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Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication

BACKGROUND: Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an...

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Autores principales: Metzger, Julia, Tonda, Raul, Beltran, Sergi, Águeda, Lídia, Gut, Marta, Distl, Ottmar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097168/
https://www.ncbi.nlm.nih.gov/pubmed/24996778
http://dx.doi.org/10.1186/1471-2164-15-562
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author Metzger, Julia
Tonda, Raul
Beltran, Sergi
Águeda, Lídia
Gut, Marta
Distl, Ottmar
author_facet Metzger, Julia
Tonda, Raul
Beltran, Sergi
Águeda, Lídia
Gut, Marta
Distl, Ottmar
author_sort Metzger, Julia
collection PubMed
description BACKGROUND: Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an insight into genetic influences on selective forces. RESULTS: Whole genome sequencing of five horses of four different populations revealed 10,193,421 single nucleotide polymorphisms (SNPs) and 1,361,948 insertion/deletion polymorphisms (indels). In comparison to horse variant databases and previous reports, we were able to identify 3,394,883 novel SNPs and 868,525 novel indels. We analyzed the distribution of individual variants and found significant enrichment of private mutations in coding regions of genes involved in primary metabolic processes, anatomical structures, morphogenesis and cellular components in non-breed horses and in contrast to that private mutations in genes affecting cell communication, lipid metabolic process, neurological system process, muscle contraction, ion transport, developmental processes of the nervous system and ectoderm in breed horses. CONCLUSIONS: Our next generation sequencing data constitute an important first step for the characterization of non-breed in comparison to breed horses and provide a large number of novel variants for future analyses. Functional annotations suggest specific variants that could play a role for the characterization of breed or non-breed horses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-562) contains supplementary material, which is available to authorized users.
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spelling pubmed-40971682014-07-18 Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication Metzger, Julia Tonda, Raul Beltran, Sergi Águeda, Lídia Gut, Marta Distl, Ottmar BMC Genomics Research Article BACKGROUND: Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an insight into genetic influences on selective forces. RESULTS: Whole genome sequencing of five horses of four different populations revealed 10,193,421 single nucleotide polymorphisms (SNPs) and 1,361,948 insertion/deletion polymorphisms (indels). In comparison to horse variant databases and previous reports, we were able to identify 3,394,883 novel SNPs and 868,525 novel indels. We analyzed the distribution of individual variants and found significant enrichment of private mutations in coding regions of genes involved in primary metabolic processes, anatomical structures, morphogenesis and cellular components in non-breed horses and in contrast to that private mutations in genes affecting cell communication, lipid metabolic process, neurological system process, muscle contraction, ion transport, developmental processes of the nervous system and ectoderm in breed horses. CONCLUSIONS: Our next generation sequencing data constitute an important first step for the characterization of non-breed in comparison to breed horses and provide a large number of novel variants for future analyses. Functional annotations suggest specific variants that could play a role for the characterization of breed or non-breed horses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-562) contains supplementary material, which is available to authorized users. BioMed Central 2014-07-04 /pmc/articles/PMC4097168/ /pubmed/24996778 http://dx.doi.org/10.1186/1471-2164-15-562 Text en © Metzger et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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
Metzger, Julia
Tonda, Raul
Beltran, Sergi
Águeda, Lídia
Gut, Marta
Distl, Ottmar
Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication
title Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication
title_full Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication
title_fullStr Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication
title_full_unstemmed Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication
title_short Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication
title_sort next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097168/
https://www.ncbi.nlm.nih.gov/pubmed/24996778
http://dx.doi.org/10.1186/1471-2164-15-562
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