title: Structure and polymorphism of the major histocompatibility complex class II region in the Japanese Crested Ibis, Nipponia nippon.
abstract: The major histocompatibility complex (MHC) is a highly polymorphic genomic region that plays a central role in the immune system. Despite its functional consistency, the genomic structure of the MHC differs substantially among organisms. In birds, the MHC-B structures of Galliformes, including chickens, have been well characterized, but information about other avian MHCs remains sparse. The Japanese Crested Ibis (Nipponia nippon, Pelecaniformes) is an internationally conserved, critically threatened species. The current Japanese population of N. nippon originates from only five founders; thus, understanding the genetic diversity among these founders is critical for effective population management. Because of its high polymorphism and importance for disease resistance and other functions, the MHC has been an important focus in the conservation of endangered species. Here, we report the structure and polymorphism of the Japanese Crested Ibis MHC class II region. Screening of genomic libraries allowed the construction of three contigs representing different haplotypes of MHC class II regions. Characterization of genomic clones revealed that the MHC class II genomic structure of N. nippon was largely different from that of chicken. A pair of MHC-IIA and -IIB genes was arranged head-to-head between the COL11A2 and BRD2 genes. Gene order in N. nippon was more similar to that in humans than to that in chicken. The three haplotypes contained one to three copies of MHC-IIA/IIB gene pairs. Genotyping of the MHC class II region detected only three haplotypes among the five founders, suggesting that the genetic diversity of the current Japanese Crested Ibis population is extremely low. The structure of the MHC class II region presented here provides valuable insight for future studies on the evolution of the avian MHC and for conservation of the Japanese Crested Ibis.
authors.affiliation: Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Yukio
authors.initials: Y
authors.lastname: Taniguchi
authors.affiliation: Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Matsumoto
authors.affiliation: Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Matsuda
authors.affiliation: Department of Agrobiology, Faculty of Agriculture, Niigata University, Niigata, Japan.
authors.forename: Takahisa
authors.initials: T
authors.lastname: Yamada
authors.affiliation: Department of Agrobiology, Faculty of Agriculture, Niigata University, Niigata, Japan.
authors.forename: Toshie
authors.initials: T
authors.lastname: Sugiyama
authors.affiliation: Field Center for Sustainable Agriculture and Forestry, Niigata University, Niigata, Japan.
authors.forename: Kosuke
authors.initials: K
authors.lastname: Homma
authors.affiliation: Sado Japanese Crested Ibis Conservation Center, Sado, Japan.
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Kaneko
authors.affiliation: Yamashina Institute for Ornithology, Abiko, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Yamagishi
authors.affiliation: Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Iwaisaki
mesh_terms: D000818:Animals; D001483:Base Sequence; D001717:Birds / Q000235:genetics*; D002645:Chickens / Q000235:genetics; D024161:Collagen Type XI / Q000235:genetics; D020451:Contig Mapping; D056727:Endangered Species; D005091:Exons / Q000235:genetics; D018703:Founder Effect; D005802:Genes, MHC Class II; D014644:Genetic Variation; D015698:Genomic Library; D006239:Haplotypes / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D012150:Polymorphism, Restriction Fragment Length; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D024161:Collagen Type XI