E. Freebern*,1, J. Jiang2, J.B. Cole3, P.M. VanRaden3, and L. Ma1
1University of Maryland, College Park, MD 20742
2North Carolina State University, Raleigh, NC 27695
3Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705
2020 J. Dairy Sci. (?)
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Genetic and genomic selection in the U.S. dairy population has achieved successful phenotypic improvement across a comprehensive set of economically important traits that involve production, reproduction, health, and body conformation. While contemporary cows differ phenotypically from their ancestors hundreds of years ago, the changes in the genome, especially those due to selection, remain to be discovered. The aim of this study is to investigate genome-wide and region-specific changes in the U.S. Holstein-Friesian (HF) cattle population between the years of 1950 to 2015. Using the U.S. dairy cooperator’ phenotypic and genomic databases hosted at CDCB, we first extracted genotype and phenotype (PTA) data of ~27,000 reference bulls and performed GWAS analyses to identify candidate QTLs. We then divided the 27,000 Holstein bulls into five bins based on birth year, 1950~1980, 1980~2000, 2000~2010, 2010~2013, 2013~2015. The allele frequency changes between the two extreme time periods were calculated to capture the difference between the earliest and most recent populations. Finally, the genomic regions with the largest allele frequency changes were compared against the QTL regions identified in GWAS analyses. To identify true genome changes due to selection from those due to random genetic drift, we implemented a gene dropping simulation approach with real pedigree and calculated thresholds of allele frequency change. The process was executed by running a simulation program in Python, which will visualize systemic changes over individual SNPs and compare them to a distribution under pure genetic drift. Observation of changes above the 99.9% threshold on the distribution may be indicative of selection and affecting dairy traits. From this evaluation of genome-wide and region-specific changes due to selection, we will identify candidate QTL regions under selection and are associated with economically important traits in the U.S. dairy population.