Theoretical and Applied Genetics

, Volume 111, Issue 2, pp 218–225 | Cite as

Temperature gradient capillary electrophoresis (TGCE)–a tool for the high-throughput discovery and mapping of SNPs and IDPs

  • An-Ping Hsia
  • Tsui-Jung Wen
  • Hsin D. Chen
  • Zhaowei Liu
  • Marna D. Yandeau-Nelson
  • Yanling Wei
  • Ling Guo
  • Patrick S. Schnable
Original Paper

Abstract

Temperature gradient capillary electrophoresis (TGCE) can be used to distinguish heteroduplex from homoduplex DNA molecules and can thus be applied to the detection of various types of DNA polymorphisms. Unlike most single nucleotide polymorphism (SNP) detection technologies, TGCE can be used even in the absence of prior knowledge of the sequences of the underlying polymorphisms. TGCE is both sensitive and reliable in detecting SNPs, small InDel (insertion/deletion) polymorphisms (IDPs) and simple sequence repeats, and using this technique it is possible to detect a single SNP in amplicons of over 800 bp and 1-bp IDPs in amplicons of approximately 500 bp. Genotyping data obtained via TGCE are consistent with data obtained via gel-based detection technologies. For genetic mapping experiments, TGCE has a number of advantages over alternative heteroduplex-detection technologies such as celery endonuclease (CELI) and denaturing high-performance liquid chromatography (dHPLC). Multiplexing can increase TGCE’s throughput to 12 markers on 94 recombinant inbreds per day. Given its ability to efficiently and reliably detect a variety of subtle DNA polymorphisms that occur at high frequency in genes, TGCE shows great promise for discovering polymorphisms and conducting genetic mapping and genotyping experiments.

Supplementary material

122_2005_1997_ESM_supp.pdf (49 kb)
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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • An-Ping Hsia
    • 1
  • Tsui-Jung Wen
    • 1
  • Hsin D. Chen
    • 1
  • Zhaowei Liu
    • 2
  • Marna D. Yandeau-Nelson
    • 3
  • Yanling Wei
    • 3
  • Ling Guo
    • 4
  • Patrick S. Schnable
    • 1
    • 5
  1. 1.Department of AgronomyIowa State UniversityAmesUSA
  2. 2.SpectruMedix CorporationState CollegeUSA
  3. 3.Interdepartmental Genetics Graduate ProgramIowa State UniversityAmesUSA
  4. 4.Bioinformatics and Computational Biology Graduate ProgramIowa State UniversityAmesUSA
  5. 5.Center for Plant GenomicsIowa State UniversityAmesUSA

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