Artificial selection on introduced Asian haplotypes shaped the genetic architecture in european commercial pigs

Mirte Bosse, Marcos Soares Lopes, Ole Madsen, Hendrik Jan Megens, Richard P.M.A. Crooijmans, Laurent A.F. Frantz, Barbara Harlizius, John W.M. Bastiaansen, Martien A.M. Groenen

Research output: Contribution to journalArticleAcademicpeer-review

11 Citations (Scopus)

Abstract

Early pig farmers in Europe importedAsian 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 thatwere 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 thatwere 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.

LanguageEnglish
Article number20152019
Number of pages9
JournalProceedings of the Royal Society. B: Biological Sciences
Volume282
Issue number1821
DOIs
Publication statusPublished - 2015

Fingerprint

artificial selection
pig
Haplotypes
haplotypes
Swine
Genes
swine
Large White
backfat
introgression
alleles
genomics
phenotype
swine breeds
allele
genome
livestock breeding
Alleles
Genome
litter size

Keywords

  • Adaptive introgression
  • Commercial breeding
  • Domestication
  • Hybridization
  • Selection
  • Sus scrofa

Cite this

@article{044363f914494424bba8378eb27b2008,
title = "Artificial selection on introduced Asian haplotypes shaped the genetic architecture in european commercial pigs",
abstract = "Early pig farmers in Europe importedAsian 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 thatwere 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 thatwere 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.",
keywords = "Adaptive introgression, Commercial breeding, Domestication, Hybridization, Selection, Sus scrofa",
author = "Mirte Bosse and {Soares Lopes}, Marcos and Ole Madsen and Megens, {Hendrik Jan} and Crooijmans, {Richard P.M.A.} and Frantz, {Laurent A.F.} and Barbara Harlizius and Bastiaansen, {John W.M.} and Groenen, {Martien A.M.}",
year = "2015",
doi = "10.1098/rspb.2015.2019",
language = "English",
volume = "282",
journal = "Proceedings of the Royal Society. B: Biological Sciences",
issn = "0962-8452",
publisher = "Royal Society, The",
number = "1821",

}

TY - JOUR

T1 - Artificial selection on introduced Asian haplotypes shaped the genetic architecture in european commercial pigs

AU - Bosse, Mirte

AU - Soares Lopes, Marcos

AU - Madsen, Ole

AU - Megens, Hendrik Jan

AU - Crooijmans, Richard P.M.A.

AU - Frantz, Laurent A.F.

AU - Harlizius, Barbara

AU - Bastiaansen, John W.M.

AU - Groenen, Martien A.M.

PY - 2015

Y1 - 2015

N2 - Early pig farmers in Europe importedAsian 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 thatwere 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 thatwere 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.

AB - Early pig farmers in Europe importedAsian 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 thatwere 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 thatwere 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.

KW - Adaptive introgression

KW - Commercial breeding

KW - Domestication

KW - Hybridization

KW - Selection

KW - Sus scrofa

U2 - 10.1098/rspb.2015.2019

DO - 10.1098/rspb.2015.2019

M3 - Article

VL - 282

JO - Proceedings of the Royal Society. B: Biological Sciences

T2 - Proceedings of the Royal Society. B: Biological Sciences

JF - Proceedings of the Royal Society. B: Biological Sciences

SN - 0962-8452

IS - 1821

M1 - 20152019

ER -