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4 results on '"Bastien Laubin"'

1. Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species

Author

Arnaud Bellec, Pierre Sourdille, Philippe Leroy, Jérôme Salse, Carole Dossat, Jean Weissenbach, Bastien Laubin, Ivan Dubois, Michel Bernard, Laurence Cattolico, Marie-Françoise Gautier, Nathalie Chantret, Philippe Joudrier, Michel Caboche, Sébastien Aubourg, François Sabot, Michel Beckert, Boulos Chalhoub, Diversité et adaptation des plantes cultivées (UMR DIAPC), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), 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), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), UMR 1097 Diversité et Adaptation des Plantes Cultivées, Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-MontpellierSupAgro (MontpellierSupAgro)-Génétique et amélioration des plantes (G.A.P.)-Diversité et Adaptation des Plantes Cultivées (DIA-PC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay

Subjects
0106 biological sciences, Chromosomes, Artificial, Bacterial, Molecular Sequence Data, Locus (genetics), Biology, CARTOGRAPHIE GENETIQUE, Genes, Plant, 01 natural sciences, Genome, Chromosomes, Plant, Conserved sequence, Evolution, Molecular, 03 medical and health sciences, Molecular evolution, Genetics, Coding region, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Codon, Molecular clock, Molecular Biology, Gene, Conserved Sequence, Triticum, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, Comparative genomics, 0303 health sciences, Base Sequence, food and beverages, Hordeum, Oryza, Introns, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], DNA, Intergenic, RIZ, 010606 plant biology & botany
Abstract

UMR DIAPC, UMR DAP équipe DGB; We study here the evolution of genes located in the same physical locus using the recently sequenced Ha locus in seven wheat genomes in diploid, tetraploid, and hexaploid species and compared them with barley and rice orthologous regions. We investigated both the conservation of microcolinearity and the molecular evolution of genes, including coding and noncoding sequences. Microcolinearity is restricted to two groups of genes (Unknown gene-2, VAMP, BGGP, Gsp-1, and Unknown gene-8 surrounded by several copies of ATPase), almost conserved in rice and barley, but in a different relative position. Highly conserved genes between wheat and rice run along with genes harboring different copy numbers and highly variable sequences between close wheat genomes. The coding sequence evolution appeared to be submitted to heterogeneous selective pressure and intronic sequences analysis revealed that the molecular clock hypothesis is violated in most cases

Published
2008
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2. Inheritance of the number and thickness of cell layers in barley aleurone tissue (Hordeum vulgare L.): an approach using F2-F3 progeny

Author

Sylvie Auroy, Catherine Ravel, Bastien Laubin, Marie-Reine Perretant, Louis Jestin, Gilles Charmet, Caroline Pont, Génétique Diversité et Ecophysiologie des Céréales (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)

Subjects
0106 biological sciences, Genetic Linkage, Population, Quantitative Trait Loci, Single-nucleotide polymorphism, Biology, Quantitative trait locus, Genes, Plant, 01 natural sciences, Chromosomes, Plant, 03 medical and health sciences, Genetic linkage, Aleurone, Botany, Genetics, education, Crosses, Genetic, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, LOCUS DES CARACTERES QUANTITATIFS, Chromosome, Chromosome Mapping, food and beverages, Hordeum, General Medicine, GENETIQUE, Phenotype, Microsatellite, Hordeum vulgare, Agronomy and Crop Science, 010606 plant biology & botany, Biotechnology, Microsatellite Repeats
Abstract

The aleurone tissue of cereal grains, nutritionally rich in minerals and vitamins, is an important target for the improvement of cereals. Inheritance of the thickness and the number of cell layers in barley aleurone was studied on the F2-F3 progeny of an Erhard Frederichen x Criolla Negra cross in which the parental lines have three or two aleurone layers, respectively. F3 grain was sampled from each F2 plant and 96.8% of the entire F3 grain population was classified as being either the 2- or 3-layer type. Using microsatellite, single nucleotide polymorphism (SNP) and morphological markers on 190 F2 plants, a linkage map was built. Three quantitative trait loci (QTLs) affecting aleurone traits were revealed on chromosome 5H (max. LOD = 5.83) and chromosome 7H (max. LOD = 4.45) by interval mapping, and on chromosome 2H by marker analysis with an unmapped marker. These QTLs were consistent with genetic sub-models involving either 2-cell type dominance for 7H and 2H, or putative partial dominance for 5H where 2-cell-layer dominance and additivity gave similar LODs. The number of aleurone cell layers and aleurone thickness were strongly correlated and QTL results for these traits were alike. An SNP marker of sal1, an orthologue of the maize multilayer aleurone gene was mapped to the 7HL chromosome arm. However, the 7H QTL did not co-locate with the barley sal1 SNP, suggesting that an additional gene is involved in determining aleurone traits. These new mapping data allow comparisons to be made with related studies.

Published
2008
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3. Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations

Author

Michel Bernard, Philippe Leroy, Thomas Wicker, Pierre Sourdille, François Sabot, Bastien Laubin, Nathalie Chantret, Romain Guyot, Boulos Chalhoub, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institute of Plant Biology, Universität Zürich [Zürich] (UZH), Unité mixte de recherche polymorphismes d'intérêt agronomique génomique appliquée aux caractères agronomiques, Institut National de la Recherche Agronomique (INRA), Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Universität Zürich [Zürich] = University of Zurich (UZH), Unité mixte de recherche polymorphismes d'intérêt agronomique génomique appliquée aux caractères agronomiques (UMR PIA-GACA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Montpellier (ENSA M), and Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Transposable element, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Genome evolution, DNA, Plant, Retrotransposon, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Species Specificity, Polyploid, Genetics, Triticeae, Molecular Biology, Triticum, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, food and beverages, Hordeum, Sequence Analysis, DNA, General Medicine, GENETIQUE, biology.organism_classification, Long terminal repeat, DNA Transposable Elements, Ploidy, Edible Grain, Genome, Plant, 010606 plant biology & botany
Abstract

Triticeae species (including wheat, barley and rye) have huge and complex genomes due to polyploidization and a high content of transposable elements (TEs). TEs are known to play a major role in the structure and evolutionary dynamics of Triticeae genomes. During the last 5 years, substantial stretches of contiguous genomic sequence from various species of Triticeae have been generated, making it necessary to update and standardize TE annotations and nomenclature. In this study we propose standard procedures for these tasks, based on structure, nucleic acid and protein sequence homologies. We report statistical analyses of TE composition and distribution in large blocks of genomic sequences from wheat and barley. Altogether, 3.8 Mb of wheat sequence available in the databases was analyzed or re-analyzed, and compared with 1.3 Mb of re-annotated genomic sequences from barley. The wheat sequences were relatively gene-rich (one gene per 23.9 kb), although wheat gene-derived sequences represented only 7.8% (159 elements) of the total, while the remainder mainly comprised coding sequences found in TEs (54.7%, 751 elements). Class I elements [mainly long terminal repeat (LTR) retrotransposons] accounted for the major proportion of TEs, in terms of sequence length as well as element number (83.6% and 498, respectively). In addition, we show that the gene-rich sequences of wheat genome A seem to have a higher TE content than those of genomes B and D, or of barley gene-rich sequences. Moreover, among the various TE groups, MITEs were most often associated with genes: 43.1% of MITEs fell into this category. Finally, the TRIM and copia elements were shown to be the most active TEs in the wheat genome. The implications of these results for the evolution of diploid and polyploid wheat species are discussed.

Published
2005
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4. Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations.

Author

François Sabot, Romain Guyot, Thomas Wicker, Nathalie Chantret, Bastien Laubin, Boulos Chalhoub, Philippe Leroy, Pierre Sourdille, and Michel Bernard

Abstract

Triticeae species (including wheat, barley and rye) have huge and complex genomes due to polyploidization and a high content of transposable elements (TEs). TEs are known to play a major role in the structure and evolutionary dynamics of Triticeae genomes. During the last 5 years, substantial stretches of contiguous genomic sequence from various species of Triticeae have been generated, making it necessary to update and standardize TE annotations and nomenclature. In this study we propose standard procedures for these tasks, based on structure, nucleic acid and protein sequence homologies. We report statistical analyses of TE composition and distribution in large blocks of genomic sequences from wheat and barley. Altogether, 3.8 Mb of wheat sequence available in the databases was analyzed or re-analyzed, and compared with 1.3 Mb of re-annotated genomic sequences from barley. The wheat sequences were relatively gene-rich (one gene per 23.9 kb), although wheat gene-derived sequences represented only 7.8% (159 elements) of the total, while the remainder mainly comprised coding sequences found in TEs (54.7%, 751 elements). Class I elements [mainly long terminal repeat (LTR) retrotransposons] accounted for the major proportion of TEs, in terms of sequence length as well as element number (83.6% and 498, respectively). In addition, we show that the gene-rich sequences of wheat genome A seem to have a higher TE content than those of genomes B and D, or of barley gene-rich sequences. Moreover, among the various TE groups, MITEs were most often associated with genes: 43.1% of MITEs fell into this category. Finally, the TRIM and copia elements were shown to be the most active TEs in the wheat genome. The implications of these results for the evolution of diploid and polyploid wheat species are discussed. [ABSTRACT FROM AUTHOR]

Published
2005
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