Genetics, Genomics, and Biological Resources in the Medaka, Oryzias latipes
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.
KeywordsSingle Nucleotide Polymorphic Body Color Amplify Fragment Length Polymorphism Female Meiosis Amplify Fragment Length Polymorphism Marker
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.
- Bateson W, Saunders ER (1901) Experimental studies in the physiology of heredity. Report to The Evolution Committee of the Royal Society of London, LondonGoogle Scholar
- 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 177:2457–2467PubMedCrossRefGoogle Scholar
- Ishihara M (1916) On the inheritance of body color of medaka (Medaka no taishoku no iden ni tsuite). Fukuoka Ikadaigaku Zashi 9:259–267Google Scholar
- Ishikawa C (1912) Genshu Kairyo Ron. Suisan Koshujo PublicationGoogle Scholar
- 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) 431:946–957CrossRefGoogle Scholar
- 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) 447:714–719CrossRefGoogle Scholar
- 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 26:121–138PubMedCrossRefGoogle Scholar
- 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 154:1773–1784PubMedGoogle Scholar
- Ojima Y, Hitotsumachi S (1969) The karyotype of the medaka, Oryzias latipes. Chrom Inf Serv 10:15–16Google Scholar
- Schmidt J (1920) Racial investigations. IV. The genetic behavior of a secondary sexual character. C R Lab Trav Carlsberg 14:1–12Google Scholar
- Tomita H (1982) Gene analysis in the medaka (Oryzias latipes). Fish Biol J Medaka 1:7–9Google Scholar
- Tomita H (1985) Study on the mutant of the medaka co and di. Fish Biol J Medaka 3:5–16Google Scholar
- Tomita H (1993) A study on the mutant pectoral-finless, pl, of medaka Oryzias latipes. Fish Biol J Medaka 5:31–32Google Scholar
- Toyama K (1916) Some examples of the Mendelian characters. Nihon Ikushugaku Kaiho 1:1–9Google Scholar
- Yamamoto T (1951) Artificial sex-reversal in the genotypic males of the medaka, Oryzias latipes. Jpn J Genet 26:245Google Scholar