title: Domestication does not narrow MHC diversity in Sus scrofa.
abstract: The Major Histocompatibility Complex (MHC) is a multigene family of outstanding polymorphism. MHC molecules bind antigenic peptides in the peptide-binding region (PBR) that consists of five binding pockets (P). In this study, we compared the genetic diversity of domestic pigs to that of the modern representatives of their wild ancestors, the wild boar, in two MHC loci, the oligomorphic DQA and the polymorphic DRB1. MHC nucleotide polymorphism was compared with the actual functional polymorphism in the PBR and the binding pockets P1, P4, P6, P7, and P9. The analysis of approximately 200 wild boars collected throughout Europe and 120 domestic pigs from four breeds (three pureblood, Pietrain, Leicoma, and Landrace, and one mixed Danbred) revealed that wild boars and domestic pigs share the same levels of nucleotide and amino acid polymorphism, allelic richness, and heterozygosity. Domestication did not appear to act as a bottleneck that would narrow MHC diversity. Although the pattern of polymorphism was uniform between the two loci, the magnitude of polymorphism was different. For both loci, most of the polymorphism was located in the PBR region and the presence of positive selection was supported by a statistically significant excess of nonsynonymous substitutions over synonymous substitutions in the PBR. P4 and P6 were the most polymorphic binding pockets. Functional polymorphism, i.e., the number and the distribution of pocket variants within and among populations, was significantly narrower than genetic polymorphism, indicative of a hierarchical action of selection pressures on MHC loci.
authors.affiliation: Laboratory of Cenetics, Evolutionary and Comparative Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
authors.forename: Katerina A
authors.initials: KA
authors.lastname: Moutou
authors.forename: Evagelia A
authors.initials: EA
authors.lastname: Koutsogiannouli
authors.forename: Costas
authors.initials: C
authors.lastname: Stamatis
authors.forename: Charalambos
authors.initials: C
authors.lastname: Billinis
authors.forename: Claudia
authors.initials: C
authors.lastname: Kalbe
authors.forename: Massimo
authors.initials: M
authors.lastname: Scandura
authors.forename: Zissis
authors.initials: Z
authors.lastname: Mamuris
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D063147:Animal Distribution; D000818:Animals; D000835:Animals, Wild / Q000235:genetics* / Q000276:immunology; D001665:Binding Sites; D005060:Europe; D005787:Gene Frequency; D005802:Genes, MHC Class II / Q000235:genetics*; D014644:Genetic Variation; D015395:Histocompatibility Antigens Class I; D000949:Histocompatibility Antigens Class II / Q000737:chemistry / Q000235:genetics*; D058751:Livestock / Q000235:genetics* / Q000276:immunology; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D018807:Polymorphism, Single-Stranded Conformational; D017434:Protein Structure, Tertiary; D012641:Selection, Genetic; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D034421:Sus scrofa / Q000235:genetics* / Q000276:immunology
chemical_list: D015395:Histocompatibility Antigens Class I; D000949:Histocompatibility Antigens Class II; C438668:swine leukocyte antigen