different, despite originating from similar breed lineages. This can lead to further characterization of biological traits unique to populations of animals within a species. The assembly of high-quality reference genomes also leads to a better understanding of genetic diversity and identification of genetic variation. This includes mitochondrial genomes, which have historically contributed to phylogenetic studies in mammalian species. The assembly of the mitochondrial genome of the Rocky Mountain bighorn sheep and the entire genome of the Rambouillet sheep presented in this dissertation contribute valuable reference resources to the scientific community. Further studies using these assemblies will aid in better defining and understanding the relationships between wild and domestic sheep, as well as genetic variation and locations of genes and regulatory elements in domestic sheep. The functional annotation of the sheep genome presented in the last two chapters of this dissertation defines the locations of transcriptional regulatory elements across the genome from a large collection of tissues. Histone modification, open chromatin, and DNA methylation are all classified as transcriptional regulatory elements and were defined in these studies. These regulatory elements were annotated on the Rambouillet reference genome to provide further resources to the community to investigate the mechanisms of gene regulation in relation to traits important to the sheep industry. Overall, this research will advance sheep research and production of economically important sheep products including meat, milk, and wool across the world.