Signatures of diversifying selection in European pig breeds

Samantha Wilkinson; Zen H Lu; Hendrik-Jan Megens; Alan L Archibald; Chris Haley; Ian J Jackson; Martien A M Groenen; Richard P M A Crooijmans; Rob Ogden; Pamela Wiener

doi:10.1371/journal.pgen.1003453

Signatures of diversifying selection in European pig breeds

Samantha Wilkinson, Zen H Lu, Hendrik-Jan Megens, Alan L Archibald, Chris Haley, Ian J Jackson, Martien A M Groenen, Richard P M A Crooijmans, Rob Ogden, Pamela Wiener

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	1003453
Number of pages	15
Journal	PLoS Genetics
Volume	9
Issue number	4
Early online date	25 Apr 2013
DOIs	https://doi.org/10.1371/journal.pgen.1003453
Publication status	Published - Apr 2013

Keywords / Materials (for Non-textual outputs)

QUANTITATIVE TRAIT LOCI
FATTY-ACID-COMPOSITION
COAT COLOR
ARTIFICIAL SELECTION
KIT-LIGAND
SKIN PIGMENTATION
COMPLEX TRAITS
TEAT NUMBER
WILD BOAR
EAR SIZE

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10.1371/journal.pgen.1003453

Signatures of diversifying selection in European pig breeds
Copyright: © 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.
Final published version, 0.98 MB

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003453

ISP1: Analysis and prediction in complex animal systems
Tenesa, A. (Principal Investigator), Archibald, A. (Co-investigator), Beard, P. (Co-investigator), Bishop, S. (Co-investigator), Bronsvoort, M. (Co-investigator), Burt, D. (Co-investigator), Freeman, T. (Co-investigator), Haley, C. (Co-investigator), Hocking, P. (Co-investigator), Houston, R. (Co-investigator), Hume, D. (Co-investigator), Joshi, A. (Co-investigator), Law, A. (Co-investigator), Michoel, T. (Co-investigator), Summers, K. (Co-investigator), Vernimmen, D. (Co-investigator), Watson, M. (Co-investigator), Wiener, P. (Co-investigator), Wilson, A. (Co-investigator), Woolliams, J. (Co-investigator), Ait-Ali, T. (Researcher), Barnett, M. (Researcher), Carlisle, A. (Researcher), Finlayson, H. (Researcher), Haga, I. (Researcher), Karavolos, M. (Researcher), Matika, O. (Researcher), Paterson, T. (Researcher), Paton, B. (Researcher), Pong-Wong, R. (Researcher), Robert, C. (Researcher) & Robertson, G. (Researcher)
Biotechnology and Biological Sciences Research Council
1/04/12 → 31/03/17
Project: Research
CORE FUNDS
Haley, C. (Principal Investigator), Cabrera-Cardenas, C. (Researcher), Navarro, P. (Researcher) & Wei, W. (Researcher)
MRC
1/10/11 → 31/03/12
Project: Research

Data from: Signatures of diversifying selection in European pig breeds
Wilkinson, S. (Creator), Lu, Z. H. (Creator), Megens, H.-J. (Creator), Archibald, A. L. (Creator), Haley, C. (Creator), Jackson, I. J. (Creator), Groenen, M. A. M. (Creator), Crooijmans, R. P. M. A. (Creator), Ogden, R. (Creator) & Wiener, P. (Creator), Dryad, 26 Apr 2013
DOI: 10.5061/dryad.c2124, https://zenodo.org/records/5024043
Dataset

Cite this

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title = "Signatures of diversifying selection in European pig breeds",

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.",

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author = "Samantha Wilkinson and Lu, \{Zen H\} and Hendrik-Jan Megens and Archibald, \{Alan L\} and Chris Haley and Jackson, \{Ian J\} and Groenen, \{Martien A M\} and Crooijmans, \{Richard P M A\} and Rob Ogden and Pamela Wiener",

note = "Funding: The work was funded by the UK Food Standards Agency; the UK Department of Environment, Food and Rural Affairs; a Genesis Faraday (Biosciences KTN) SPARK award; Institute Strategic Grant funding from the UK Biotechnology and Biological Sciences Research Council (BBSRC); and the European Research Council under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC grant \#ERC-2009-AdG: 249894 (SelSweep project). SW acknowledges studentship funding from BBSRC and the Rare Breeds Survival Trust",

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doi = "10.1371/journal.pgen.1003453",

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AU - Wilkinson, Samantha

AU - Lu, Zen H

AU - Megens, Hendrik-Jan

AU - Archibald, Alan L

AU - Haley, Chris

AU - Jackson, Ian J

AU - Groenen, Martien A M

AU - Crooijmans, Richard P M A

AU - Ogden, Rob

AU - Wiener, Pamela

N1 - Funding: The work was funded by the UK Food Standards Agency; the UK Department of Environment, Food and Rural Affairs; a Genesis Faraday (Biosciences KTN) SPARK award; Institute Strategic Grant funding from the UK Biotechnology and Biological Sciences Research Council (BBSRC); and the European Research Council under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC grant #ERC-2009-AdG: 249894 (SelSweep project). SW acknowledges studentship funding from BBSRC and the Rare Breeds Survival Trust

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N2 - 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.

AB - 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.

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KW - FATTY-ACID-COMPOSITION

KW - COAT COLOR

KW - ARTIFICIAL SELECTION

KW - KIT-LIGAND

KW - SKIN PIGMENTATION

KW - COMPLEX TRAITS

KW - TEAT NUMBER

KW - WILD BOAR

KW - EAR SIZE

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DO - 10.1371/journal.pgen.1003453

M3 - Article

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SN - 1553-7404

VL - 9

JO - PLoS Genetics

JF - PLoS Genetics

IS - 4

M1 - 1003453

ER -

Signatures of diversifying selection in European pig breeds

Abstract

Keywords / Materials (for Non-textual outputs)

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Projects

ISP1: Analysis and prediction in complex animal systems

CORE FUNDS

Datasets

Data from: Signatures of diversifying selection in European pig breeds

Cite this