title: An assessment of population structure in eight breeds of cattle using a whole genome SNP panel.
abstract: BACKGROUND
  Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from Bos indicus and Bos taurus.
  
  
  RESULTS
  Two thousand six hundred and forty one single nucleotide polymorphisms (SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds.
  
  
  CONCLUSIONS
  The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the Bos taurus and Bos indicus breeds. When the Bos indicus breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the Bos taurus breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada. mckaysd@missouri.edu
authors.forename: Stephanie D
authors.initials: SD
authors.lastname: McKay
authors.forename: Robert D
authors.initials: RD
authors.lastname: Schnabel
authors.forename: Brenda M
authors.initials: BM
authors.lastname: Murdoch
authors.forename: Lakshmi K
authors.initials: LK
authors.lastname: Matukumalli
authors.forename: Jan
authors.initials: J
authors.lastname: Aerts
authors.forename: Wouter
authors.initials: W
authors.lastname: Coppieters
authors.forename: Denny
authors.initials: D
authors.lastname: Crews
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Dias Neto
authors.forename: Clare A
authors.initials: CA
authors.lastname: Gill
authors.forename: Chuan
authors.initials: C
authors.lastname: Gao
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Mannen
authors.forename: Zhiquan
authors.initials: Z
authors.lastname: Wang
authors.forename: Curt P
authors.initials: CP
authors.lastname: Van Tassell
authors.forename: John L
authors.initials: JL
authors.lastname: Williams
authors.forename: Jeremy F
authors.initials: JF
authors.lastname: Taylor
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Moore
mesh_terms: D000704:Analysis of Variance; D000818:Animals; D002417:Cattle / Q000235:genetics*; D003433:Crosses, Genetic; D005819:Genetic Markers; D005828:Genetics, Population; D016678:Genome / Q000235:genetics*; D005838:Genotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers