Skip to main content
SpringerLink
Log in

DNA amplification fingerprinting: A strategy for genome analysis

  • Review
  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

Abstract

A novel strategy to detect genetic differences among organisms, DNA amplification fingerprinting (DAF), uses a thermostable DNA polymerase directed by usually one short (≥5 bp) oligonucleotide primer of arbitrary sequence to amplify short segments of genomic DNA and generate a range of DNA extension products. These products can be analyzed by polyacrylamide gel electrophoresis and silver staining. DAF is rapid and sensitive and is independent of cloning and prior genetic characterization. Here we describe this new methodology, its application to plant genotyping, and its perspectives in DNA fingerprinting and genome mapping.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Abbreviations

DAF:

DNA amplification fingerprinting

AFLP:

amplification fragment length polymorphism

PCR:

polymerase chain reaction

cM:

centimorgan

STS:

sequence-tagged sites

IRS:

interspersed repetitive sequences

References

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

    Article  PubMed  CAS  Google Scholar 

  • Bassam, B.J., Caetano-Anollés and P.M. Gresshoff. 1991a. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196:80–83.

    Article  PubMed  CAS  Google Scholar 

  • Bassam, B.J., G. Caetano-Anollés and P.M. Gresshoff. 1991b. DNA amplification fingerprinting and its potential application for genome analysis. InCurrent Topics in Plant Molecular Biology, Vol. 1 (ed. P.M. Gresshoff), pp. 8–16 Chapman and Hall, New York.

    Google Scholar 

  • Bernatzky, R. and S.D. Tanksley. 1986. Towards a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112:887–898.

    PubMed  CAS  Google Scholar 

  • Beckmann, J.S. and M. Soller. 1986. Restriction fragment length polymorphisms and the genetic improvement of agricultural species. Euphytica 35:111–124.

    Article  Google Scholar 

  • Boerwinkle, E., W. Xiong, E. Fourest and L. Chan. 1989. Rapid typing of tandemly repeated hypervariable loci by the polymerase chain reaction:application to the apolipoprotein B 3′ hypervariable region. Proc. Natl. Acad. Sci. USA 86:212–216.

    Article  PubMed  CAS  Google Scholar 

  • Botstein, D., R.L. White, M. Skolnick and R.W. Davis. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32:314–331.

    PubMed  CAS  Google Scholar 

  • Caetano-Anollés G., B.J. Bassam and P.M. Gresshoff. 1991. DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Bio/Technology 9:553–557.

    Article  PubMed  Google Scholar 

  • Chang, C., J.L. Bowman, A.W. DeJohn, E.S. Lander, and E.M. Meyerowitz. 1988. Restriction fragment length polymorphism linkage map forArabidopsis thaliana. Proc. Natl. Acad. Sci. USA 85:6856–6860.

    Article  PubMed  CAS  Google Scholar 

  • Cox, D.R., M. Burmeister, E. R. Price, S. Kim and R.M. Myers. 1990. Radiation hybrid mapping:a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science 250:245–250.

    Article  PubMed  CAS  Google Scholar 

  • Donis-Keller, H., P. Green, C. Helms, S. Cartinhour, B. Weiffenbach, K. Stephens, T.P. Keith, D.W. Bowden, D.R. Smith, E.S. Lander, D. Botstein, G. Akots, K.S. Rediker, T. Gravius, V.A. Brown, M.B. Rising, C. Parker, J.A. Powers, D.E. Watt, E.R. Kauffman, A. Bricker, P. Phipps, H. Muller-Kahle, T.R. Fulton, S. Ng, J.W. Schumm, J.C. Braman, R.G. Knowlton, D.F. Barker, S.M. Crooks, S.E. Lincoln, M.J. Daly and J. Abrahamson. 1987. A genetic linkage map of the human genome. Cell 51:319–337.

    Article  PubMed  CAS  Google Scholar 

  • Erlich, H.A., D. Gelfand and J.J. Sninsky. 1991. Recent advances in the polymerase chain reaction. Science 252:1643–1651.

    Article  PubMed  CAS  Google Scholar 

  • Golenberg, E. M., D.E. Giannasi, M.T. Clegg, C.J. Smiley, M. Durbin, D. Henderson and G. Zurawski. 1990. Chloroplast DNA sequence from a mioceneMagnolia species. Nature 344:656–658.

    Article  PubMed  CAS  Google Scholar 

  • Goodwin, P.H. and S.L. Annis. 1991. Rapid identification of genetic variation and pathotype ofLeptosphaeria maculans by random amplified polymorphic DNA assay. Appl. Environ. Microbiol. 57:2482–2486.

    PubMed  CAS  Google Scholar 

  • Green, E.D., and M.V. Olson. 1990. Chromosomal region of the cystic fibrosis gene in yeast artificial chromosomes:a model for human genome mapping. Science 250:94–98.

    Article  PubMed  CAS  Google Scholar 

  • Helentjaris, T., W. Slocum, S. Wright, A. Schaefer and J. Nienhuis. 1986. Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms. Theor. Appl. Genet. 72:761–769.

    Article  CAS  Google Scholar 

  • Helentjaris, T., D. Weber and S. Wright. 1988. Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms Genetics 118:353–363.

    PubMed  CAS  Google Scholar 

  • Hagelberg, E., I.C. Gray and A.J. Jeffreys. 1991. Identification of the skeletal remains of a murder victim by DNA analysis. Nature 352:427–429.

    Article  PubMed  CAS  Google Scholar 

  • Horn, G.T., B. Richards and K.W. Klinger. 1989. Amplification of a highly polymorphic VNTR segment by the polymerase chain reaction. Nucleic Acids Res. 17:2140.

    Article  PubMed  CAS  Google Scholar 

  • Jeffreys, A.J., V. Wilson and S.L. Thein. 1985a. Hypervariable ‘minisatellite’ regions in human DNA. Nature 314:67–732.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Jeffreys, A.J., R. Neumann and V. Wilson. 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  PubMed  CAS  Google Scholar 

  • Keim, P., B.W. Diers, T.C. Olson and R.C. Shoemaker. 1990. RFLP mapping in soybean:association between marker loci and variation in quantitative traits. Genetics 126:735–742.

    PubMed  CAS  Google Scholar 

  • Landegren, U., R. Kaiser, C.T. Caskey and L. Hood. 1988. DNA diagnostics. Molecular techniques and automation. Science 242:229–237.

    Article  PubMed  CAS  Google Scholar 

  • Landry, B.S., R.V. Kesseli, B. Farrara and R.W. Michelmore. 1987. Genetics 116: 331–337.

    PubMed  CAS  Google Scholar 

  • Li, H., U.B. Gyllensten, X. Cui, R.K. Saiki, H.A. Erlich and N. Arnheim. 1988. Amplification and analysis of DNA sequences in single human sperm and diploid cells. Nature 335:414–417.

    Article  PubMed  CAS  Google Scholar 

  • Li, H., X. Cui and N. Arnheim. 1990. Direct electrophoretic detection of the allelic state of single DNA molecules in human sperm by using the polymerase chain reaction. Proc. Natl. Acad. Sci. USA 87:4580–4584.

    Article  PubMed  CAS  Google Scholar 

  • Lichter, P., C.C. Tang, K. Call, G. Hermanson, G.A. Evans, D. Housman and D.C. Ward. 1990. High-resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 247:64–69.

    Article  PubMed  CAS  Google Scholar 

  • Mullis, K.B. and F.A. Faloona. 1987. Specific synthesis of DNAin vitro via the polymerase catalyzed reaction. Meth. Enzymol. 255:335–350.

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Ochman, H., A.S. Gerber and D.L. Hartl. 1988. Genetic applications of an inverse polymerase chain reaction. Genetics 120:621–623.

    PubMed  CAS  Google Scholar 

  • Olson, M., L. Hood, C. Cantor and D. Botstein. 1989. A common language for physical mapping of the human genome. Science 245:1434–1435.

    Article  PubMed  CAS  Google Scholar 

  • Orita, M., H. Iwahana, H. Kanazawa, K. Hayashi and T. Sekiya. 1989a. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 86:2766–2770.

    Article  PubMed  CAS  Google Scholar 

  • Orita, M., Y. Suzuki, T. Sekiya and K. Hayashi. 1989b. Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics 5:874–879.

    Article  PubMed  CAS  Google Scholar 

  • Pääbo, S. 1989. Ancient DNA:extraction, characterization, molecular cloning and enzymatic amplification. Proc. Natl. Acad. Sci. USA 86:1939–1943.

    Article  PubMed  Google Scholar 

  • Paterson, A.W., E.S. Lander, J.D. Hewitt, S. Peterson, S.E. Lincoln and S.D. Tanksley. 1988. Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335:721–726

    Article  PubMed  CAS  Google Scholar 

  • Saiki, R.K., D.H. Gelfand, S. Stoffel, S.J. Scharf, R. Higuchi, G.T. Horn and H.A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491.

    Article  PubMed  CAS  Google Scholar 

  • Tanksley, S.D. and J. Hewitt. 1988. Use of molecular markers in breeding for soluble solids content in tomato—a re-examination. Theor. Appl. Genet. 75:811–823.

    Article  CAS  Google Scholar 

  • Tautz, D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17:6463–6472.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Ward, E.R. and G.C. Jen. 1990. Isolation of single copy sequence clones from a yeast artificial chromosome library of randomly shearedArabidopsis thaliana DNA. Plant Mol. Biol. 14:561–568.

    Article  PubMed  CAS  Google Scholar 

  • Watkins, P.C. 1988. Restriction fragment length polymorphism (RFLP):applications in human chromosome mapping and genetic disease research. Biotechniques 6:310–320.

    Article  PubMed  CAS  Google Scholar 

  • Weising, K., B. Beyermann, J. Ramser and G. Kahl. 1991. Plant DNA fingerprinting with radioactive and digoxigenated oligonucleotide probes complementary to simple repetitive DNA sequences. Electrophoresis 12:159–169.

    Article  PubMed  CAS  Google Scholar 

  • Welsh, J. and M. McClelland. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucl. Acids Res. 18:7213–7218.

    Article  PubMed  CAS  Google Scholar 

  • Welsh, J., C. Petersen and M. McClelland. 1991. Polymorphisms generated by arbitrarily primed PCR in the mouse:application to strain identification and genetic mapping. Nucl. Acids Res. 19:303–306.

    Article  PubMed  CAS  Google Scholar 

  • Welsh, J., R.J. Honeycutt, M. McClelland and B.W.S. Sobral. Parentage determination in maize hybrids using the arbitrarilyprimned polymerase chain reaction (AP-PCR). Theor. Appl. Genet (in press).

  • Williams, J.G.K., A.R. Kubelik, K.J. Livak, J.A. Rafalski and S.V. Tingey. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:6531–6535.

    Article  PubMed  CAS  Google Scholar 

  • Wyman, A.R. and R. White. 1980. A highly polymorphic locus in human DNA. Proc. Natl. Acad. Sci. USA 77:6754–6758.

    Article  PubMed  CAS  Google Scholar 

  • Wong, Z., V. Wilson, A.J. Jeffreys and S.L. Thien. 1986. Cloning of a selected fragment from a human DNA ‘fingerprint’:isolation of an extremely polymorphic minisatellite. Nucleic Acids Res. 14:4607–4616.

    Article  Google Scholar 

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

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Plant Molecular Genetics, Institute of Agriculture and Center for Legume Research, The University of Tennessee, 37901-1071, Knoxville, TN, USA

    Gustavo Caetano-Anollés, Brant J. Bassam & Peter M. Gresshoff

Authors
  1. Gustavo Caetano-Anollés
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Brant J. Bassam
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Peter M. Gresshoff
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Caetano-Anollés, G., Bassam, B.J. & Gresshoff, P.M. DNA amplification fingerprinting: A strategy for genome analysis. Plant Mol Biol Rep 9, 294–307 (1991). https://doi.org/10.1007/BF02672006

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02672006

Key Words

Search

Navigation