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A practical approach to detect ancestral haplotypes in livestock populations

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  • Enrique Sanchez Molano
  • Dimitrios Tsiokos
  • Dimitrios Chatziplis
  • Hossein Jorjani
  • Lorenzo Degano
  • Clara Diaz
  • Attilio Rossoni
  • Hermann Schwarzenbacher
  • Franz Seefried
  • Luis Varona
  • Daniele Vicario
  • Ezequiel Nicolazzi
  • Georgios Banos

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    Rights statement: © 2016 The Author(s). Open Access This 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.

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    Licence: Creative Commons: Attribution (CC-BY)

Original languageEnglish
Pages (from-to)91
JournalBMC Genetics
Publication statusPublished - 24 Jun 2016


Background: The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle.

Results: The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content.

Conclusion: In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations.

    Research areas

  • Ancestral haplotypes, Population dynamics, Selection signatures, Cattle

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