Current status of medaka genetics and genomics. The Medaka Genome Initiative (MGI).

Publisher Summary This chapter focuses on the current status of medaka genetics and genomics. The egg-laying killifish medaka, Oryzias latipes, is an old (100 years) and well-established genetic model system for developmental genetics and many other areas of biological and environmental research. Genetics in medaka offers several advantages; for example, the availability of divergent, completely inbred strains and a genome of only 800 Mb, less than half the size of the zebrafish genome. Also, as a practical aspect, the sexes are easily distinguished in medaka, in contrast to zebrafish, facilitating breeding in general and genetic studies in particular. Like zebrafish, medaka is suitable for forward genetics based on chemically induced mutations and might even be advantageous in certain aspects. The medaka genome is less than half the size of the zebrafish genome and is highly polymorphic in nucleotide sequences without large-scale rearrangements. Although the comparison of all mutant phenotypes in medaka and zebrafish is not possible, it is clear that many mutants in medaka display phenotypes previously undescribed in zebrafish. Transposable elements are a major source of mutations. Large-scale medaka expressed sequence tag (EST) analysis and gene mapping are essential for positional cloning of the genes responsible for mutants and the genomewide comparison of linkage relationships among vertebrate species. The development of bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) cloning systems has revolutionized genome analysis in vertebrates. Chromosome analysis of medaka started long before the emergence of mammalian cytogenetics.

[1]  M. Carl,et al.  Mutations affecting liver development and function in Medaka, Oryzias latipes, screened by multiple criteria , 2004, Mechanisms of Development.

[2]  M. Schartl,et al.  Genomic organization and expression of the doublesex-related gene cluster in vertebrates and detection of putative regulatory regions for DMRT1. , 2001, Genomics.

[3]  G. McVean,et al.  Evidence for Selective Advantage of Pathogenic FGFR2 Mutations in the Male Germ Line , 2003, Science.

[4]  V. Korzh,et al.  Fish development and genetics : the zebrafish and medaka models , 2004 .

[5]  Thorsten Henrich,et al.  MEPD: a Medaka gene expression pattern database , 2003, Nucleic Acids Res..

[6]  A. Shimada,et al.  The Japanese medaka, Oryzias latipes, as a new model organism for studying environmental germ-cell mutagenesis. , 1994, Environmental health perspectives.

[7]  M. Schartl,et al.  Common spontaneous sex-reversed XX males of the medaka Oryzias latipes. , 2003, Genetics.

[8]  T. Henrich,et al.  Mutations affecting the formation of posterior lateral line system in Medaka, Oryzias latipes , 2004, Mechanisms of Development.

[9]  H. Baier,et al.  Loss of eyes in zebrafish caused by mutation of chokh/rx3 , 2003, EMBO reports.

[10]  M. Kinoshita,et al.  The see-through medaka: A fish model that is transparent throughout life , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Thorsten Henrich,et al.  A systematic genome-wide screen for mutations affecting organogenesis in Medaka, Oryzias latipes , 2004, Mechanisms of Development.

[12]  J. Volff,et al.  Molecular cloning and characterization of DMRT genes from the medaka Oryzias latipes and the platyfish Xiphophorus maculatus. , 2002, Gene.

[13]  H. Baier,et al.  A radiation hybrid map of the zebrafish genome , 1999, Nature Genetics.

[14]  N. Shimizu,et al.  The medaka rs-3 locus required for scale development encodes ectodysplasin-A receptor , 2001, Current Biology.

[15]  T. Henrich,et al.  Transposon-mediated enhancer trapping in medaka. , 2003, Gene.

[16]  Y. Wakamatsu,et al.  Establishment of a pluripotent cell line derived from a medaka (Oryzias latipes) blastula embryo. , 1994, Molecular marine biology and biotechnology.

[17]  T. Todo,et al.  Identification of radiation-sensitive mutants in the Medaka, Oryzias latipes , 2004, Mechanisms of Development.

[18]  M. Kinoshita,et al.  Fertile and diploid nuclear transplants derived from embryonic cells of a small laboratory fish, medaka (Oryzias latipes). , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Y. Yan,et al.  Zebrafish comparative genomics and the origins of vertebrate chromosomes. , 2000, Genome research.

[20]  Akihiro Shima,et al.  A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. , 2004, Genome research.

[21]  Thorsten Henrich,et al.  A genetic screen for mutations affecting embryonic development in medaka fish (Oryzias latipes) , 2000, Mechanisms of Development.

[22]  N. Shimizu,et al.  Nucleotide sequence of the MHC class I genomic region of a teleost, the medaka (Oryzias latipes) , 2002, Immunogenetics.

[23]  A. Shimada,et al.  Evidence for recent invasion of the medaka fish genome by the Tol2 transposable element. , 2000, Genetics.

[24]  N. Shimizu,et al.  A novel third gonadotropin-releasing hormone receptor in the medaka Oryzias latipes: evolutionary and functional implications. , 2003, Gene.

[25]  A. Shimada,et al.  The Medaka as a Model for Studying Germ-Cell Mutagenesis and Genomic Instability , 2001, Marine Biotechnology.

[26]  A. Iida,et al.  The medaka fish Tol2 transposable element can undergo excision in human and mouse cells , 2003, Journal of Human Genetics.

[27]  H. Hori,et al.  Transposable Elements in Medaka Fish , 2002, Zoological science.

[28]  M. Hagmann,et al.  Homologous Recombination and DNA-End Joining Reactions in Zygotes and Early Embryos of Zebrafish (Danio rerio) and Drosophila melanogaster , 1998, Biological chemistry.

[29]  Shuichi Asakawa,et al.  DMY is a Y-specific DM-domain gene required for male development in the medaka fish , 2002, Nature.

[30]  M. Schartl,et al.  A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[31]  M. Westerfield,et al.  GSD: a genetic screen database , 2004, Mechanisms of Development.

[32]  Gen Tamiya,et al.  Complete sequence and gene map of a human major histocompatibility complex , 1999 .

[33]  Yunhan Hong,et al.  Efficiency of cell culture derivation from blastula embryos and of chimera formation in the medaka (Oryzias latipes) depends on donor genotype and passage number , 1998, Development Genes and Evolution.

[34]  T. Henrich,et al.  Mutations affecting retinotectal axonal pathfinding in Medaka, Oryzias latipes , 2004, Mechanisms of Development.

[35]  M. Brilliant,et al.  Mutations in the human orthologue of the mouse underwhite gene (uw) underlie a new form of oculocutaneous albinism, OCA4. , 2001, American journal of human genetics.

[36]  T. Iwamatsu.  Stages of normal development in the medaka Oryzias latipes , 1994, Mechanisms of Development.

[37]  Yunhan Hong,et al.  An ES-like cell line from the marine fish Sparus aurata: Characterization and chimaera production , 2002, Transgenic Research.

[38]  A. Meyer,et al.  Genome duplication, a trait shared by 22000 species of ray-finned fish. , 2003, Genome research.

[39]  T. Henrich,et al.  Mutations affecting gonadal development in Medaka, Oryzias latipes , 2004, Mechanisms of Development.

[40]  H. Gutzeit,et al.  Primary culture of medaka (Oryzias latipes) testis: a test system for the analysis of cell proliferation and differentiation , 2003, Cell and Tissue Research.

[41]  M. Schartl,et al.  Absence of the Candidate Male Sex-Determining Gene dmrt1b(Y) of Medaka from Other Fish Species , 2003, Current Biology.

[42]  T. Henrich,et al.  Mutations affecting early distribution of primordial germ cells in Medaka (Oryzias latipes) embryo , 2004, Mechanisms of Development.

[43]  Y. Kuwahara,et al.  γ‐Ray exposure accelerates spermatogenesis of medaka fish, Oryzias latipes , 2003 .

[44]  Yunhan Hong,et al.  Activation of the mouse Oct4 promoter in medaka embryonic stem cells and its use for ablation of spontaneous differentiation , 2004, Mechanisms of Development.

[45]  M. Carl,et al.  Mutations affecting retina development in Medaka , 2004, Mechanisms of Development.

[46]  O. Ohara,et al.  Mutations affecting thymus organogenesis in Medaka, Oryzias latipes , 2004, Mechanisms of Development.

[47]  A. Bradley,et al.  Formation of germ-line chimaeras from embryo-derived teratocarcinoma cell lines , 1984, Nature.

[48]  L. Joly,et al.  The LN54 radiation hybrid map of zebrafish expressed sequences. , 2001, Genome research.

[49]  R. Plasterk,et al.  Molecular Reconstruction of Sleeping Beauty , a Tc1-like Transposon from Fish, and Its Transposition in Human Cells , 1997, Cell.

[50]  M. Flajnik,et al.  Molecular Cloning of C4 Gene and Identification of the Class III Complement Region in the Shark MHC 1 , 2003, The Journal of Immunology.

[51]  Thorsten Henrich,et al.  Large-scale expression screening by automated whole-mount in situ hybridization , 2004, Mechanisms of Development.

[52]  N. Kuroda,et al.  Molecular cloning and linkage analysis of complement C3 and C4 genes of the Japanese medaka fish , 2000, Immunogenetics.

[53]  Tadashi Sato,et al.  Oryzias curvinotus Has DMY, a Gene That Is Required for Male Development in the Medaka, O. latipes , 2003, Zoological science.

[54]  A. Shimada,et al.  Development of a possible nonmammalian test system for radiation-induced germ-cell mutagenesis using a fish, the Japanese medaka (Oryzias latipes). , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Y. Ishikawa,et al.  Medakafish as a model system for vertebrate developmental genetics. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[56]  M. Kondo,et al.  A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. , 2000, Genetics.

[57]  M. Flajnik,et al.  Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system. , 2001, Immunity.

[58]  J. Klein,et al.  Linkage Relationships of Genes Coding for α2‐Macroglobulin, C3 and C4 in the Zebrafish: Implications for the Evolution of the Complement and Mhc Systems , 2002, Scandinavian journal of immunology.

[59]  H. Mitani,et al.  Four functionally distinct C-type natriuretic peptides found in fish reveal evolutionary history of the natriuretic peptide system , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Y L Wang,et al.  Zebrafish hox clusters and vertebrate genome evolution. , 1998, Science.

[61]  H. Himmelbauer,et al.  A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing , 2004, Mechanisms of Development.

[62]  Yunhan Hong,et al.  Pluripotency and differentiation of embryonic stem cell lines from the medakafish (Oryzias latipes) , 1996, Mechanisms of Development.

[63]  H. Hori,et al.  Homogeneity in the structure of the medaka fish transposable element Tol2. , 1999, Genetical research.

[64]  N. Shimizu,et al.  Human BAC library: construction and rapid screening. , 1997, Gene.

[65]  H. Hori,et al.  Gene Transfer and Cloning of Flanking Chromosomal Regions Using the Medaka Fish Tol2 Transposable Element , 2002, Marine Biotechnology.

[66]  Yunhan Hong,et al.  Mitf expression is sufficient to direct differentiation of medaka blastula derived stem cells to melanocytes , 2003, Development.

[67]  Songlin Chen,et al.  Derivation of a pluripotent embryonic cell line from red sea bream blastulas , 2003 .

[68]  H. B. Goodrich.  A study of the development of mendelian characters in Oryzias latipes , 1927 .

[69]  D A Kane,et al.  The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. , 1996, Development.

[70]  M. Schartl,et al.  Production of medakafish chimeras from a stable embryonic stem cell line. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[71]  M. Kinoshita,et al.  Establishment of medaka (Oryzias latipes) transgenic lines with the expression of green fluorescent protein fluorescence exclusively in germ cells: A useful model to monitor germ cells in a live vertebrate , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[72]  A. Shimada,et al.  Genetic linkage map of a fish, the Japanese medaka Oryzias latipes. , 1995, Molecular marine biology and biotechnology.

[73]  A. Shimada,et al.  Mutations in the gene encoding B, a novel transporter protein, reduce melanin content in medaka , 2001, Nature Genetics.

[74]  Yunhan Hong,et al.  Establishment of a normal medakafish spermatogonial cell line capable of sperm production in vitro. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[75]  Y. Kuwahara,et al.  A Critical Stage in Spermatogenesis for Radiation-Induced Cell Death in the Medaka Fish, Oryzias latipes , 2002, Radiation research.

[76]  Monte Westerfield,et al.  The Zebrafish Information Network: the zebrafish model organism database , 2005, Nucleic Acids Res..

[77]  S. Taourit,et al.  A mutation in the MATP gene causes the cream coat colour in the horse , 2003, Genetics Selection Evolution.

[78]  A. Schier,et al.  Efficient recovery of ENU-induced mutations from the zebrafish germline. , 1994, Genetics.

[79]  N. Shimizu,et al.  Construction of a BAC library derived from the inbred Hd-rR strain of the teleost fish, Oryzias latipes. , 2001, Genes & genetic systems.

[80]  J. Wittbrodt,et al.  An in situ hybridization screen for the rapid isolation of differentially expressed genes , 2000, Development Genes and Evolution.

[81]  K. Kawakami,et al.  Identification of a functional transposase of the Tol2 element, an Ac-like element from the Japanese medaka fish, and its transposition in the zebrafish germ lineage. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[82]  M. Schartl,et al.  Medaka — a model organism from the far east , 2002, Nature Reviews Genetics.

[83]  R. M. Krol,et al.  Use of the Japanese Medaka (Oryzias latipes) and Guppy (Poecilia reticulata) in Carcinogenesis Testing Under National Toxicology Program Protocols , 2003, Toxicologic pathology.

[84]  M. Carl,et al.  Mutations affecting somite formation in the Medaka (Oryzias latipes) , 2004, Mechanisms of Development.

[85]  A. Schier,et al.  A genetic screen for mutations affecting embryogenesis in zebrafish. , 1996, Development.

[86]  M. Carl,et al.  Genetic dissection of the formation of the forebrain in Medaka, Oryzias latipes , 2004, Mechanisms of Development.

[87]  K. Okazaki,et al.  Strain difference in establishment of mouse embryonic stem (ES) cell lines. , 1994, The International journal of developmental biology.