Strong signatures of selection in the domestic pig genome
Open accessAbstract
Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig--the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1, PLAG1, and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other domestic animals and in humans. Most European domestic pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in domestic pigs, most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted pigs, carrying the Dominant white, Patch, or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals and how alleles in domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection.
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- Authors
- Rubin, C.-J., Megens, H.-J., Barrio, A. M., Maqbool, K., Sayyab, S., Schwochow, D., Wang, C., Carlborg, Ö., Jern, P., Jørgensen, C. B., Archibald, A. L., Fredholm, M., Groenen, M. A. M., & Andersson, L.
- Affiliations
- Uppsala University (SE)
- Wageningen University & Research (NL)
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden;
- Departments of cAnimal Breeding and Genetics and
- Swedish University of Agricultural Sciences (SE)
- University of Copenhagen (DK)
- Roslin Institute (GB)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2012-11-14
- Volume
- 109
- Issue
- 48
- Pages
- 19529-19536
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3511700
- OpenAlex
- W1977314055
- Cited by
- 652
- References
- 52
- Citations by year
- 2026: 19 · 2025: 34 · 2024: 51 · 2023: 47 · 2022: 68 · 2021: 48 · 2020: 58 · 2019: 51 · 2018: 46 · 2017: 41 · 2016: 44 · 2015: 64 · 2014: 51 · 2013: 26 · 2012: 1
- FWCI
- 26.92
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/I025328/1, BBS/E/D/20211554, BBS/E/D/20211550)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- domestic pigs, Sus scrofa, domestication, positive selection, selective sweeps, quantitative trait loci, vertebral number, NR6A1, PLAG1, LCORL, structural variants, gene duplication, dominant white spotting, coat color, relaxed purifying selection, nonsynonymous substitutions
- MeSH terms
- Amino Acid Sequence, Animals, Animals, Domestic, Homozygote, Molecular Sequence Data, Selection, Genetic, Swine, Genome, Sequence Homology, Amino Acid, Quantitative Trait Loci, DNA Copy Number Variations
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