144 results on '"Paux E"'
Search Results
2. Fine mapping of LrSV2, a race-specific adult plant leaf rust resistance gene on wheat chromosome 3BS
- Author
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Diéguez, M. J., Pergolesi, M. F., Velasquez, S. M., Ingala, L., López, M., Darino, M., Paux, E., Feuillet, C., and Sacco, F.
- Published
- 2014
- Full Text
- View/download PDF
3. Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat
- Author
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Bassi, F. M., Kumar, A., Zhang, Q., Paux, E., Huttner, E., Kilian, A., Dizon, R., Feuillet, C., Xu, S. S., and Kianian, S. F.
- Published
- 2013
- Full Text
- View/download PDF
4. A multiple resistance locus on chromosome arm 3BS in wheat confers resistance to stem rust (Sr2), leaf rust (Lr27) and powdery mildew
- Author
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Mago, R., Tabe, L., McIntosh, R. A., Pretorius, Z., Kota, R., Paux, E., Wicker, T., Breen, J., Lagudah, E. S., Ellis, J. G., and Spielmeyer, W.
- Published
- 2011
- Full Text
- View/download PDF
5. Genetic diversity and linkage disequilibrium studies on a 3.1-Mb genomic region of chromosome 3B in European and Asian bread wheat (Triticum aestivum L.) populations
- Author
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Hao, C. Y., Perretant, M. R., Choulet, F., Wang, L. F., Paux, E., Sourdille, P., Zhang, X. Y., Feuillet, C., and Balfourier, Francois
- Published
- 2010
- Full Text
- View/download PDF
6. Evaluation of the genetic variability of homoeologous group 3 SSRS in bread wheat
- Author
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Chebotar, S., Sourdille, P., Paux, E., Balfourier, F., Feuillet, C., and Bernard, M.
- Published
- 2009
- Full Text
- View/download PDF
7. BAC-derived markers for assaying the stem rust resistance gene, Sr2, in wheat breeding programs
- Author
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McNeil, M. D., Kota, R., Paux, E., Dunn, D., McLean, R., Feuillet, C., Li, D., Kong, X., Lagudah, E., Zhang, J. C., Jia, J. Z., Spielmeyer, W., Bellgard, M., and Appels, R.
- Published
- 2008
- Full Text
- View/download PDF
8. Mating system and recombination affect molecular evolution in four Triticeae species
- Author
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HAUDRY, A., CENCI, A., GUILHAUMON, C., PAUX, E., POIRIER, S., SANTONI, S., DAVID, J., and GLÉMIN, S.
- Published
- 2008
9. Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome
- Author
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Ilc, T., Gautier Arista, Raquel Tavares, Nicolas Navrot, Eric Duchene, Amandine Velt, Frédéric Choulet, Paux, E., Véronique Fischer, Nelson, D., Philippe Hugueney, Daniele Werck Reichhart, Camille Rustenholz Russell, Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-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), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Department of Microbiology, Immunology and Biochemistry [Memphis, TN, États-Unis], The University of Tennessee Health Science Center [Memphis] (UTHSC), The authors acknowledge the support of the French Agence Nationale de la Recherche to the InteGrape project (ANR-13-BSV6-0010). The doctoral fellowship of Tina Ilc was funded by the People Programme (Marie Curie Actions) of the European Union's 7th Framework Programme (FP7/2007-2013) under REA Grant Agreement 289217. The doctoral fellowship of Gautier Arista was funded by INRA and the Région Alsace., ANR-13-BSV6-0010,InteGrape,Analyse intégrative des familles de gènes impliquées dans la biosynthèse des terpènes aromatiques chez la vigne(2013), European Project: 289217,EC:FP7:PEOPLE,FP7-PEOPLE-2011-ITN,P4FIFTY(2012), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - UFC (UMR 6249) (LCE), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Dupuis, Christine, Blanc 2013 - Analyse intégrative des familles de gènes impliquées dans la biosynthèse des terpènes aromatiques chez la vigne - - InteGrape2013 - ANR-13-BSV6-0010 - Blanc 2013 - VALID, and Development of Cytochrome P450 Enzymes for the Chemical Manufacturing Industries - P4FIFTY - - EC:FP7:PEOPLE2012-01-01 - 2015-12-31 - 289217 - VALID
- Subjects
Bioinformatics ,[SDV]Life Sciences [q-bio] ,lcsh:Medicine ,Gene Expression ,Plant Science ,Genome Complexity ,Plant Genetics ,Biosynthesis ,Research and Analysis Methods ,Biochemistry ,Gene Expression Regulation, Enzymologic ,Fruits ,Database and Informatics Methods ,Cytochrome P-450 Enzyme System ,Gene Expression Regulation, Plant ,Gene Types ,Genetics ,Plant Genomics ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Vitis ,lcsh:Science ,Flowering Plants ,Plant Proteins ,lcsh:R ,Organisms ,Biology and Life Sciences ,Eukaryota ,Computational Biology ,food and beverages ,Molecular Sequence Annotation ,Berries ,Genomics ,Plants ,Genome Analysis ,Genome Annotation ,[SDV] Life Sciences [q-bio] ,lcsh:Q ,Grapevine ,Plant Biotechnology ,Sequence Analysis ,Sequence Alignment ,Genome, Plant ,Pseudogenes ,Research Article ,Biotechnology - Abstract
International audience; Cytochromes P450 are enzymes that participate in a wide range of functions in plants, from hormonal signaling and biosynthesis of structural polymers, to defense or communication with other organisms. They represent one of the largest gene/protein families in the plant kingdom. The manual annotation of cytochrome P450 genes in the genome of Vitis vinifera PN40024 revealed 579 P450 sequences, including 279 complete genes. Most of the P450 sequences in grapevine genome are organized in physical clusters, resulting from tandem or segmental duplications. Although most of these clusters are small (2 to 35, median = 3), some P450 families, such as CYP76 and CYP82, underwent multiple duplications and form large clusters of homologous sequences. Analysis of gene expression revealed highly specific expression patterns, which are often the same within the genes in large physical clusters. Some of these genes are induced upon biotic stress, which points to their role in plant defense, whereas others are specifically activated during grape berry ripening and might be responsible for the production of berry-specific metabolites, such as aroma compounds. Our work provides an exhaustive and robust annotation including clear identification, structural organization, evolutionary dynamics and expression patterns for the grapevine cytochrome P450 families, paving the way to efficient functional characterization of genes involved in grapevine defense pathways and aroma biosynthesis.
- Published
- 2018
10. Towards Positional Cloning of Qyld.Idw-3B, a Major QTL for Grain Yield Per Se in Durum Wheat
- Author
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Graziani M., MACCAFERRI, MARCO, Paux E., Feuillet E., Sanguineti M. C., Massi A., SALVI, SILVIO, TUBEROSA, ROBERTO, Graziani M., Maccaferri M., Salvi S., Paux E., Feuillet E., Sanguineti M.C., Massi A., and Tuberosa R.
- Subjects
QTL ,Positional cloning ,GRAIN YIELD ,DURUM WHEAT - Published
- 2012
11. Validation of Qyld.idw-3B, a major QTL for grain yield and related morphophysiological traits in durum wheat
- Author
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GRAZIANI, MARTA, MACCAFERRI, MARCO, SANGUINETI, MARIA CORINNA, CORNETI, SIMONA, STEFANELLI, SANDRA, DEMONTIS A., MASSI A., PAUX E., SALSE J., FEUILLET C., TUBEROSA, ROBERTO, GRAZIANI M., MACCAFERRI M., SANGUINETI M.C., CORNETI S., STEFANELLI S., DEMONTIS A., MASSI A., PAUX E., SALSE J., FEUILLET C., and TUBEROSA R.
- Subjects
grain yield, QTL, wheat - Published
- 2011
12. Towards the fine mapping of a major QTL on chromosome 3BS for yield and plant vigour in durum wheat
- Author
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GRAZIANI, MARTA, MACCAFERRI, MARCO, SANGUINETI, MARIA CORINNA, STEFANELLI, SANDRA, TUBEROSA, ROBERTO, PAUX E., SALSE J., CHOULET F., FEUILLET C., DEMONTIS A., GRAZIANI M., MACCAFERRI M., SANGUINETI M.C., PAUX E., SALSE J., CHOULET F., FEUILLET C., STEFANELLI S., DEMONTIS A., and TUBEROSA R.
- Published
- 2010
13. Searching for QTLs to enhance yield stability in durum wheat
- Author
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MACCAFERRI, MARCO, SANGUINETI, MARIA CORINNA, BASSI, FILIPPO, CORNETI, SIMONA, STEFANELLI, SANDRA, TUBEROSA, ROBERTO, GRAZIANI M., DEMONTIS A., MASSI A., AMMAR K., PAUX E., FEUILLET C., MACCAFERRI M., SANGUINETI M.C., GRAZIANI M., BASSI F., CORNETI S., STEFANELLI S., DEMONTIS A., MASSI A., AMMAR K., PAUX E., FEUILLET C., and TUBEROSA R.
- Published
- 2010
14. Fine mapping of QYld.idw-3B, a major QTL on chromosome 3BS for yield in durum wheat
- Author
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GRAZIANI M., PAUX E., SALSE J., CHOULET F., FEUILLET C., DEMONTIS A., MACCAFERRI, MARCO, SANGUINETI, MARIA CORINNA, STEFANELLI, SANDRA, TERRACCIANO, IRMA, TUBEROSA, ROBERTO, GRAZIANI M., MACCAFERRI M., SANGUINETI M.C., PAUX E., SALSE J., CHOULET F., FEUILLET C., STEFANELLI S., DEMONTIS A., TERRACCIANO I., and TUBEROSA R.
- Published
- 2010
15. Fine mapping of two major QTLs on chromosomes 2BL and 3BS controlling yield in durum wheat
- Author
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GRAZIANI, MARTA, ALOISIO, IRENE, MACCAFERRI, MARCO, SANGUINETI, MARIA CORINNA, TUBEROSA, ROBERTO, PAUX E., SALSE J., CHOULET F., FEUILLET C., DEMONTIS A., GRAZIANI M., ALOISIO I., MACCAFERRI M., PAUX E., SALSE J., CHOULET F., FEUILLET C., SANGUINETI M.C., DEMONTIS A., and TUBEROSA R.
- Published
- 2010
16. Towards the fine mapping of two major QTLs for grain yield in durum wheat
- Author
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GRAZIANI M., PAUX E., SALSE J., FEUILLET C., DEMONTIS A., MACCAFERRI, MARCO, ALOISIO, IRENE, SANGUINETI, MARIA CORINNA, TUBEROSA, ROBERTO, FRISON E., GRANER A., TUBEROSA R., GRAZIANI M., MACCAFERRI M., ALOISIO I., PAUX E., SALSE J., FEUILLET C., SANGUINETI M.C., DEMONTIS A., and TUBEROSA R.
- Published
- 2010
17. Fine mapping of two major durum wheat QTLs for grain yield identified under different water availabilities
- Author
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MACCAFERRI, MARCO, ALOISIO, IRENE, CORNETI, SIMONA, SANGUINETI, MARIA CORINNA, TUBEROSA, ROBERTO, PAUX E., SALSE J., FAURE S., SOURDILLE P., FEUILLET C., DEMONTIS A., MASSI A., GRAZIANI M., MACCAFERRI M., ALOISIO I., PAUX E., SALSE J., FAURE S., SOURDILLE P., FEUILLET C., CORNETI S., SANGUINETI M.C., DEMONTIS A., MASSI A., GRAZIANI M., and TUBEROSA R.
- Published
- 2009
18. Towards the fine mapping of two major QTLs for grain yield and related morpho-physiological traits in durum wheat
- Author
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ALOISIO, IRENE, MACCAFERRI, MARCO, CORNETI, SIMONA, SANGUINETI, MARIA CORINNA, TUBEROSA, ROBERTO, PAUX E., SALSE J., FAURE S., SOURDILLE P., FEUILLET C., DEMONTIS A., MASSI A., ALOISIO I., MACCAFERRI M., PAUX E., SALSE J., FAURE S., SOURDILLE P., FEUILLET C., CORNETI S., SANGUINETI M.C., DEMONTIS A., MASSI A., and TUBEROSA R.
- Published
- 2009
19. Ancient hybridizations among the ancestral genomes of bread wheat
- Author
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Marcussen, T., Sandve, S., Heier, L., Spannagl, M., Pfeifer, M., Jakobsen, K., Wulff, B., Steuernagel, B., Mayer, K., Olsen, O.-A., Rogers, J., Dole el, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A., Sourdille, Pierre, Endo, T., Kubalakova, M., ihalikova, J., Dubska, Z., Vrana, J., perkova, R., imkova, H., Febrer, M., Clissold, L., McLay, K., Singh, K., Chhuneja, P., Singh, N., Khurana, J., Akhunov, E., Choulet, F., Alberti, A., Barbe, Valérie, Wincker, P., Kanamori, H., Kobayashi, F., Itoh, T., Matsumoto, T., Sakai, H., Tanaka, T., Wu, J., Ogihara, Y., Handa, H., Maclachlan, P., Sharpe, A., Klassen, D., Edwards, D., Batley, J., Lien, S., Caccamo, M., Ayling, S., Ramirez-Gonzalez, R., Clavijo, B., Wright, J., Martis, M., Mascher, M., Chapman, J., Poland, J., Scholz, U., Barry, K., Waugh, R., Rokhsar, D., Muehlbauer, G., Stein, N., Gundlach, H., Zytnicki, M., Jamilloux, V., Quesneville, H., Wicker, T., Faccioli, P., Colaiacovo, M., Stanca, A., Budak, H., Cattivelli, L., Glover, N., Pingault, L., Paux, E., Sharma, S., Appels, R., Bellgard, M., Chapman, B., Nussbaumer, T., Bader, K., Rimbert, H., Wang, S., Knox, R., Kilian, A., Alaux, M., Alfama, F., Couderc, L., Guilhot, N., Viseux, C., Loaec, M., Keller, B., Praud, S., Norwegian University of Life Sciences (NMBU), Helmholtz-Zentrum München (HZM), Helmholtz Centre Munich, Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health - Helmholtz Center München (GmbH), John Innes Centre [Norwich], Eversole Associates, Bayer Corporation, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Laboratoire d'hydrodynamique (LadHyX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), Consiglio Nazionale delle Ricerche (CNR), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), 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)-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)-Université Paris-Saclay, Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Seismological Laboratory, California Institute of Technology (CALTECH), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Department of Physics, University of Tokyo, The University of Tokyo (UTokyo), National Institute for Environmental Studies (NIES), Université de Lille, Sciences et Technologies, The University of Western Australia (UWA), Leibniz Institute of Plant Genetics and Crop Plant Research, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), Consiglio per la Ricerca e Sperimentazione in Agricoltura, Climate Research Division [Toronto], Environment and Climate Change Canada, School of Biosciences, University of Birmingham [Birmingham], Centre for Comparative Genomics, Murdoch University, Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, BIOGEMMA, Centre de Recherche de Chappes, Diversity Arrays Technology Pty Ltd (DArT P/L), Institute of plant biology, Universität Zürich [Zürich] = University of Zurich (UZH), Research Council of Norway 199387Biotechnology and Biological Sciences Research Council (BBSRC) BB/J003166/1,BBS/E/T/000PR6193National Science Foundation (NSF) - Directorate for Computer & Information Science & Engineering (CISE) 1126709, Helmholtz Zentrum München = German Research Center for Environmental Health, Biotechnology and Biological Sciences Research Council (BBSRC), Laboratoire Chrono-environnement (UMR 6249) (LCE), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Oslo (UiO), The Sainsbury Laboratory (TSL), and Norwegian Research Council 199387
- Subjects
0106 biological sciences ,TRITICUM ,GENES ,[SDV]Life Sciences [q-bio] ,Biology ,Genes, Plant ,01 natural sciences ,Genome ,Evolution, Molecular ,Polyploidy ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,03 medical and health sciences ,Polyploid ,Phylogenetics ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Gene ,DRAFT GENOME ,Phylogeny ,AEGILOPS-TAUSCHII ,030304 developmental biology ,2. Zero hunger ,Genetics ,0303 health sciences ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Multidisciplinary ,Phylogenetic tree ,A-GENOME ,myr ,food and beverages ,Bread ,EVOLUTION ,ALIGNMENT ,DOMESTICATION ,Hybridization, Genetic ,Hybrid speciation ,Ploidy ,Genome, Plant ,010606 plant biology & botany ,PACKAGE - Abstract
International audience; The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor similar to 7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.
- Published
- 2014
20. A unified classification system for eukaryotic transposable elements should reflect their phylogeny Reply
- Author
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Wicker, T., Francois Sabot, Hua, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., San Miguel, P., Alejandro Schulman, Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), and Nicolas, Christine
- Subjects
[SDV.BA] Life Sciences [q-bio]/Animal biology ,[SDV.BA]Life Sciences [q-bio]/Animal biology - Published
- 2009
21. Insertion site-based polymorphism: A Swiss army knife for wheat genomics
- Author
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Paux E, Gao L, Faure S, Choulet F, Roger D, Chevalier K, Saintenac C, Balfourier F, Paux K, Cakir M, Brunel D, Le Paslier M-C, Krugman T, Gandon B, Nevo E, Bernard M, Sourdille P, and Feuillet, C
- Subjects
Wheat breeding ,Wheat genetics - Published
- 2008
22. Genetic map of wheat chromosome 3BS including SV2; an adult plant leaf rust resistance gene
- Author
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Ingala L, Diéguez MJ, Pergolesi F, López M, Paux E, Feuillet, C, and Sacco F
- Subjects
Wheat breeding ,Wheat genetics - Published
- 2008
23. Recombination analysis on bread wheat chromosome 3B
- Author
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Saintenac C, Paux E, Choulet F, Faure S, Philippon J, Boyer D, Bernard M, Feuillet, C, and Sourdille P
- Subjects
Wheat breeding ,Wheat genetics - Published
- 2008
24. High-resolution radiation hybrid mapping in wheat: an essential tool for the construction of the wheat physical maps
- Author
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Michalak, M, Kumar, A, Riera-Lizarazu, O, Gu, Y, Paux, E, Choulet, F, Feuillet, C, Kumar, S, Goyal, A, Tiwari, V, Dogramaci, M, Hegstad, J, Peckrul, A, Kalavacharla, V, Hossain, K, Balyan, HS, Dhaliwal, HS, Gupta, PK, Randhawa, GS, Maan, SS, and Kianian, SF
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Wheat breeding ,Wheat genetics - Published
- 2008
25. The Big B of Bread wheat - 3B - exploring the structure; function; and evolution of the hexaploid wheat genome
- Author
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Paux, E, Sourdille, P, Salse, J, Saintenac, C, Choulet, F, Leroy, P, Korol, AB, Spielmeyer, W, Lagudah, E, Somers, D, Kilian, A, Allaux, M, Bergès, H, Appels R, Dolezel, J, Bernard, M, and Feuillet, C
- Subjects
Wheat breeding ,Wheat genetics - Published
- 2008
26. Air quality and engine emission at Paris CDG airport during AIRPUR field campaigns
- Author
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Lelievre, C. P., Magnani, G., Ramaroson, R., Gouriou, F., Talbaut, M., Frejafon, E., Schuermann, G., Schaefer, K., Cornier, I., Emeis, S., Vannier, F., Paux, E., Copalle, A., and Perros, P.
- Published
- 2006
27. Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model
- Author
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Bogard, M., primary, Ravel, C., additional, Paux, E., additional, Bordes, J., additional, Balfourier, F., additional, Chapman, S. C., additional, Le Gouis, J., additional, and Allard, V., additional
- Published
- 2014
- Full Text
- View/download PDF
28. Preparation of the first European working standard for phenylalanine determination in dried blood spots
- Author
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Dhondt, J L, primary, Loeber, J G, additional, Elvers, L H, additional, and Paux, E, additional
- Published
- 1998
- Full Text
- View/download PDF
29. NEWBORN SCREENING FOR SICLE CELL DISEASE IN FRANCE. 523
- Author
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Bardakdjian-Michau, J., primary, Galacteros, F., additional, Elion, J., additional, Ducrocq, R., additional, Feingold, J., additional, Farriaux, J. P., additional, Paux, E., additional, Girot, R., additional, Maier-Redelsperger, M., additional, Lena-Russo, D., additional, Giraud, F., additional, Briard, M. L., additional, Rey, J., additional, Dhondt, J. L., additional, and North, M. L., additional
- Published
- 1997
- Full Text
- View/download PDF
30. Détection néonatale de la drépanocytose en France métropolitaine
- Author
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Galactéros, F, primary, Bardakdjian-Michau, J, additional, Galactéros, F, additional, Dhondt, J.L, additional, Farriaux, J.P, additional, Paux, E, additional, Ducrocq, D, additional, Elion, J, additional, Feingold, J, additional, Girot, R, additional, Maier-Redolsperger, M, additional, Lena Russo, D, additional, Giraud, F, additional, North, M.L, additional, Briard, M.L, additional, and Rey, J, additional
- Published
- 1996
- Full Text
- View/download PDF
31. Need for a standardized procedure in the preparation of phenylalanine calibrators
- Author
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Dhondt, J.L., primary, Paux, E., additional, and Farriaux, J.P., additional
- Published
- 1996
- Full Text
- View/download PDF
32. Evaluation of an enzymatic, colorimetric method for the neonatal screening of phenylketonuria
- Author
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Dhondt, J.L., primary and Paux, E., additional
- Published
- 1993
- Full Text
- View/download PDF
33. A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block
- Author
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Breen, J, Wicker, T, Kong, X, Juncheng, Z, Ma, W, Feuillet, C, Paux, E, Appels, R, and Bellgard, M
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2. Zero hunger
34. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces
- Author
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Choulet, F, Wicker, T, Rustenholz, C, Paux, E, Salse, J, Leroy, P, Schlub, S, Le Paslier, M C, Magdelenat, G, Gonthier, C, Couloux, A, Budak, H, Breen, J, Pumphrey, M, Liu, S, Kong, X, Jia, J, Gut, M, Brunel, D, Anderson, J A, Gill, B S, Appels, R, Keller, B, and Feuillet, C
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2. Zero hunger
35. Le dosage de la trypsine immunoréactive sur éluat de sang séché : données techniques et application au dépistage néonatal de la mucoviscidose
- Author
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Duarte-Hazenfeldt, M., primary, Dhondt, J.L., additional, Farriaux, J.P., additional, Paux, E., additional, and Braula-Reis, A., additional
- Published
- 1989
- Full Text
- View/download PDF
36. DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum
- Author
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Kumar Ajay, Bassi Filippo M, Paux Etienne, Al-Azzam Omar, de Jimenez Monika, Denton Anne M, Gu Yong Q, Huttner Eric, Kilian Andrzej, Kumar Sachin, Goyal Aakash, Iqbal Muhammad J, Tiwari Vijay K, Dogramaci Munevver, Balyan Harindra S, Dhaliwal Harcharan S, Gupta Pushpendra K, Randhawa Gursharn S, Feuillet Catherine, Pawlowski Wojciech P, and Kianian Shahryar F
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Non homologous end joining ,Physical mapping ,Gamma radiation ,Deletion mutant ,Chromatin ,Wheat chromosome 3B ,Radiation hybrid ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The uneven distribution of recombination across the length of chromosomes results in inaccurate estimates of genetic to physical distances. In wheat (Triticum aestivum L.) chromosome 3B, it has been estimated that 90% of the cross over events occur in distal sub-telomeric regions representing 40% of the chromosome. Radiation hybrid (RH) mapping which does not rely on recombination is a strategy to map genomes and has been widely employed in animal species and more recently in some plants. RH maps have been proposed to provide i) higher and ii) more uniform resolution than genetic maps, and iii) to be independent of the distribution patterns observed for meiotic recombination. An in vivo RH panel was generated for mapping chromosome 3B of wheat in an attempt to provide a complete scaffold for this ~1 Gb segment of the genome and compare the resolution to previous genetic maps. Results A high density RH map with 541 marker loci anchored to chromosome 3B spanning a total distance of 1871.9 cR was generated. Detailed comparisons with a genetic map of similar quality confirmed that i) the overall resolution of the RH map was 10.5 fold higher and ii) six fold more uniform. A significant interaction (r = 0.879 at p = 0.01) was observed between the DNA repair mechanism and the distribution of crossing-over events. This observation could be explained by accepting the possibility that the DNA repair mechanism in somatic cells is affected by the chromatin state in a way similar to the effect that chromatin state has on recombination frequencies in gametic cells. Conclusions The RH data presented here support for the first time in vivo the hypothesis of non-casual interaction between recombination hot-spots and DNA repair. Further, two major hypotheses are presented on how chromatin compactness could affect the DNA repair mechanism. Since the initial RH application 37 years ago, we were able to show for the first time that the iii) third hypothesis of RH mapping might not be entirely correct.
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- 2012
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37. Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development
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Capron Delphine, Mouzeyar Said, Boulaflous Aurélia, Girousse Christine, Rustenholz Camille, Laugier Christel, Paux Etienne, and Bouzidi Mohamed
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Botany ,QK1-989 - Abstract
Abstract Background Wheat grains are an important source of food, stock feed and raw materials for industry, but current production levels cannot meet world needs. Elucidation of the molecular mechanisms underlying wheat grain development will contribute valuable information to improving wheat cultivation. One of the most important mechanisms implicated in plant developmental processes is the ubiquitin-proteasome system (UPS). Among the different roles of the UPS, it is clear that it is essential to hormone signaling. In particular, E3 ubiquitin ligases of the UPS have been shown to play critical roles in hormone perception and signal transduction. Results A NimbleGen microarray containing 39,179 UniGenes was used to study the kinetics of gene expression during wheat grain development from the early stages of cell division to the mid-grain filling stage. By comparing 11 consecutive time-points, 9284 differentially expressed genes were identified and annotated during this study. A comparison of the temporal profiles of these genes revealed dynamic transcript accumulation profiles with major reprogramming events that occurred during the time intervals of 80-120 and 220-240°Cdays. The list of the genes expressed differentially during these transitions were identified and annotated. Emphasis was placed on E3 ligase and hormone-related genes. In total, 173 E3 ligase coding genes and 126 hormone-related genes were differentially expressed during the cell division and grain filling stages, with each family displaying a different expression profile. Conclusions The differential expression of genes involved in the UPS and plant hormone pathways suggests that phytohormones and UPS crosstalk might play a critical role in the wheat grain developmental process. Some E3 ligase and hormone-related genes seem to be up- or down-regulated during the early and late stages of the grain development.
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- 2012
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38. Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome
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Philippe Romain, Choulet Frédéric, Paux Etienne, van Oeveren Jan, Tang Jifeng, Wittenberg Alexander HJ, Janssen Antoine, van Eijk Michiel JT, Stormo Keith, Alberti Adriana, Wincker Patrick, Akhunov Eduard, van der Vossen Edwin, and Feuillet Catherine
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Sequencing projects using a clone-by-clone approach require the availability of a robust physical map. The SNaPshot technology, based on pair-wise comparisons of restriction fragments sizes, has been used recently to build the first physical map of a wheat chromosome and to complete the maize physical map. However, restriction fragments sizes shared randomly between two non-overlapping BACs often lead to chimerical contigs and mis-assembled BACs in such large and repetitive genomes. Whole Genome Profiling (WGP™) was developed recently as a new sequence-based physical mapping technology and has the potential to limit this problem. Results A subset of the wheat 3B chromosome BAC library covering 230 Mb was used to establish a WGP physical map and to compare it to a map obtained with the SNaPshot technology. We first adapted the WGP-based assembly methodology to cope with the complexity of the wheat genome. Then, the results showed that the WGP map covers the same length than the SNaPshot map but with 30% less contigs and, more importantly with 3.5 times less mis-assembled BACs. Finally, we evaluated the benefit of integrating WGP tags in different sequence assemblies obtained after Roche/454 sequencing of BAC pools. We showed that while WGP tag integration improves assemblies performed with unpaired reads and with paired-end reads at low coverage, it does not significantly improve sequence assemblies performed at high coverage (25x) with paired-end reads. Conclusions Our results demonstrate that, with a suitable assembly methodology, WGP builds more robust physical maps than the SNaPshot technology in wheat and that WGP can be adapted to any genome. Moreover, WGP tag integration in sequence assemblies improves low quality assembly. However, to achieve a high quality draft sequence assembly, a sequencing depth of 25x paired-end reads is required, at which point WGP tag integration does not provide additional scaffolding value. Finally, we suggest that WGP tags can support the efficient sequencing of BAC pools by enabling reliable assignment of sequence scaffolds to their BAC of origin, a feature that is of great interest when using BAC pooling strategies to reduce the cost of sequencing large genomes.
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- 2012
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39. Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources
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Waugh Robbie, Feuillet Catherine, Choulet Frédéric, Morris Jenny, Hedley Pete E, Rustenholz Camille, and Paux Etienne
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B). However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.
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- 2010
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40. LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes
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Feuillet Catherine, Mester David, Paux Etienne, Frenkel Zeev, and Korol Abraham
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC) software, which often results in short contig lengths (of 3-5 clones before merging) as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs). Results To address these problems, we propose a novel approach that: (i) reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii) obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii) explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv) performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v) uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC) were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize. Conclusions The results show that compared to other methods, LTC enables the construction of highly reliable and longer contigs (5-12 clones before merging), the detection of "weak" connections in contigs and their "repair", and the elongation of contigs obtained by other assembly methods.
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- 2010
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41. A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block
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Ma Wujun, Zhang Juncheng, Kong Xiuying, Wicker Thomas, Breen James, Paux Etienne, Feuillet Catherine, Appels Rudi, and Bellgard Matthew
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Botany ,QK1-989 - Abstract
Abstract Background The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The ctg1034 contig completed in this paper was initially studied because it was assigned to the Sr2 resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features. Results BAC shotgun sequencing of the hexaploid wheat (Triticum aestivum cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig ctg1034 into a 783,553 bp genomic sequence. This ctg1034 sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. The ctg1034 gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, even though the intergenic space and introns were divergent. Conclusion We propose that ctg1034 is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containing gypsy LTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and orientation within the gene island. Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824
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- 2010
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42. A new genomic resource dedicated to wood formation in Eucalyptus
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Couloux Arnaud, Wincker Patrick, Paux Etienne, Ladouce Nathalie, Servant Florence, Clemente Hélène, Rengel David, Sivadon Pierre, and Grima-Pettenati Jacqueline
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Botany ,QK1-989 - Abstract
Abstract Background Renowned for their fast growth, valuable wood properties and wide adaptability, Eucalyptus species are amongst the most planted hardwoods in the world, yet they are still at the early stages of domestication because conventional breeding is slow and costly. Thus, there is huge potential for marker-assisted breeding programs to improve traits such as wood properties. To this end, the sequencing, analysis and annotation of a large collection of expressed sequences tags (ESTs) from genes involved in wood formation in Eucalyptus would provide a valuable resource. Results We report here the normalization and sequencing of a cDNA library from developing Eucalyptus secondary xylem, as well as the construction and sequencing of two subtractive libraries (juvenile versus mature wood and vice versa). A total of 9,222 high quality sequences were collected from about 10,000 cDNA clones. The EST assembly generated a set of 3,857 wood-related unigenes including 2,461 contigs (Cg) and 1,396 singletons (Sg) that we named 'EUCAWOOD'. About 65% of the EUCAWOOD sequences produced matches with poplar, grapevine, Arabidopsis and rice protein sequence databases. BlastX searches of the Uniref100 protein database allowed us to allocate gene ontology (GO) and protein family terms to the EUCAWOOD unigenes. This annotation of the EUCAWOOD set revealed key functional categories involved in xylogenesis. For instance, 422 sequences matched various gene families involved in biosynthesis and assembly of primary and secondary cell walls. Interestingly, 141 sequences were annotated as transcription factors, some of them being orthologs of regulators known to be involved in xylogenesis. The EUCAWOOD dataset was also mined for genomic simple sequence repeat markers, yielding a total of 639 putative microsatellites. Finally, a publicly accessible database was created, supporting multiple queries on the EUCAWOOD dataset. Conclusion In this work, we have identified a large set of wood-related Eucalyptus unigenes called EUCAWOOD, thus creating a valuable resource for functional genomics studies of wood formation and molecular breeding in this economically important genus. This set of publicly available annotated sequences will be instrumental for candidate gene approaches, custom array development and marker-assisted selection programs aimed at improving and modulating wood properties.
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- 2009
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43. A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R
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Lelley Tamas, Town Christopher D, Šimková Hana, Šafář Jan, Suchánková Pavla, Kopecký David, Havránková Miroslava, Kofler Robert, Paux Etienne, Bartoš Jan, Feuillet Catherine, and Doležel Jaroslav
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Botany ,QK1-989 - Abstract
Abstract Background Rye (Secale cereale L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of agronomically important genes for wheat improvement. The short arm of rye chromosome 1 (1RS), in particular is rich in useful genes, and as it may increase yield, protein content and resistance to biotic and abiotic stress, it has been introgressed into wheat as the 1BL.1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding. Results Here, we report on BAC end sequencing of 1,536 clones from two 1RS-specific BAC libraries. We obtained 2,778 (90.4%) useful sequences with a cumulative length of 2,032,538 bp and an average read length of 732 bp. These sequences represent 0.5% of 1RS arm. The GC content of the sequenced fraction of 1RS is 45.9%, and at least 84% of the 1RS arm consists of repetitive DNA. We identified transposable element junctions in BESs and developed insertion site based polymorphism markers (ISBP). Out of the 64 primer pairs tested, 17 (26.6%) were specific for 1RS. We also identified BESs carrying microsatellites suitable for development of 1RS-specific SSR markers. Conclusion This work demonstrates the utility of chromosome arm-specific BAC libraries for targeted analysis of large Triticeae genomes and provides new sequence data from the rye genome and molecular markers for the short arm of rye chromosome 1.
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- 2008
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44. A diverse panel of 755 bread wheat accessions harbors untapped genetic diversity in landraces and reveals novel genetic regions conferring powdery mildew resistance.
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Leber R, Heuberger M, Widrig V, Jung E, Paux E, Keller B, and Sánchez-Martín J
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- Genome-Wide Association Study, Plant Breeding, Bread, Iran, Genetic Variation, Plant Diseases genetics, Disease Resistance genetics, Triticum genetics
- Abstract
Key Message: A bread wheat panel reveals rich genetic diversity in Turkish, Pakistani and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies. Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel. Population structure analysis of this panel based on the TaBW35K SNP array revealed an increased genetic diversity compared to 632 landraces genotyped in an earlier study and 17 high-quality sequenced wheat accessions. The additional genetic diversity found here mostly originated from Turkish, Iranian and Pakistani landraces. We characterized the LandracePLUS panel for resistance to ten diverse isolates of the fungal pathogen powdery mildew. Performing genome-wide association studies and dividing the panel further by a targeted subsetting approach for accessions of distinct geographical origin, we detected several known and already cloned genes, including the Pm2a gene. In addition, we identified 22 putatively novel powdery mildew resistance loci that represent useful sources for resistance breeding and for research on the mildew-wheat pathosystem. Our study shows the value of assembling trait-customized collections and utilizing a diverse range of pathogen races to detect novel loci. It further highlights the importance of integrating landraces of different geographical origins into future diversity studies., (© 2024. The Author(s).)
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- 2024
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45. All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity.
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Papon N, Lasserre-Zuber P, Rimbert H, De Oliveira R, Paux E, and Choulet F
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- Genome, Plant, Polyploidy, Evolution, Molecular, Triticum genetics, DNA Transposable Elements
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Bread wheat (Triticum aestivum L.) is a major crop and its genome is one of the largest ever assembled at reference-quality level. It is 15 Gb, hexaploid, with 85% of transposable elements (TEs). Wheat genetic diversity was mainly focused on genes and little is known about the extent of genomic variability affecting TEs, transposition rate, and the impact of polyploidy. Multiple chromosome-scale assemblies are now available for bread wheat and for its tetraploid and diploid wild relatives. In this study, we computed base pair-resolved, gene-anchored, whole genome alignments of A, B, and D lineages at different ploidy levels in order to estimate the variability that affects the TE space. We used assembled genomes of 13 T. aestivum cultivars (6x = AABBDD) and a single genome for Triticum durum (4x = AABB), Triticum dicoccoides (4x = AABB), Triticum urartu (2x = AA), and Aegilops tauschii (2x = DD). We show that 5%-34% of the TE fraction is variable, depending on the species divergence. Between 400 and 13,000 novel TE insertions per subgenome were detected. We found lineage-specific insertions for nearly all TE families in di-, tetra-, and hexaploids. No burst of transposition was observed and polyploidization did not trigger any boost of transposition. This study challenges the prevailing idea of wheat TE dynamics and is more in agreement with an equilibrium model of evolution., (© 2023 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)
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- 2023
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46. Wheat Ym2 originated from Aegilops sharonensis and confers resistance to soil-borne Wheat yellow mosaic virus infection to the roots.
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Mishina K, Suzuki T, Oono Y, Yamashita Y, Zhu H, Ogawa T, Ohta M, Doman K, Xu W, Takahashi D, Miyazaki T, Tagiri A, Soma C, Horita H, Nasuda S, De Oliveira R, Paux E, Chen G, Pourkheirandish M, Wu J, Liu C, and Komatsuda T
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- Plant Proteins genetics, Plant Proteins metabolism, Plant Roots genetics, Plant Roots metabolism, Plant Roots virology, Cloning, Molecular, Transcription, Genetic, Phylogeny, Plant Diseases, Aegilops genetics, Aegilops metabolism, Triticum genetics, Triticum metabolism, Triticum virology
- Abstract
Wheat yellow mosaic virus (WYMV) is a pathogen transmitted into its host's roots by the soil-borne vector Polymyxa graminis . Ym1 and Ym2 genes protect the host from the significant yield losses caused by the virus, but the mechanistic basis of these resistance genes remains poorly understood. Here, it has been shown that Ym1 and Ym2 act within the root either by hindering the initial movement of WYMV from the vector into the root and/or by suppressing viral multiplication. A mechanical inoculation experiment on the leaf revealed that the presence of Ym1 reduced viral infection incidence, rather than viral titer, while that of Ym2 was ineffective in the leaf. To understand the basis of the root specificity of the Ym2 product, the gene was isolated from bread wheat using a positional cloning approach. The candidate gene encodes a CC-NBS-LRR protein and it correlated allelic variation with respect to its sequence with the host's disease response. Ym2 (B37500) and its paralog (B35800) are found in the near-relatives, respectively, Aegilops sharonensi s and Aegilops speltoides (a close relative of the donor of bread wheat's B genome), while both sequences, in a concatenated state, are present in several accessions of the latter species . Structural diversity in Ym2 has been generated via translocation and recombination between the two genes and enhanced by the formation of a chimeric gene resulting from an intralocus recombination event. The analysis has revealed how the Ym2 region has evolved during the polyploidization events leading to the creation of cultivated wheat.
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- 2023
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47. A second-generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives.
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Zhang J, Debernardi JM, Burguener GF, Choulet F, Paux E, O'Connor L, Enk J, and Dubcovsky J
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- Cost-Benefit Analysis, Polyploidy, Promoter Regions, Genetic, Chromatin, Triticum genetics, Genome, Plant
- Abstract
As genome resources for wheat (Triticum L.) expand at a rapid pace, it is important to update targeted sequencing tools to incorporate improved sequence assemblies and regions of previously unknown significance. Here, we developed an updated regulatory region enrichment capture for wheat and other Triticeae species. The core target space includes sequences from 2-Kbp upstream of each gene predicted in the Chinese Spring wheat genome (IWGSC RefSeq Annotation v1.0) and regions of open chromatin identified with an assay for transposase-accessible chromatin using sequencing from wheat leaf and root samples. To improve specificity, we aggressively filtered candidate repetitive sequences using a combination of nucleotide basic local alignment search tool (BLASTN) searches to the Triticeae Repetitive Sequence Database (TREP), identification of regions with read over-coverage from previous target enrichment experiments, and k-mer frequency analyses. The final design comprises 216.5 Mbp of predicted hybridization space in hexaploid wheat and showed increased specificity and coverage of targeted sequences relative to previous protocols. Test captures on hexaploid and tetraploid wheat and other diploid cereals show that the assay has broad potential utility for cost-effective promoter and open chromatin resequencing and general-purpose genotyping of various Triticeae species., (© 2022 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)
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- 2023
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48. Capturing Wheat Phenotypes at the Genome Level.
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Hussain B, Akpınar BA, Alaux M, Algharib AM, Sehgal D, Ali Z, Aradottir GI, Batley J, Bellec A, Bentley AR, Cagirici HB, Cattivelli L, Choulet F, Cockram J, Desiderio F, Devaux P, Dogramaci M, Dorado G, Dreisigacker S, Edwards D, El-Hassouni K, Eversole K, Fahima T, Figueroa M, Gálvez S, Gill KS, Govta L, Gul A, Hensel G, Hernandez P, Crespo-Herrera LA, Ibrahim A, Kilian B, Korzun V, Krugman T, Li Y, Liu S, Mahmoud AF, Morgounov A, Muslu T, Naseer F, Ordon F, Paux E, Perovic D, Reddy GVP, Reif JC, Reynolds M, Roychowdhury R, Rudd J, Sen TZ, Sukumaran S, Ozdemir BS, Tiwari VK, Ullah N, Unver T, Yazar S, Appels R, and Budak H
- Abstract
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat ( Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence., Competing Interests: HB and BA are employed by Montana BioAg Inc., VK is employed by KWS, TU is employed by Ficus Biotechnology, and PD is employed by Florimond Desprez Group. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Hussain, Akpınar, Alaux, Algharib, Sehgal, Ali, Aradottir, Batley, Bellec, Bentley, Cagirici, Cattivelli, Choulet, Cockram, Desiderio, Devaux, Dogramaci, Dorado, Dreisigacker, Edwards, El-Hassouni, Eversole, Fahima, Figueroa, Gálvez, Gill, Govta, Gul, Hensel, Hernandez, Crespo-Herrera, Ibrahim, Kilian, Korzun, Krugman, Li, Liu, Mahmoud, Morgounov, Muslu, Naseer, Ordon, Paux, Perovic, Reddy, Reif, Reynolds, Roychowdhury, Rudd, Sen, Sukumaran, Ozdemir, Tiwari, Ullah, Unver, Yazar, Appels and Budak.)
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- 2022
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49. Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding.
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Aury JM, Engelen S, Istace B, Monat C, Lasserre-Zuber P, Belser C, Cruaud C, Rimbert H, Leroy P, Arribat S, Dufau I, Bellec A, Grimbichler D, Papon N, Paux E, Ranoux M, Alberti A, Wincker P, and Choulet F
- Subjects
- Breeding, Chromosomes, Sequence Analysis, DNA methods, Genome, Triticum genetics
- Abstract
Background: The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions, but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost., Results: Here, we report on an optimized procedure based on long reads produced on the Oxford Nanopore Technology PromethION device to assemble the genome of the French bread wheat cultivar Renan., Conclusions: We provide the most contiguous chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-sequencing data, this resource will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide a framework to generate high-quality assemblies of complex genomes using ONT., (© The Author(s) 2022. Published by Oxford University Press GigaScience.)
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- 2022
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50. Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection.
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Paux E, Lafarge S, Balfourier F, Derory J, Charmet G, Alaux M, Perchet G, Bondoux M, Baret F, Barillot R, Ravel C, Sourdille P, Le Gouis J, and On Behalf Of The Breedwheat Consortium
- Abstract
There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production. To address these challenges, new and innovative knowledge, resources, tools, and methods to facilitate breeding are needed. This starts with the development of high throughput genomic tools including single nucleotide polymorphism (SNP) arrays, high density molecular marker maps, and full genome sequences. Such powerful tools are essential to perform genome-wide association studies (GWAS), to implement genomic and phenomic selection, and to characterize the worldwide diversity. This is also useful to breeders to broaden the genetic basis of elite varieties through the introduction of novel sources of genetic diversity. Improvement in varieties particularly relies on the detection of genomic regions involved in agronomical traits including tolerance to biotic (diseases and pests) and abiotic (drought, nutrient deficiency, high temperature) stresses. When enough resolution is achieved, this can result in the identification of candidate genes that could further be characterized to identify relevant alleles. Breeding must also now be approached through in silico modeling to simulate plant development, investigate genotype × environment interactions, and introduce marker-trait linkage information in the models to better implement genomic selection. Breeders must be aware of new developments and the information must be made available to the world wheat community to develop new high-yielding varieties that can meet the challenge of higher wheat production in a sustainable and fluctuating agricultural context. In this review, we compiled all knowledge and tools produced during the BREEDWHEAT project to show how they may contribute to face this challenge in the coming years.
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- 2022
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