Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep

In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of “dairy breed...

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Main Authors:	Gutiérrez-Gil, Beatriz, Arranz, Juan Jose, Pong-Wong, Ricardo, García-Gámez, Elsa, Kijas, James, Wiener, Pamela
Format:	Online
Language:	English
Published:	Public Library of Science 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006912/

id	pubmed-4006912
recordtype	oai_dc
spelling	pubmed-40069122014-05-09 Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep Gutiérrez-Gil, Beatriz Arranz, Juan Jose Pong-Wong, Ricardo García-Gámez, Elsa Kijas, James Wiener, Pamela Research Article In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of “dairy breeds.” This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep. Public Library of Science 2014-05-01 /pmc/articles/PMC4006912/ /pubmed/24788864 http://dx.doi.org/10.1371/journal.pone.0094623 Text en © 2014 Gutiérrez-Gil et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Gutiérrez-Gil, Beatriz Arranz, Juan Jose Pong-Wong, Ricardo García-Gámez, Elsa Kijas, James Wiener, Pamela
spellingShingle	Gutiérrez-Gil, Beatriz Arranz, Juan Jose Pong-Wong, Ricardo García-Gámez, Elsa Kijas, James Wiener, Pamela Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep
author_facet	Gutiérrez-Gil, Beatriz Arranz, Juan Jose Pong-Wong, Ricardo García-Gámez, Elsa Kijas, James Wiener, Pamela
author_sort	Gutiérrez-Gil, Beatriz
title	Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep
title_short	Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep
title_full	Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep
title_fullStr	Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep
title_full_unstemmed	Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep
title_sort	application of selection mapping to identify genomic regions associated with dairy production in sheep
description	In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of “dairy breeds.” This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep.
publisher	Public Library of Science
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006912/
_version_	1612084370111201280

Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep

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