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

Bosse M, Megens HJ, Frantz LA, Madsen O, Larson G, Paudel Y, Duijvesteijn N, Harlizius B, Hagemeijer Y, Crooijmans RP, Groenen MA - Nat Commun (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands.

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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Experimental setup for the introgression detectionArrows indicate the comparisons between groups that are used for the IBD detection. Individuals from the LW breed are used for all pairwise comparisons with individuals from two geographical and functional groups: EUWB and ASDom. The blue arrow indicates the human-mediated introgression from ASDom in to LW.
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Figure 1: Experimental setup for the introgression detectionArrows indicate the comparisons between groups that are used for the IBD detection. Individuals from the LW breed are used for all pairwise comparisons with individuals from two geographical and functional groups: EUWB and ASDom. The blue arrow indicates the human-mediated introgression from ASDom in to LW.

Mentions: We identified haplotypes in the LW pigs that were identical by decent (IBD) with individuals from both the original source of domestication, the European wild boars (EUWB), and the source of introgression, the Asian domestic group (ASDom, Fig. 1). Individuals from different locations in Europe were used to represent the source of domestication, whereas individuals from three different Asian breeds were used to represent the pool of putative introgressed haplotypes (see Supplementary Table 1 and Supplementary Methods for details). Average genetic differentiation (Fst, as defined by Weir and Cockerham20) between the LW and ASDom was 0.33 (s.d. 0.23, s.e. 0.0008), while the average Fst value between LW and EUWB was 0.16 (s.d. 0.17, s.e. 0.0006). These results show that the genomes of the LW pigs still share greater similarity with their EUWB ancestors than with ASDom. We used an other independent method to further verify the existence of gene flow between ASDom and LW after lineage divergence between Asian and European Sus scrofa (D-statistics21, see Methods). We computed this statistic for each possible trio between (LW, ASDom and EUWB), and (LW, EUWB, ASDom) so that a significantly negative D (Z< −4) imply admixture between ASDom and LW. Our results demonstrate that all LW individuals possess roughly an equal degree of admixture with Asian pigs over their entire genomes, reflecting the human-mediated hybridization with Asian domestics in the late eighteenth and early nineteenth century (D = −0.083±0.015, Z = −20).


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

Bosse M, Megens HJ, Frantz LA, Madsen O, Larson G, Paudel Y, Duijvesteijn N, Harlizius B, Hagemeijer Y, Crooijmans RP, Groenen MA - Nat Commun (2014)

Experimental setup for the introgression detectionArrows indicate the comparisons between groups that are used for the IBD detection. Individuals from the LW breed are used for all pairwise comparisons with individuals from two geographical and functional groups: EUWB and ASDom. The blue arrow indicates the human-mediated introgression from ASDom in to LW.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4225517&req=5

Figure 1: Experimental setup for the introgression detectionArrows indicate the comparisons between groups that are used for the IBD detection. Individuals from the LW breed are used for all pairwise comparisons with individuals from two geographical and functional groups: EUWB and ASDom. The blue arrow indicates the human-mediated introgression from ASDom in to LW.
Mentions: We identified haplotypes in the LW pigs that were identical by decent (IBD) with individuals from both the original source of domestication, the European wild boars (EUWB), and the source of introgression, the Asian domestic group (ASDom, Fig. 1). Individuals from different locations in Europe were used to represent the source of domestication, whereas individuals from three different Asian breeds were used to represent the pool of putative introgressed haplotypes (see Supplementary Table 1 and Supplementary Methods for details). Average genetic differentiation (Fst, as defined by Weir and Cockerham20) between the LW and ASDom was 0.33 (s.d. 0.23, s.e. 0.0008), while the average Fst value between LW and EUWB was 0.16 (s.d. 0.17, s.e. 0.0006). These results show that the genomes of the LW pigs still share greater similarity with their EUWB ancestors than with ASDom. We used an other independent method to further verify the existence of gene flow between ASDom and LW after lineage divergence between Asian and European Sus scrofa (D-statistics21, see Methods). We computed this statistic for each possible trio between (LW, ASDom and EUWB), and (LW, EUWB, ASDom) so that a significantly negative D (Z< −4) imply admixture between ASDom and LW. Our results demonstrate that all LW individuals possess roughly an equal degree of admixture with Asian pigs over their entire genomes, reflecting the human-mediated hybridization with Asian domestics in the late eighteenth and early nineteenth century (D = −0.083±0.015, Z = −20).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen 6708 WD, The Netherlands.

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.

Show MeSH
Related in: MedlinePlus