Skip to main content
SpringerLink
Log in

New Technologies for Ultra-High Throughput Genotyping in Plants

  • Protocol
  • First Online:
Plant Genomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 513))

Summary

Molecular genetic markers represent one of the most powerful tools for the analysis of plant genomes and the association of heritable traits with underlying genetic variation. Molecular marker technology has developed rapidly over the last decade, with the development of high-throughput genotyping methods. Two forms of sequence-based marker, simple sequence repeats (SSRs), also known as microsatellites and single nucleotide polymorphisms (SNPs) now predominate applications in modern plant genetic analysis, along the anonymous marker systems such as amplified fragment length polymorphisms (AFLPs) and diversity array technology (DArT). The reducing cost of DNA sequencing and increasing availability of large sequence data sets permits the mining of this data for large numbers of SSRs and SNPs. These may then be used in applications such as genetic linkage analysis and trait mapping, diversity analysis, association studies and marker-assisted selection. Here, we describe automated methods for the discovery of molecular markers and new technologies for high-throughput, low-cost molecular marker genotyping. Genotyping examples include multiplexing of SSRs using Multiplex-Ready® marker technology (MRT); DArT genotyping; SNP genotyping using the Invader® assay, the single base extension (SBE), oligonucleotide ligation assay (OLA) SNPlex™ system, and Illumina GoldenGate™ and Infinium® methods.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Gupta, P.K., Roy, J.K., and Prasad, M. (2001) Single nucleotide polymorphisms: A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr. Sci. 80, 524–535.

    CAS  Google Scholar 

  2. Brumfield, R.T., Beerli, P., Nickerson, D.A., and Edwards, S.V. (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol. Evol. 18, 249–256.

    Article  Google Scholar 

  3. Collins, A., Lau, W. and De la Vega, F.M. (2004) Mapping genes for common diseases: The case for genetic (LD) maps. Hum. Hered. 58, 2–9.

    Article  PubMed  Google Scholar 

  4. Rafalski, A. (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5, 94–100.

    Article  PubMed  CAS  Google Scholar 

  5. Edwards, D., Forster, J.W., Chagné, D., and Batley, J. (2007) What are SNPs?, in Association Mapping in Plants (Oraguzie, N.C., Rikkerink, E.H.A., Gardiner, S.E., and De Silva, H.N., eds.), Springer, NY, 41–52.

    Chapter  Google Scholar 

  6. Batley, J. and Edwards, D. (2007) SNP applications in plants, in Association Mapping in Plants (Oraguzie, N.C., Rikkerink, E.H.A., Gardiner, S.E. and, De Silva, H.N. eds.) Springer, NY, 95–102.

    Chapter  Google Scholar 

  7. Edwards, D., Batley, J., Cogan, N.O.I., Forster, J.W., and Chagné, D. (2007) Single nucleotide polymorphism discovery, in Association Mapping in Plants (Oraguzie, N.C., Rikkerink, E.H.A., Gardiner, S.E., and De Silva, H.N. eds.) Springer, NY, 53–76.

    Chapter  Google Scholar 

  8. Syvanen, A.C. (2001) Genotyping single nucleotide polymorphisms. Nat. Rev. Genet. 2, 930–942.

    Article  PubMed  CAS  Google Scholar 

  9. Tóth, G., Gáspári, Z., and Jurka, J. (2000) Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Res. 10, 967–981.

    Article  PubMed  Google Scholar 

  10. Katti, M.V., Ranjekar, P.K., and Gupta, V.S. (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol. Biol. Evol. 18, 1161–1167.

    Article  PubMed  CAS  Google Scholar 

  11. Schlötterer, C. (2000) Evolutionary dynamics of microsatellite DNA. Nucleic Acids Res. 20, 211–215.

    Article  Google Scholar 

  12. Tautz, D. (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17, 6463–6471.

    Article  PubMed  CAS  Google Scholar 

  13. Powell, W., Machray, G.C., and Provan, J. (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1, 215–222.

    Google Scholar 

  14. Subramanian, S., Mishra, R.K., and Singh, L. (2003) Genome-wide analysis of microsatellite repeats in humans: Their abundance and density in specific genomic regions. Genome Biol. 4, R13.

    Article  PubMed  Google Scholar 

  15. Awadalla, P. and Ritland, K. (1997) Microsatellite variation and evolution in the Mimulus guttatus species complex with contracting mating systems. Mol. Biol. Evol. 14, 1023–1034.

    PubMed  CAS  Google Scholar 

  16. Moxon, E.R. and Wills, C. (1999) DNA microsatellites: Agents of evolution. Sci. Am. 280, 94–99.

    Article  PubMed  CAS  Google Scholar 

  17. Kashi, Y., King, D., and Soller, M. (1997) Simple sequence repeats as a source of quantitative genetic variation. Trends Genet. 13, 74–78.

    Article  PubMed  CAS  Google Scholar 

  18. Gupta, 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.

    Article  CAS  Google Scholar 

  19. Mortimer, J., Batley, J., Love, C., Logan, E., and Edwards, D. (2005) Simple sequence repeat (SSR) and GC distribution in the Arabidopsis thaliana genome. J. Plant Biotechnol. 7, 17–25.

    Google Scholar 

  20. Li, Y.-C., Korol, A.B., Fahima, T., Beiles, A., and Nevo, E. (2002) Microsatellites: Genomic distribution, putative functions and mutational mechanisms: A review. Mol. Ecol.11, 2453–2465.

    Article  PubMed  Google Scholar 

  21. Jaccoud, D., Peng, K., Feinstein, D., and Kilian, A. (2001) Diversity arrays: A solid state technology for sequence information independent genotyping. Nucleic Acids Res. 29, e25.

    Article  PubMed  CAS  Google Scholar 

  22. Xia, L., Peng, K., Yang, S., Wenzl, P., de Vicente, C., Fregene, M., and Kilian, A. (2005) DArT for high-throughput genotyping of cassava (Manihot esculenta) and its wild relatives. Theor. Appl. Genet. 110, 1092–1098.

    Article  PubMed  CAS  Google Scholar 

  23. Yang, S., Pang, W., Ash, G., Harper, J., Carling, J., Wenzl, P., Huttner, E., and Kilian, A. (2006) Low level of genetic diversity in cultivated pigeonpea compared to its wild relatives is revealed by diversity arrays technology (DArT). Theor. Appl. Genet. 113, 585–595.

    Article  PubMed  CAS  Google Scholar 

  24. Xie, Y., McNally, K., Li, C.Y., Leung, H., and Zhu, Y.Y. (2006) A high-throughput genomic tool: Diversity array technology complementary for rice genotyping. J. Integr. Plant Biol. 48, 1069–1076.

    Article  CAS  Google Scholar 

  25. Akbari, M., Wenzl, P., Vanessa, C., Carling, J., Xia, L., Yang, S., Uszynski, G., Mohler, V., Lehmensiek, A., Kuchel, H., Hayden, M.J., Howes, N., Sharp, P., Rathmell, B., Vaughan, P., Huttner, E., and Kilian, A. (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor. Appl. Genet. 113, 1409–1420.

    Article  PubMed  CAS  Google Scholar 

  26. Wenzl, P., Li, H., Carling, J., Zhou, M., Raman, H., Paul, E., Hearnden, P., Maier, C., Xia, L., Caig, V., Ovesna, J., Cakir, M., Poulsen, D., Wang, J., Raman, R., Smith, K.P., Muehlbauer, G.J., Chalmers, K.J., Kleinhofs, A., Huttner, E., and Kilian, A. (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and phenotypic traits. BMC Genom. 7, 206.

    Article  Google Scholar 

  27. Wenzl, P., Carling, J., Kudrna, D., Jaccoud, D., Huttner, E., Kleinhofs, A., and Kilian, A. (2004) Diversity arrays technology (DArT) for whole-genome profiling of barley. PNAS. 101, 9915–9920.

    Article  PubMed  CAS  Google Scholar 

  28. Ewing, B. and Green, P. (1998a) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186–194.

    CAS  Google Scholar 

  29. Ewing, B., Hillier, L., Wendl, M.C., and Green, P. (1998b) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185.

    CAS  Google Scholar 

  30. Barker, G., Batley, J., O'Sullivan, H., Edwards, K.J., and Edwards, D. (2003) Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19, 421–422.

    Article  PubMed  CAS  Google Scholar 

  31. Batley, J., Barker, G., O'Sullivan, H., Edwards, K.J., and Edwards, D. (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol. 132, 84–91.

    Article  PubMed  CAS  Google Scholar 

  32. Savage, D., Batley, J., Erwin, T., Logan, E., Love, C.G., Lim, G.A.C., Mongin, E., Barker, G., Spangenberg, G.C., and Edwards, D. (2005) SNPServer: A real-time SNP discovery tool. Nucleic Acids Res. 33, W493–W495.

    Article  PubMed  CAS  Google Scholar 

  33. Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Genome Res. 9, 868–877.

    Article  PubMed  CAS  Google Scholar 

  34. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410.

    PubMed  CAS  Google Scholar 

  35. Edwards, K.J., Barker, J.H.A., Daly, A., Jones, C., and Karp, A. (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20, 758–760.

    PubMed  CAS  Google Scholar 

  36. Robinson, A.J., Love, C.G., Batley, J., Barker, G., and Edwards, D. (2004) Simple sequence repeat marker loci discovery using SSRPrimer. Bioinfomatics 20, 1475–1476.

    Article  CAS  Google Scholar 

  37. Jewell, E., Robinson, A., Savage, D., Erwin, T., Love, C.G., Lim, G.A.C., Li, X., Batley, J., Spangenberg, G.C., and Edwards, D. (2006) SSR Primer and SSR Taxonomy Tree: Biome SSR discovery. Nucleic Acids Res. 34, W656–W659.

    Article  PubMed  CAS  Google Scholar 

  38. Hapmap, C.A. (2003) The International HapMap Project: The International HapMap Consortium. Nature 426, 789–796.

    Article  Google Scholar 

  39. Mein, C.A., Barratt, B.J., Dunn, M.G., Siegmund, T., Smith, A.N., Esposito, L., Nutland, S., Stevens, H.E., Wilson, A.J., Phillips, M.S., Jarvis, N., Law, S., De Arruda, M., and Todd, J.A. (2000) Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation. Genome Res. 10, 330–343.

    Article  PubMed  CAS  Google Scholar 

  40. Olivier, M. (2005) The Invader® assay for SNP genotyping. Mutat. Res. 573, 103–110.

    Article  PubMed  CAS  Google Scholar 

  41. Olivier, M., Chuang, L.M., Chang, M.S., Chen, Y.T., Pei, D., Ranade, K., de Witte, A., Allen, J., Tran, N., Curb, D., Pratt, R., Neefs, H., de Arruda, M., Law, S., Neri, B., Wang, L., and Cox, D.R. (2002) High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology. Nucleic Acids Res. 30, e53.

    Article  PubMed  Google Scholar 

  42. Gupta, M., Nirunsuksiri, W., Schulenberg, G., Hartl, T., Novak, S., Bryan, J., Vanopdorp, N., Bing, J., and Thompson, S. (2008) A non-PCR-based Invader® assay quantitatively detects single-copy genes in complex plant genomes. Mol. Breeding 21,173–181.

    Google Scholar 

  43. Fan, J.-B., Oliphant, A., Shen, R., Kermani, B.G., Garcia, F., Gunderson, K.L., Hansen, M., Steemers, F., Butler, S.L., Deloukas, P., Galver, L., Hunt, S., McBride, C., Bibikova, M., Rubano, T., Chen, J., Wickham, E., Doucet, D., Chang, W., Campbell, D., Zhang, B., Kruglyak, S., Bentley, D., Haas, J., Rigault, P., Zhou, L., Stuelpnagel, J., and Chee, M.S. (2003) Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol. 68, 69–78.

    Article  PubMed  CAS  Google Scholar 

  44. Gunderson, K.L., Steemers, F.J., Lee, G., Mendoza, L.G., and Chee, M.S. (2005) A genome-wide scalable SNP genotyping assay using microarray technology. Nat. Genet. 37, 549–554.

    Article  PubMed  CAS  Google Scholar 

  45. Pastinen, T., Kurg, A., Metspalu, A., Peltonen, L., and Syvänen, A.-C. (1997) Minisequencing: A specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 7, 606–614.

    PubMed  CAS  Google Scholar 

  46. Batley, J., Mogg, R., Edwards, D., O'Sullivan, H., and Edwards, K.J. (2003). A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. Mol. Breeding 11, 111–120.

    Article  CAS  Google Scholar 

  47. Ekstroem, B., Alderborn, A., and Hammerling, U. (2000) Pyrosequencing for SNPs. Proceedings of SPIE—The International Society for Optical Engineering 3926, 134–139.

    CAS  Google Scholar 

  48. Chen, J., Iannone, M.A., Li, M.-S., Taylor, J.D., Rivers, P., Nelsen, A.J., Slentz-Kesler, K.A., Roses, A., and Weiner, M.P. (2000) A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res. 10, 549–557.

    Article  PubMed  CAS  Google Scholar 

  49. Haff, L.A. and Smirnov, I.P. (1997) Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res. 7, 378–388.

    PubMed  CAS  Google Scholar 

  50. Hsu, T.M., Chen, X., Duan, S., Miller, R.D., and Kwok, P.-Y. (2001) Universal SNP genotyping assay with fluorescence polarization detection. BioTechniques 31, 560–570.

    PubMed  CAS  Google Scholar 

  51. Törjek, O., Berger, D., Meyer, B.C., Müssig, C., Schmid, K.J., Sörensen, T.R., Weisshaar, B., Mitchell-Olds, T., and Altmann, T. (2003) Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis. Plant J. 36, 122–140.

    Article  PubMed  Google Scholar 

  52. Landegren, U., Kaiser, R., Sanders, J., and Hood, L. (1988) A ligase-mediated gene detection technique. Science 241, 1077–1080.

    Article  PubMed  CAS  Google Scholar 

  53. Tobler, A.R., Short, S., Andersen, M.R., Paner, T.M., Briggs, J.C., Lambert, S.M., Wu, P.P., Wang, Y., Spoonde, A.Y., Koehler, R.T., Peyret, N., Chen, C., Broomer, A.J., Ridzon, D.A., Zhou, H., Hoo, B.S., Hayashibara, K.C., Leong, L.N., Ma, C.N., Rosenblum, B.B., Day, J.P., Ziegle, J.S., de la Vega, F.M., Rhodes, M.D., Hennessy, K.M., and Wenz, H.M. (2005) The SNPlex genotyping system: A flexible and scalable platform for SNP genotyping. J. Biomol. Tech. 16, 398–406.

    PubMed  Google Scholar 

  54. Green, P. (1994) Phrap, unpublished. www.phrap.org

    Google Scholar 

  55. Gordon, D., Abajian, C. and, Green, P. (1998) Consed: A graphical tool for sequence finishing. Genome Res. 8, 195–202.

    PubMed  CAS  Google Scholar 

  56. Marth, G.T., Korf, I., Yandell, M.D., Yeh, R.T., Gu, Z.J., Zakeri,, H., Stitziel,, N.O., Hillier, L., Kwok,, P.Y. and, Gish,, W.R. (1999) A general approach to single nucleotide polymorphism discovery. Nat. Genet. 23, 452–456.

    Article  PubMed  CAS  Google Scholar 

  57. Chagné, D., Batley, J., Edwards, D., and Forster, J.W. (2007) Single nucleotide polymorphisms genotyping in plants, in Association Mapping in Plants (Oraguzie, N.C., Rikkerink, E.H.A., Gardiner, S.E. and, De Silva, H.N., eds.), Springer, NY, 77–94.

    Chapter  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. ARC Centre for Integrated Legume Research, University of Queensland, Brisbane, Australia

    Jacqueline Batley

Authors
  1. Nikki Appleby
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. David Edwards
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jacqueline Batley
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jacqueline Batley .

Editor information

Editors and Affiliations

    Rights and permissions

    Reprints and permissions

    Copyright information

    © 2009 Humana Press, a part of Springer Science+Business Media, LLC

    About this protocol

    Cite this protocol

    Appleby, N., Edwards, D., Batley, J. (2009). New Technologies for Ultra-High Throughput Genotyping in Plants. In: Gustafson, J., Langridge, P., Somers, D. (eds) Plant Genomics. Methods in Molecular Biology™, vol 513. Humana Press. https://doi.org/10.1007/978-1-59745-427-8_2

    Download citation

    • DOI: https://doi.org/10.1007/978-1-59745-427-8_2

    • Published:

    • Publisher Name: Humana Press

    • Print ISBN: 978-1-58829-997-0

    • Online ISBN: 978-1-59745-427-8

    • eBook Packages: Springer Protocols

    Publish with us

    Policies and ethics

    Search

    Navigation