Research Abstracts Online
January - December 2011
University of Minnesota Twin Cities
College of Veterinary Medicine
of Veterinary Population Medicine
PI: Molly E. McCue
Genetic Epidemiology and Population Genetics in Domestic Horse Populations
The primary focus of this research group is to study genetic disease in the domestic horse populations. They are studying several diseases that serve as biomedical models for human disease and are of relevance to the domestic horse. Most of these studies involve genome-wide association studies (GWAS) on datasets generated from the equine 50,000 SNP genotyping array.
In addition to using MSI resources for data analysis for these data analyses, they use MSI to host an online survey service to communicate with potential study participants. This application makes use of the MySQL database server as well as a live website that is hosted on the MSI web server. The researchers use PHP to communicate between the two components. In the future they plan to make moderate use of the database services as well as implementing further web interfaces for our database, possibly using CGI.
A secondary focus of this group is explaining the diversity between and within horse breeds, with a special interest in the impact of breed demographic on mapping strategies, and the study of signatures of selection in the genome, resulting from selective breeding strategies. Using Elmo, they have just completed analysis of 825 horses from 35 breeds. They have extended this project and are in the process of identifying Ancestry Informative Markers, which will be tested using STRUCTURE, again with Elmo. Finally, the group also has four different projects using next-generation sequencing, two with targeted enrichment of small regions of the genome (1-6Mb), and two using RNA-deq for gene expression and transcriptome analysis.
Krista Fritz, Research Associate
Eric Graalum, Graduate Student
Annette McCoy, Research Associate
Jessica Petersen, Research Associate
Aaron Rendahl, Faculty Collaborator
Rob James Schaefer, Staff