A genome-wide scan for signatures of directional selection in domesticated pigs

BMC Genomics
Sunjin MoonHeebal Kim

Abstract

Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an F ST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated ...Continue Reading

References

Oct 1, 1992·Genetics·R R HudsonW P Maddison
Feb 1, 1974·Genetical Research·J M Smith, J Haigh
Feb 19, 2004·Nature Reviews. Genetics·Leif Andersson, Michel Georges
Feb 24, 2006·PLoS Biology·Benjamin F VoightJonathan K Pritchard
Jun 17, 2006·Science·P C SabetiE S Lander
May 22, 2008·Genetics·Andreia J AmaralMartien A M Groenen
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Feb 13, 2009·Nature·Michael D Purugganan, Dorian Q Fuller
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 9, 2010·Annual Review of Pharmacology and Toxicology·Colleen M Niswender, P Jeffrey Conn
Jan 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Joshua M AkeyMark W Neff
Mar 12, 2010·Journal of Psychiatric Research·Mònica GratacòsXavier Estivill
May 24, 2011·The Journal of Biological Chemistry·Sunitha MeruvuElisabetta Mueller
Jun 21, 2011·BMC Bioinformatics·David H Alexander, Kenneth Lange
Sep 3, 2011·Proceedings. Biological Sciences·Pamela Wiener, Samantha Wilkinson
Feb 22, 2012·PLoS Biology·James W KijasUNKNOWN International Sheep Genomics Consortium Members
Nov 16, 2012·Proceedings of the National Academy of Sciences of the United States of America·Carl-Johan RubinLeif Andersson
Nov 16, 2012·Nature·Martien A M GroenenLawrence B Schook
Apr 23, 2013·Neuropharmacology·Richard M O'ConnorJohn F Cryan
May 3, 2013·PLoS Genetics·Samantha WilkinsonPamela Wiener
May 16, 2013·Nature Communications·Guo-dong WangYa-ping Zhang
Nov 12, 2013·Bioinformatics·Ida Moltke, Anders Albrechtsen
Mar 4, 2014·PLoS Genetics·Saber QanbariHenner Simianer

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Citations

Mar 31, 2016·Genetics, Selection, Evolution : GSE·Martien A M Groenen
Nov 4, 2016·Scientific Reports·Yuhua FuChangchun Li
Oct 28, 2017·Asian-Australasian Journal of Animal Sciences·Taehyung KwonHeebal Kim
Nov 9, 2017·Genetics, Selection, Evolution : GSE·Beatriz Gutiérrez-GilJuan-Jose Arranz
Oct 11, 2017·Genome Biology and Evolution·Yaling ZhuLusheng Huang
Mar 1, 2019·PloS One·Letícia Borges JoaquimDanísio Prado Munari
Jul 4, 2018·Nature Ecology & Evolution·Hui XiangShuai Zhan
Jun 5, 2019·Animals : an Open Access Journal From MDPI·Ligang WangShutang Feng
Jan 9, 2019·Frontiers in Genetics·Martin Johnsson

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Datasets Mentioned

BETA
SRP052927

Methods Mentioned

BETA
MDS
electrophoresis

Software Mentioned

SAMtools
ADMIMXTURE
ADMIXTURE
rehh
iHS
PLINK
Picard Tools
HaploView
Genome Analysis ToolKit
RelateAdmix

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