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

Mirte Bosse (), Hendrik-Jan Megens, Laurent A. F. Frantz, Ole Madsen, Greger Larson, Yogesh Paudel, Naomi Duijvesteijn, Barbara Harlizius, Yanick Hagemeijer, Richard P. M. A. Crooijmans and Martien A. M. Groenen
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Mirte Bosse: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands
Hendrik-Jan Megens: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands
Laurent A. F. Frantz: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands
Ole Madsen: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands
Greger Larson: Durham Evolution and Ancient DNA, Durham University
Yogesh Paudel: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands
Naomi Duijvesteijn: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands
Barbara Harlizius: TOPIGS Research Center IPG
Yanick Hagemeijer: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands
Richard P. M. A. Crooijmans: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands
Martien A. M. Groenen: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands

Nature Communications, 2014, vol. 5, issue 1, 1-8

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms5392

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