Animal Science, Department of


First Advisor

Jessica L. Petersen

Second Advisor

Daniel C. Ciobanu

Third Advisor

Audrey L. Atkin

Date of this Version


Document Type



A Thesis Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science, Major: Animal Science, Under the Supervision of Professor Jessica L. Petersen Lincoln, Nebraska: April 2022

Copyright © 2022 Alexa McKenna Barber,


Genome annotation has a direct impact on the success of genomic studies. Transcriptome analyses and chromatin immunoprecipitation and sequencing (ChIP-seq) have been used to functionally annotate genomes. These methods can identify protein-coding genes, non-coding transcripts, and cis-regulatory elements across the genome. The primary objective of the first study was to functionally annotate the equine genome through the assessment of nine tissues: adipose, brain, heart, lamina, liver, lung, skeletal, muscle, testis, and ovary. In the first project, 150 bp, paired-end RNA sequencing (RNA-seq) libraries were generated in stallion tissues and compared to previously generated mare RNA-seq libraries to quantify variation in gene expression due to sex and tissue type. On average, each tissue expressed (> 10 transcripts per million) over 8,000 genes, and adipose, liver, and skeletal muscle each had over 900 genes differentially expressed due to sex (P adj

The third study examined genomic variation associated with a congenital defect, perosomus elumbis, (PE) in Angus cattle. The affected calf was still-born, displaying lumbar aplasia, and arthrogryposis. Whole-genome sequencing of 31 Angus cattle identified a frameshift mutation in PTK7 as a candidate variant for the development of PE in an Angus calf. Despite the implication of PTK7 in similar phenotypes, additional research is needed to verify the etiology of PE in Angus cattle.

Advisor: Jessica L. Petersen