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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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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. |
format | Online Article Text |
id | pubmed-4662009 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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