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PCR-based marker systems

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DNA-Based Markers in Plants

Part of the book series: Advances in Cellular and Molecular Biology of Plants ((CMBP,volume 6))

Abstract

There has been a continual evolution in methods used to determine the genetic makeup of individuals. The complete genetic makeup or genotype of an individual is represented by its entire DNA sequence; however, until entire genomes can be sequenced with little effort, geneticists will continue to rely on genetic markers as a means of characterising the genotypic variation of individuals.

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References

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

    PubMed  CAS  Google Scholar 

  • Allard, R.W. (1956) Formulas and tables to facilitate the calculation of recombination value in heredity. Hilgardia 24: 235–278.

    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

    Google Scholar 

  • Caetano-Anolles, G., Bassam, B.J., and Gresshoff, P.M. (1991) DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Bio/Technology 9: 292–305.

    Google Scholar 

  • Caetano-Anolles, G., and Gresshoff, P.M. (1994) DNA amplification fingerprinting using arbitrary mini-hairpin oligonucleotide primers. Bio/Technology 12: 619–623.

    Article  PubMed  CAS  Google Scholar 

  • Caetano-Anolles, G., and Gresshoff, P.M. (1996) Generation of sequence signatures from DNA amplification fingerprints with mini-hairpin and microsatellite primers. Biotechniques 20: 1044–1056.

    PubMed  CAS  Google Scholar 

  • Caetano-Anolles, G., Bassam, B.J., and Gresshoff, P.M. (1993) Enhanced detection of polymorphic DNA by multiple arbitrary amplicon profiling of endonuclease digested DNA: identification of markers tightly linked to the supernodulation locus of soybean. Mol. Gen. Genet. 241: 57–64.

    Google Scholar 

  • Caetano-Anolles, G. (1994) MAAP: a versatile and universal tool for genome analysis. Plant Mol. Biol. 25: 1011–1026.

    Google Scholar 

  • Caetano-Anolles, G. (1996) Scanning of nucleic acids by in vitro amplification: New developments and applications. Nature Biotechnolgy 14: 1668–1674.

    Google Scholar 

  • Callahan, L.M., Weaver, K.R., Caetano-Anolles, G., Bassam, B.J., and Gresshoff, P.M. (1993) DNA fingerprinting of turfgrasses. Int. Turfgrass Soc. Res. J. 7: 761–767.

    Google Scholar 

  • Carlson, J.E., Tulsieram, L.K., Glaubitz, J.C., Luk, V., Kauffeldt, C., and Rutledge, R. (1991) Segregation of random amplified DNA markers in Fl progeny of conifers. Theor. Appl. Genet. 83: 194–200.

    Google Scholar 

  • Cifarelli, R.A., Gallitelli, M., and Cellini, F. (1995) Random amplified hybridization microsatellites (RAHM): isolation of a new class of microsatellite-containing DNA clones. Nucleic Acids Res. 23: 3802–3803.

    Article  PubMed  CAS  Google Scholar 

  • Cregan, P. (1997) Soybean SSR marker development - application in legumes. Final Program and Abstracts Guide, Plant and Animal Genome V, Abs. W74, p 45.

    Google Scholar 

  • D’Ovidio, R., and Anderson, O.P. (1994) PCR analysis to distinguish between alleles of a member of a multigene family correlated with wheat bread-making quality. Theor. Appl. Genet. 88: 759–763.

    Google Scholar 

  • Edwards, A., Hammond, H.A., Jin, L., Caskey, C.T., and Chakraborty, R. (1992) Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics 12: 241–253.

    Article  PubMed  CAS  Google Scholar 

  • Eng, C. and Vijg, J. (1997) Genetic testing: the problems and the promise. Nature Biotechnology 15: 422–426.

    Article  PubMed  CAS  Google Scholar 

  • Fischer, S.G. and Lerman, L.S. (1979) Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell 16: 191–200.

    Article  PubMed  CAS  Google Scholar 

  • Guta, M., Chyi, Y.-S., Romero-Severson, J., and Owen, J.L. (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor. Appl. Genet. 89: 998–1006.

    Google Scholar 

  • Haff, L.A. and Smirnov, I.P. (1997) Multiplex genotyping of PCR products with MassTag-labeled primers. Nucleic Acids Res. 25: 3749–3750.

    Article  PubMed  CAS  Google Scholar 

  • Hill, M., Witsenboer, H., Zabeau, M., Vos, P., Kesseli, R., and Michelmore, R. (1996) PCR-based fingerprinting using AFLPs as a tool for studying genetic relationships in Lactuca spp. Theor. Appl. Genet. 93: 1202–1210.

    Google Scholar 

  • Konieczny, A., and Ausubel, F.M. (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. The Plant J. 4: 403–410.

    Article  CAS  Google Scholar 

  • Kuppuswami, M.N., Hoffmann, J.W., Kasper, C.K., Spitzer, S.G., Groce, S.L., and Bajaj, S.P. (1991) Single nucleotide primer extension to detect genetic diseases: Experimental application to hemophilia B (factor IX) and cystic fibrosis genes. Proc. Natl. Acad. Sci. USA 88: 1143–1147.

    Google Scholar 

  • Marshall, E. (1997) The hunting of the SNP. Science 278: 2047.

    Article  CAS  Google Scholar 

  • Maughan, P.J, Saghai Maroof, M.A., and Buss, G.R. (1995) Microsatellite and amplified sequence length polymorphisms in cultivated and wild soybean. Genome 38: 715–723.

    Article  PubMed  CAS  Google Scholar 

  • Monforte, J.A. and Becker, C.H. (1997) High-throughput DNA analysis by time-of-flight mass spectrometry. Nature Medicine 3: 360–362.

    Article  PubMed  CAS  Google Scholar 

  • Myers, R.M., Sheffield, V.C., and Cox, D.R. (1988) Detection of single base changes in DNA: ribonuclease cleavage and denaturing gradient gel electrophoresis In: K.E. Davies (ed.), Genome Analysis: A Practical Approach. pp. 95–139. IRL Press, Oxford.

    Google Scholar 

  • Nikiforov, T.T., Rendle, R.B., Goelet, P., Rogers, Y-H., Kotewicz, M.L., Anderson, S., Trainor, G.L., and Knapp, M.R. (1994) Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res. 22: 4167–4175.

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

  • Menendez, C.M., Hall, A.E., and Gepts, P. (1997) A genetic-linkage map of cowpea (VignaUnguiculata) developed from a cross between 2 inbred, domesticated lines. Theor. Appl. Genet. 95: 1210–1217.

    Google Scholar 

  • Mohler, V., and Jahoor, A. (1996) Allele-specific amplification of polymorphic sites for the detection of powdery mildew resistance loci in cereals. Theor. Appl. Genet. 93: 1078–1082.

    Google Scholar 

  • Morgante, M. and Vogel, J.M. (1996) Compound microsatellite primers for the detection of genetic polymorphisms. World Patent Organization WO96/17082.

    Google Scholar 

  • Nandi, S., Subudhi, P.K., Senadhira, D., Manigbas, N.L., Senmandi, S., and Huang, N. (1997) Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Mol. Gen. Genet. 255: 1–8.

    Google Scholar 

  • Parks, C., Chang, L.-S., and Shenk, T. (1991) A polymerase chain reaction mediated by a single primer: cloning of genomic sequences adjacent to a serotonin receptor protein coding region. Nucleic Acids Res. 19: 7155–7160.

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

  • Powell, W., Thomas, W.T.B., Baird, E., Lawrence, P., Booth, A., Harrower, B., McNicol, J.W., and Waugh, R. (1997) Analysis of quantitative traits in barley by the use of amplfied fragment length polymorphisms. Heredity 79: 48–59.

    Article  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.

    Google Scholar 

  • Richardson, T., Cato, S., Ramser, J., Kahl, G., and Weising, K. (1995) Hybridization of microsatellites to RAPD: a new source of polymorphic markers. Nucleic Acids Res. 23: 3798–3799.

    Article  PubMed  CAS  Google Scholar 

  • Saiki, R.K., Scharf, S. Faloona, F., Mullis, K.B., Horn, G.T., Erlich, H.A. and Arnheim, N. (1985) Enzymatic amplification of ß-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230: 1350–1354.

    CAS  Google Scholar 

  • Sax, K. (1923) The association of size differences with seed coat pattern and pigmentation in Phaseolus vulgarus. Genetics 8: 552: 560.

    Google Scholar 

  • Stuber, C.W. and Goodman M.M. (1983) Allozyme genotypes for popular and historically important inbred lines of corn, Zea mays L. USDA Agric. Res. Results, Southern Ser., No. 16.

    Google Scholar 

  • Syvanen, A.-C., Aalto-Setala, K., Harju, L., Kontula, K., and Soderlund, H. (1990) A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics 8: 684–692.

    Article  CAS  Google Scholar 

  • Tingey, S.V., Rafalski, J.A., and Williams, J.G.K. (1992) Genetic analysis with RAPD markers. In: Proceedings of the Symposium, Applications of RAPD Technology to Plant Breeding. Crop Sci. Soc./Amer. Soc. Hort. Sci./Amer. Genet. Assoc. p 3–8.

    Google Scholar 

  • To, K.-Y., Liu, C.-I., Liu, S.-T., and Chang, Y.-S. (1993) Detection of point mutations in the chloroplast genome by single-stranded conformation polymorphism analysis. Plant J. 3: 183–186.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Vuylsteke, M., Anonise, R., Bastiaans, E., Senior M., Stuber, C., and Kuiper, M. (1997) A high density AFLP Linkage map of Zea mays L. Final Program and Abstracts Guide, Plant and Animal Genome V, Abs. P206, p 104.

    Google Scholar 

  • Wang, D., Sapolsky, R., Spencer, J., Rioux, J., Kruglyak, L., Hubbell, E., Ghandour, G., Hawkins, T., Hudson, T., Lipshutz, R., and Lander, E. (1996) Toward a third generation genetic map of the human genome based on bi-allelic polymorphisms. Am. J. Human Genet. 59 supplement p. A3.

    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 

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

    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 

  • Williams, K.J., Fisher, J.M., and Langridge, P. (1996) Development of a PCR-based allele-specific assay from an RFLP probe linked to resistance to cereal cyst nematode in wheat. Genome 39: 798–801.

    Article  PubMed  CAS  Google Scholar 

  • Wu, K.-S., Jones, R., Danneberger, L., and P.A. Scolnik (1994) Detection of microsatellite polymorphisms without cloning Nucleic Acids Res. 22: 3257–3258.

    Article  CAS  Google Scholar 

  • Xu, L. and Hall, B.G. (1994) SASA: a simplified, reliable method for allele-specific amplification of polymorphic sites. BioTechniques 6: 44–45.

    Google Scholar 

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

    Google Scholar 

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Author information

Authors and Affiliations

  1. Monsanto, Agricultural Technology, Molecular Breeding Group, Ankeny, IA, 50021, USA

    Robert Reiter

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  1. Robert Reiter
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Editors and Affiliations

  1. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108-6026, USA

    Ronald L. Phillips

  2. Laboratory of Plant Cell and Molecular Biology, University of Florida, Gainesville, Florida, 32611-0690, USA

    Indra K. Vasil

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© 2001 Springer Science+Business Media Dordrecht

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Reiter, R. (2001). PCR-based marker systems. In: Phillips, R.L., Vasil, I.K. (eds) DNA-Based Markers in Plants. Advances in Cellular and Molecular Biology of Plants, vol 6. Springer, Dordrecht. https://doi.org/10.1007/978-94-015-9815-6_2

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  • DOI: https://doi.org/10.1007/978-94-015-9815-6_2

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-90-481-5672-6

  • Online ISBN: 978-94-015-9815-6

  • eBook Packages: Springer Book Archive

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