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DNA Fingerprinting: Approaches and Applications pp 243–262Cite as

Cloning of Hypervariable Minisatellite and Simple Sequence Microsatellite Repeats for DNA Fingerprinting of Important Aquacultural Species of Salmonids and Tilapia

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Part of the book series: Experientia Supplementum ((EXS,volume 58))

Summary

DNA fingerprints reveal a class of highly polymorphic variable number tandem repeat (VNTR) loci that offer considerable potential as genetic markers in aquaculture and fisheries research. We have obtained DNA fingerprints from three commercially important fish species, Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss) and tilapia (Oreochromis niloticus) using the Jeffreys polycore probes, 33.15 and 33.6. The complexity of multilocus fingerprints, however, limits their utility in many contexts. To circumvent this problem we have cloned a number of highly polymorphic VNTRs for use as genetic markers: minisatellites from salmon and tilapia, and microsatellites from rainbow trout.

Both mini- and microsatellite loci appear to be abundant in fish genomes. Discrete classes of minisatellites, distinguishable by their hybridization to the 33.15 and 33.6 probes, occur in both salmonids and tilapia. Minisatellite arrays isolated from genomic libraries show a tendency, particularly in salmon, to occur in clusters. Cross-hybridization data suggest that polymorphic mini- and microsatellite loci are conserved in related salmonids.

We expect VNTR markers to find applications in quantititative genetic analyses, assessment of inbreeding, and identification of particular strains in aquaculture. In fisheries research VNTRs will offer logistic advantages over conventional genetic markers and may facilitate high resolution analyses of genotype/environment interactions.

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References

  • Ali, S., Muller C. R., and Epplen, J. T. (1986) DNA fingerprinting by oligonucleotide probes specific for simple repeats. Hum. Genet. 74: 239–243.

    Article  Google Scholar 

  • Allendorf, F. W., and Thorgaard, G. H. (1984) Tetraploidy and the evolution of salmonid fishes. In: Turner, B. J. (ed.) Evolutionary Genetics of Fishes, Plenum, New York, pp. 1–54.

    Google Scholar 

  • Anon. (1989) Report of Dublin meeting on genetic threats to wild stocks from salmon aquaculture. North Atlantic Salmon Conservation Organization (NASCO) paper CNL(89)19. Edinburgh, Scotland, 33 pp.

    Google Scholar 

  • Armour, J. A. L., Wong, Z., Wilson, V., Royle, N. J., and Jeffreys, A. J. (1989) Sequences flanking the repeat arrays of human minisatellites: association with tandem and dispersed repeat elements. Nucleic Acids Res. 17: 4925–4935.

    Article  Google Scholar 

  • Armour, J. A. L., Povey, S., Jeremiah, S., and Jeffreys, A. J. (1990) Systematic cloning of human minisatellites from ordered array charomid libraries. Genomics 8: 501–512.

    Article  Google Scholar 

  • Benton, W. D., and Davis, R. W. (1977) Screening) gt recombinant clones by hybridization to single plaques in situ. Science 196: 180.

    Google Scholar 

  • Burke, T., and Bruford, M. W. (1987) DNA fingerprinting in birds. Nature 327: 149–152.

    Article  Google Scholar 

  • Burke, T., Davies, N. B., Bruford, M. W., and Hatchwell, B. J. (1989) Parental care and mating behaviour of polyandrous dunnocks Prunella modularis related to paternity by DNA fingerprinting. Nature 338: 249–251.

    Article  Google Scholar 

  • Chimini, G., Mattei, M.-G., Passage, E., Nguyen, C., Boretto, J., Mattei, J.-F., Jordan, B. R. (1989) In situ hybridization and pulsed-field gel analysis define two major minisatellite loci: 1q23 for minisatellite 33.6 and 7q35-q36 for minisatellite 33.15. Genomics 5: 316–324.

    Article  Google Scholar 

  • Davidson, W. S., Birt, T. P., and Green, J. M. (1989) A review of genetic variation in Atlantic salmon, Salmo salar L., and its importance for stock identification, enhancement programmes and aquaculture. J. Fish. Biol. 34: 547–560.

    Article  Google Scholar 

  • Feinberg, A. P., and Vogelstein, B. (1983) A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132: 6–13.

    Article  Google Scholar 

  • Feinberg, A. P., and Vogelstein, B. (1984) Addendum. Anal. Biochem. 137: 266–267.

    Google Scholar 

  • Fields, R. W., Johnson, K. R., and Thorgaard, G. H. (1989) DNA fingerprints in rainbow trout detected by hybridization with DNA of bacteriophage M13. Trans. Am. Fish. Soc. 118: 78–81.

    Article  Google Scholar 

  • Fowler, S. J., Gill, P., Werrett, D. J., and Higgs, D. R. (1988) Individual specific DNA fingerprints from a hypervariable region probe: alpha-globin 3’HVR. Hum. Genet. 79: 142–146.

    Article  Google Scholar 

  • Georges, M., Lequarre, A.-S., Castelli, M., Hanset, R., and Vassart, G. (1988) DNA fingerprinting in domestic animals using four different minisatellite probes. Cytogenet. Cell. Genet. 47: 127–131.

    Article  Google Scholar 

  • Graves, J. E., Ferris, S. D., and Dizon, A. E. (1984) Close genetic similarity of Atlantic and Pacific skipjack tuna (Katsuonis pelamis) demonstrated with restriction endonuclease analysis of mitochondrial DNA. Mar. Biol. 79: 315–319.

    Article  Google Scholar 

  • Gyllensten, U. B., Jakobsson, S., Temrin, H., and Wilson, A.C. (1989) Nucleotide sequence and genomic organization of bird minisatellites. Nucleic Acids Res. 17: 2203–2215.

    Article  Google Scholar 

  • Hallerman, E. M., and Beckmann, J. S. (1988) DNA-level polymorphism as a tool in fisheries science. Can. J. Fish. Aquat. Sci. 45: 1075–1087.

    Article  Google Scholar 

  • Hanotte, O., Burke, T., Armour, J. A., and Jeffreys, A. J. (1991) Hypervariable minisatellite DNA sequences in the Indian peafowl Pavo cristatus. Genomics 9: 587–597.

    Article  Google Scholar 

  • Harris, A. S., Bieger, S., Doyle, R. W., and Wright, J. M. (1991) DNA fingerprinting of tilapia. Oreochromis niloticus, and its application to aquaculture genetics. Aquaculture 92: 157–163.

    Article  Google Scholar 

  • Jarman, A. P., Nicholls, R. D., Weatherall, D. J., Clegg, J. B., and Higgs, D. R. (1986) Molecular characterization of a hypervariable region downstream of the human a-globin gene cluster. EMBO J. 5: 1857–1863.

    Google Scholar 

  • Jarman, A. P., and Wells, R. A. (1989) Hypervariable minisatellites: recombinators or innocent bystanders? Trends Genet. 5: 367–371.

    Article  Google Scholar 

  • Jeffreys, A. J., Wilson, V., and Thein, S. L. (1985a) Hypervariable “minisatellite” regions in human DNA. Nature 314: 67–73.

    Article  Google Scholar 

  • Jeffreys, A. J., Wilson, V., and Thein, S. L. (1985b) Individual-specific “fingerprints” of human DNA. Nature 316: 76–79.

    Article  Google Scholar 

  • Jeffreys, A. J., Wilson, V., Thein, S. L., Weatherall, D. J., and Ponder, B. A. J. (1986) DNA “fingerprints” and segregation analysis of multiple markers in human pedigrees. Am. J. Hum. Genet. 39: 11–24.

    Google Scholar 

  • Jeffreys, A. J., and Morton, D. B. (1987) DNA fingerprints of dogs and cats. Animal Genet. 18: 1–15.

    Article  Google Scholar 

  • Jeffreys, A. J., Wilson, V., Kelly, R., Taylor, B. A., and Bulfield, G. (1987) Mouse DNA `fingerprints’: analysis of chromosome localization and germ-line stability of hypervariable loci in recombinant inbred strains. Nucleic Acids Res. 15: 2823–2837.

    Article  Google Scholar 

  • Jeffreys, A. J., Royle, N. J., Wilson, V., and Wong, Z. (1988a) Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA. Nature 332: 278–281.

    Article  Google Scholar 

  • Jeffreys, A. J., Wilson, V., Neumann R., and Keyte, J. (1988b) Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells. Nucleic Acids Res. 16: 10953–10971.

    Article  Google Scholar 

  • Jeffreys, A. J., Neumann, R., and Wilson, V. (1990) Repeat unit sequence variation in minisatellites: a novel source of DNA polymorphism for studying variation and mutation by single molecule analysis. Cell 60: 473–485.

    Article  Google Scholar 

  • Kam, J. M., Brenner, S., Barnett, L., and Casareni, G. (1980) Novel bacteriophage R cloning vector. Proc. Natl. Acad. Sci. USA 77: 5172.

    Article  Google Scholar 

  • Kashi, Y., Iraqi, F., Tikochinski, Y., Ruzitsky, B., Nave, A., Beckmann, J. S., Friedmann, A., Soller, M., and Gruenbaum, Y. (1990) (TG) uncovers a sex-specific hybridization pattern in cattle. Genomics 7: 31–36.

    Article  Google Scholar 

  • Kelly, R., Bulfield, G., Collick, A., Gibbs, M., and Jeffreys, A. J. (1989) Characterization of a highly unstable mouse minisatellite locus: evidence for somatic mutation during early development. Genomics 5: 844–856.

    Article  Google Scholar 

  • Kessler, C., and Holtke, H.-J. (1986) Specificity of restriction endonucleases and methylases — a review (Edition 2). Gene 47: 1–153.

    Article  Google Scholar 

  • Kornfield, I. (1984) Descriptive genetics of cichlid fishes. In: Turner, B. J. (ed.) Evolutionary Genetics of Fishes, Plenum, New York, pp. 591–616.

    Google Scholar 

  • Kuhnlein, U., Zadworny, D., Dawe, Y., Fairfull, R. W., and Gavora, J. S. (1990) Assessment of inbreeding by DNA fingerprinting: development of a calibration curve using defined strains of chickens. Genetics 125: 161–165.

    Google Scholar 

  • Litt, M., and Luty, J.A. (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet. 44: 397–401.

    Google Scholar 

  • Lloyd, M. A., Fields, M. J., and Thorgaard, G. H. (1989) BKm minisatellite sequences are not sex associated but reveal DNA fingerprint polymorphisms in rainbow trout. Genome 32: 865–868.

    Article  Google Scholar 

  • Love, J. M., Knight, A. M., McAleer, M. A., and Todd, J. A. (1990) Towards construction of a high resolution map of the mouse genome using PC R-analysed microsatellites. Nucleic Acids Res. 18: 4123–4130.

    Article  Google Scholar 

  • Moav, R., Brody, T., Wohlfarth, G., and Hulata, G. (1976) Applications of electrophoretic genetic markers to fish breeding. I. Advantages and methods. Aquaculture 9: 217–228.

    Article  Google Scholar 

  • Mork, J., and Sundnes, G. (1985a) Haemoglobin polymorphism in Atlantic cod (Gadus morhua): allele frequency variation between year classes in a Norwegian fjord stock. Helgolander Meersunters 39: 55–62.

    Article  Google Scholar 

  • Mork J., and Sundnes, G. (1985b) O-group cod (Gadus morhua) in captivity: differential survival of certain genotypes. Helgolander Meeresunters 39: 63–70.

    Article  Google Scholar 

  • Nakamura, Y., Leppert, M., O’Connell, P., Wolff, R., Holm, T., Culver, M., Martin, C., Fujimoti, E. Hoff, M., Kumlin, E., and White, R. (1987) Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 235: 1616–1622.

    Google Scholar 

  • Nanda, I., Feichtinger, W., Schmid, M., Schroder, J. H., Zischler, H., and Epplen, J. T. (1990) Simple repetitive sequences are associated with differentiation of the sex chromosomes in the guppy fish. J. Mol. Evol. 30: 456–462.

    Article  Google Scholar 

  • Rogaev, E.I. (1990) Simple human DNA-repeats associated with genomic hypervariability, flanking the genomic retroposons and similar to retroviral sites. Nucleic Acids Res. 18: 1879–1885.

    Article  Google Scholar 

  • Royle, N. J., Clarkson, R. E., Wong, Z., and Jeffreys, A. J. (1988) Clustering of hypervariable minisatellites in the proterminal regions of human autosomes. Genomics 3: 352–360.

    Article  Google Scholar 

  • Ryman, N., and Utter, F. (eds.) (1987) Population Genetics and Fishery Management, University of Washington, Seattle.

    Google Scholar 

  • Ryskov, A. P., Jincharadze, A. G., Prosnyak, M. I., Ivanov, P. L., and Limborska, S. A. (1988) M13 phage DNA as a universal marker for DNA fingerprinting of animals, plants and microorganisms. FEBS Letters 233: 388–392.

    Article  Google Scholar 

  • Schafer, R., Zischler, H., and Epplen, J. T. (1988) (CAC)s, a very informative oligonucleotide for DNA fingerprinting. Nucleic Acids Res. 16: 51–96.

    Article  Google Scholar 

  • Smith, P. J., Birley, A. J., Jamieson, A., and Bishop, C. A. (1989) Mitochondrial DNA in the Atlantic cod, Gadus morhua: lack of genetic divergence between eastern and western populations. J. Fish. Biol. 34: 369–377.

    Article  Google Scholar 

  • Taggart, J. B., and Ferguson, A. (1986) Electrophoretic evaluation of a supplemental stocking programme for brown trout, Salmo trutta L. Aquaculture and Fisheries Management 17: 155–162.

    Google Scholar 

  • Tautz, D. (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17: 6463–6471.

    Article  Google Scholar 

  • Tautz, D., and Renz, M. (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res. 12: 4127–4138.

    Article  Google Scholar 

  • Tautz, D., Trick, M., and Dover, G. A. (1986) Cryptic simplicity in DNA is a major source of DNA variation. Nature 332: 652–658.

    Article  Google Scholar 

  • Tave, D. (1986) Genetics for fish hatchery managers. AVI, Westport, Connecticut.

    Google Scholar 

  • Thomas, W. K., Pääbo, S., Villablanca, F. X., and Wilson, A. C. (1990) Spatial and temporal continuity of kangaroo rat populations shown by sequencing mitochrondrial DNA from museum specimens. J. Mol. Evol. 31: 101–112.

    Article  Google Scholar 

  • Turner, B. J., Elder, J. F. Jr., Laughlin, T. F., and Davis, W. P. (1990) Genetic variation in clonal vertebrates detected by simple-sequence DNA fingerprinting. Proc. Natl. Acad. Sci. USA 87: 5653–5657.

    Article  Google Scholar 

  • Uraiwan, S., and Doyle, R.W. (1986) Replicate variance and the choice of selection procedure for tilapia (Oreochromis niloticus) stock improvement in Thailand. Aquaculture 57: 27–35.

    Article  Google Scholar 

  • Vassart, G., Georges, M., Monsieur, R., Brocas, H., Lequarre, A.-S., and Christophe, D. (1987) A sequence of M13 phage detects hypervariable minisatellites in human and animal DNA. Science 235: 683–684.

    Article  Google Scholar 

  • Vergnaud, G. (1989) Polymers of random short oligonucleotides detect polymorphic loci in the human genome. Nucleic Acids Res. 17: 7623–7630.

    Article  Google Scholar 

  • Vogelstein, B., and Gillespie, D. (1979) Preparative and analytical purification of DNA from agarose. Proc. Natl. Acad. Sci. USA 76: 615–619.

    Article  Google Scholar 

  • Waldman, J. R., Grossfield, J., and Wirgin, I. (1988) Review of stock discrimination techniques for striped bass. N. Am. J. Fish. Management 8: 410–425.

    Article  Google Scholar 

  • Weber, J. L., and May, P. E. (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44: 388–396.

    Google Scholar 

  • Westneat, D. F., Noon, W. A., Reeve, H. K., and Aquadro, C. F. (1988) Improved hybridization conditions for DNA ‘fingerprints’ probed with M13. Nucleic Acids Res. 16: 4161.

    Article  Google Scholar 

  • Wong, Z., Wilson, V., Patel, I., Povey, S., and Jeffreys, A. J. (1987) Characterization of a panel of highly variable minisatellites cloned from human DNA. Ann. Hum. Genet. 51: 269–288.

    Article  Google Scholar 

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Authors and Affiliations

  1. Marine Gene Probe Laboratory and Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4J1

    P. Bentzen, A. S. Harris & J. M. Wright

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  1. P. Bentzen
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  2. A. S. Harris
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  3. J. M. Wright
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Editors and Affiliations

  1. Dept. Zoology, University of Leicester, LE1 7RH, Leicester, England

    Terry Burke

  2. Institut für Tierzucht, Universität Bern, 3012, Bern, Switzerland

    Gaudenz Dolf

  3. Dept. Genetics, University of Leicester, LE1 7RH, Leicester, England

    Alec J. Jeffreys

  4. UCSF-HSE 1556, Box # 0554, 94143-0554, San Francisco, CA, USA

    Roger Wolff

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Bentzen, P., Harris, A.S., Wright, J.M. (1991). Cloning of Hypervariable Minisatellite and Simple Sequence Microsatellite Repeats for DNA Fingerprinting of Important Aquacultural Species of Salmonids and Tilapia. In: Burke, T., Dolf, G., Jeffreys, A.J., Wolff, R. (eds) DNA Fingerprinting: Approaches and Applications. Experientia Supplementum, vol 58. Birkhäuser Basel. https://doi.org/10.1007/978-3-0348-7312-3_17

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  • DOI: https://doi.org/10.1007/978-3-0348-7312-3_17

  • Publisher Name: Birkhäuser Basel

  • Print ISBN: 978-3-0348-7314-7

  • Online ISBN: 978-3-0348-7312-3

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