Skip to main content
Log in

Development of a single-copy nuclear DNA sequence marker for the detection of artificially caused genetic introgressions in Japanese wild medaka populations

  • Methods and Resources Article
  • Published:
Conservation Genetics Resources Aims and scope Submit manuscript

Abstract

Medaka (comprising two species Oryzias latipes and Oryzias sakaizumii) is a small freshwater fish that is globally used as an experimental model organism. Wild Japanese medaka populations have been declining and their genetic diversity has been affected by extensive artificial introduction of non-native populations and ‘himedaka’, an orange-red variety derived from O. latipes, which is a commercially popular in Japan. To detect artificially caused genetic introgression in wild medaka populations, we developed a novel and effective nuclear markers. Sequencing analysis of a single-copy nuclear DNA (scnDNA) belonging to linkage group 21 (LG21b) was performed to identify specific haplotype in O. sakaizumii, nine genetically localized groups of O. latipes, and himedaka populations. A total of 28 haplotypes were identified from the 16 tested wild populations. Of the 28 haplotypes, 27 were considered specific to O. sakaizumii and to each genetically localized group of O. latipes; thus, these haplotypes could be used as diagnostic markers to detect artificially caused genetic introgression. Eight haplotypes were confirmed in himedaka, and four were considered specific to himedaka. Our tests involved direct sequencing of the 3′-sequence of the LG21b region as a diagnostic marker, which effectively detected artificially caused genetic introgression in wild populations. Analysis of the actual level of genetic introgression will be improved by incorporating the new scnDNA marker in combination with conventional DNA markers of medaka.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Allendorf FW, Leary RF, Spruell P, Wenburg JK (2001) The problems with hybrids: setting conservation guidelines. Trends Ecol Evol 16:613–622

    Article  Google Scholar 

  • Annett B, Gerlach G, King TL, Whiteley AR (2012) Conservation genetics of remnant coastal brook trout populations at the southern limit of their distribution: population structure and effects of stocking. Trans Am Fish Soc 141:1399–1410

    Article  Google Scholar 

  • Asai T, Senou H, Hosoya K (2011) Oryzias sakaizumii, a new ricefish from northern Japan (Teleostei: Adrianichthydae). Ichthyol Explor Freshw 22:289–299

    Google Scholar 

  • Brito P, Edwards SV (2009) Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135:439–455

    Article  Google Scholar 

  • Estoup A, Largiader CR, Cornuet J-M, Gharbi K, Presa P, Guyomard R (2000) Juxtaposed microsatellite systems as diagnostic markers for admixture: an empirical evaluation with brown trout (Salmo trutta) as model organism. Mol Ecol 9:1873–1886

    Article  CAS  Google Scholar 

  • Frankham R, Ballow JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Fukamachi S, Shimada A, Shima A (2001) Mutation in the gene encoding B, a novel transporter protein, reduce melanin contend in medaka. Nat Genet 28:381–385

    Article  CAS  Google Scholar 

  • Hirai N, Torii Y, Matsuoka H, Ishii M (2017) Genetic diversity and intrusion of alien populations of Oryzias latipes in Osaka Prefecture, central Japan. Jpn J Environ Entomol Zool 28:47–54

    Google Scholar 

  • Hosoya K (2000) The circumstances and protection in Japanese ricefish, “Medaka”. J Jpn Soc Water Env 23:135–139

    Google Scholar 

  • Iguchi Y, Nakao R, Takata K, Kitagawa T (2017) Re-examination of the native mitotype within wild populations of Japanese medaka (Oryzias latipes) in the Kanto region, Japan. Jpn J Ichthyol 64:11–18

    Google Scholar 

  • Iguchi Y, Kume K, Kitagawa T (2018) Natural hybridization between two Japanese medaka species (Oryzias latipes and Oryzias sakaizumii) observed in the Yura River basin, Kyoto, Japan. Ichthyol Res 64:116–119

    Google Scholar 

  • Kasahara M et al (2007) The medaka draft genome and insights into vertebrate genome evolution. Nature 447:714–719

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • King TL, Lubinski BA, Burnham-Curtis MK, Stott W, Morgan RP II (2012) Tools for the management and conservation of genetic diversity in brook trout (Salvelinus fontinalis): tri- and tetranucleotide microsatellite markers for the assessment of genetic diversity, phylogeography, and historical demographics. Conserv Genet Resour 4:539–543

    Article  Google Scholar 

  • Koyama N, Kitagawa T (2009) Mitochondrial DNA originating from the orange-red type commercial varieties of Oryzias latipes (himedaka) detected in wild populations inhabiting the Yamato River System, Nara Prefecture. Jpn J Ichthyol 56:153–157

    Google Scholar 

  • Koyama N, Mori T, Nakai K, Kitagawa T (2011) Genetic composition of commercial strains of Oryzias latipes revealed by mtDNA analysis. Jpn J Icthyol 58:81–86

    Google Scholar 

  • Ministry of the Environment Government of Japan (2018) Red list 2018, Ministry of the Environment. http://www.env.go.jp/index.html. Accessed 1 Sept 2018

  • Moore WS (1995) Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49:718–726

    PubMed  Google Scholar 

  • Moritz C (1994) Defining ‘evolutionarily significant units’ for conservation. Trends Ecol Evol 9:373–375

    Article  CAS  Google Scholar 

  • Nakai K, Nakao R, Fukamachi S, Koyama N, Kitagawa T (2011) Genetic analysis of Medaka (Oryzias latipes) populations in the Yamato River, Nara prefecture, Japan: detection of the b allele responsible for the himedaka phenotype. Jpn J Ichthyol 58:189–193

    Google Scholar 

  • Nakao R, Kitagawa T (2015) Differences in the behavior and ecology of wild type medaka (Oryzias latipes complex) and an orange commercial variety (himedaka). J Exp Zool 323:349–358

    Article  Google Scholar 

  • Nakao R, Iguchi Y, Koyama N, Nakai K, Kitagawa T (2017) Current status of genetic disturbances in wild medaka populations (Oryzias latipes species complex) in Japan. Ichthyol Res 64:116–119

    Article  Google Scholar 

  • Naruse K, Tanaka M, Takeda H (2014) A model for organogenesis, human disease, and evolution. Springer, Berlin

    Google Scholar 

  • Sakaizumi M (1990) Intraspecific variation of Japanese medaka from genetic analyses. In: Egami N, Yamafami K, Shima A (eds) Biology of medaka. Tokyo Univ. Press, Tokyo, pp 143–161

    Google Scholar 

  • Schultheis AS, Davis N, Page JT, Fenwick AM, Bond JE, Shiozawa DK (2014) Comparative transcriptomics allows for rapid development of population-level nuclear markers in Hesperoperla pacifica (Plecoptera: Perlidae). Freshw Sci 33:364–373

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  Google Scholar 

  • Yamamoto T (1975) Medaka (killfish): biology and strains. Keigaku Publishing, Tokyo

    Google Scholar 

  • Yokota H, Kuwahara N, Nakano E, Eguchi S (2014) Genotype distribution in wild populations medaka inhabiting the Muko river system and the actual state of genetic introgression from the demonstrated orange-red fish (hi-medaka). Bull Kansai Org Nat Cons 36:53–58

    Google Scholar 

  • Zhang DX, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol 12:563–584

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We sincerely thank Dr. M. Kobayashi (ICU), Dr. M. Fukui (KESC), Dr. M. Maegata (KU), Dr. A. Munakata (MDU), Mr. T. Hagiwara (GEF), and other colleagues for helping with specimen collection. The samples in Yakushima Island were provided by Y. Kano (DSKU) under a fund “Development of mitigation and adaptation technologies to climate change in the sectors of agriculture, forestry, and fisheries” by the Ministry of Agriculture, Forestry and Fisheries, Japan. We are grateful to Dr. K. Hosoya, Dr. D. Hayasaka, Dr. M. Mori, Dr. T. Ito, and other members of our laboratory for their useful advice and helping with specimen sampling and fieldwork. We would like to thank Editage (www.editage.jp) for English language editing. This study complies with the current laws of Japan.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Tadao Kitagawa.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Iguchi, Y., Nakao, R., Takata, K. et al. Development of a single-copy nuclear DNA sequence marker for the detection of artificially caused genetic introgressions in Japanese wild medaka populations. Conservation Genet Resour 12, 311–317 (2020). https://doi.org/10.1007/s12686-019-01106-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12686-019-01106-x

Keywords

Navigation