Analysis of Single Nucleotide Polymorphisms in the Cattle Genome and Epigenome
Stassen, Emily
Stassen, Emily
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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.
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11:00 AM
1:00pm-3:00pm
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1:00pm-3:00pm
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Date
2019-01-01