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A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm

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Abstract

Several DNA marker systems and associated techniques are available today for fingerprinting plant germplasm but information on their relative usefulness in particular crops is limited. The study investigated PCR based DNA fingerprinting in a set of 39 potato cultivars using RAPDs (20 primers), ISSRs (6 primers), AFLPs (2 primers) and SSRs (5 primer pairs). Results show that each of the four techniques can on their own, individually identify each cultivar, but that techniques differ in the mean number of profiles generated per primer (or primer pair) per cultivar, referred to as Genotype Index (GI). The order of merit based on this criterium and in this material was AFLPs (GI = 1.0), a multi-locus SSR (GI = 0.77),RAPDs (GI = 0.53), ISSRs (GI = 0.47) and single locus SSRs (GI = 0.36). Problems in relating banding patterns to individual loci and alleles for polyploid genomes, using these techniques as they are currently employed, are also discussed.

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References

  • Akkaya, M.S., A.A. Bhagwat & P.B. Cregan, 1992. Length polymorphism of simple sequence repeat DNA in soybean. Genetics 132: 1131–1139.

    PubMed  CAS  Google Scholar 

  • Becker, J. & M. Heun, 1995. Barley microsatellites: allele variation and mapping. Plant Mol Biol 27: 835–845.

    Article  PubMed  CAS  Google Scholar 

  • Charters, Y.M., A. Robertson, M.J. Wilkinson & G. Ramsay, 1996. PCR analysis of oilseed rape cultivars (Brassica napus L. ssp. oleifera) using 50–anchored simple sequence repeat (SSR) primers. Theor Appl Genet 92: 442–447.

    Article  CAS  Google Scholar 

  • Cregan, P.B., 1992. Simple sequence repeat DNA length polymorphisms. Probe 2: 18–22.

    Google Scholar 

  • Crow, J.F., 1986. Basic concepts in population, quantitative, and evolutionary genetics. Library of Congress Cataloging. Freeman and company, New York.

    Google Scholar 

  • Demeke, T., D.R. Lynch, L.M. Kawchuk, G.C. Kozub & J.D. Armstrong, 1996. Genetic diversity of potato determined by random amplified polymorphic DNA analysis. Plant Cell Reports 15: 662–667.

    Article  CAS  Google Scholar 

  • Devis, K.M., G.J. Bryan, A.J. Collins, P. Stephenson & R. Gale, 1995. Application of two microsatellite sequences in wheat storage proteins as molecular markers. Theor Appl Genet 90: 247–252.

    Google Scholar 

  • Edwards, K., C. Johnstone & C. Thompson, 1991. A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucl Acids Res 19(6): 1349.

    PubMed  CAS  Google Scholar 

  • Fisher, P.J., R.C. Gardner & T.E. Richardson, 1996. Single locus microsatellites isolated using 50 anchored PCR. Nucl Acids Res 24(21): 4369–4371.

    Article  PubMed  CAS  Google Scholar 

  • Golembiewski, R.C., T.K. Danneberger & P.M. Sweeney, 1997. Potential of RAPD markers for use in the identification of creeping bentgrass cultivars. Crop Science 37: 212–214.

    Article  CAS  Google Scholar 

  • Halldén, C., M. Hansen, N.-O. Nilsson, A. Hjerdin & T. Säll, 1996. Competition as a source of errors in RAPD analysis. Theor Appl Genet 93: 1185–1192.

    Article  Google Scholar 

  • Hantula, J., M. Dusabenygasani & R.C. Hamelin, 1996. Random amplified microsatellites (RAMS)-a novel method for characterizing genetic variation within fungi. Eur J For Path 26: 159–166.

    Google Scholar 

  • Hartl, D.L., 1988. A primer of population genetics (2nd ed). Sinauer Associates, INC-Publishers, Massachusetts.

    Google Scholar 

  • He, G. & S. Prakash, 1997. Identification of polymorphic DNA markers in cultivated peanut (Arachis hypogaea L.). Euphytica 97: 143–149.

    Article  CAS  Google Scholar 

  • Hosaka, K., M. More & K. Ogawa, 1994. Genetic relationships of Japanese potato cultivars assessed by RAPD analysis. Am Potato J 71: 535–546.

    Google Scholar 

  • Iqbal, M.J. & A.L. Rayburn, 1994. Stability of RAPD markers for determining cultivar specific DNA profiles in rye (Secale cereale L.). Euphytica 75: 215–220.

    Article  CAS  Google Scholar 

  • Jondle, R.J., 1992. Legal aspects of varietal protection using molecular markers, pp. 50–52. In Applications of RAPD technology to plant breeding. Joint Plant Breeding symposia series.

  • Jones, C.J., K.J. Edwards, S. Castaglione, M.O. Winfield, F. Sala, C. van de Wiel, G. Bredemeijer, B. Vosman, M. Matthes, A. Maly, R. Brettschneider, P. Bettini, M. Buiatti, E. Maestri, A. Malcevschi, N. Marmiroli, R. Aert, G. Volckaert, J. Rueda, R. Linaacero, A. Vazque & A. Karp, 1997. Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Molecular Breeding 3: 381–390.

    Article  CAS  Google Scholar 

  • Kantety, R.V., X. Zeng, J.L. Bennetzen & B.E. Zehr, 1995. Assessment of genetic diversity in dent and popcorn (Zea mays L.) inbred lines using inter-simple sequence repeat (ISSR) amplification. Molecular Breeding 1: 365–373.

    Article  CAS  Google Scholar 

  • Karp, A. & K. Edwards, 1998. DNA markers: a global overview. In: G. Caetano-Annolés & P.M. Gresshoff (Eds.), DNA Markers: Protocols, Applications and Overviews, pp. 1–14. Wiley-VCH, New York.

    Google Scholar 

  • Kawchuck, L.M., D.R. Lynch, J. Thomas, B. Penner, D. Sillito & F. Kulcsar, 1996. Characterization of Solanum tuberosum simple sequence repeats and application to potato cultivar identification. Am Potato J 73: 325–335.

    Google Scholar 

  • Khandka, D.K., A. Nejidat & A. Golan-Goldhirsh, 1996. Polymorphism and DNA markers for asparagus cultivars identified by random amplified polymorphic DNA. Euphytica 87: 39–44.

    Article  CAS  Google Scholar 

  • Lanham, P.G. & R.M. Brennan, 1998. Characterization of the genetic resources of redcurrent (Ribes rubrum: subf. Ribesia) using anchored microsatellite markers. Theor Appl Genet 96: 917–921.

    Article  CAS  Google Scholar 

  • Lin, J.-J., J. Kuo, J. Ma, J.A. Saunders, H.S. Beard, M.H. MacDonald, W. Kenworthy, G.N. Ude & B.L. Mattews, 1996. Identification of molecular markers in soybean: comparing RFLP, RAPD, and AFLP DNA mapping techniques. Plant Mol Biol Rep 14: 156–169.

    CAS  Google Scholar 

  • Lui, Z. & G.R. Furnier, 1993. Comparison of allozyme, RFLP, and RAPD markers for revealing genetic variation within and between trembling aspen and bigtooth aspen. Theor Appl Genet 87: 97–105.

    Google Scholar 

  • Marshal, D.R. & R.W. Allard, 1970. Isozyme polymorphisms in natural populations of Avena fatua and A. barbata. Heredity 25: 373–382.

    Google Scholar 

  • Matthes, M.C., A. Daly & K.J. Edwards, 1998. Amplified Fragment Length Polymorphism (AFLP). In: A. Karp, P.G. Isaac & D.S. Ingram (Eds.), Molecular tools for screening biodiversity, pp. 183–192. Chapman & Hall, London.

    Google Scholar 

  • Milbourne, D., R. Meyer, J.E. Bradshaw, E. Baird, N. Bonar, J. Provan, W. Powell & R. Waugh, 1997. Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato. Molecular Breeding 3: 127–136.

    Article  CAS  Google Scholar 

  • Mohan, M., S. Nair, A. Bhagwat, T.G. Krishna, M. Yano, C.R. Bhatio & T. Sasaki, 1997. Genome mapping, molecular markers and marker-assisted selection in crop plants. Molecular Breeding 3: 87–103.

    Article  CAS  Google Scholar 

  • Morgante, M. & A.M. Olivieri, 1993. PCR-amplified microsatellites in plant genetics. The Plant Journal 3: 175–182.

    Article  PubMed  CAS  Google Scholar 

  • Nei, M., 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70: 3321–3323.

    Article  PubMed  CAS  Google Scholar 

  • Powell, W., M. Morgante, C. Andre, M. Hanafey, J. Vogel, S. Tingey & A. Rafalski, 1996. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 2: 225–238.

    Article  CAS  Google Scholar 

  • Provan, J., W. Powell & R. Waugh, 1996a. Microsatellite analysis of relationships within cultivated potato (Solanum tuberosum). Theor Appl Genet 92: 1078–1084.

    Article  CAS  Google Scholar 

  • Provan, J., W. Powell & R. Waugh, 1996b. Analysis of cultivated potato (Solanum tuberosum) using intermicrosatellite amplification. Genome 39: 767–769.

    CAS  PubMed  Google Scholar 

  • Rafalski, J.A., S.V. Tingey & J.G.K. Williams, 1991. RAPD markers-a new technology for genetic mapping and plant breeding. AgBiotech News and Information 3(4): 645–648.

    Google Scholar 

  • Russell, R.J., J.D. Fuller, M. Macaulay, B.G. Hats, A. Jahoor, W. Powell & R.Waugh, 1997. Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95: 714–722.

    Article  CAS  Google Scholar 

  • Smith, S., 1998. Cultivar identification and varietal protection. In: G. Caetano-Annolés & P.M. Gresshoff (Eds.), DNA Markers: Protocols, Applications and Overviews, pp. 383–400. Wiley-VCH, New York.

    Google Scholar 

  • Sosinski, B. & D.S. Douches, 1996. Using polymerase chain reaction-based DNA amplification to fingerprint North American potato cultivars. HortScience 31(1): 130–133.

    Google Scholar 

  • Taramino, G. & S. Tingey, 1996. Simple sequence repeats for germplasm analysis and mapping in maize. Genome 39: 277–287.

    PubMed  CAS  Google Scholar 

  • Vogel, J.M., A. Rafalski, W. Powell, M. Morgante, C. Andre, M. Hanafey & S.V. Tingey, 1996. Application of genetic diagnostics to plant genome analysis and plant breeding. HortScience 31(7): 1107–1108.

    Google Scholar 

  • Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. van der Lee, M. Hornes, A. Frijters, J. Pot, J. Peleman, M. Kuiper & M. Zabeau, 1995. AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23(21): 4407–4414.

    PubMed  CAS  Google Scholar 

  • Vos, P. & M. Kuiper, 1998. AFLP analysis. In: G. Caetano-Annolés & P.M. Gresshoff (Eds.), DNA Markers: Protocols, Applications and Overviews, pp. 115–131. Wiley-VCH, New York.

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Zietkiewics, E., A. Rafalski & D. Labuda, 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20: 176–183.

    Article  Google Scholar 

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Authors and Affiliations

  1. ARC Roodeplaat, Vegetable and Ornamental Plant Institute, Private Bag X293, Pretoria, 0001, Republic of South Africa

    C.E. McGregor & M.M. Greyling

  2. Department of Genetics, University of Stellenbosch, Private Bag X1, Matieland, Stellenbosch, 7602, Republic of South Africa

    C.A. Lambert, J.H. Louw & L. Warnich

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  1. C.E. McGregor
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  2. C.A. Lambert
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  3. M.M. Greyling
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  4. J.H. Louw
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  5. L. Warnich
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McGregor, C., Lambert, C., Greyling, M. et al. A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica 113, 135–144 (2000). https://doi.org/10.1023/A:1003925620546

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