title: Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression.
abstract: The independent domestication of local wild boar populations in Asia and Europe about 10,000 years ago led to distinct European and Asian pig breeds, each with very different phenotypic characteristics. During the Industrial Revolution, Chinese breeds were imported to Europe to improve commercial traits in European breeds. Here we demonstrate the presence of introgressed Asian haplotypes in European domestic pigs and selection signatures on some loci in these regions, using whole genome sequence data. The introgression signatures are widespread and the Asian haplotypes are rarely fixed. The Asian introgressed haplotypes are associated with regions harbouring genes involved in meat quality, development and fertility. We identify Asian-derived non-synonymous mutations in the AHR gene that associate with increased litter size in multiple European commercial lines. These findings demonstrate that increased fertility was an important breeding goal for early nineteenth century pig farmers, and that Asian variants of genes related to this trait were preferentially selected during the development of modern European pig breeds.
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands.
authors.forename: Mirte
authors.initials: M
authors.lastname: Bosse
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands.
authors.forename: Hendrik-Jan
authors.initials: HJ
authors.lastname: Megens
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands.
authors.forename: Laurent A F
authors.initials: LA
authors.lastname: Frantz
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands.
authors.forename: Ole
authors.initials: O
authors.lastname: Madsen
authors.affiliation: Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, DH1 3LE Durham, UK.
authors.forename: Greger
authors.initials: G
authors.lastname: Larson
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands.
authors.forename: Yogesh
authors.initials: Y
authors.lastname: Paudel
authors.affiliation: 1] Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands [2] TOPIGS Research Center IPG, 6640 AA Beuningen, The Netherlands.
authors.forename: Naomi
authors.initials: N
authors.lastname: Duijvesteijn
authors.affiliation: TOPIGS Research Center IPG, 6640 AA Beuningen, The Netherlands.
authors.forename: Barbara
authors.initials: B
authors.lastname: Harlizius
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands.
authors.forename: Yanick
authors.initials: Y
authors.lastname: Hagemeijer
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands.
authors.forename: Richard P M A
authors.initials: RP
authors.lastname: Crooijmans
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands.
authors.forename: Martien A M
authors.initials: MA
authors.lastname: Groenen
mesh_terms: D000818:Animals; D001208:Asia; D005060:Europe; D005298:Fertility / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D013552:Swine