Proceeding of Veterinary and Animal Science Days 2015, 15th- 17th  July,  Milan, Italy 

riviste.unimi.it/index.php/haf                                                                                 1 

   

 

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STEPHANIE  MCKAY 

 

Dr. Stephanie McKay was born 

and raised in Texas where she 

attended Texas A&M University 

and received her undergraduate 

degrees in Biochemistry and 

Genetics. While working as a full 

time lab technician in a bovine 

genomics laboratory, Dr. McKay 

worked on her M.S. in Veterinary 

Microbiology. After receiving her 

Master's degree, Stephanie 

ventured to the University of 

Alberta in Edmonton, Alberta, 

Canada where she received her 

Ph.D. in Animal Science in 2007. 

Dr. McKay has had varied 

research experience including 

generating transgenic mice, 

working in Biohazardous disease 

related laboratories and 

predominantly working with the 

bovine genome. Her work with 

the bovine genome started as an 

undergraduate student and has 

evolved with time as research 

with the bovine genome has 

grown. Currently the McKay lab 

performs genetic, genomic, 

epigenetic and epigenomic work 

with beef cattle. Our primary 

interest is identifying the 

proportion of epigenetic 

variation associated with 

complex traits. 

 
 

Stephanie.McKay@uvm.edu 

To What Extent Does DNA Methylation 

Affect Phenotypic Variation in Cattle? 

Stephanie McKAY
1
 

1 
University of Vermont, Department of Animal Veterinary Sciences, 304 

Terrill Hall570 Main St. Burlington, VT 05405USA. 

MAIN LECTURE 

 
DNA methylation is an environmentally influenced epigenetic modification that 
regulates gene transcription and has the potential to influence variation in 
economically important phenotypes in agricultural species. We have utilized a 
novel approach to evaluate the relationship between genetic and epigenetic 
variation and downstream phenotypes. To begin with, we have integrated RNA-
Seq and methyl binding domain sequencing (MBD-Seq) data in order to determine 
the extent to which DNA methylation affects phenotypic variation in economically 
important traits of cattle. MBD-Seq is a technique that involves the sample 
enrichment of methylated genomic regions followed by their next-generation 
sequencing. This study utilized Illumina next generation sequencing technology to 
perform both RNA-Seq and MBD-Seq. NextGENe software (SoftGenetics, State 
College, PA) was employed for quality trimming and aligning the sequence reads 
to the UMD3.1 bovine reference genome, generating counts of matched reads 
and methylated peak identification. Subsequently, we identified and quantified 
genome-wide methylated regions and characterized the extent of differential 
methylation and differential expression between two groups of animals with 
extreme phenotypes. The program edgeR from the R software package (version 
3.0.1) was employed for identifying differentially methylated regions and regions 
of differential expression. Finally, Partial Correlation with Information Theory 
(PCIT) was performed to identify transcripts and methylation events that exhibit 
differential hubbing. A differential hub is defined as a gene network hub that is 
more highly connected in one treatment group than the other. This analysis 
produced every possible pair-wise interaction that subsequently enabled us to 
look at network interactions of how methylation affects expression. (co-
expression, co-methylation, methylation x expression). Genomic regions of 
interest derived from this analysis were then aligned to previously identified QTL 
and GWAS regions using Animal QTL database. The approach described here has 
provided us with evidence that QTL and GWAS regions overlay genomic regions 
where methylation may regulate transcription.