title: Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs.
abstract: Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708WD, The Netherlands mirte.bosse@wur.nl.
authors.forename: Mirte
authors.initials: M
authors.lastname: Bosse
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708WD, The Netherlands Topigs Norsvin Research Center, Beuningen 6640AA, The Netherlands.
authors.forename: Marcos S
authors.initials: MS
authors.lastname: Lopes
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708WD, The Netherlands.
authors.forename: Ole
authors.initials: O
authors.lastname: Madsen
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708WD, The Netherlands.
authors.forename: Hendrik-Jan
authors.initials: HJ
authors.lastname: Megens
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708WD, The Netherlands.
authors.forename: Richard P M A
authors.initials: RP
authors.lastname: Crooijmans
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708WD, The Netherlands.
authors.forename: Laurent A F
authors.initials: LA
authors.lastname: Frantz
authors.affiliation: Topigs Norsvin Research Center, Beuningen 6640AA, The Netherlands.
authors.forename: Barbara
authors.initials: B
authors.lastname: Harlizius
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708WD, The Netherlands.
authors.forename: John W M
authors.initials: JW
authors.lastname: Bastiaansen
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708WD, The Netherlands.
authors.forename: Martien A M
authors.initials: MA
authors.lastname: Groenen
mesh_terms: D050154:Adiposity / Q000235:genetics; D000818:Animals; D001208:Asia; D001947:Breeding; D005060:Europe; D006239:Haplotypes; D006824:Hybridization, Genetic; D008098:Litter Size / Q000235:genetics; D034421:Sus scrofa / Q000235:genetics*
keywords: Sus scrofa; adaptive introgression; commercial breeding; domestication; hybridization; selection