Genome signature of artificial selection for milk yield in Holstein cattle

T.S. Sonstegard1, L. Ma3, J.B. Cole2, G.R. Wiggans2, B.A. Crooker3, C.P. Van Tassell1,2, B.D. Mariani4, and Y. Da3

1Bovine Functional Genomics and 2Animal Improvement Programs Laboratories, Agricultural Research Service, USDA, Beltsville, MD 20705-2350

3Department of AnimalScience, University of Minnesota, St. Paul, MN 55108

4Genetics and In Vitro Fertilization Institute, Fairfax, VA 20151


Artificial selection for high milk yield in Holstein cattle over the past forty years achieved tremendous increases in milk yield but saw an unintended consequence of declined fertility. It was unknown how artificial selection changed the Holstein genome and what genome changes were associated with the phenotypic changes. By contrasting the genome-wide single nucleotide polymorphism of cattle populations with and without being subjected to selection pressure and by comparing cattle in different selection stages, extensive allele frequency changes across the Holstein genome were revealed. Using genome-wide analysis of extended haplotype homozygosity and SNP-phenotype association between the selected and unselected populations, a number of selection signatures associated with milk yield were localized to specific genes or chromosome regions. Some of the regions had opposite effects on fertility measured by daughter pregnancy rate, suggesting an antagonistic mechanism underlying milk yield and fertility.