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9 results on '"Annick Dubois"'

1. Dynamique de la Chromatine , développement des plantes, ingéniérie épigénomique

Author

François Roudier, Annick Dubois, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and ANR-18-CE12-0014,ChromAuxi,Décodage de la réponse auxine à l'interface ARFs-chromatine(2018)

Subjects
0106 biological sciences, QH301-705.5, Computer science, [SDV]Life Sciences [q-bio], Health, Toxicology and Mutagenesis, plant, Computational biology, Review, 01 natural sciences, Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, 03 medical and health sciences, Genome regulation, Genetics, Epigenome editing, CRISPR, Cellular dynamics, Biology (General), epigenome engineering, 030304 developmental biology, 0303 health sciences, CRISPR-dCas9, Epigenome, Chromatin, CRISPR-dC9as9, epigenome editing, Medicine, chromatin, Transcription (software), Function (biology), 010606 plant biology & botany
Abstract

International audience; CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss how recent progress in plants and animals provides new routes to investigate the function of chromatin regulators and address the complexity of associated regulations that are often interconnected. While efficient transcriptional engineering methodologies have been developed and can be used as tools to alter the chromatin state of a locus, examples of direct manipulation of chromatin regulators remain scarce in plants. These reports also reveal pitfalls and limitations of epigenome engineering approaches that are nevertheless informative as they are often associated with locus- and context-dependent features, which include DNA accessibility, initial chromatin and transcriptional state or cellular dynamics. Strategies implemented in different organisms to overcome and even take advantage of these limitations are highlighted, which will further improve our ability to establish the causality and hierarchy of chromatin dynamics on genome regulation.

Published
2021

2. Biosynthesis of 2-Phenylethanol in Rose Petals Is Linked to the Expression of One Allele of RhPAAS

Author

Fabrice Foucher, Philippe Vergne, Mohammed Bendahmane, Emilie Cavel, Aymeric Roccia, Laurence Hibrand-Saint Oyant, Judit Szécsi, Sylvie Baudino, Tatiana Thouroude, Aurélie Rius Bony, Jean-Claude Caissard, Annick Dubois, Julien Jeauffre, Jana Machenaud, Laboratoire BVpam, Université Jean Monnet [Saint-Étienne] (UJM), Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (BVPAM), Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Region Auvergne-Rhone-Alpes, INRA, France, CNRS GDR MediatEC 3658, ANR Rosascent, Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, Candidate gene, Physiology, Population, Quantitative Trait Loci, Plant Science, Flowers, Quantitative trait locus, Biology, Rosa, 01 natural sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cultivar, Allele, education, Alleles, Hybrid, Plant Proteins, 2. Zero hunger, education.field_of_study, Vase life, food and beverages, Articles, Phenylethyl Alcohol, Biosynthetic Pathways, Odorants, Petal, 010606 plant biology & botany
Abstract

International audience; Floral scent is one of the most important characters in horticultural plants. Roses (Rosa spp.) have been cultivated for their scent since antiquity. However, probably by selecting for cultivars with long vase life, breeders have lost the fragrant character in many modern roses, especially the ones bred for the cut flower market. The genetic inheritance of scent characters has remained elusive so far. In-depth knowledge of this quantitative trait is thus very much needed to breed more fragrant commercial cultivars. Furthermore, rose hybrids harbor a composite genomic structure, which complexifies quantitative trait studies. To understand rose scent inheritance, we characterized a segregating population from two diploid cultivars, Rosa × hybrida cv H190 and Rosa wichurana, which have contrasting scent profiles. Several quantitative trait loci for the major volatile compounds in this progeny were identified. One among these loci contributing to the production of 2-phenylethanol, responsible for the characteristic odor of rose, was found to be colocalized with a candidate gene belonging to the 2-phenylethanol biosynthesis pathway: the PHENYLACETALDEHYDE SYNTHASE gene RhPAAS. An in-depth allele-specific expression analysis in the progeny demonstrated that only one allele was highly expressed and was responsible for the production of 2-phenylethanol. Unexpectedly, its expression was found to start early during flower development, before the production of the volatile 2-phenylethanol, leading to the accumulation of glycosylated compounds in petals.; Analyse des composés du parfum dans une population en ségrégation qui montre que la synthèse du2-phenylethanol est liée à l'expression d'un allèle deu gène de laphenylacetaldehyde synthase dans les pétales

Published
2019

3. ROSE GENOMICS: CHALLENGES AND PERSPECTIVES

Author

Olivier Raymond, Mohammed Bendahmane, Annick Dubois, Judit Szécsi, Jérémy Just, Philippe Vergne, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Flanders Research Institute for Agriculture, Fisheries and Food (ILVO). BEL., École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Rose (mathematics), 0303 health sciences, [SDV]Life Sciences [q-bio], food and beverages, Genomics, Horticulture, Biology, 01 natural sciences, 03 medical and health sciences, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, genome, Rosaceae, 030304 developmental biology, 010606 plant biology & botany
Abstract

International audience; Cultivated roses have a very ancient history. Artificial crossing led to what is today perceived as modern rose cultivars. Impressively, these modern rose cultivars were established from less than 10 species, which have contributed to the origin of the about 35,000 existing rose cultivars. Roses exhibit an extraordinary diversity of traits, both of economic and scientific importance. Several recent studies have been marked as important milestones on the journey towards deeply understanding the molecular and genetic mechanisms that govern these traits, yet we still lack information on the genome sequences of rose species and cultivars, especially those that heavily participated to rose domestication and breeding programs.

Published
2015

4. Genetics and genomics of flower initiation and development in roses

Author

Manuel Le Bris, Olivier Raymond, Mohammed Bendahmane, Annick Dubois, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Avignon Université (AU), Biologie Vegetale Department of the French 'Institut National de la Recherche Agronomique, École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Time Factors, Physiology, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Color, Plant Development, morphogenesis, POWDERY MILDEW RESISTANCE, Genomics, Flowers, Plant Science, Cut flowers, Biology, Genes, Plant, Rosa, 01 natural sciences, HYBRIDA L, DIPLOROSES, Anthocyanins, 03 medical and health sciences, Gene Expression Regulation, Plant, Flowering Newsletter Review, Ornamental plant, Botany, genomics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, MOLECULAR CHARACTERIZATION, Domestication, Plant Proteins, rose, 030304 developmental biology, BUD BURST, Volatile Organic Compounds, 0303 health sciences, FLORAL IDENTITY GENES, fungi, food and beverages, FLAVONOBIOSYNTHETIC-PATHWAY, AGROBACTERIUM-TUMEFACIENS, biology.organism_classification, O-METHYLTRANSFERASES, Plant development, Phenotype, Flower, Petal, MADS-BOX GENES, 010606 plant biology & botany
Abstract

International audience; Roses hold high symbolic value and great cultural importance in different societies throughout human history. They are widely used as garden ornamental plants, as cut flowers, and for the production of essential oils for the perfume and cosmetic industries. Domestication of roses has a long and complex history, and the rose species have been hybridized across vast geographic areas such as Europe, Asia, and the Middle East. The domestication processes selected several flower characters affecting floral quality, such as recurrent flowering, double flowers, petal colours, and fragrance. The molecular and genetic events that determine some of these flower characters cannot be studied using model species such as Arabidopsis thaliana, or at least only in a limited manner. In this review, we comment on the recent development of genetic, genomic, and transcriptomic tools for roses, and then focus on recent advances that have helped unravel the molecular mechanisms underlying several rose floral traits.

Published
2013

5. Biosynthesis of monoterpene scent compounds in roses

Author

Stéphanie Huguet, Julien Jeauffre, Sophie Meyer, Raymonde Baltenweck, Sylvie Baudino, Michel Rohmer, Annick Dubois, Aymeric Roccia, Mohammed Bendahmane, Fabrice Foucher, Romain Hecquet, Patricia Claudel, Laurence Hibrand-Saint Oyant, Philippe Hugueney, Jean-Claude Caissard, Florence Nicolè, Pulu Sun, Frédéric Jullien, Jean-Louis Magnard, Olivier Raymond, Philippe Vergne, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM), Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Institut Le Bel, Region Rhone-Alpes, CNRS [GDR 2827], ENS Lyon, INRA, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (BVPAM), Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire BVpam, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Louis Pasteur - Strasbourg I, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)

Subjects
0106 biological sciences, Rose, pyrophosphatase, Monoterpene, [SDV]Life Sciences [q-bio], Biology, plastide, Biosynthesis, 01 natural sciences, Nudix hydrolase, Terpene, 03 medical and health sciences, chemistry.chemical_compound, Botany, donnée de séquence moléculaire, Cultivar, odeur, 2-phenylethanol, Geranyl diphosphate, biosynthesis, rose, monoterpene, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, fungi, food and beverages, Metabolic pathway, Enzyme, Biochemistry, chemistry, transcriptome, Geraniol, 010606 plant biology & botany
Abstract

Stop to smell the roses Some roses smell beautiful, yet others only look beautiful. Magnard et al. leveraged this distinction to study the biosynthesis of geraniol, a monoterpene alcohol in rose scent (see the Perspective by Tholl and Gershenzon). Enzymes known for geraniol synthesis in other plants, such as basil, did not seem to provide that function for roses. Instead, a diphosphohydrolase, which functions in the cytoplasm of cells in rose petals, generates the geraniol emitted by fragrant roses. Identification of the enzyme and its gene enables marker-assisted breeding to put the perfume back into beauty. Science , this issue p. 81 ; see also p. 28

Published
2015

6. Transcriptome database resource and gene expression atlas for the rose

Author

Rossitza Atanassova, Sylvie Baudino, Ludovic Cottret, Aymeric Roccia, Soulaiman Sakr, Annick Dubois, Olivier Raymond, Jérôme Gouzy, Manuel Le Bris, Fabrice Foucher, Jean-Paul Onesto, Benjamin Pouvreau, Sébastien Carrère, Mohammed Bendahmane, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Institut de Recherches Historiques du Septentrion (IRHiS) - UMR 8529 (IRHiS), Université de Lille-Centre National de la Recherche Scientifique (CNRS), AIP-Bioressources programme, 'Biologie Vegetale' Department of the French 'Institut National de la Recherche Agronomique', 'Genetique et Amelioration des Plantes' Department of the French 'Institut National de la Recherche Agronomique', and Centre National de la Recherche Scientifique (CNRS)-Université de Lille

Subjects
0106 biological sciences, Gene Expression, Polymerase Chain Reaction, 01 natural sciences, Genome, scent compound, Transcriptome, Gene Expression Regulation, Plant, functional-characterization, Arabidopsis, Databases, Genetic, Gene expression, [SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture, Plant Proteins, rose, Expressed Sequence Tags, 2. Zero hunger, Regulation of gene expression, Genetics, 0303 health sciences, Expressed sequence tag, biology, o-methyltransferases, High-Throughput Nucleotide Sequencing, BIOTECHNOLOGY & APPLIED MICROBIOLOGY, homolog, product-moment correlation, phenylacetaldehyde reductase, Multigene Family, Rose, Gene expression atlas, PRODUCT-MOMENT CORRELATION, POLLEN DEVELOPMENT, PHENYLACETALDEHYDE REDUCTASE, FUNCTIONAL-CHARACTERIZATION, O-METHYLTRANSFERASES, SCENT COMPOUND, ARABIDOPSIS, BIOSYNTHESIS, EVOLUTION, HOMOLOG, Prunus, DNA microarray, Genome, Plant, Plant Shoots, Research Article, Biotechnology, lcsh:QH426-470, lcsh:Biotechnology, Rosa, Fragaria, 03 medical and health sciences, lcsh:TP248.13-248.65, evolution, RNA, Messenger, Gene, 030304 developmental biology, pollen development, biology.organism_classification, lcsh:Genetics, arabidopsis, biosynthesis, transcriptome, Software, 010606 plant biology & botany
Abstract

Background For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce. Results Here, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways. Conclusions The study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy.

Published
2012

7. Genomic approach to study floral development genes in Rosa sp

Author

Philippe Vergne, Sandrine Balzergue, Fabrice Legeai, Julien Jeauffre, Mohammed Bendahmane, Arnaud Remay, Jean-Pierre Renou, Tatiana Thouroude, Aurelie Chauvet, Annick Dubois, Fabrice Foucher, Marie-Laure Martin-Magniette, Yann Pecrix, Shu-Hua Yang, Véronique Boltz, Stéphane Janczarski, Olivier Raymond, Manuel Le Bris, Marion Maene, Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Génétique et Horticulture (GenHort), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Génétique et Horticulture (GENHORT), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-Institut National d'Horticulture, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Service de Gynécologie et Obstétrique [Rennes] = Gynaecology [Rennes], CHU Pontchaillou [Rennes], This work was funded by the 'Biologie Vegetale' and the 'Genetique et Amelioration des Plantes' Departments of the French Institut National de la Recherche Agronomique, and by the Region Rhones-Alpes. Dr. Maene, Dr. Pecrix and Dr. Remay were supported by funds from the Region Rhone Alpes (Dr. Maene), The Region PACA (Dr. Pecrix) and by a joint grant from Region Pays de la Loire and the French 'Institut National de la Recherche Agronomique' (Dr. Remay). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., Bendahmane, Mohammed, École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut National d'Horticulture-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Service de Gynécologie et Obstétrique [Rennes], Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CHU Pontchaillou [Rennes]-Hôpital Sud, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Paul Cézanne - Aix-Marseille 3-Centre National de la Recherche Scientifique (CNRS)-Avignon Université (AU)-Université de Provence - Aix-Marseille 1, Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1)

Subjects
0106 biological sciences, initiation florale, Floral development, Microarrays, Plant genetics, Gene Identification and Analysis, lcsh:Medicine, F62 - Physiologie végétale - Croissance et développement, Plant Science, 01 natural sciences, microscopie électronique à balayage, F30 - Génétique et amélioration des plantes, Transcriptomes, Meristems, Transcriptome, rosa, Gene Expression Regulation, Plant, Floraison, Databases, Genetic, lcsh:Science, rosa genetics, molecular sequence annotation, meristem genetics, genes, developmental genetics, multidisciplinary sciences, science and technology, Flowering Plants, Roses, Oligonucleotide Array Sequence Analysis, Plant Growth and Development, Expressed Sequence Tags, Genetics, 0303 health sciences, Expressed sequence tag, Multidisciplinary, Vegetal Biology, mrna, phytogénétique, Gene Expression Regulation, Developmental, food and beverages, Genomics, Plants, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ABC model of flower development, stade de développement, Meristem initiation, analyse microarray, puce à adn, rosier, Méristème, Sequence databases, DNA microarray, Research Article, expression des gènes, Meristem, Flowers, Biology, Genes, Plant, Real-Time Polymerase Chain Reaction, génomique, Molecular Genetics, 03 medical and health sciences, Genome Analysis Tools, Botany, Transcription factors, Gene Regulation, Genes, Developmental, Stade de développement végétal, Gene Networks, Gene, 030304 developmental biology, lcsh:R, stade de floraison, fungi, méristème floral, Molecular Sequence Annotation, lcsh:Q, Gene expression, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Biologie végétale, Developmental Biology, 010606 plant biology & botany
Abstract

International audience; Cultivated for centuries, the varieties of rose have been selected based on a number of flower traits. Understanding the genetic and molecular basis that contributes to these traits will impact on future improvements for this economically important ornamental plant. In this study, we used scanning electron microscopy and sections of meristems and flowers to establish a precise morphological calendar from early rose flower development stages to senescing flowers. Global gene expression was investigated from floral meristem initiation up to flower senescence in three rose genotypes exhibiting contrasted floral traits including continuous versus once flowering and simple versus double flower architecture, using a newly developed Affymetrix microarray (Rosa1_Affyarray) tool containing sequences representing 4765 unigenes expressed during flower development. Data analyses permitted the identification of genes associated with floral transition, floral organs initiation up to flower senescence. Quantitative real time PCR analyses validated the mRNA accumulation changes observed in microarray hybridizations for a selection of 24 genes expressed at either high or low levels. Our data describe the early flower development stages in Rosa sp, the production of a rose microarray and demonstrate its usefulness and reliability to study gene expression during extensive development phases, from the vegetative meristem to the senescent flower.

Published
2011

8. Tinkering with the C-function : a molecular frame for the selection of double flowers in cultivated roses

Author

Sylvie Baudino, Véronique Boltz, Philippe Vergne, Nicolas B. Langlade, Olivier Raymond, Mohammed Bendahmane, Marion Maene, Annick Dubois, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (BVPAM), Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)

Subjects
0106 biological sciences, Models, Anatomic, Gynoecium, Stamen, lcsh:Medicine, Plant Biology, MADS Domain Proteins, Flowers, Rosa, 01 natural sciences, 03 medical and health sciences, Plant Biology/Plant Genetics and Gene Expression, Plant Biology/Plant Growth and Development, Gene Expression Regulation, Plant, Botany, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:Science, Domestication, Molecular Biology, In Situ Hybridization, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Hybrid, Plant Proteins, 0303 health sciences, Volatile Organic Compounds, Vegetal Biology, Multidisciplinary, biology, Agamous, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, lcsh:R, fungi, food and beverages, Gene Expression Regulation, Developmental, Genetic Variation, biology.organism_classification, Phenotype, Developmental Biology/Plant Growth and Development, RHAG, biology.protein, Hybridization, Genetic, lcsh:Q, Petal, Biologie végétale, 010606 plant biology & botany, Research Article
Abstract

Background Roses have been cultivated for centuries and a number of varieties have been selected based on flower traits such as petal form, color, and number. Wild-type roses have five petals (simple flowers), whereas high numbers of petals (double flowers) are typical attributes of most of the cultivated roses. Here, we investigated the molecular mechanisms that could have been selected to control petal number in roses. Methodology/Principal Findings We have analyzed the expression of several candidate genes known to be involved in floral organ identity determination in roses from similar genetic backgrounds but exhibiting contrasting petal numbers per flower. We show that the rose ortholog of AGAMOUS (RhAG) is differentially expressed in double flowers as compared to simple flowers. In situ hybridization experiments confirm the differential expression of RhAG and demonstrate that in the double-flower roses, the expression domain of RhAG is restricted toward the center of the flower. Conversely, in simple-flower roses, RhAG expression domain is wider. We further show that the border of RhAG expression domain is labile, which allows the selection of rose flowers with increased petal number. Double-flower roses were selected independently in the two major regions for domestication, China and the peri-Mediterranean areas. Comparison of RhAG expression in the wild-type ancestors of cultivated roses and their descendants both in the European and Chinese lineages corroborates the correlation between the degree of restriction of RhAG expression domain and the number of petals. Our data suggests that a restriction of RhAG expression domain is the basis for selection of double flowers in both the Chinese and peri-Mediterranean centers of domestication. Conclusions/Significance We demonstrate that a shift in RhAG expression domain boundary occurred in rose hybrids, causing double-flower phenotype. This molecular event was selected independently during rose domestication in Europe/Middle East and in China.

Published
2010

9. Genome-wide analysis of gene expression during early Arabidopsis flower development

Author

Elliot M. Meyerowitz, José Luis Riechmann, Annick Dubois, Marcio Alves-Ferreira, Frank Wellmer, Division of Biology [Pasadena], California Institute of Technology (CALTECH), and NIGMS NIH HHS [GM45697], [R01 GM045697]

Subjects
0106 biological sciences, Cancer Research, Time Factors, Transcription, Genetic, Arabidopsis, génome végétal, Plant Science, QH426-470, 01 natural sciences, Gene Expression Regulation, Plant, Arabidopsis thaliana, Genetics (clinical), Oligonucleotide Array Sequence Analysis, Plant Proteins, Genetics/Genomics, Regulation of gene expression, Genetics, régulation de l'expression génique, 0303 health sciences, Vegetal Biology, biology, Gene Expression Regulation, Developmental, food and beverages, ABC model of flower development, Genome, Plant, Research Article, Transcriptional Activation, lcsh:QH426-470, Evolution, Flowers, Development, Genes, Plant, protéine végétale, 03 medical and health sciences, activation de la transcription, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, transcription génétique, Gene, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, développement de la fleur, Gene Expression Profiling, fungi, biology.organism_classification, floral development, Gene expression profiling, lcsh:Genetics, Arabidopsis (Thale Cress), profilage génétique, Genetics/Gene Expression, Flower formation, Caltech Library Services, Biologie végétale, 010606 plant biology & botany
Abstract

Detailed information about stage-specific changes in gene expression is crucial for the understanding of the gene regulatory networks underlying development. Here, we describe the global gene expression dynamics during early flower development, a key process in the life cycle of a plant, during which floral patterning and the specification of floral organs is established. We used a novel floral induction system in Arabidopsis, which allows the isolation of a large number of synchronized floral buds, in conjunction with whole-genome microarray analysis to identify genes with differential expression at distinct stages of flower development. We found that the onset of flower formation is characterized by a massive downregulation of genes in incipient floral primordia, which is followed by a predominance of gene activation during the differentiation of floral organs. Among the genes we identified as differentially expressed in the experiment, we detected a significant enrichment of closely related members of gene families. The expression profiles of these related genes were often highly correlated, indicating similar temporal expression patterns. Moreover, we found that the majority of these genes is specifically up-regulated during certain developmental stages. Because co-expressed members of gene families in Arabidopsis frequently act in a redundant manner, these results suggest a high degree of functional redundancy during early flower development, but also that its extent may vary in a stage-specific manner., Synopsis The development of flowers is one of the characteristic features of higher plants. In an effort to gain detailed insights into the molecular processes underlying flower development, the authors have analyzed the expression of the genes of the small plant Arabidopsis thaliana, which is widely used by biologists for the study of plant development, during the early stages of flower formation. To this end, they used DNA microarray analysis, a technology that allows the simultaneous detection of thousands of gene transcripts in a single experiment. Because young floral buds of Arabidopsis are minute and are difficult to dissect, the authors established a system that allows the simultaneous induction of a large number of flowers on a single plant. Using this system, they identified groups of genes, many of them novel or uncharacterized, that are highly active during distinct stages of flower development. These genes are likely involved in controlling the various developmental changes that take place during the formation of flowers. The authors also found that many of these genes are closely related in sequence, suggesting that they might be involved in similar or identical processes, and thus uncovering a large degree of potential functional redundancy during flower development.

Published
2006

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