title: Epigenomics and bolting tolerance in sugar beet genotypes.
abstract: In sugar beet (Beta vulgaris altissima), bolting tolerance is an essential agronomic trait reflecting the bolting response of genotypes after vernalization. Genes involved in induction of sugar beet bolting have now been identified, and evidence suggests that epigenetic factors are involved in their control. Indeed, the time course and amplitude of DNA methylation variations in the shoot apical meristem have been shown to be critical in inducing sugar beet bolting, and a few functional targets of DNA methylation during vernalization have been identified. However, molecular mechanisms controlling bolting tolerance levels among genotypes are still poorly understood. Here, gene expression and DNA methylation profiles were compared in shoot apical meristems of three bolting-resistant and three bolting-sensitive genotypes after vernalization. Using Cot fractionation followed by 454 sequencing of the isolated low-copy DNA, 6231 contigs were obtained that were used along with public sugar beet DNA sequences to design custom Agilent microarrays for expression (56k) and methylation (244k) analyses. A total of 169 differentially expressed genes and 111 differentially methylated regions were identified between resistant and sensitive vernalized genotypes. Fourteen sequences were both differentially expressed and differentially methylated, with a negative correlation between their methylation and expression levels. Genes involved in cold perception, phytohormone signalling, and flowering induction were over-represented and collectively represent an integrative gene network from environmental perception to bolting induction. Altogether, the data suggest that the genotype-dependent control of DNA methylation and expression of an integrative gene network participate in bolting tolerance in sugar beet, opening up perspectives for crop improvement.
authors.affiliation: Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, 45067 Orléans, France INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans, France SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark, B-3300 Tienen, Belgium.
authors.forename: Claire
authors.initials: C
authors.lastname: Hébrard
authors.affiliation: Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, 2 Research Blvd., Box 9627, Mississippi State, MS 39762, USA.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Peterson
authors.affiliation: SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark, B-3300 Tienen, Belgium.
authors.forename: Glenda
authors.initials: G
authors.lastname: Willems
authors.affiliation: Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, 45067 Orléans, France INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Delaunay
authors.affiliation: IMAXIO/HELIXIO, Biopôle Clermont-Limagne, Saint-Beauzire, F-63360, France.
authors.forename: Béline
authors.initials: B
authors.lastname: Jesson
authors.affiliation: SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark, B-3300 Tienen, Belgium.
authors.forename: Marc
authors.initials: M
authors.lastname: Lefèbvre
authors.affiliation: SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark, B-3300 Tienen, Belgium.
authors.forename: Steve
authors.initials: S
authors.lastname: Barnes
authors.affiliation: Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, 45067 Orléans, France INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans, France stephane.maury@univ-orleans.fr.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Maury
mesh_terms: D027461:Beta vulgaris / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D035264:Flowers / Q000235:genetics / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins
keywords: Bolting tolerance; differentially expressed gene; differentially methylated region; epigenomics; microarray; sugar beet; vernalization.