title: Characterizing homozygosity across United States, New Zealand and Australian Jersey cow and bull populations.
abstract: BACKGROUND
  Dairy cattle breeding objectives are in general similar across countries, but environment and management conditions may vary, giving rise to slightly different selection pressures applied to a given trait. This potentially leads to different selection pressures to loci across the genome that, if large enough, may give rise to differential regions with high levels of homozygosity. The objective of this study was to characterize differences and similarities in the location and frequency of homozygosity related measures of Jersey dairy cows and bulls from the United States (US), Australia (AU) and New Zealand (NZ).
  
  
  RESULTS
  The populations consisted of a subset of genotyped Jersey cows born in US (n = 1047) and AU (n = 886) and Jersey bulls progeny tested from the US (n = 736), AU (n = 306) and NZ (n = 768). Differences and similarities across populations were characterized using a principal component analysis (PCA) and a run of homozygosity (ROH) statistic (ROH45), which counts the frequency of a single nucleotide polymorphism (SNP) being in a ROH of at least 45 SNP. Regions that exhibited high frequencies of ROH45 and those that had significantly different ROH45 frequencies between populations were investigated for their association with milk yield traits. Within sex, the PCA revealed slight differentiation between the populations, with the greatest occurring between the US and NZ bulls. Regions with high levels of ROH45 for all populations were detected on BTA3 and BTA7 while several other regions differed in ROH45 frequency across populations, the largest number occurring for the US and NZ bull contrast. In addition, multiple regions with different ROH45 frequencies across populations were found to be associated with milk yield traits.
  
  
  CONCLUSIONS
  Multiple regions exhibited differential ROH45 across AU, NZ and US cow and bull populations, an interpretation is that locations of the genome are undergoing differential directional selection. Two regions on BTA3 and BTA7 had high ROH45 frequencies across all populations and will be investigated further to determine the gene(s) undergoing directional selection.
authors: Department of Animal Science, North Carolina State University, Raleigh, NC, 27695-7627, USA. jthoward@ncsu.edu.
authors: Jeremy T
authors: JT
authors: Howard
authors: Department of Animal Science, North Carolina State University, Raleigh, NC, 27695-7627, USA. christian_maltecca@ncsu.edu.
authors: Christian
authors: C
authors: Maltecca
authors: Dairy Futures Cooperative Research Centre, 5 Ring Road, Bundoora, Victoria, 3083, Australia. mekonnen.haile-mariam@depi.vic.gov.au.|Biosciences Research Division, Department of Environment and Primary Industries Victoria, 5 Ring Road, Bundoora, 3083, Australia. mekonnen.haile-mariam@depi.vic.gov.au.
authors: Mekonnen
authors: M
authors: Haile-Mariam
authors: Dairy Futures Cooperative Research Centre, 5 Ring Road, Bundoora, Victoria, 3083, Australia. ben.hayes@depi.vic.gov.au.|La Trobe University, Bundoora, Victoria, 3086, Australia. ben.hayes@depi.vic.gov.au.|Biosciences Research Division, Department of Environment and Primary Industries Victoria, 5 Ring Road, Bundoora, 3083, Australia. ben.hayes@depi.vic.gov.au.
authors: Ben J
authors: BJ
authors: Hayes
authors: Dairy Futures Cooperative Research Centre, 5 Ring Road, Bundoora, Victoria, 3083, Australia. jennie.pryce@depi.vic.gov.au.|La Trobe University, Bundoora, Victoria, 3086, Australia. jennie.pryce@depi.vic.gov.au.|Biosciences Research Division, Department of Environment and Primary Industries Victoria, 5 Ring Road, Bundoora, 3083, Australia. jennie.pryce@depi.vic.gov.au.
authors: Jennie E
authors: JE
authors: Pryce
mesh_terms: D000818:Animals; D001315:Australia; D002417:Cattle / Q000235:genetics*; D003612:Dairying; D005260:Female; D014644:Genetic Variation; D016678:Genome; D055106:Genome-Wide Association Study; D006720:Homozygote; D008297:Male; D009520:New Zealand; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D000068618:Selective Breeding; D014481:United States