Aquarium Sciences and Conservation

, Volume 1, Issue 2, pp 91–104

DNA fingerprinting: application to conservation of the CITES-listed dragon fish, Scleropages formosus (Osteoglossidae)

  • A.A. Fernando
  • L.C. Lim
  • K. Jeyaseelan
  • S.W. Teng
  • M.C. Liang
  • C.K. Yeo
Article

Abstract

Since 1975,CITES has listed the dragon fish, Scleropages formosus, as anendangered species. In 1995, a captive-bred population was set upby a commercial fish farm with assistance from the PrimaryProduction Department in Singapore. Other farms in Indonesia andMalaysia followed suit. These populations have contributed to animmediate conservation of the species. Due to very high demandfor this ornamental fish, these venues may be its last sanctuary.

DNA fingerprints of the dragon fish were obtained by different methods from the green, red and gold varieties grown in a Singapore fish farm to determine which method was most suitable in providing information on genetic variability. Because a DNA fingerprint is a pattern made up of DNA fragments that are resolved by electrophoresis, each individual has its own unique ‘fingerprint’ due to a genetic make-up different from another individual. Thus, genetic variability was best studied by developing DNA fingerprints.

Firstly, restriction fragment length polymorphisms (RFLPs) were obtained. DNA fragments formed by cleavage with nine restriction endonucleases used singly were hybridized individually to four non-radioactively labelled probes to give RFLPs. The RFLPs for each variety were similar and genomic DNA from each variety had many binding sites to the probes. This made differentiating RFLPs specific to individual varieties difficult. Secondly, random amplified polymorphic DNA (RAPD) fingerprints were developed. DNA fragments that were resolved on a denaturing polyacrylamide gel were hybridized to seven arbitrary primers used singly. RAPD fingerprints for each variety were different for each primer tested. The similarity index indicated low genetic variability between varieties. Lastly, DNA was screened for microsatellite loci which refer to short tandem repeats of two or three bases. The occurrence of other microsatellite loci, their chromosome location and frequency is being investigated while primers have been designed to detect more loci by the polymerase chain reaction. As this method provides undisputed and reproducible evidence of relatedness and stock identification, and can be applied for long-term management of domesticated populations through pedigree construction and evaluation of heterozygosity, it is the preferred choice to determine genetic variability

Endangered fish DNA fingerprinting RFLP RAPD Microsatellites Captive-bred 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

REFERENCES

  1. Anonymous (1987) Our Common Future. World Commission on Environment and Development (WCED). Oxford, UK: Oxford University Press.Google Scholar
  2. Anonymous (1992) Expert consultation on utilization and conservation of aquatic genetic resources. Grottaferrata, Italy, 9-13 November 1992. FAO Fisheries Report No. 491.Google Scholar
  3. Anonymous (1993) Checklist of Fish and Invertebrates Listed in CITES Appendices. Peterborough, UK: World Conservation Monitoring Centre, Joint Nature Conservation Committee. 171 pp.Google Scholar
  4. Beacham, T.D., Withler, R.E. and Stevens, T.A. (1996) Stock identification of chinoock salmon (Oncorhynchus tshawytscha) using minisatellite DNA variation. Canadian Journal of Fisheries and Aquatic Sciences 53, 380–394.Google Scholar
  5. Berg, D.E., Akopyants, N.S. and Kersulyte, D. (1994) Fingerprinting microbial genomes using RAPD or AP-PCR method. Methods in Molecular and Cellular Biology 5, 13–24.Google Scholar
  6. Cheong, L. (1993) Singapore's Dragon fish connection. OFI Journal 5, 7–8.Google Scholar
  7. Cheong, L. (1994) Singapore's Dragon fish connection. Part II: Making it all come together. OFI Journal 9, 16.Google Scholar
  8. Clark, A.G. and Lanigan, C.M.S. (1993) Prospects for estimating dinucleotide divergence with RAPDs. Molecular Biology and Evolution 10 1096–1111.Google Scholar
  9. Dawes, J. and Cheong, L. (1994) Captive-bred Dragon fish from Singapore. Aquaristics (May) 9–11. PETS Europe 6 (3).Google Scholar
  10. Dinesh, K.R., Phang, V.P.E., Lim, T.M., Chua, K.L. and Tan, T.W. (1993) DNA polymorphisms in colour mutants of Tiger Barb, Barbus tetrazona, by arbitrary primed polymerase chain reaction. In Penman, D., Roongratri, N. and McAndrew, B., eds, Proceedings of the AADCP International Workshop on Genetics in Aquaculture and Fisheries, Stirling, UK: Stirling UniversityGoogle Scholar
  11. Ehrlich, P.R. and Ehrlich, A.H. (1981) Extinction: The Causes and Consequences of the Disappearance of Species. New York: Random House.Google Scholar
  12. Falconer, D.S. and McKay, T.F.C. (1996) Introduction to Quantitative Genetics, 4th edn. Essex, UK. Longman Press.Google Scholar
  13. Georges, M., Lequarré, A.-S., Castelli, M., Hanset, R. and Vassart, G. (1988) DNA fingerprinting in domestic animals using four different minisatellite probes. Cytogenetics and Cell Genetics 47, 127–134.Google Scholar
  14. Gilbert, J. (ed.) (1984) The Complete Aquarist's Guide to Freshwater Tropical Fishes. Italy: Eurobook Ltd. pp. 226.Google Scholar
  15. Gill, P., Jeffreys, A.J. and Werrett, D.J. (1985) Forensic applications of DNA "fingerprints". Nature 318, 577–579.Google Scholar
  16. Greenwood, P.H., Rosen, D.E., Weitzman, S.H. and Myers, G.S. (1996) Phyletic studies of teleostean fishes, with a provisional classification of living forms. Bulletin of the American Museum of Natural History 131, 338–456.Google Scholar
  17. Hedrick, P.W. and Miller, P. (1992) Conservation genetics: theory and management of captive populations. In Sandlund, O.T., Hindar, K. and Brown, A.H.D., eds, Conservation of Biodiversity for Sustainable Development, Norway: Scandinavian University Press, pp. 70–87.Google Scholar
  18. Janzen, D.H. (1992) A south-north perspective on science in the management, use, and economic development of biodiversity. In Sandlund, O.T., Hindar, K. and Brown, A.H.D., eds, Conservation of Biodiversity for Sustainable Development, Norway: Scandinavian University Press, pp. 27–52.Google Scholar
  19. Jeffreys, A.J., Wilson, V. and Thein, S.L. (1985a) Hypervariable "minisatellite" regions in human DNA. Nature 314, 67–73.Google Scholar
  20. Jeffreys, A.J., Wilson, V. and Thein, S.L. (1985b) Individual-specific "fingerprints" of human DNA. Nature 316, 76–79.Google Scholar
  21. Jin, L. and Chakraborty, R. (1994) Population dynamics of DNA fingerprinting patterns within and between populations. Genetical Research 63, 1–9.Google Scholar
  22. Johnson, J.E. and Hubbs, C. (1989) Status and conservation of poeciliid fishes. In Meffe, G.K. and Snelson, F.F., Jr, eds, Ecology and Evolution of Livebearing Fishes (Poeciliidae), (Prentice Hall Advanced Reference Series) Engelwood Cliffs, NJ: Prentice-Hall, pp. 301–317.Google Scholar
  23. Kodera, H., Igarashi, T., Kuroiwa, N., Maeda, H., Mitani, S., Mori, I. and Yamazaki, K. (1996) Jurassic Fishes. New York: T.F.H. Publ. Inc., pp. 12, 42-44.Google Scholar
  24. Lim, L.C., Ho, K.H., Cheong, L. and Teo, S.H. (1995) Production of red dragon fish, Scleropages formosus (Muller and Schlegel), by captive breeding. Paper presented at the 12th PPD Seminar, 29 Sep. 1995.Google Scholar
  25. Maitland, P.S. and Evans, D. (1986) The role of captive breeding in the conservation of fish species. International Zoo Yearbook 24/25, 66–74.Google Scholar
  26. Mathe, J., Eisenmann, C. and Seitz, A. (1993) Paternity testing of endangered species of birds by DNA fingerprinting with non-radioactive labeled oligonucleotide probes. In Pena, S.D.J., Chakraborty, R., Epplen, J.T. and Jeffreys, A.J., eds, DNA Fingerprinting: State of the Science, Basel, Switzerland: Birkhauser Verlag}, pp. 387–93.Google Scholar
  27. Meffe, G.K. (1986) Conservation genetics and the management of endangered fishes. Fisheries 11, 14–23.Google Scholar
  28. Morgan, D.H.W. (1995) Implications of the CITES regulations for the ornamental aquatics industry. In Dawes, J.D., Cheong, L., Lim, L.C., Phang, V., Lim, K.K. and Tan, L.L., eds., Proceedings of the 4th International Aquarium Fish and Accessories Exhibition and Conference. Singapore, pp. 70–80.Google Scholar
  29. Myers, N. (1989) Deforestation Rates in Tropical Forests and their Climatic Implications. London, UK: Friends of the Earth.Google Scholar
  30. Nei, M. and Li, W.H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the USA 76, 5269–5273.Google Scholar
  31. Rinne, J.N., Johnson, J.E., Jensen, B.L., Ruger, A.W. and Sorenson, R. (1986) The role of hatcheries in management and recovery of threatened and endangered fishes. In Stroud, R.H., ed., Fisheries Management, Bethesda, MD: American Fisheries Society, pp. 271–286.Google Scholar
  32. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. pp. 9.31-9.51, B4-B23.Google Scholar
  33. Sandlund, O.T., Hindar, K. and Brown, A.H.D. (eds) (1992) Conservation of Biodiversity for Sustainable Development. Norway: Scandinavian University Press, pp. 9–11.Google Scholar
  34. Schaäfer, R., Zischler, H., Birsner, U., Becker, A. and Epplen, J.T. (1988) Optimized oligonucleotide probes for DNA fingerprinting. Electrophoresis 9, 369–374.Google Scholar
  35. Slettan, A., Olsaker, I. and Lie, Ø. (1995) Atlantic Salmon, Salmo salar microsatellites at the SSOSL25, SSOSL85, SSOSL311, SSOSL417 loci. Animal Genetics 26, 281–282.Google Scholar
  36. Southern, E.M. (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. Journal of Molecular Biology 98, 503–517.Google Scholar
  37. Tave, D. (1995) Selective breeding programs for medium-sized fish farms. FAO Fisheries Technical Paper No. 352, 122 pp.Google Scholar
  38. Toney, D.P. (1974) Observations on the propagation and rearing of two endangered fish species in a hatchery environment. Proceedings of the Annual Conference of the Western Association of Game and Fish Commissioners 59, 252–259.Google Scholar
  39. Wainscoat, J.C., Hill, A.V., Boyce, A.L., Flint, J., Hernandez, M., Thein, S.L., Old, J.M., Lynch, J.R., Falusi, A.G. and Weatherall, D.J. (1986) Evolutionary relationships of human populations from an analysis of nuclear DNA polymorphisms. Nature 319, 491–493.Google Scholar
  40. Ward, R.D. and Grewe, P.M. (1994) Appraisal of molecular genetic techniques in fisheries. Reviews in Fish Biology and Fisheries 4, 300–325. Google Scholar
  41. Weber, J.L. (1990) Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics 7, 524–530.Google Scholar
  42. Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research 18, 7213–7218.Google Scholar
  43. Williams, J.G.K., Kubelik, A.R., Livak, J., Rafalski, J.A. and Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18, 6531–6535.Google Scholar
  44. Williams, J.G.K., Hanaffy, M.K., Rafalski, J.A. and Tingey, S.V. (1993) Genetic analysis using random amplified polymorphic DNA markers. Methods in Enzymology 218, 704–740.Google Scholar
  45. Winterø, A.K., Fredholm, M. and Thomsen, P.D. (1992) Variable (dG-dT)n.(dC-dA)n sequences in the porcine genome. Genomics 12, 281–288.Google Scholar
  46. Wright, J.M. (1993) DNA fingerprinting of fishes. In Hochachka, P.W. and Mommesen, T.P., eds, Biochemistry and Molecular Biology of fishes, Vol. 2, Amsterdam, Netherlands: Elsevier pp. 57-91Google Scholar
  47. Wright, J.M. and Bentzen, P. (1994) Microsatellites: genetic markers for the future. Reviews in Fish Biology and Fisheries 4, 384–388.Google Scholar
  48. Wu, K.S. and Tanksley, S.D. (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Molecular and General Genetics 241, 225–235.Google Scholar

Copyright information

© Chapman and Hall 1997

Authors and Affiliations

  • A.A. Fernando
    • 1
  • L.C. Lim
    • 2
  • K. Jeyaseelan
    • 3
  • S.W. Teng
    • 1
  • M.C. Liang
    • 1
  • C.K. Yeo
    • 1
  1. 1.Chemical Process & Biotechnology DepartmentSingapore PolytechnicSingapore
  2. 2.Ornamental Fish Section, Primary Production DepartmentMinistry of National DevelopmentLorong ChencharuSingapore
  3. 3.Department of BiochemistryNational University of SingaporeSingapore Kent RidgeSingapore

Personalised recommendations