Chapter 4. Single Nucleotide Polymorphisms: Detection Techniques and Their Potential for Genotyping and Genome Mapping

  1. Prof. Dr. Khalid Meksem5,
  2. Prof. Dr. Günter Kahl6
  1. Günter Kahl6,
  2. Andrea Mast1,
  3. Nigel Tooke2,
  4. Richard Shen3,
  5. Dirk van den Boom4

Published Online: 28 APR 2005

DOI: 10.1002/3527603514.ch4

Book Title

The Handbook of Plant Genome Mapping: Genetic and Physical Mapping

The Handbook of Plant Genome Mapping: Genetic and Physical Mapping

Additional Information

How to Cite

Kahl, G., Mast, A., Tooke, N., Shen, R. and van den Boom, D. (2005) Single Nucleotide Polymorphisms: Detection Techniques and Their Potential for Genotyping and Genome Mapping, in The Handbook of Plant Genome Mapping: Genetic and Physical Mapping (eds K. Meksem and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/3527603514.ch4

Editor Information

  1. 5

    Dept. Plant, Soil, Agriculture Southern Illinois University, Carbondale, IL 629, USA

  2. 6

    Plant Molecular Biology Biocentre and GenXPro Johann Wolfgang Goethe University Marie-Curie-Strasse 9 60439 Frankfurt am Main, Germany

Author Information

  1. 1

    Third Wave Technologies, 502 South Rosa Road, Madison, WI 53719-1256, USA

  2. 2

    Biotage AB, Kungsgatan 76, 753 18 Uppsala, Sweden

  3. 3

    Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA 92121-1975, USA

  4. 4

    SEQUENOM, Inc., 3595 John Hopkins Court, San Diego, CA 92121, USA

  5. 6

    Plant Molecular Biology Biocentre and GenXPro Johann Wolfgang Goethe University Marie-Curie-Strasse 9 60439 Frankfurt am Main, Germany

Publication History

  1. Published Online: 28 APR 2005
  2. Published Print: 26 JAN 2005

ISBN Information

Print ISBN: 9783527311163

Online ISBN: 9783527603510

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CHAPTER TOOLS

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Keywords:

  • plant genome mapping;
  • genetic mapping;
  • single nucleotide polymorphisms;
  • detection techniques;
  • SNP analysis I;
  • SNP analysis II: pyrosequencing;
  • SNP analysis III: a scalable high-multiplex SNP genotyping platform;
  • SNP analysis IV: high-throughput SNP analysis by MALDI-TOF MS

Summary

This chapter contains sections titled:

  • Introduction

  • Selected Techniques

    • SNP Analysis I: The Invader Technology

      • Introduction

      • Cleavase Enzymes

      • Oligonucleotides and Structure

      • Probe Cycling and Signal Amplification

      • DNA Format

      • RNA Format

      • Alternate Detection Formats

      • Specificity

      • Robustness

      • Invader Applications

      • Conclusion

    • SNP Analysis II: Pyrosequencing

      • Introduction

      • SNP Genotyping Using Pyrosequencing Technology

      • Allele Frequency Quantification

      • Haplotyping

    • SNP Analysis III: A Scalable High-multiplex SNP Genotyping Platform

      • Introduction

      • The Illumina Genotyping Platform

      • Genotyping Data

      • Conclusion

    • SNP Analysis IV: High-throughput SNP Analysis by MALDI-TOF MS

      • Introduction

      • SNP Analysis Using the Massarray Platform

  • Conclusions and Perspectives

  • Acknowledgments

  • References

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