title: Recent artificial selection in U.S. Jersey cattle impacts autozygosity levels of specific genomic regions.
abstract: BACKGROUND
  Genome signatures of artificial selection in U.S. Jersey cattle were identified by examining changes in haplotype homozygosity for a resource population of animals born between 1953 and 2007. Genetic merit of this population changed dramatically during this period for a number of traits, especially milk yield. The intense selection underlying these changes was achieved through extensive use of artificial insemination (AI), which also increased consanguinity of the population to a few superior Jersey bulls. As a result, allele frequencies are shifted for many contemporary animals, and in numerous cases to a homozygous state for specific genomic regions. The goal of this study was to identify those selection signatures that occurred after extensive use of AI since the 1960, using analyses of shared haplotype segments or Runs of Homozygosity. When combined with animal birth year information, signatures of selection associated with economically important traits were identified and compared to results from an extended haplotype homozygosity analysis.
  
  
  RESULTS
  Overall, our results reveal that more recent selection increased autozygosity across the entire genome, but some specific regions increased more than others. A genome-wide scan identified more than 15 regions with a substantial change in autozygosity. Haplotypes found to be associated with increased milk, fat and protein yield in U.S. Jersey cattle also consistently increased in frequency.
  
  
  CONCLUSIONS
  The analyses used in this study was able to detect directional selection over the last few decades when individual production records for Jersey animals were available.
authors.affiliation: United States Department of Agriculture, Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, MD, 20705, USA. ekim5@iastate.edu.|Department of Animal Science, Iowa State University, Ames, IA, 50011, USA. ekim5@iastate.edu.
authors.forename: Eui-Soo
authors.initials: ES
authors.lastname: Kim
authors.affiliation: United States Department of Agriculture, Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, MD, 20705, USA. tad.sonstegard@ars.usda.gov.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011, USA. mfrothsc@iastate.edu.
authors.forename: Max F
authors.initials: MF
authors.lastname: Rothschild
mesh_terms: D000818:Animals; D002417:Cattle; D005787:Gene Frequency; D016678:Genome; D005838:Genotype; D006239:Haplotypes; D006720:Homozygote; D007315:Insemination, Artificial; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic / Q000235:genetics*; D014481:United States