Advertisement

Medaka pp 339-350 | Cite as

Human Population Genetics Meets Medaka

  • Hiroki Oota
  • Hiroshi Mitani

Abstract

A significant feature of Medaka (Oryzias latipes) is its well-known genetic, morphological and physiological diversity. Population studies of medaka have shown that it is a promising candidate for a “vertebrate” model system of population genetics. The study of genome diversity in humans is one of the key postgenome sequencing projects, accomplished by analyzing genetic polymorphisms in human populations, although in most cases little is known as to what functional differences are induced by polymorphisms and what effect they have on human adaptation. We expect that Medaka populations can be a useful model to examine the relationship between allelic functional differences and habitat environment as an analogy of human populations. Herein we review the potential usefulness of Medaka in the study of human population genetics.

Keywords

Inbred Strain Solute Carrier Family Intrapopulation Diversity Substitution Ratio Oryzias Latipes 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Adams SH, Chui C, Schilbach SL, Yu XX, Goddard AD, Grimaldi JC, Lee J, Dowd P, Colman S, Lewin DA (2001) BFIT, a unique acyl-CoA thioesterase induced in thermogenic brown adipose tissue: cloning, organization of the human gene and assessment of a potential link to obesity. Biochem J 360:135–142.PubMedCrossRefGoogle Scholar
  2. Altshuler D, Daly MJ, Lander ES (2008) Genetic mapping in human disease. Science 322:881–888.PubMedCrossRefGoogle Scholar
  3. Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L (2008) Natural selection has driven population differentiation in modern humans. Nat Genet 40:340–345.PubMedCrossRefGoogle Scholar
  4. Bodmer W, Bonilla C (2008) Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40:695–701.PubMedCrossRefGoogle Scholar
  5. Burton PR, Clayton DG, Cardon LR, Craddock N, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand WH, Samani NJ, Todd JA, Donnelly P, Barrett JC, Davison D, Easton D, Evans DM, Leung HT, Marchini JL, Morris AP, Spencer CC, Tobin MD, Attwood AP, Boorman JP, Cant B, Everson U, Hussey JM, Jolley JD, Knight AS, Koch K, Meech E, Nutland S, Prowse CV, Stevens HE, Taylor NC, Walters GR, Walker NM, Watkins NA, Winzer T, Jones RW, McArdle WL, Ring SM, Strachan DP, Pembrey M, Breen G, St Clair D, Caesar S, Gordon-Smith K, Jones L, Fraser C, Green EK, Grozeva D, Hamshere ML, Holmans PA, Jones IR, Kirov G, Moskivina V, Nikolov I, O’Donovan MC, Owen MJ, Collier DA, Elkin A, Farmer A, Williamson R, McGuffin P, Young AH, Ferrier IN, Ball SG, Balmforth AJ, Barrett JH, Bishop TD, Iles MM, Maqbool A, Yuldasheva N, Hall AS, Braund PS, Dixon RJ, Mangino M, Stevens S, Thompson JR, Bredin F, Tremelling M, Parkes M, Drummond H, Lees CW, Nimmo ER, Satsangi J, Fisher SA, Forbes A, Lewis CM, Onnie CM, Prescott NJ, Sanderson J, Matthew CG, Barbour J, Mohiuddin MK, Todhunter CE, Mansfield JC, Ahmad T, Cummings FR, Jewell DP, et al. (2007) Association scan of 14, 500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Nat Genet 39:1329–1337.PubMedCrossRefGoogle Scholar
  6. Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez RD, Civello D, Adams MD, Cargill M, Clark AG (2005) Natural selection on protein-coding genes in the human genome. Nature 437:1153–1157.PubMedCrossRefGoogle Scholar
  7. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203–218.PubMedCrossRefGoogle Scholar
  8. Egami N (1953) Studies on the variation of the number of the anal fin rays in Oryzias latipes. I. Geographical variation in wild populations. (In Japanese, with English abstract). Jpn J Ichthyol 3:87–89.Google Scholar
  9. Egami N (1954) Geographical variation in the male characters of the fish Oryzias latipes. Annot Zool Jpn 27:7–12.Google Scholar
  10. Egami N (1971a) Further notes on the life span of the teleost, Oryzias latipes. Exp Geront 6:379–382.CrossRefGoogle Scholar
  11. Egami N (1971b) The medaka, Oryzias latipes (teleost fish) as a laboratory animal. The ICLA Asian Pacific Meeting of LaboratoryAnimals, Tokyo and Inuyama, 20–25 September, 1971.Google Scholar
  12. Faisst AM, Alvarez-Bolado G, Treichel D, Gruss P (2002) Rotatin is a novel gene required for axial rotation and left-right specification in mouse embryos. Mech Dev 113:15–28.PubMedCrossRefGoogle Scholar
  13. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Sun W, Wang H, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallee C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851–861.PubMedCrossRefGoogle Scholar
  14. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csuros M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222–234.PubMedCrossRefGoogle Scholar
  15. Hancock AM, Witonsky DB, Gordon AS, Eshel G, Pritchard JK, Coop G, Di Rienzo A (2008) Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genet 4:e32.PubMedCrossRefGoogle Scholar
  16. Hirayama M, Mitani H, Watabe S (2006) Temperature-dependent growth rates and gene expression patterns of various medaka Oryzias latipes cell lines derived from different populations. J Comp Physiol [B] 176:311–320.CrossRefGoogle Scholar
  17. Hyodo-Tagichi Y (1996) Inbred strains of the medaka, Oryzias latipes. Fish Biol J Medaka 8:11–14.Google Scholar
  18. Hyodo-Taguchi Y (1980) Establishment of inbred strains of the teleost, Oryzias latipes (in Japanese with English abstract). Zool Mag 89:283–301.Google Scholar
  19. Ishikawa Y, Yoshimoto M, Yamamoto N, Ito H (1999) Different brain morphologies from different genotypes in a single teleost species, the medaka (Oryzias latipes). Brain Behav Evol 53:2–9.PubMedCrossRefGoogle Scholar
  20. 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 S, 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 IT, Takeda H, Morishita S, Kohara Y (2007) The medaka draft genome and insights into vertebrate genome evolution. Nature 447:714–719.PubMedCrossRefGoogle Scholar
  21. Katsumura T, Oda S, Mano S, Suguro N, Watanabe K, Mitani H, Oota H, Kawamura S (2009) Genetic differentiation among local populations of medaka fish (Oryzias latipes) evaluated through grid- and deme-based sampling. Gene 443(1–2):170–177.PubMedCrossRefGoogle Scholar
  22. Kimura T, Shimada A, Sakai N, Mitani H, Naruse K, Takeda H, Inoko H, Tamiya G, Shinya M (2007) Genetic analysis of craniofacial traits in the medaka. Genetics 177:2379–2388.PubMedCrossRefGoogle Scholar
  23. Magtoon W, Nadee N, Higsdhitani T, Takata K, Uwa H (1992) Karyotype evolution and geographical distribution of the Thai-medaka, Oryzias minutillus, in Thailand. J Fish Biol 41:489–497.CrossRefGoogle Scholar
  24. Matsumoto Y, Oota H, Asaoka Y, Nishina H, Watanabe K, Bujnicki JM, Oda S, Kawamura S, Mitani H (2009) Medaka: a promising model animal for comparative population genomics. BMC Res Notes 2:88.PubMedCrossRefGoogle Scholar
  25. Mitani H, Naruse K, Shima A (1989) Eurythermic and stenothermic growth of cultured fish cells and their thermosensitivity. J Cell Sci 93 (Pt 4):731–737.PubMedGoogle Scholar
  26. Miyagawa T, Kawashima M, Nishida N, Ohashi J, Kimura R, Fujimoto A, Shimada M, Morishita S, Shigeta T, Lin L, Hong SC, Faraco J, Shin YK, Jeong JH, Okazaki Y, Tsuji S, Honda M, Honda Y, Mignot E, Tokunaga K (2008) Variant between CPT1B and CHKB associated with susceptibility to narcolepsy. Nat Genet 40:1324–1328.PubMedCrossRefGoogle Scholar
  27. Naruse K, Hori H, Shimizu N, Kohara Y, Takeda H (2004) Medaka genomics: a bridge between mutant phenotype and gene function. Mech Dev 121:619–628.PubMedCrossRefGoogle Scholar
  28. Nelson (1994) Fishes of the world. Wiley, New York.Google Scholar
  29. Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andres AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, Indap A, Bustamante CD, Clark AG (2009) Darwinian and demographic forces affecting human protein coding genes. Genome Res 19:838–849.PubMedCrossRefGoogle Scholar
  30. Oota H, Kitano T, Jin F, Yuasa I, Wang L, Ueda S, Saitou N, Stoneking M (2002) Extreme mtDNA homogeneity in continental Asian populations. Am J Phys Anthropol 118:146–153.PubMedCrossRefGoogle Scholar
  31. Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW, Pritchard JK (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Res 19:826–837.PubMedCrossRefGoogle Scholar
  32. Roberts TR (1998) Systematic observations on tropical Asian medakas or rice fishes of the genus Oryzias, with descriptions of four new species. Ichthyol Res 45:213–224.CrossRefGoogle Scholar
  33. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES (2006) Positive natural selection in the human lineage. Science 312:1614–1620.PubMedCrossRefGoogle Scholar
  34. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Sun W, Wang H, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallee C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, ­Taillon-Miller P, Xiao M, Tsui LC, et al. (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913–918.PubMedCrossRefGoogle Scholar
  35. Sakaizumi M (1986) Genetic-divergence in wild populations of medaka, Oryzias latipes (Pisces, Oryziatidae) from Japan and China. Genetica 69:119–125.CrossRefGoogle Scholar
  36. Sakaizumi M, Joen S (1987) Two divergent groups in the wild populations of medaka Oryzias latipes (Pisces: Oryziatidae) in Korea. Korean J Limnol 20:13–20.Google Scholar
  37. Sakaizumi M, Moriwaki K, Egami N (1983) Allozymic variation and regional differentiation in wild populations of the fish Oryzias latipes. Copeia 2:311–318.CrossRefGoogle Scholar
  38. Sakaizumi M, Suzuki H, Sakaizumi M, Suzuki H, Moriwaki K, Kominami R, Muramastu M (1984). Geographic variation of ribosomal-RNA gene structure in wild populations of the medaka Oryzias latipes. Jpn J Genet 59(6):651–651.Google Scholar
  39. Shima A, Mitani H (2004) Medaka as a research organism: past, present and future. Mech Dev 121:599–604.PubMedCrossRefGoogle Scholar
  40. Shima A, Shimada A, Komura J, Isa K, Naruse K, Sakaizumi M, Egami N (1985) The preservation and utilization of wild populations of the medaka, Oryzias latipes. Medaka 3:1–4.Google Scholar
  41. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450:219–232.PubMedCrossRefGoogle Scholar
  42. 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.PubMedCrossRefGoogle Scholar
  43. Tamura K, Subramanian S, Kumar S (2004) Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21:36–44.PubMedCrossRefGoogle Scholar
  44. The Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69–87.CrossRefGoogle Scholar
  45. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437:1299–1320.CrossRefGoogle Scholar
  46. Wittbrodt J, Shima A, Schartl M (2002) Medaka—a model organism from the far east. Nat Rev Genet 3:53–64.PubMedCrossRefGoogle Scholar
  47. Yamahira K, Nishida T (2009) Latitudinal variation in axial patterning of the medaka (Actinopterygii: Adrianichthyidae): Jordan’s rule is substantiated by genetic variation in abdominal vertebral number. Biol J Linnean Society 96:856–866.CrossRefGoogle Scholar
  48. Yamahira K, Nishida T, Arakawa A, Iwasaki H (2009) Heritability and genetic correlation of abdominal versus caudal vertebral number in the medaka (Actinopterygii: Adrianichthyidae): genetic constraints on evolution of axial patterning? Biol J Linnean Society 96:867–874.CrossRefGoogle Scholar
  49. Yamahira K, Takeshi K (2008) Variation in juvenile growth rates among and within latitudinal populations of the medaka. Populat Ecol 50:3–8.CrossRefGoogle Scholar
  50. Young JH, Chang YP, Kim JD, Chretien JP, Klag MJ, Levine MA, Ruff CB, Wang NY, Chakravarti A (2005) Differential susceptibility to hypertension is due to selection during the out-of-Africa expansion. PLoS Genet 1:e82.PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2010

Authors and Affiliations

  1. 1.Department of Integrated Biosciences, Graduate School of Frontier ScienceThe University of TokyoKashiwaJapan
  2. 2.Department of AnatomyKitasato University School of MedicineSagamiharaJapan

Personalised recommendations