Signatures of diversifying selection in European pig breeds

Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, bod...

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Published inPLoS genetics Vol. 9; no. 4; p. e1003453
Main Authors Wilkinson, Samantha, Lu, Zen H, Megens, Hendrik-Jan, Archibald, Alan L, Haley, Chris, Jackson, Ian J, Groenen, Martien A M, Crooijmans, Richard P M A, Ogden, Rob, Wiener, Pamela
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 01.04.2013
Public Library of Science (PLoS)
Subjects
Agriculture
Animals
artificial selection
Biological diversity
Biology
Breeding
coat color
Comparative analysis
complex traits
ear size
fatty-acid-composition
Genetics
Genome
Genomes
Genomics
Hogs
Identification and classification
kit-ligand
Livestock
Observations
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Selection, Genetic
Single nucleotide polymorphisms
skin pigmentation
Sus scrofa - genetics
Swine
teat number
wild boar
United Kingdom
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Abstract Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.
AbstractList Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.
  Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.
Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition. The domestic pig, an important source of protein worldwide, was domesticated from the ancestral wild boar in multiple locations throughout the world. In Europe, local types were developed following domestication, but phenotypically distinct breeds only arose in the eighteenth century with the advent of systematic breeding. Recently developed molecular tools for pigs (as well as other livestock species) now allow a genetic characterisation of breed histories, including identification of regions of the genome that have been under selection in the establishment of breeds. We have applied these tools to identify genomic regions associated with breed development in a set of commercial and traditional pig breeds. We found strong evidence of genetic differentiation between breeds near genes associated with traits that are used to define breed standards, such as ear morphology and coat colour, as well as in regions of the genome that are associated with pork production traits. It is well documented that crosses with Asian pigs have been used to modify European breeds. We have found evidence of genetic influence from Asian pigs in European breeds, again in regions of the genome associated with breed standard characteristics, including ear shape and coat colour, as well as production traits.
Audience Academic
Author Groenen, Martien A M
Crooijmans, Richard P M A
Ogden, Rob
Lu, Zen H
Wilkinson, Samantha
Megens, Hendrik-Jan
Haley, Chris
Wiener, Pamela
Archibald, Alan L
Jackson, Ian J
AuthorAffiliation The University of Queensland, Australia
4 Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
3 MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
2 Animal Breeding and Genomics Centre, Wageningen UR, Wageningen, The Netherlands
AuthorAffiliation_xml – name: 3 MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
– name: The University of Queensland, Australia
– name: 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
– name: 2 Animal Breeding and Genomics Centre, Wageningen UR, Wageningen, The Netherlands
– name: 4 Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
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ContentType Journal Article
Copyright COPYRIGHT 2013 Public Library of Science
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2013 Wilkinson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Wilkinson S, Lu ZH, Megens H-J, Archibald AL, Haley C, et al. (2013) Signatures of Diversifying Selection in European Pig Breeds. PLoS Genet 9(4): e1003453. doi:10.1371/journal.pgen.1003453
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– notice: 2013 Wilkinson et al 2013 Wilkinson et al
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– notice: 2013 Wilkinson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Wilkinson S, Lu ZH, Megens H-J, Archibald AL, Haley C, et al. (2013) Signatures of Diversifying Selection in European Pig Breeds. PLoS Genet 9(4): e1003453. doi:10.1371/journal.pgen.1003453
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content type line 23
Analyzed the data: SW ZHL H-JM PW. Wrote the paper: SW PW. Collected and genotyped biological samples: ALA H-JM MAMG RPMAC RO. Conceived the analysis: SW PW. Provided comments and suggestions regarding data analysis and the manuscript: ALA RPMAC CH H-JM MAMG ZHL IJJ RO. Approved the final manuscript: SW ZHL H-JM ALA CH IJJ MAMG RPMAC RO PW.
Current address: Animal and Veterinary Sciences, Scotland's Rural College, The Roslin Insitute Building, Easter Bush, Midlothian, United Kingdom
The authors have declared that no competing interests exist.
OpenAccessLink https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636142/
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Snippet Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large...
  Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large...
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StartPage e1003453
SubjectTerms Agriculture
Animals
artificial selection
Biological diversity
Biology
Breeding
coat color
Comparative analysis
complex traits
ear size
fatty-acid-composition
Genetics
Genome
Genomes
Genomics
Hogs
Identification and classification
kit-ligand
Livestock
Observations
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Selection, Genetic
Single nucleotide polymorphisms
skin pigmentation
Sus scrofa - genetics
Swine
teat number
wild boar
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Title Signatures of diversifying selection in European pig breeds
URI https://www.ncbi.nlm.nih.gov/pubmed/23637623
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https://doaj.org/article/24684a7970954a73b149eecc02d671a2
http://dx.doi.org/10.1371/journal.pgen.1003453
Volume 9
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