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

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 sign...

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Autores principales: Makina, Sithembile O., Muchadeyi, Farai C., van Marle-Köster, Este, Taylor, Jerry F., Makgahlela, Mahlako L., Maiwashe, Azwihangwisi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662009/
https://www.ncbi.nlm.nih.gov/pubmed/26612660
http://dx.doi.org/10.1186/s12711-015-0173-x
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author Makina, Sithembile O.
Muchadeyi, Farai C.
van Marle-Köster, Este
Taylor, Jerry F.
Makgahlela, Mahlako L.
Maiwashe, Azwihangwisi
author_facet Makina, Sithembile O.
Muchadeyi, Farai C.
van Marle-Köster, Este
Taylor, Jerry F.
Makgahlela, Mahlako L.
Maiwashe, Azwihangwisi
author_sort Makina, Sithembile O.
collection PubMed
description 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)). 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-015-0173-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-46620092015-11-28 Genome-wide scan for selection signatures in six cattle breeds in South Africa Makina, Sithembile O. Muchadeyi, Farai C. van Marle-Köster, Este Taylor, Jerry F. Makgahlela, Mahlako L. Maiwashe, Azwihangwisi Genet Sel Evol Research Article 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)). 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-015-0173-x) contains supplementary material, which is available to authorized users. BioMed Central 2015-11-26 /pmc/articles/PMC4662009/ /pubmed/26612660 http://dx.doi.org/10.1186/s12711-015-0173-x Text en © Makina et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Makina, Sithembile O.
Muchadeyi, Farai C.
van Marle-Köster, Este
Taylor, Jerry F.
Makgahlela, Mahlako L.
Maiwashe, Azwihangwisi
Genome-wide scan for selection signatures in six cattle breeds in South Africa
title Genome-wide scan for selection signatures in six cattle breeds in South Africa
title_full Genome-wide scan for selection signatures in six cattle breeds in South Africa
title_fullStr Genome-wide scan for selection signatures in six cattle breeds in South Africa
title_full_unstemmed Genome-wide scan for selection signatures in six cattle breeds in South Africa
title_short Genome-wide scan for selection signatures in six cattle breeds in South Africa
title_sort genome-wide scan for selection signatures in six cattle breeds in south africa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662009/
https://www.ncbi.nlm.nih.gov/pubmed/26612660
http://dx.doi.org/10.1186/s12711-015-0173-x
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