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

M. Bosse, H.J.W.C. Megens, L.A.F. Frantz, O. Madsen, Y. Paudel, N. Duijvestein, R.P.M.A. Crooijmans, M. Groenen

Research output: Contribution to journalArticleAcademicpeer-review

51 Citations (Scopus)

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.
LanguageEnglish
Article number4392
Number of pages8
JournalNature Communications
Volume5
DOIs
Publication statusPublished - 2014

Fingerprint

swine
genes
Haplotypes
Sus scrofa
Swine
Genes
fertility
Fertility
Litter Size
signatures
Meat
Breeding
Meats
genome
loci
mutations
Genome
Mutation
Population

Keywords

  • hydrocarbon dioxin receptor
  • recent positive selection
  • haplotype structure
  • molecular characterization
  • reproductive traits
  • domestic pig
  • wide snp
  • evolution
  • models
  • polymorphisms

Cite this

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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.",
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Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression. / Bosse, M.; Megens, H.J.W.C.; Frantz, L.A.F.; Madsen, O.; Paudel, Y.; Duijvestein, N.; Crooijmans, R.P.M.A.; Groenen, M.

In: Nature Communications, Vol. 5, 4392, 2014.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Bosse, M.

AU - Megens, H.J.W.C.

AU - Frantz, L.A.F.

AU - Madsen, O.

AU - Paudel, Y.

AU - Duijvestein, N.

AU - Crooijmans, R.P.M.A.

AU - Groenen, M.

PY - 2014

Y1 - 2014

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AB - 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.

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KW - reproductive traits

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KW - evolution

KW - models

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