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A new approach to extending the wheat marker pool by anchored PCR amplification of compound SSRs

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Abstract

A study was undertaken to determine the utility in bread wheat of anchored PCR for the development of single locus SSR markers targeted at compound repeat motifs. In anchored PCR, microsatellite amplification is achieved using a single primer complementary to the flanking sequence, and one which anchors to the repeat junction of the compound SSR. The recovery rate of useable markers was found to be similar (43%) to that reported for conventionally generated SSRs. Thus, anchored PCR can be used to reduce the costs of marker development, since it requires that only half the number of primers be synthesised. Where fluorescence-based platforms are used, marker deployment costs are lower, since only the anchoring primers need to be labelled. In addition, anchored PCR improves the recovery of useful markers, as it allows assays to be generated from microsatellite clones with repeat sequences located close to their ends, a situation where conventional PCR amplification fails as two flanking primers cannot be designed. Strategies to permit the large-scale development of compound SSR markers amplified by anchored PCR are discussed.

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Acknowledgements

The authors thank the members of the Wheat Microsatellite Consortium who kindly gave their permission to publish the sequences of microsatellite clones included in this manuscript. This research was supported by the Value Added Wheat CRC, and Grains Research and Development Corporation, Australia, the Biotechnology and Biological Sciences Research Council, UK, and the International Atomic Energy Agency (IAEA RCA-11023).

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Authors and Affiliations

  1. Plant Breeding Institute, Cobbitty, University of Sydney, PMB 11, Camden, NSW, 2570 Australia

    M. J. Hayden, D. Khatkar & P. J. Sharp

  2. Value Added Wheat CRC, LB 1345, PO North Ryde, NSW, 2113 Australia

    M. J. Hayden & P. J. Sharp

  3. Crop Genetics Department, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK

    P. Stephenson, A. M. Logojan, C. Rogers, R. M. D. Koebner & J. W. Snape

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  1. M. J. Hayden
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  2. P. Stephenson
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  3. A. M. Logojan
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  4. D. Khatkar
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  5. C. Rogers
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  6. R. M. D. Koebner
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  7. J. W. Snape
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  8. P. J. Sharp
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Correspondence to M. J. Hayden.

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Communicated by P. Langridge

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Hayden, M.J., Stephenson, P., Logojan, A.M. et al. A new approach to extending the wheat marker pool by anchored PCR amplification of compound SSRs. Theor Appl Genet 108, 733–742 (2004). https://doi.org/10.1007/s00122-003-1480-0

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  • DOI: https://doi.org/10.1007/s00122-003-1480-0

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