Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression

• Published in: Nature communications Vol. 5; no. 1; p. 4392
• Main Authors: Bosse, Mirte, Megens, Hendrik-Jan, Frantz, Laurent A. F., Madsen, Ole, Larson, Greger, Paudel, Yogesh, Duijvesteijn, Naomi, Harlizius, Barbara, Hagemeijer, Yanick, Crooijmans, Richard P. M. A., Groenen, Martien A. M.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 15.07.2014; Nature Publishing Group; Nature Pub. Group
• Subjects: 631/181/457; 631/208/1348; 631/208/728; Animals; Asia; domestic pig; Europe; evolution; Fertility - genetics; Genomics - methods; haplotype structure; Haplotypes - genetics; Humanities and Social Sciences; Humans; hydrocarbon dioxin receptor; molecular characterization; multidisciplinary; polymorphisms; recent positive selection; reproductive traits; Science; Science (multidisciplinary); Swine; wide snp; Asia; Europe
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms5392

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. Domestication of wild boar populations has led to phenotypically distinct European and Asian pig breeds. Here, the authors show that Asian haplotypes that have introgressed into European pig breeds harbour genes that control economically important traits such as meat quality, development and fertility.