Skip to main content
SpringerLink
Log in
SpringerLink
Log in

Multilocus DNA fingerprinting and genetic relatedness in plants: A case study with banana and tomato

  • Chapter
Molecular Ecology and Evolution: Approaches and Applications

Part of the book series: Experientia Supplementum ((EXS,volume 69))

Summary

The technique of DNA fingerprinting is frequently used for studies of genetic diversity and relatedness in a wide range of organisms. In humans and animals, multilocus fingerprints are mainly applied to paternity and identity test cases, behavioral ecology, and the analysis of population structures. In plants and fungi, the frequent occurrence of “low-variability” fingerprint patterns additionally allows to use multilocus fingerprinting for studying taxonomical problems at an intraspecific level. In the present article, we (1) present an overview of such approaches in a series of plant species, (2) summarize our attempts to estimate genetic relationships within two cultivated plant species, banana and tomato, by band sharing data derived from oligonucleotide fingerprints, and (3) discuss the limitations and potentials of multilocus fingerprinting for the determination of genetic relatedness.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

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

    Article  PubMed  CAS  Google Scholar 

  • Arnold, M.L., Buckner, C.M. and Robinson, J.J. (1991) Pollen-mediated introgression and hybrid speciation in Lousiana irises. Proc. Natl. Acad. Sci. USA 88: 1398–1402.

    Article  PubMed  CAS  Google Scholar 

  • Arnold, M.L. (1993) Iris nelsonii (Iridaceae): Origin and genetic composition of a homoploid hybrid species. Am. J. Bot. 80: 577–583.

    Article  Google Scholar 

  • Bachmann, K. (1992) Nuclear DNA markers in angiosperm taxonomy. Acta. Bot. Neerl. 39(4): 369–384.

    Google Scholar 

  • Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. (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 

  • Brown, J.K.M., O’dell M., Simpson, C.G. and Wolfe, M.S. (1990) The use of DNA polymorphisms to test hypotheses about a population of Erysiphe graminis f.sp. hordei. Plant Pathol. 39: 391–401.

    Article  CAS  Google Scholar 

  • Bruford, M.W., Hanotte, O., Brookfield, J.F.Y. and Burke, T. (1992) Single-locus and multilocus DNA fingerprinting. In: A.R. Hoelzel (ed): Molecular Genetic Analysis of Populations: A Practical Approach, IRL Press Oxford, pp. 225–269.

    Google Scholar 

  • Burke, T. (1989) DNA fingerprinting and other methods for the study of mating success. Trends Ecol. Evol. 4: 139–144.

    Article  PubMed  CAS  Google Scholar 

  • Burke, T., Dolf, G., Jeffreys, A.J. and Wolff, R. (1991) DNA fingerprinting: Approaches and Applications. Birkhäuser Verlag, Basel.

    Book  Google Scholar 

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

    PubMed  Google Scholar 

  • Chalmers, K.J., Waugh, R., Sprent, J.I., Simons, A.J. and Powell, W. (1992) Detection of genetic variation between and within populations of Gliricidia sepium and G. maculata using RAPD markers. Heredity 69: 465–472.

    Article  PubMed  Google Scholar 

  • Crawford, D.J., Brauner, S., Cosner, M.B. and Stuessy, T.F. (1993) Use of RAPD markers to document the origin of the intergeneric hybrid × Margyracaena skottsbergii (Rosaceae) on the Juan Fernandez Islands. Am. J. Bot. 80: 89–92.

    Article  CAS  Google Scholar 

  • Dallas, J.F. (1988) Detection of DNA “fingerprints” of cultivated rice by hybridization with a human minisatellite DNA probe. Proc. Natl. Acad. Sci. USA 85: 6831–6835.

    Article  PubMed  CAS  Google Scholar 

  • Dawson, I.K., Chalmers, K.J. and Waugh, R., Powell, W. (1993) Detection and analysis of genetic variation in Hordeum spontaneum populations from Israel using RAPD markers. Mol. Ecol. 2: 151–159.

    Article  PubMed  CAS  Google Scholar 

  • Demeke, T., Adams, R.P. and Chibbar, R. (1992) Potential taxonomic use of random amplified polymorphic DNA (RAPD): a case study with Brassica. Theor. Appl. Genet. 84: 990–994.

    CAS  Google Scholar 

  • Epplen, J.T. (1992) The methodology of multilocus DNA fingerprinting using radioactive and nonradioactive oligonucleotide probes specific for simple repeat motifs. In: A. Chrambach, M.J. Dunn and B.J. Radola (eds): Advances in Electrophoresis, Vol 5., VCH, Weinheim, pp. 59–112.

    Google Scholar 

  • Eskew, D.L., Caetano-Anollés, G., Bassam, B.J. and Gresshoff, P.M. (1993) DNA amplification fingerprinting of the Azolla-Anabaena symbiosis. Plant Mol. Biol. 21: 363–373.

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein, J. (1990) PHYLIP Manual Version 3.3. University of California, Berkeley.

    Google Scholar 

  • Gilbert, D.A., Packer, C., Pusey, A.E., Stephens, J.C. and O’Brien, S.J. (1991) Analytical DNA fingerprinting in lions: parentage, genetic diversity, and kinship. J. Hered. 82: 378–386.

    PubMed  CAS  Google Scholar 

  • Hadrys, H., Balick, M. and Schierwater, B. (1992) Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol. Ecol. 1: 55–63.

    Article  PubMed  CAS  Google Scholar 

  • Halward, T., Stalker, T., La Rue, E. and Kochert, G. (1992) Use of singleprimer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.). Plant Mol. Biol. 18: 315–325.

    Article  PubMed  CAS  Google Scholar 

  • Hanotte, O., Bruford, M.W. and Burke, T. (1992) Multilocus DNA fingerprints in gallinaceous birds: general approach and problems. Heredity 68: 481–494.

    Article  PubMed  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Jeffreys, A.J. and Morton, D.B. (1987) DNA fingerprints of dogs and cats. Anim. Genet. 18: 1–5.

    Article  PubMed  CAS  Google Scholar 

  • Jung, C., Pillen, K., Frese, L., Fähr, S. and Melchinger, A.E. (1993) Phylogenetic ralation-ships between cultivated and wild species of the genus Beta revealed by DNA “fingerprinting”. Theor. Appl. Genet. 86: 449–457.

    Article  CAS  Google Scholar 

  • Kaemmer, D., Afza, R., Weising, K., Kahl, G. and Novak, F.J. (1992a) Oligonucleotide and amplification fingerprinting of wild species and cultivars of Banana (Musa spp.). Bio/Technology 10: 1030–1035.

    Article  PubMed  CAS  Google Scholar 

  • Kaemmer, D., Ramser, J., Schön, M., Weigand, F., Saxena, M.C., Driesel, A.J., Kahl, G. and Weising, K. (1992b) DNA fingerprinting of fungal genomes: a case study with Ascochyta rabiei. BTF 10, Adv. Mol. Genet. 5: 255–270.

    CAS  Google Scholar 

  • Kistler, H.C., Momol, E.A. and Benny, U. (1991) Repetitive genomic sequences for determining relatedness among strains of Fusarium oxysporum. Phytopathol. 81: 331–336.

    Article  CAS  Google Scholar 

  • Kuhnlein, U., Dawe, Y., Zadworny, D. and Gavora, J.S. (1989) DNA fingerprinting: a tool for determining genetic distances betweens trains of poultry. Theor. Appl. Genet. 77: 669–672.

    Google Scholar 

  • Levy, M., Ramao, J., Marchetti, M.A. and Hamer, J.E. (1991) DNA fingerprinting with a dispersed repeated sequence resolves pathotype diversity in the rice blast fungus. Plant Cell 3: 95–102.

    PubMed  CAS  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.

    PubMed  CAS  Google Scholar 

  • Lynch, M. (1988) Estimation of relatedness by DNA fingerprinting. Mol. Biol. Evol. 5: 584–599.

    PubMed  CAS  Google Scholar 

  • Lynch, M. (1990) The similarity index and DNA fingerprinting. Mol. Biol. Evol. 7: 478–484.

    PubMed  CAS  Google Scholar 

  • Lynch, M. (1991) Analysis of population genetic structure by DNA fingerprinting. In: T. Burke, G. Dolf, A.J. Jeffreys and R. Wolff (eds): DNA Fingerprinting: Approaches and Applications. Birkhäuser Verlag, Basel, pp. 113–126.

    Chapter  Google Scholar 

  • Meyer, W., Lieckfeldt, E., Wöstemeyer, J. and Borner, T. (1992) DNA fingerprinting for differentiating aggressivity groups of the rape seed pathogen Leptosphaeria maculans. Mycol. Res. 96: 651–657.

    Article  CAS  Google Scholar 

  • Miller, J.C. and Tanksley, S.D. (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor. Appl. Genet. 80: 437–448.

    CAS  Google Scholar 

  • Munthali, M., Ford-Lloyd, B.V. and Newbury, H.J. (1992) The random amplification of polymorphic DNA for fingerprinting plants. PCR Meth. Appl. 1: 274–276.

    Article  CAS  Google Scholar 

  • Nei, M. and Li, W.H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76: 5269–5273.

    Article  PubMed  CAS  Google Scholar 

  • Nybom, H. and Hall, H.K. (1991) Minisatellite DNA ‘fingerprints’ can distinguish Rubus cultivars and estimate their degree of relatedness. Euphytica 53: 107–114.

    Article  CAS  Google Scholar 

  • Packer, C., Gilbert, D.A., Pusey A.E. and O’Brien, S.J. (1991) A molecular genetic analysis of kinship and cooperation in African lions. Nature 351: 562–565.

    Article  CAS  Google Scholar 

  • Parent, J.G. and Page, D. (1992) Identification of raspberry cultivars by nonradioactive DNA fingerprinting. Hort Science 27: 1008–1110.

    Google Scholar 

  • Patwary, M.U., MacKay, R.M. and Van der Meer, J.P. (1993) Revealing genetic markers in Gelidum vagum (Rhodophyta) through the random amplified polymorphic DNA (RAPD) technique. J. Phycol. 29: 216–222.

    Article  CAS  Google Scholar 

  • Pena, S.D.J., Chakraborty, R., Epplen, J.T. and Jeffreys, A.J. (1993) DNA Fingerprinting: State of the Science. Birkhäuser, Basel.

    Book  Google Scholar 

  • Poulsen, G.B., Kahl, G., Weising, K. (1993) Abundance and polymorphism of simple repetitive DNA sequences in Brassica napus L. Theor. Appl. Genet. 85: 994–1000.

    Article  CAS  Google Scholar 

  • Reeve, H.K., Westneat, D.F., Noon, W.A., Sherman, P.W. and Aquadro, C.F. (1990) DNA “fingerprinting” reveals high levels of inbreeding in colonies of the eusocial naked mole-rat. Proc. Natl. Acad. Sci. USA 87: 2496–2500.

    Article  PubMed  CAS  Google Scholar 

  • Reiter, R.S., Williams, J.G.K., Feldmann, K.A., Rafalski, J.A., Tingey, S.V. and Scolnik, P.A. (1992) Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs. Proc. Natl. Acad. Sci. USA 89: 1477–1481.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Schierwater, B., Ender, A. and Streit, B. (1993) The use of RAPD markers for molecular phylogenies. Verh. Dtsch. Zool. Ges. 86: 58.

    Google Scholar 

  • Schmid, J., Voss, E. and Soll, D.R. (1990) Computer-assisted methods for assessing strain relatedness in Candida albicans by fingerprinting with the moderately repetitive sequence Ca3. J. Clin. Microbiol. 28: 1236–1243.

    PubMed  CAS  Google Scholar 

  • Sharon, D., Hillel, J., Vainstein, A. and Lavi, U. (1992) Application of DNA fingerprints for identification and genetic analysis of Carica papaya and other Carica species. Euphytica 62: 119–126.

    Article  CAS  Google Scholar 

  • Sneath, P.H.A. and Sokal, R.R. (1973) Numerical Taxonomy. Freeman, San Francisco.

    Google Scholar 

  • Sokal, R.R. and Rohlf, F.J. (1981) Biometry. Freeman, San Francisco.

    Google Scholar 

  • Swofford, D.L. and Olsen, G.J. (1990) Phylogeny reconstruction. In: D.M. Hillis and C. Moritz (eds): Molecular Systematics. Sinauer Publishers, Sunderland, pp. 411–501.

    Google Scholar 

  • Swofford, D.L. (1991) PAUP. Phylogenetic analysis using parsimony. Version 3.0. Illinois Natural History Survey, Champaign, IL.

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Thormann, C.E. and Osborn, T.C. (1993) Use of RAPD and RFLP markers for germplasm evaluation. In: M. Neff (ed.): Application of RAPD technology to Plant Breeding, ASHS Publishers, St Paul MN, USA, pp. 9–11.

    Google Scholar 

  • Vainstein, A., Hillel, J. and Tzuri, G. (1991) Assessment of genetic relatedness in carnation by DNA fingerprint analysis. Euphytica 56: 225–229.

    Article  Google Scholar 

  • Van Coppenolle, V., Watanabe, I., Van Hove, C., Second, G., Huang, N. and McCouch, S.R. (1993) Genetic diversity and phylogeny analysis of Azolla based on DNA amplification by arbitrary primers. Genome 36: 686–693.

    Article  PubMed  Google Scholar 

  • Van Heusden, A.W., Van der Voort, J.R. and Bachmann, K. (1991) Oligo-(GATA) fingerprints identify clones in asexual dandelions Taraxacum (Asteraceae). Fingerprint News 3(2): 13–15.

    Google Scholar 

  • Van Heusden, A.W. and Bachmann, K. (1992) Genotype relationships in Microseris elegans (Asteraceae, Lactuceae) revealed by DNA amplification from arbitrary primers (RAPDs). Plant Syst. Evol. 179: 221–233.

    Article  Google Scholar 

  • Van Houten, W.H.J., Van Heusden, A.W., Rouppe vd Voort, K., Raijmann, L. and Bachmann, K. (1991) Hypervariable DNA fingerprint loci in Microseris pygmaea (Asteraceae, Lactuceae). Bot. Acta. 104: 252–256.

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Vuylsteke, D.R., Swennen, R.L. and Ortiz, R. (1993) Development and performance of black sigatoka-resistant tetraploid hybrids of plantain (Musa spp, AAB group). Euphytica 65: 33–42.

    Article  Google Scholar 

  • Warnock, S.J. (1988) A review of taxonomy and phylogeny of the genus Lycopersicon. Hort Sci. 23: 669–673.

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Weising, K., Ramser, J., Kaemmer, D., Kahl, G. and Epplen, J.T. (1991b) Oligonucleotide fingerprinting in plants and fungi. In: G. Dolf, T. Burke, A.J. Jeffreys and R. Wolff (eds): DNA Fingerprinting, Approaches and Applications. Birkhäuser, Basel, pp. 312–329.

    Chapter  Google Scholar 

  • Weising, K., Kaemmer, D., Epplen, J.T., Weigand, F., Saxena, M. and Kahl, G. (1991c) DNA fingerprinting of Ascochyta rabiei with synthetic oligodeoxynucleotides. Curr. Genet. 19: 483–489.

    Article  CAS  Google Scholar 

  • Weising, K., Kaemmer, D., Weigand, F., Kahl, G. and Epplen, J.T. (1992) Oligonucleotide fingerprinting reveals various probe dependent levels of informativeness in chickpea (Cicer arietinum). Genome 35: 436–442.

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Wetton, J.H., Carter, R.E., Parkin, D.T. and Walters, D. (1987) Demographic study of a wild house sparrow population by DNA fingerprinting. Nature 327: 147–149.

    Article  PubMed  CAS  Google Scholar 

  • Wilkie, S.E., Isaac, P.G. and Slater, R.J. (1993) Random amplified polymorphic DNA (RAPD) markers for genetic analysis in Allium. Theor. Appl. Genet. 86: 497–504.

    Article  CAS  Google Scholar 

  • Williams, C.E. and St.Clair, D.A. (1993) Phenetic relationships and levels of variability detected by restriction fragment length polymorphism and random amplified polymorphic DNA analysis in cultivated and wild accessions of Lycopersicon esculentum. Genome 36: 619–630.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Plant Molecular Biology Group, University of Frankfurt, D-60054, Frankfurt, Germany

    K. Weising, J. Ramser, D. Kaemmer & G. Kahl

Authors
  1. K. Weising
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. Ramser
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. D. Kaemmer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. G. Kahl
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Zoologisches Institut, Universität Frankfurt, Siesmayerstr. 70, D-60054, Frankfurt, Germany

    B. Schierwater  & B. Streit  & 

  2. Department of Biology, Yale University, 165 Prospect St., New Haven, CT, 06511, USA

    G. P. Wagner

  3. Department of Entomology, American Museum of Natural History, 79th Street at Central Park West, New York, NY, 10024, USA

    R. DeSalle

Additional information

Dedicated to the memory of Frantisek Novak (Joint FAO/IAEA Program, Plant Breeding Unit, Seibersdorf Laboratories, Vienna), a good friend and colleague.

Rights and permissions

Reprints and permissions

Copyright information

© 1994 Springer Basel AG

About this chapter

Cite this chapter

Weising, K., Ramser, J., Kaemmer, D., Kahl, G. (1994). Multilocus DNA fingerprinting and genetic relatedness in plants: A case study with banana and tomato. In: Schierwater, B., Streit, B., Wagner, G.P., DeSalle, R. (eds) Molecular Ecology and Evolution: Approaches and Applications. Experientia Supplementum, vol 69. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-7527-1_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-0348-7527-1_4

  • Publisher Name: Birkhäuser, Basel

  • Print ISBN: 978-3-0348-7529-5

  • Online ISBN: 978-3-0348-7527-1

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation