Abstract
Oryzias latipes, also known as the medaka or Japanese killifish, has long been considered one of the most powerful animal models in the field of genetics. The Japanese researchers Toyama and Ishikawa confirmed the Mendelian law of inheritance in medaka in 1910, one of the earliest and most prominent achievements in vertebrate genetics. Medaka Y-linked inheritance was subsequently reported in 1921 by Aida, representing the first report of this phenomenon in animals. Yamamoto established the first sex linkage map for medaka and described the differences in recombination frequency between sexes. He also reported for the first time, autosomal linkage between the i and ci loci in fish. Following the development of PCR technology, several attempts were made to construct a genome-wide genetic linkage map in medaka, zebrafish, pufferfish, and other fish species. In the initial stages of these experiments, fingerprint-type markers were used as they did not require any prior genome knowledge. In the later phases, single-locus type markers that amplify specific regions of the genome in the presence of sequence information were used. The map generated using the single-locus type markers enabled researchers to compare the linkage relationships between orthologous genes. The teleosts underwent specific whole genome duplication (third WGD). Finally, the medaka genome sequencing project, in addition to the Tetraodon genome project, provided a high-quality draft genome sequence for both medaka and Tetraodon. These data confirmed the third WGD, allowed the successful reconstruction of the preduplicated proto-chromosomes, and described a potential scenario that all led to the generation of the present medaka, Tetraodon, and zebrafish genomes. This analysis also identified the highly conserved synteny of the orthologous genes present in the teleost fishes.
Over the past 100 years of medaka research, numerous important biological resources have been developed. The first resource included the body color mutants such as the orange-red and white medaka. The d-rR strain was the first of these strains to be established and served the specific purpose of linking genetic sex with body color. To date, more than 600 mutants have been reported. In terms of genetic resources, more than 3,000 primer sequences that specifically amplify medaka genomic regions and medaka genome sequences are now widely available via genome browsers. The bacterial artificial chromosome (BAC) and Fosmid clones cover the vast majority of the medaka genome, and 355,000 full-length cDNA clones and expressed sequence tags (ESTs) are also now available. Importantly, most of these resources are publicly available through the National BioResource Project Medaka.
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References
Aida T (1921) On the inheritance of color in a freshwater fish, Aplocheilus latipes Temminck and Schlegel, with special reference to sex-linked inheritance. Genetics 6:554–573
Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang YL, Westerfield M, Ekker M, Postlethwait JH (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282:1711–1714
Bateson W, Saunders ER (1901) Experimental studies in the physiology of heredity. Report to The Evolution Committee of the Royal Society of London, London
Bouza C, Hermida M, Pardo BG, Fernandez C, Fortes GG, Castro J, Sanchez L, Presa P, Perez M, Sanjuan A, de Carlos A, Alvarez-Dios JA, Ezcurra S, Cal RM, Piferrer F, Martinez P (2007) A microsatellite genetic map of the turbot (Scophthalmus maximus). Genetics 177:2457–2467
Castle WE, Allen GM (1903) The heredity of albinism. Proc Am Acad Arts Sci 38:603–622
Fukamachi S, Shimada A, Shima A (2001) Mutations in the gene encoding B, a novel transporter protein, reduce melanin content in medaka. Nat Genet 28:381–385
Fukamachi S, Asakawa S, Wakamatsu Y, Shimizu N, Mitani H, Shima A (2004a) Conserved function of medaka pink-eyed dilution in melanin synthesis and its divergent transcriptional regulation in gonads among vertebrates. Genetics 168:1519–1527
Fukamachi S, Sugimoto M, Mitani H, Shima A (2004b) Somatolactin selectively regulates proliferation and morphogenesis of neural-crest derived pigment cells in medaka. Proc Natl Acad Sci USA 101:10661–10666
Hashimoto S, Suzuki Y, Kasai Y, Morohoshi K, Yamada T, Sese J, Morishita S, Sugano S, Matsushima K (2004) 5′-end SAGE for the analysis of transcriptional start sites. Nat Biotechnol 22:1146–1149
Ishihara M (1916) On the inheritance of body color of medaka (Medaka no taishoku no iden ni tsuite). Fukuoka Ikadaigaku Zashi 9:259–267
Ishikawa C (1912) Genshu Kairyo Ron. Suisan Koshujo Publication
Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard R, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, de Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Crollius HR (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (Lond) 431:946–957
Kai W, Kikuchi K, Fujita M, Suetake H, Fujiwara A, Yoshiura Y, Ototake M, Venkatesh B, Miyaki K, Suzuki Y (2005) A genetic linkage map for the tiger pufferfish, Takifugu rubripes. Genetics 171:227–238
Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Kasai Y, Jindo T, Kobayashi D, Shimada A, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto SI, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Morishita S, Kohara Y (2007) The medaka draft genome and insights into vertebrate genome evolution. Nature (Lond) 447:714–719
Kimura T, Jindo T, Narita T, Naruse K, Kobayashi D, Shin-I T, Kitagawa T, Sakaguchi T, Mitani H, Shima A, Kohara Y, Takeda H (2004) Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics. Mech Dev 121:915–932
Kimura T, Yoshida K, Shimada A, Jindo T, Sakaizumi M, Mitani H, Naruse K, Takeda H, Inoko H, Tamiya G, Shinya M (2005) Genetic linkage map of medaka with polymerase chain reaction length polymorphisms. Gene (Amst) 363:24–31
Koga A, Inagaki H, Bessho Y, Hori H (1995) Insertion of a novel transposable element in the tyrosinase gene is responsible for an albino mutation in the medaka fish, Oryzias latipes. Mol Gen Genet 249:400–405
Koga A, Suzuki M, Inagaki H, Bessho Y, Hori H (1996) Transposable element in fish. Nature (Lond) 383:30
Kondo M, Nagao E, Mitani H, Shima A (2001a) Differences in recombination frequencies during female and male meioses of the sex chromosomes of the medaka, Oryzias latipes. Genet Res 78:23–30
Kondo S, Kuwahara Y, Kondo M, Naruse K, Mitani H, Wakamatsu Y, Ozato K, Asakawa S, Shimizu N, Shima A (2001b) The medaka rs-3 locus required for scale development encodes ectodysplasin-A receptor. Curr Biol 11:1202–1206
Maruyama K, Sugano S (1994) Oligo-capping: a simple method to replace the cap structure of eukaryotic messenger-RNAs with oligoribonucleotides. Gene (Amst) 138:171–174
Matsuda M, Nagahama Y, Shinomiya A, Sato T, Matsuda C, Kobayashi T, Morrey CE, Shibata N, Asakawa S, Shimizu N, Hori H, Hamaguchi S, Sakaizumi M (2002) DMY is a Y-specific DM-domain gene required for male development in the medaka fish. Nature (Lond) 417:559–563
Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, Shirai SM, Nishida M (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 26:121–138
Morgan TH (1910) Sex limited inheritance in Drosophila. Science 22:120–122
Murphy WJ, Eizirik E, O’Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS (2001) Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348–2351
Nakamura S, Saito D, Tanaka M (2008) Generation of transgenic medaka using modified bacterial artificial chromosome. Dev Growth Differ 50:415–419
Nanda I, Kondo M, Hornung U, Asakawa S, Winkler C, Shimizu A, Shan Z, Haaf T, Shimizu N, Shima A, Schmid M, Schartl M (2002) A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes. Proc Natl Acad Sci USA 99:11778–11783
Naruse K, Fukamachi S, Mitani H, Kondo M, Matsuoka T, Kondo S, Hanamura N, Morita Y, Hasegawa K, Nishigaki R, Shimada A, Wada H, Kusakabe T, Suzuki N, Kinoshita M, Kanamori A, Terado T, Kimura H, Nonaka M, Shima A (2000) A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. Genetics 154:1773–1784
Naruse K, Hori H, Shimizu N, Kohara Y, Takeda H (2004a) Medaka genomics: a bridge between mutant phenotype and gene function. Mech Dev 121:619–628
Naruse K, Tanaka M, Mita K, Shima A, Postlethwait J, Mitani H (2004b) A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res 14:820–828
Ohtsuka M, Makino S, Yoda K, Wada H, Naruse K, Mitani H, Shima A, Ozato K, Kimura M, Inoko H (1999) Construction of a linkage map of the medaka (Oryzias latipes) and mapping of the Da mutant locus defective in dorsoventral patterning. Genome Res 9:1277–1287
Ojima Y, Hitotsumachi S (1969) The karyotype of the medaka, Oryzias latipes. Chrom Inf Serv 10:15–16
Rexroad CE, Palti Y, Gahr SA, Vallejo RL (2008) A second generation genetic map for rainbow trout (Oncorhynchus mykiss). BMC Genet 9:74
Schmidt J (1920) Racial investigations. IV. The genetic behavior of a secondary sexual character. C R Lab Trav Carlsberg 14:1–12
Takehana Y, Nagai N, Matsuda M, Tsuchiya K, Sakaizumi M (2003) Geographic variation and diversity of the cytochrome b gene in Japanese wild populations of medaka, Oryzias latipes. Zool Sci 20:1279–1291
Tomita H (1982) Gene analysis in the medaka (Oryzias latipes). Fish Biol J Medaka 1:7–9
Tomita H (1985) Study on the mutant of the medaka co and di. Fish Biol J Medaka 3:5–16
Tomita H (1993) A study on the mutant pectoral-finless, pl, of medaka Oryzias latipes. Fish Biol J Medaka 5:31–32
Toyama K (1916) Some examples of the Mendelian characters. Nihon Ikushugaku Kaiho 1:1–9
Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA-fingerprinting. Nucleic Acids Res 23:4407–4414
Wada H, Naruse K, Shimada A, Shima A (1995) Genetic-linkage map of a fish, the Japanese medaka Oryzias latipes. Mol Mar Biol Biotechnol 4:269–274
Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218
Winge O (1922) One-sided masculine and sex-linked inheritance in Lebistes reticulatus. J Genet 12:145–162
Yamamoto T (1951) Artificial sex-reversal in the genotypic males of the medaka, Oryzias latipes. Jpn J Genet 26:245
Yamamoto T (1953) Artificially induced sex-reversal in genotypic males of the medaka (Oryzias latipes). J Exp Zool 123:571–594
Yamamoto T (1958) Artificial induction of functional sex-reversal in genotypic females of the medaka (Oryzias latipes). J Exp Zool 137:227–264
Yamamoto T (1964) Linkage map of sex chromosomes in the medaka, Oryzias latipes. Genetics 50:59–64
Yamamoto T, Oikawa T (1973) Linkage between albino (i) and color interfere (ci) in the medaka Oryzias latipes. Jpn J Genet 48:315–329
Yamanoue Y, Miya M, Matsuura K, Yagishita N, Mabuchi K, Sakai H, Katoh M, Nishida M (2007) Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences. Mol Phylogenet Evol 45:89–101
Acknowledgments
I thank Dr. Kawasaki for sending me the interesting papers of Bateson and Castle and discussion on earlier work on Mendelism. I also thank Drs. Yoshizaki, Shimada, Okubo, and Yoshikuni for sending me the interesting papers on the study of Mendelism published by Japanese researchers in the early 20th century. I express my great thanks to all members of the medaka genome sequencing project and especially to Drs. Takeda, Morishita, and Kohara for their excellent leadership of the medaka genome project. The medaka genome project was supported by a Grant-in-Aid for Scientific Research on Priority Area “Genome” from the Ministry of Education, Culture, Sports, Science and Technology Japan (MEXT) and Japan Science and Technology Corporation (JST). NBRP Medaka is supported by MEXT, Japan.
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Naruse, K. (2011). Genetics, Genomics, and Biological Resources in the Medaka, Oryzias latipes . In: Naruse, K., Tanaka, M., Takeda, H. (eds) Medaka. Springer, Tokyo. https://doi.org/10.1007/978-4-431-92691-7_2
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DOI: https://doi.org/10.1007/978-4-431-92691-7_2
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