title: A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT.
abstract: The Dominant White (I/KIT) locus is one of the major coat color loci in the pig. Previous studies showed that the Dominant White (I) and Patch (IP) alleles are both associated with a duplication including the entire KIT coding sequence. We have now constructed a BAC contig spanning the three closely linked tyrosine kinase receptor genes PDGFRA-KIT-KDR. The size of the duplication was estimated at about 450 kb and includes KIT, but not PDGFRA and KDR. Sequence analysis revealed that the duplication arose by unequal homologous recombination between two LINE elements flanking KIT. The same unique duplication breakpoint was identified in animals carrying the I and IP alleles across breeds, implying that Dominant White and Patch alleles are descendants of a single duplication event. An unexpected finding was that Piétrain pigs carry the KIT duplication, since this breed was previously assumed to be wild type at this locus. Comparative sequence analysis indicated that the distinct phenotypic effect of the duplication occurs because the duplicated copy lacks some regulatory elements located more than 150 kb upstream of KIT exon 1 and necessary for normal KIT expression.
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 597, S-751 24 Uppsala, Sweden.
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Giuffra
authors.forename: Anna
authors.initials: A
authors.lastname: Törnsten
authors.forename: Stefan
authors.initials: S
authors.lastname: Marklund
authors.forename: Erik
authors.initials: E
authors.lastname: Bongcam-Rudloff
authors.forename: Patrick
authors.initials: P
authors.lastname: Chardon
authors.forename: James M H
authors.initials: JM
authors.lastname: Kijas
authors.forename: Susan I
authors.initials: SI
authors.lastname: Anderson
authors.forename: Alan L
authors.initials: AL
authors.lastname: Archibald
authors.forename: Leif
authors.initials: L
authors.lastname: Andersson
mesh_terms: D000483:Alleles; D000818:Animals; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial; D020451:Contig Mapping; D016521:Electrophoresis, Gel, Pulsed-Field; D020440:Gene Duplication; D005799:Genes, Dominant / Q000235:genetics; D006200:Hair Color / Q000235:genetics*; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D008969:Molecular Sequence Data; D010641:Phenotype; D019009:Proto-Oncogene Proteins c-kit / Q000235:genetics*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013552:Swine / Q000235:genetics*
chemical_list: D019009:Proto-Oncogene Proteins c-kit