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Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting—peak ratios) method

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Abstract

Polysomic inheritance frequently results in the simultaneous occurrence of several microsatellite DNA alleles on a single locus. The MAC-PR (microsatellite DNA allele counting—peak ratios) method was recently developed for the analysis of polyploid plants and makes use of the quantitative values for microsatellite allele peak areas. To date, this approach has only been used in plants with known genetic relationships. We report here the application of MAC-PR for the first time to random samples of unknown pedigrees. We analysed six microsatellite loci using a set of tetraploid ornamental rose (Rosa × hybrida L.) varieties. For each locus, all alleles were analysed in pairwise combinations in order to determine their copy number in the individual samples. This was accomplished by calculating the ratios between the peak areas for two alleles in all of the samples where these two alleles occurred together. The allele peak ratios observed were plotted in a histogram, and those histograms that produced at least two well-separated groups were selected for further analysis. Mean allelic peak ratio values for these groups were compared to the relationships expected between alleles in hypothetical configurations of the locus investigated. Using this approach, we were able to assign precise allelic configurations (the actual genotype) to almost all of the varieties analysed for five of the six loci investigated. MAC-PR also appears to be a very effective tool for detecting ‘null’ alleles in polyploid species.

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Acknowledgements

Financial support was received from the Erik Philip-Sörensen Foundation and the Commission of the European Communities, specific Research programme ‘Quality of Life and Management of Living Resources’, QLRT-2001-01278 ‘Genetic evaluation of European rose resources for conservation and horticultural use’. It does not necessarily reflect its views and in no way anticipates the Commission’s future policy in this area.

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Authors and Affiliations

  1. Department of Biodiversity and Breeding, Plant Research International, P.O. Box 16, 6700 AA, Wageningen, The Netherlands

    G. D. Esselink & B. Vosman

  2. Balsgård-Department of Crop Science, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 291 94, Kristianstad, Sweden

    H. Nybom

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  1. G. D. Esselink
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  2. H. Nybom
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  3. B. Vosman
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Correspondence to H. Nybom.

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Communicated by C. Möllers

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Esselink, G.D., Nybom, H. & Vosman, B. Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting—peak ratios) method. Theor Appl Genet 109, 402–408 (2004). https://doi.org/10.1007/s00122-004-1645-5

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  • DOI: https://doi.org/10.1007/s00122-004-1645-5

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