title: Strong signatures of selection in the domestic pig genome.
abstract: 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.
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology,  Uppsala University, SE-751 23 Uppsala,  Sweden.
authors.forename: Carl-Johan
authors.initials: CJ
authors.lastname: Rubin
authors.forename: Hendrik-Jan
authors.initials: HJ
authors.lastname: Megens
authors.forename: Alvaro
authors.initials: A
authors.lastname: Martinez Barrio
authors.forename: Khurram
authors.initials: K
authors.lastname: Maqbool
authors.forename: Shumaila
authors.initials: S
authors.lastname: Sayyab
authors.forename: Doreen
authors.initials: D
authors.lastname: Schwochow
authors.forename: Chao
authors.initials: C
authors.lastname: Wang
authors.forename: Örjan
authors.initials: Ö
authors.lastname: Carlborg
authors.forename: Patric
authors.initials: P
authors.lastname: Jern
authors.forename: Claus B
authors.initials: CB
authors.lastname: Jørgensen
authors.forename: Alan L
authors.initials: AL
authors.lastname: Archibald
authors.forename: Merete
authors.initials: M
authors.lastname: Fredholm
authors.forename: Martien A M
authors.initials: MA
authors.lastname: Groenen
authors.forename: Leif
authors.initials: L
authors.lastname: Andersson
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000829:Animals, Domestic / Q000235:genetics*; D056915:DNA Copy Number Variations; D016678:Genome; D006720:Homozygote; D008969:Molecular Sequence Data; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D017386:Sequence Homology, Amino Acid; D013552:Swine / Q000235:genetics*