title: Genome-wide scan for selection signatures in six cattle breeds in South Africa.
abstract: BACKGROUND
  The detection of selection signatures in breeds of livestock species can contribute to the identification of regions of the genome that are, or have been, functionally important and, as a consequence, have been targeted by selection.
  
  
  METHODS
  This study used two approaches to detect signatures of selection within and between six cattle breeds in South Africa, including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31) and Holstein (n = 29). The first approach was based on the detection of genomic regions in which haplotypes have been driven towards complete fixation within breeds. The second approach identified regions of the genome that had very different allele frequencies between populations (F ST).
  
  
  CONCLUSIONS
  Forty-seven candidate genomic regions were identified as harbouring putative signatures of selection using both methods. Twelve of these candidate selected regions were shared among the breeds and ten were validated by previous studies. Thirty-three of these regions were successfully annotated and candidate genes were identified. Among these genes the keratin genes (KRT222, KRT24, KRT25, KRT26, and KRT27) and one heat shock protein gene (HSPB9) on chromosome 19 between 42,896,570 and 42,897,840 bp were detected for the Nguni breed. These genes were previously associated with adaptation to tropical environments in Zebu cattle. In addition, a number of candidate genes associated with the nervous system (WNT5B, FMOD, PRELP, and ATP2B), immune response (CYM, CDC6, and CDK10), production (MTPN, IGFBP4, TGFB1, and AJAP1) and reproductive performance (ADIPOR2, OVOS2, and RBBP8) were also detected as being under selection.
  
  
  CONCLUSIONS
  The results presented here provide a foundation for detecting mutations that underlie genetic variation of traits that have economic importance for cattle breeds in South Africa.
authors.affiliation: Agricultural Research Council-Animal Production Institute, Private Bag X 2, Irene, 0062, South Africa. qwabes@arc.agric.za.|Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X 20, Hatfield, 0028, South Africa. qwabes@arc.agric.za.
authors.forename: Sithembile O
authors.initials: SO
authors.lastname: Makina
authors.affiliation: Agricultural Research Council-Biotechnology Platform, Private Bag X 5, Onderstepoort, 0110, South Africa. muchadeyif@arc.agric.za.
authors.forename: Farai C
authors.initials: FC
authors.lastname: Muchadeyi
authors.affiliation: Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X 20, Hatfield, 0028, South Africa. evm.koster@up.ac.za.
authors.forename: Este
authors.initials: E
authors.lastname: van Marle-Köster
authors.affiliation: Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. taylorjerr@missouri.edu.
authors.forename: Jerry F
authors.initials: JF
authors.lastname: Taylor
authors.affiliation: Agricultural Research Council-Animal Production Institute, Private Bag X 2, Irene, 0062, South Africa. MMakgahlela@arc.agric.za.
authors.forename: Mahlako L
authors.initials: ML
authors.lastname: Makgahlela
authors.affiliation: Agricultural Research Council-Animal Production Institute, Private Bag X 2, Irene, 0062, South Africa. norman@arc.agric.za.|Department of Animal, Wildlife and Grassland Sciences, University of Free State, Bloemfontein, 9300, South Africa. norman@arc.agric.za.
authors.forename: Azwihangwisi
authors.initials: A
authors.lastname: Maiwashe
mesh_terms: D000483:Alleles; D000818:Animals; D001947:Breeding; D002417:Cattle; D033481:Chromosomes, Mammalian; D019295:Computational Biology / Q000379:methods; D005787:Gene Frequency; D056726:Genetic Association Studies; D005819:Genetic Markers; D016678:Genome; D055106:Genome-Wide Association Study / Q000379:methods; D023281:Genomics / Q000379:methods; D006239:Haplotypes; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D013019:South Africa
chemical_list: D005819:Genetic Markers