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Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana

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Abstract

Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds of restriction site based polymorphisms between genotypes and does not require DNA sequence information or site-specific oligonucleotides. This paper demonstrates the potential of DArT for genetic mapping by validating the quality and molecular basis of the markers, using the model plant Arabidopsis thaliana. Restriction fragments from a genomic representation of the ecotype Landsberg erecta (Ler) were amplified by PCR, individualized by cloning and spotted onto glass slides. The arrays were then hybridized with labeled genomic representations of the ecotypes Columbia (Col) and Ler and of individuals from an F2 population obtained from a Col × Ler cross. The scoring of markers with specialized software was highly reproducible and 107 markers could unambiguously be ordered on a genetic linkage map. The marker order on the genetic linkage map coincided with the order on the DNA sequence map. Sequencing of the Ler markers and alignment with the available Col genome sequence confirmed that the polymorphism in DArT markers is largely a result of restriction site polymorphisms.

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Acknowledgements

We thank Andy Pereira for providing seeds from the A. thaliana ecotypes Ler, Col and from the F2 population used for mapping. We also thank our colleagues Gerard van der Linden, Mark Kemper, Mark Fiers and Hong Tran (Plant Research International) and Eric Huttner (DArT Pty./Ltd.) for constructive discussions during the course of this work and of manuscript preparation. This project was supported by a travel grant from the Netherlands Organization for Scientific Research (NWO)

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Authors and Affiliations

  1. Department of Plant Sciences, Laboratory of Plant Breeding, The Graduate School Experimental Plant Sciences, Wageningen University and Research Centre, P.O. Box 386, 6700, AJ Wageningen, The Netherlands

    Alexander H. J. Wittenberg & Richard G. F. Visser

  2. Plant Research International, Wageningen University and Research Centre, P.O. Box 16, 6700, AA Wageningen, The Netherlands

    Alexander H. J. Wittenberg, Theo van der Lee & Henk J. Schouten

  3. Diversity Arrays Technology Pty. Ltd, G.P.O. Box 3200, Canberra, ACT 2601, Australia

    Cyril Cayla & Andrzej Kilian

  4. Center for the Application of Molecular Biology to International Agriculture, G.P.O. Box 3200, Canberra, ACT 2601, Australia

    Andrzej Kilian

Authors
  1. Alexander H. J. Wittenberg
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  2. Theo van der Lee
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  3. Cyril Cayla
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  4. Andrzej Kilian
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  5. Richard G. F. Visser
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  6. Henk J. Schouten
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Correspondence to Henk J. Schouten.

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Wittenberg, A.H.J., Lee, T.v.d., Cayla, C. et al. Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana. Mol Genet Genomics 274, 30–39 (2005). https://doi.org/10.1007/s00438-005-1145-6

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  • DOI: https://doi.org/10.1007/s00438-005-1145-6

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