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Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes

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Abstract

A panel of 13 sugar beet lines and one genotype each of the Beta vulgaris cultivars red beet and Swiss chard, and B. vulgaris ssp. maritima were used to identify polymorphisms in alignments of genomic DNA sequences derived from 315 EST- and 43 non-coding RFLP-derived loci. In sugar beet lines, loci of expressed genes showed an average SNP frequency of 1/72 bp, 1 in 58 bp in non-coding sequences, increasing to 1/47 bp upon the addition of the remaining genotypes. Within analysed DNA fragments, alleles at different SNP positions displayed linkage disequilibrium indicative of haplotype structures. On average 2.7 haplotypes were found in sugar beet lines, and haplotype conservation in expressed genes appeared to exceed 500 bp in length. Seven different genotyping techniques including SNP detection by MALDI-TOF mass spectrometry, pyrosequencing and fluorescence scanning of labelled nucleotides were employed to perform 712 segregation analyses for 538 markers in three F2 populations. Functions were predicted for 492 mapped sequences. Genetic maps comprised 305 loci covering 599.8 cM in population K1, 241 loci distributed over 636.6 cM in population D2, and 166 loci over 507.1 cM in population K2, respectively. Based on 156 markers common to more than one population an integrated map was constructed with 524 loci covering 664.3 cM. For 377 loci the genome positions of the most similar sequences from A. thaliana were identified, but little evidence for previously presented ancestral genome structures was found.

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Acknowledgment

The project was supported by the GABI (Genomanalyse im biologischen System Pflanze) initiative funded by Bundesministerium für Bildung und Forschung (Germany). Funding by grants with the numbers 0312283A, 0312283B, 0312283E, 0312283H, and 0312283D/0 is gratefully acknowledged.

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Authors and Affiliations

  1. Department of Plant Breeding and Yield Physiology, Max-Planck-Institute for Plant Breeding Research (MPIZ), Carl-von-Linné Weg 10, 50827, Cologne, Germany

    Katharina Schneider, Thomas Rosleff Soerensen, Silke Möhring & Bernd Weisshaar

  2. GSF-National Research Center for Environment and Health, Institute for Radiation Protection, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany

    Katharina Schneider

  3. TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Gatersleben, Germany

    Dagmar Kulosa, Martin Heine, Gregor Durstewitz, Andreas Polley & Martin Ganal

  4. Institute of Genome Research, University of Bielefeld, 33594, Bielefeld, Germany

    Thomas Rosleff Soerensen & Bernd Weisshaar

  5. Institute for Plant Breeding and Plant Protection, Martin-Luther-University Halle-Wittenberg, 06099, Halle, Germany

    Eberhard Weber & Emma Tahiro

  6. Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098, Kiel, Germany

    Jamsari, Jens Lein, Uwe Hohmann & Christian Jung

  7. KWS SAAT AG, Grimsehlstrasse 31, 37555, Einbeck, Germany

    Britta Schulz

  8. Strube-Dieckmann, Saatzucht Dieckmann GmbH & Co. KG, Kirchhorster Str. 16, 31688, Nienstaedt, Germany

    Georg Koch

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  1. Katharina Schneider
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  16. Christian Jung
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Correspondence to Katharina Schneider.

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Communicated by R. Waugh.

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Schneider, K., Kulosa, D., Soerensen, T.R. et al. Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theor Appl Genet 115, 601–615 (2007). https://doi.org/10.1007/s00122-007-0591-4

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