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Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (Quercus spp.)

Authors

  • E. GUICHOUX,

    1. INRA, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
    2. University of Bordeaux, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
    3. Centre de Recherche Pernod-Ricard, F-94000 Créteil, France
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  • L. LAGACHE,

    1. INRA, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
    2. University of Bordeaux, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
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  • S. WAGNER,

    1. INRA, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
    2. University of Bordeaux, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
    3. University of Bonn, Steinmann Institut, D-53115 Bonn, Germany
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  • P. LÉGER,

    1. INRA, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
    2. University of Bordeaux, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
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  • R.J. PETIT

    1. INRA, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
    2. University of Bordeaux, UMR Biodiversité Gènes & Communautés 1202, F-33610 Cestas, France
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Rémy J. Petit, INRA-Univ. Bordeaux, UMR BIOGECO, 69 route d’Arcachon, 33612 Cestas, France, Fax: +33557122881; E-mail: petit@pierroton.inra.fr

Abstract

Multiplex PCR is a fast and cost-effective technique allowing increased genotyping throughput of microsatellites. We developed two multiplexes for Quercus petraea and Q. robur, a 12-plex of EST-SSRs (eSSRs) and an 8-plex of genomic SSRs (gSSRs). We studied the origin of allele calling errors at the human reader and software levels. We showed that the robustness of allele identification can be improved by binning on raw peak sizes prior to genetic data analysis. We checked through simulation the power of these markers for species delimitation and hybrid detection. The resolution achieved with all 20 markers was greatly improved compared to that of previous studies based on a subset of the markers. Preliminary PCR tests suggest that these multiplexes might be useful to study other oak species as well. The strategy used for multiplex microsatellite development (from PCR conditions to the definition of allele calling rules) should be broadly applicable.

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