Abstract
Advancements in sequencing technology have provided the ability to study the genome at a more in-depth level than ever before. Understanding how changes in the genome from single base pairs to insertions and deletions can increase our knowledge of the biological factors influencing phenotypic traits. Analysis of sheep whole genome sequence was utilized to compare variant callers and analyze genetic variation between breeds. This first study showed that utilization of whole genome sequence and thus the ability to compare genetic variation from a greater number of Single Nucleotide Polymorphisms (SNPs) provides greater separation between genetically similar breeds. The second study aimed to identify genetic associations with rhino lamb, a semi-lethal disease in sheep where newborns struggle to stand or suckle and often die from lack of nutrition. Utilization of a genome-wide association study and run of homozygosity identified a region on chromosome 15 associated with the disease. Through the use of fine mapping, haplotypes within the CELF1 gene were associated with the disease. Advances in the length and accuracy of sequencing have enabled the creation of telomere-to-telomere (T2T) assemblies. The third study depicts the creation of two goat haploid T2T assemblies from Saanen, a dairy breed, and Kiko, a meat breed. Assembly of these two different haplotypes allowed for comparison of centromere and rDNA regions that can be informative in studying evolution between breeds and species. Being able to create complete genome assemblies provides a roadmap to where genes and regulatory elements are located. This can increase the ability to detect and associate genetic changes with important phenotypic traits. Identification of genetic variation throughout the genome is crucial, but as only about 2% of the genome is protein coding, most of the genetic variation that exists does not reside within genes. Many studies have identified genetic variation within regulatory elements however it can be difficult to associate which gene(s) they influence. Characterization of the genome structure can enable the association of genomic interactions can provide insight into how genes are regulated and increase biological understanding of gene function. The fourth study characterized the 3D genome in fetal goat tissues and compared similarities and differences between three tissues, lung, muscle, and spleen. This study identified tissue specific DNA contacts, some of which identify genes known to play a crucial role in their specific tissue. There are many aspects of the genome from changes in base pairs to different genomic interactions that affect biological function resulting in tissue and breed differences. Understanding these genomic differences can help in utilization of genetic variation for selective breeding to increase efficiency and food supply.