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

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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.

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References

  • Bhattramakki D, Dolan M, Hanafey M, Wineland R, Vaske D, Register JC III, Tingey SV, Rafalski A (2002) Insertion-deletion polymorphisms in 3′ regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol 48:539–547

    Article  CAS  PubMed  Google Scholar 

  • Brown JJ, Mattes MG, O‘Reilly C, Shepherd NS (1989) Molecular characterization of rDt, a maize transposon of the “Dotted” controlling element system. Mol Gen Genet 215:239–244

    Article  CAS  PubMed  Google Scholar 

  • Brown GR, Gill GP, Wheeler NC, Megraw RA, Neale DB (2002) Searching for genes underlying quantitative variation in confiner wood properties: candidate genes, single nucleotide polymorphisms, and an association study in Loblolly pine (Pinus taeda). In: Plant, Anim Microbe Genome 10th Conf. San Diego

    Google Scholar 

  • Cato SA, Gardner RC, Kent J, Richardson TE (2001) A rapid PRC-based method for genetically mapping ESTs. Theor Appl Genet 120:296–306

    Article  Google Scholar 

  • Ching A, Rafalski A (2002) Rapid genetic mapping of ESTs using SNP pyrosequencing and Indel analysis. Cell Mol Biol Lett 7:803–810

    CAS  PubMed  Google Scholar 

  • Colbert T, Till BJ, Tompa R, Reynolds S, Steine MN, Yeung AT, McCallum CM, Comai L, Henikoff S (2001) High-throughput screening for induced point mutations. Plant Physiol 126:480–484

    Article  CAS  PubMed  Google Scholar 

  • Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Henikoff S (2004) Efficient discovery of DNA polymorphisms in natural populations by ecotilling. Plant J 37:778–786

    Article  CAS  PubMed  Google Scholar 

  • Dellaporta A (1994) Plant DNA miniprep and microprep: version 2.1–2.3. In: Freeling M, Walbot V (eds) The maize handbook. Springer, Berlin Heidelberg New York, pp 522–525

    Google Scholar 

  • Kota R, Wolf M, Michalek W, Graner A (2001) Application of denaturing high-performance liquid chromatography for mapping of single nucleotide polymorphisms in barley (Hordeum vulgare L). Genome 44:523–528

    Article  CAS  PubMed  Google Scholar 

  • Kristensen VN, Kelefiotis D, Kristensen T, Borresen-Dale AL (2001) High-throughput methods for detection of genetic variation (324, 326 passim). Biotechniques 30:318–322

    CAS  PubMed  Google Scholar 

  • Lee M, Sharopova N, Beavis WD, Grant D, Katt M, Blair D, Hallauer A (2002) Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population. Plant Mol Biol 48:453–461

    Article  CAS  PubMed  Google Scholar 

  • Lemieux B (2001) Plant genotyping based on analysis of single nucleotide polymorphisms using microarrays. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CABI Publ, Wallingford, pp 47–58

    Google Scholar 

  • Li Q, Liu Z, Monroe H, Culiat CT (2002) Integrated platform for detection of DNA sequence variants using capillary array electrophoresis. Electrophoresis 23:1499–1511

    Article  CAS  PubMed  Google Scholar 

  • Martins-Lopes P, Zhang H, Koebner R (2001) Detection of single nucleotide mutations in wheat using single strand conformation polymorphism gels. Plant Mol Biol Rep 19:159–162

    CAS  Google Scholar 

  • McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeted screening for induced mutations. Nat Biotechnol 18:455–457

    Article  CAS  PubMed  Google Scholar 

  • Murphy KM, Hafez MJ, Philips J, Yarnell K, Gutshall KR, Berg KD (2003) Evaluation of temperature gradient capillary electrophoresis for detection of the Factor V Leiden mutation. Mol Diagn 7:35–40

    PubMed  Google Scholar 

  • Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res 9:163–171

    CAS  PubMed  Google Scholar 

  • Neuffer MG (1994) Mutagenesis. In: Freeling M, Walbot V (eds) The maize handbook. Springer, Berlin Heidelberg New York, pp 212–219

    Google Scholar 

  • Paris M, Jones MGK, Eglinton JK (2002) Genotyping single nucleotide polymorphisms for selection of barley beta-amylase alleles. Plant Mol Biol Rep 20:149–159

    CAS  Google Scholar 

  • Prince JA, Brookes AJ (2001) Towards high-throughput genotyping of SNPs by dynamic allele-specific hybridization. Expert Rev Mol Diagn 1:352–358

    Article  CAS  PubMed  Google Scholar 

  • Qi X, Bakht S, Devos KM, Gale MD, Osbourn A (2001) L-RCA (ligation-rolling circle amplification): a general method for genotyping of single nucleotide polymorphisms (SNPs). Nucleic Acids Res 29:e116

    Article  CAS  PubMed  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    CAS  PubMed  Google Scholar 

  • See D, Kanazin V, Talbert H, Blake T (1998) Primer mediated detection of single nucleotide polymorphisms. Barley Newsl 42

  • Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T, Duru N, Polacco M, Edwards K, Ruff T, Register JC, Brouwer C, Thompson R, Velasco R, Chin E, Lee M, Woodman-Clikeman W, Long MJ, Liscum E, Cone K, Davis G, Coe EH Jr (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–481

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This research was funded by competitive grants from the National Science Foundation Plant Genome Program (award numbers: DBI-9975868 and DBI-0321711). Support was also provided by Hatch Act and State of Iowa funds.

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Authors and Affiliations

  1. Department of Agronomy, Iowa State University, Ames, IA, 50011, USA

    An-Ping Hsia, Tsui-Jung Wen, Hsin D. Chen & Patrick S. Schnable

  2. SpectruMedix Corporation, State College, PA, 16803, USA

    Zhaowei Liu

  3. Interdepartmental Genetics Graduate Program, Iowa State University, Ames, IA, 50011, USA

    Marna D. Yandeau-Nelson & Yanling Wei

  4. Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, 50011, USA

    Ling Guo

  5. Center for Plant Genomics, Iowa State University, Ames, IA, 50011, USA

    Patrick S. Schnable

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  1. An-Ping Hsia
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  2. Tsui-Jung Wen
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  3. Hsin D. Chen
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  4. Zhaowei Liu
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  5. Marna D. Yandeau-Nelson
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  6. Yanling Wei
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  8. Patrick S. Schnable
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Correspondence to Patrick S. Schnable.

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Communicated by H.C. Becker

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Hsia, AP., Wen, TJ., Chen, H.D. et al. Temperature gradient capillary electrophoresis (TGCE)–a tool for the high-throughput discovery and mapping of SNPs and IDPs. Theor Appl Genet 111, 218–225 (2005). https://doi.org/10.1007/s00122-005-1997-5

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  • DOI: https://doi.org/10.1007/s00122-005-1997-5

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