Genic DNA methylation changes during in vitro organogenesis: organ specificity and conservation between parental lines of epialleles

Authors

  • Stéphane Maury,

    Corresponding author
    1. Laboratoire de Biologie des Ligneux et des Grandes Cultures, UPRES EA 1207, USC1328 ARCHE INRA, rue de Chartres, BP 6759, Faculté des Sciences, Université d’Orléans, 45067 Orléans cedex 2, France
      e-mail: stephane.maury@univ-orleans.fr
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    • These authors contributed equally to this work.

  • Marie-Véronique Trap-Gentil,

    1. Laboratoire de Biologie des Ligneux et des Grandes Cultures, UPRES EA 1207, USC1328 ARCHE INRA, rue de Chartres, BP 6759, Faculté des Sciences, Université d’Orléans, 45067 Orléans cedex 2, France
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    • These authors contributed equally to this work.

  • Claire Hébrard,

    1. Laboratoire de Biologie des Ligneux et des Grandes Cultures, UPRES EA 1207, USC1328 ARCHE INRA, rue de Chartres, BP 6759, Faculté des Sciences, Université d’Orléans, 45067 Orléans cedex 2, France
    2. SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark,B-3300 Tienen, Belgium
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  • Guy Weyens,

    1. SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark,B-3300 Tienen, Belgium
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  • Alain Delaunay,

    1. Laboratoire de Biologie des Ligneux et des Grandes Cultures, UPRES EA 1207, USC1328 ARCHE INRA, rue de Chartres, BP 6759, Faculté des Sciences, Université d’Orléans, 45067 Orléans cedex 2, France
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  • Steve Barnes,

    1. SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark,B-3300 Tienen, Belgium
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  • Marc Lefebvre,

    1. SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark,B-3300 Tienen, Belgium
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  • Claude Joseph

    1. Laboratoire de Biologie des Ligneux et des Grandes Cultures, UPRES EA 1207, USC1328 ARCHE INRA, rue de Chartres, BP 6759, Faculté des Sciences, Université d’Orléans, 45067 Orléans cedex 2, France
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e-mail: stephane.maury@univ-orleans.fr

Abstract

During differentiation, in vitro organogenesis calls for the adjustment of the gene expression program toward a new fate. The role of epigenetic mechanisms including DNA methylation is suggested but little is known about the loci affected by DNA methylation changes, particularly in agronomic plants for witch in vitro technologies are useful such as sugar beet. Here, three pairs of organogenic and non-organogenic in vitro cell lines originating from different sugar beet (Beta vulgaris altissima) cultivars were used to assess the dynamics of DNA methylation at the global or genic levels during shoot or root regeneration. The restriction landmark genome scanning for methylation approach was applied to provide a direct quantitative epigenetic assessment of several CG methylated genes without prior knowledge of gene sequence that is particularly adapted for studies on crop plants without a fully sequenced genome. The cloned sequences had putative roles in cell proliferation, differentiation or unknown functions and displayed organ-specific DNA polymorphism for methylation and changes in expression during in vitro organogenesis. Among them, a potential ubiquitin extension protein 6 (UBI6) was shown, in different cultivars, to exhibit repeatable variations of DNA methylation and gene expression during shoot regeneration. In addition, abnormal development and callogenesis were observed in a T-DNA insertion mutant (ubi6) for a homologous sequence in Arabidopsis. Our data showed that DNA methylation is changed in an organ-specific way for genes exhibiting variations of expression and playing potential role during organogenesis. These epialleles could be conserved between parental lines opening perspectives for molecular markers.

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