Signatures of diversifying selection in European pig breeds

• Published in: PLoS 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
• Language: English
• 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
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1003453

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.