Presentation Title
Analysis of Single Nucleotide Polymorphisms in the Cattle Genome and Epigenome
Abstract
DNA methylation, an important epigenetic marker, is believed to play an important role in phenotype variability. It is therefore important to understand the link between the genome and the epigenome. This study focuses on identifying polymorphisms in the bovine genome and epigenome, which can be compared to identify links between genetic and epigenetic variation. Brain tissues of each of 8 Red Angus x Simmental steers underwent whole genome bisulfite sequencing (WGBS) to identify methylated cytosines. Fastq sequencing files were trimmed with Trim Galore using a phred score of 20. Trimmed reads were aligned to a bovine reference index using BSseeker2 and the bowtie2 aligner. BSseeker2 was further used to call for methylation levels. Coverage statistics and polymorphisms were determined with CGmap Tools for three brain tissues: Amygdala, Cingulate Gyrus, and Periaquaductal Gray. The genetic and epigenetic polymorphisms were then analyzed and compared to identify correlating patterns. These data provide insight into the relationship between single nucleotide polymorphisms in the genome and epigenome to begin uncovering the impact of cattle’s genetics on their epigenetic markers.
Primary Faculty Mentor Name
Dr. Stephanie McKay
Graduate Student Mentors
Bonnie Cantrell, Suraj Bhattarai
Faculty/Staff Collaborators
Bonnie Cantrell (University of Vermont), Shuli Liu (USDA and China Agricultural University), Nathan Jebbett (University of Vermont), Robert C. Switzer III (NeuroScience Associates, Inc.), Eugene Delay (University of Vermont), Steven Zinn (University of Connecticut), Sharon Aborn (University of Connecticut), Jane O’Neil (University of Vermont), Julia Sjoquist (University of Vermont), Joseph Waksman (University of Vermont), Hannah Lachance (University of Vermont), Brenda Murdoch (University of Idaho), Rick Funston (University of Nebraska), Robert Weaber (Kansas State University), George Liu (USDA), Stephanie McKay (University of Vermont)
Status
Graduate
Student College
College of Arts and Sciences
Program/Major
Cellular, Molecular and Biomedical Sciences
Primary Research Category
Biological Sciences
Analysis of Single Nucleotide Polymorphisms in the Cattle Genome and Epigenome
DNA methylation, an important epigenetic marker, is believed to play an important role in phenotype variability. It is therefore important to understand the link between the genome and the epigenome. This study focuses on identifying polymorphisms in the bovine genome and epigenome, which can be compared to identify links between genetic and epigenetic variation. Brain tissues of each of 8 Red Angus x Simmental steers underwent whole genome bisulfite sequencing (WGBS) to identify methylated cytosines. Fastq sequencing files were trimmed with Trim Galore using a phred score of 20. Trimmed reads were aligned to a bovine reference index using BSseeker2 and the bowtie2 aligner. BSseeker2 was further used to call for methylation levels. Coverage statistics and polymorphisms were determined with CGmap Tools for three brain tissues: Amygdala, Cingulate Gyrus, and Periaquaductal Gray. The genetic and epigenetic polymorphisms were then analyzed and compared to identify correlating patterns. These data provide insight into the relationship between single nucleotide polymorphisms in the genome and epigenome to begin uncovering the impact of cattle’s genetics on their epigenetic markers.