title: Primary analysis of DNA polymorphisms in the TRIM region (MHC subregion) of the Japanese quail, Coturnix japonica.
abstract: Based on sequences of two cosmid clones from Japanese quail (Coturnix japonica, Coja), we confirmed that the syntenic cluster, GNB2L1∼BTN1∼BTN2, is located in the quail TRIM subregion of the quail major histocompatibility complex (MHC Coja) region. These cosmids also included four CjBG loci and one CjLEC locus; therefore, the quail TRIM subregion was thought to be adjacent to the BG/LEC subregion. We then identified three polymorphic markers - CjHEP21, CjTRIM39.2 and CjBTN2 - in the TRIM subregion that may be useful for the functional analysis of the MHC-Coja region. We examined MHC-Coja sequences from 321 individual quails sampled from 11 inbred strains, and we found eight alleles for each of the three genes - CjHEP21, CjTRIM39.2 and CjBTN2. These polymorphisms represent the first avian DNA markers in the TRIM subregion. Additionally, we discovered a quail-specific VNTR (variable number of long tandem repeats, 133-137 bp) in intron 7 of CjBTN2. We identified 25 haplotypes in the sample of 321 quail; these haplotypes comprised combinations of all 24 alleles of the three polymorphic genes. We suggest that there are two recombination hotspots, one between each pair of adjacent loci. All strains, except AMRP, contained multiple haplotypes; the AMRP strain contained a single, apparently fixed haplotype.
authors.affiliation: Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.
authors.forename: Shingo
authors.initials: S
authors.lastname: Suzuki
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Hosomichi
authors.forename: Kana
authors.initials: K
authors.lastname: Yokoyama
authors.forename: Kaoru
authors.initials: K
authors.lastname: Tsuda
authors.forename: Hiromi
authors.initials: H
authors.lastname: Hara
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Yoshida
authors.forename: Akira
authors.initials: A
authors.lastname: Fujiwara
authors.forename: Makoto
authors.initials: M
authors.lastname: Mizutani
authors.forename: Takashi
authors.initials: T
authors.lastname: Shiina
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Kono
authors.forename: Kei
authors.initials: K
authors.lastname: Hanzawa
mesh_terms: D000483:Alleles; D000818:Animals; D003360:Cosmids / Q000235:genetics; D003370:Coturnix / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics; D006239:Haplotypes / Q000235:genetics; D007438:Introns / Q000235:genetics; D008285:Major Histocompatibility Complex / Q000235:genetics*; D018598:Minisatellite Repeats / Q000235:genetics; D005810:Multigene Family / Q000235:genetics; D011110:Polymorphism, Genetic / Q000235:genetics*; D000075370:Receptors for Activated C Kinase; D011956:Receptors, Cell Surface / Q000235:genetics
chemical_list: D000075370:Receptors for Activated C Kinase; D011956:Receptors, Cell Surface; D004247:DNA