Genome‑wide scan for selection signatures in six cattle breeds in South Africa

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dc.contributor.author Makina, Sthembile O.
dc.contributor.author Muchadeyi, Farai C.
dc.contributor.author Van Marle-Koster, Este
dc.contributor.author Taylor, Jerry F.
dc.contributor.author Makgahlela, Mahlako L.
dc.contributor.author Maiwashe, Azwihangwisi
dc.date.accessioned 2017-02-24T06:07:32Z
dc.date.available 2017-02-24T06:07:32Z
dc.date.issued 2015-11-26
dc.description Additional file 1: Table S1. Symbols and names for all annotated candidate genes. en_ZA
dc.description.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 (FST). RESULTS AND DISCUSSION : 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. en_ZA
dc.description.department Animal and Wildlife Sciences en_ZA
dc.description.librarian am2017 en_ZA
dc.description.sponsorship ARC en_ZA
dc.description.uri http://gsejournal.biomedcentral.com/ en_ZA
dc.identifier.citation Makina, SO, Muchadeyi, FC, Van Marle‑Köster, E, Taylor, JF, Makgahlela, ML & Maiwashe, A 2015, 'Genome‑wide scan for selection signatures in six cattle breeds in South Africa', Genetics Selection Evolution, vol. 47, art. no. 92, pp. 1-14. en_ZA
dc.identifier.issn 0999-193X (print)
dc.identifier.issn 1297-9686 (online)
dc.identifier.other 10.1186/s12711-015-0173-x
dc.identifier.uri http://hdl.handle.net/2263/59158
dc.language.iso en en_ZA
dc.publisher BioMed Central en_ZA
dc.rights © 2015 Makina et al. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License. en_ZA
dc.subject Cattle breeds en_ZA
dc.subject Zebu cattle en_ZA
dc.subject Signatures en_ZA
dc.subject South Africa (SA) en_ZA
dc.title Genome‑wide scan for selection signatures in six cattle breeds in South Africa en_ZA
dc.type Article en_ZA


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