Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.

<h4>Background</h4>Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity.<h4>Methodology/main findings</h4>Genome wide...

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Autores principales:	Andreia J Amaral, Luca Ferretti, Hendrik-Jan Megens, Richard P M A Crooijmans, Haisheng Nie, Sebastian E Ramos-Onsins, Miguel Perez-Enciso, Lawrence B Schook, Martien A M Groenen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6b0748904af647a6b104f33ee6da9267
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spelling	oai:doaj.org-article:6b0748904af647a6b104f33ee6da92672021-11-18T06:56:17ZGenome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.1932-620310.1371/journal.pone.0014782https://doaj.org/article/6b0748904af647a6b104f33ee6da92672011-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21483733/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity.<h4>Methodology/main findings</h4>Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ∼2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar.<h4>Conclusions/significance</h4>These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection.Andreia J AmaralLuca FerrettiHendrik-Jan MegensRichard P M A CrooijmansHaisheng NieSebastian E Ramos-OnsinsMiguel Perez-EncisoLawrence B SchookMartien A M GroenenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 4, p e14782 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Andreia J Amaral Luca Ferretti Hendrik-Jan Megens Richard P M A Crooijmans Haisheng Nie Sebastian E Ramos-Onsins Miguel Perez-Enciso Lawrence B Schook Martien A M Groenen Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.
description	<h4>Background</h4>Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity.<h4>Methodology/main findings</h4>Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ∼2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar.<h4>Conclusions/significance</h4>These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection.
format	article
author	Andreia J Amaral Luca Ferretti Hendrik-Jan Megens Richard P M A Crooijmans Haisheng Nie Sebastian E Ramos-Onsins Miguel Perez-Enciso Lawrence B Schook Martien A M Groenen
author_facet	Andreia J Amaral Luca Ferretti Hendrik-Jan Megens Richard P M A Crooijmans Haisheng Nie Sebastian E Ramos-Onsins Miguel Perez-Enciso Lawrence B Schook Martien A M Groenen
author_sort	Andreia J Amaral
title	Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.
title_short	Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.
title_full	Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.
title_fullStr	Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.
title_full_unstemmed	Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.
title_sort	genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled dna.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/6b0748904af647a6b104f33ee6da9267
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Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.

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