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21 results on '"Canaguier, Aurelie"'

1. Nanopore adaptive sampling to identify the NLR-gene family in melon (Cucumis melo L.)

Author

Belinchon-Moreno, Javier, primary, Berard, Aurelie, additional, Canaguier, Aurelie, additional, Chovelon, Veronique, additional, Cruaud, Corinne, additional, Engelen, Stefan, additional, Feriche-Linares, Rafael, additional, Le-Clainche, Isabelle, additional, Lagnel, Jacques, additional, Marande, William, additional, Rittener-Ruff, Vincent, additional, Hinsinger, Damien, additional, Boissot, Nathalie, additional, and Faivre Rampant, Patricia, additional

Published
2023
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2. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Author

Chalhoub, Boulos, Denoeud, France, Liu, Shengyi, Parkin, Isobel A. P., Tang, Haibao, Wang, Xiyin, Chiquet, Julien, Belcram, Harry, Tong, Chaobo, Samans, Birgit, Corréa, Margot, Da Silva, Corinne, Just, Jérémy, Falentin, Cyril, Koh, Chu Shin, Le Clainche, Isabelle, Bernard, Maria, Bento, Pascal, Noel, Benjamin, Labadie, Karine, Alberti, Adriana, Charles, Mathieu, Arnaud, Dominique, Guo, Hui, Daviaud, Christian, Alamery, Salman, Jabbari, Kamel, Zhao, Meixia, Edger, Patrick P., Chelaifa, Houda, Tack, David, Lassalle, Gilles, Mestiri, Imen, Schnel, Nicolas, Le Paslier, Marie-Christine, Fan, Guangyi, Renault, Victor, Bayer, Philippe E., Golicz, Agnieszka A., Manoli, Sahana, Lee, Tae-Ho, Thi, Vinh Ha Dinh, Chalabi, Smahane, Hu, Qiong, Fan, Chuchuan, Tollenaere, Reece, Lu, Yunhai, Battail, Christophe, Shen, Jinxiong, Sidebottom, Christine H. D., Wang, Xinfa, Canaguier, Aurélie, Chauveau, Aurélie, Bérard, Aurélie, Deniot, Gwenaëlle, Guan, Mei, Liu, Zhongsong, Sun, Fengming, Lim, Yong Pyo, Lyons, Eric, Town, Christopher D., Bancroft, Ian, Wang, Xiaowu, Meng, Jinling, Ma, Jianxin, Pires, J. Chris, King, Graham J., Brunel, Dominique, Delourme, Régine, Renard, Michel, Aury, Jean-Marc, Adams, Keith L., Batley, Jacqueline, Snowdon, Rod J., Tost, Jorg, Edwards, David, Zhou, Yongming, Hua, Wei, Sharpe, Andrew G., Paterson, Andrew H., Guan, Chunyun, and Wincker, Patrick

Published
2014

5. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla: the French-Italian public consortium for grapevine genome characterization

Author

Jaillon, Olivier, Aury, Jean-Marc, Noel, Benjamin, Policriti, Alberto, Clepet, Christian, Casagrande, Alberto, Choisne, Nathalie, Aubourg, Sebastien, Vitulo, Nicola, Jubin, Claire, Vezzi, Alessandro, Legeai, Fabrice, Hugueney, Philippe, Dasilva, Corinne, Horner, David, Mica, Erica, Jublot, Delphine, Poulain, Julie, Bruyere, Clemence, Billault, Alain, Segurens, Beatrice, Gouyvenoux, Michel, Ugarte, Edgardo, Cattonaro, Federica, Anthouard, Veronique, Vico, Virginie, Del Fabbro, Cristian, Alaux, Michael, Gaspero, Gabriele Di, Dumas, Vincent, Felice, Nicoletta, Paillard, Sophie, Juman, Irena, Moroldo, Marco, Scalabrin, Simone, Canaguier, Aurelie, Clainche, Isabelle Le, Malacrida, Giorgio, Durand, Eleonore, Pesole, Graziano, Laucou, Valerie, Chatelet, Philippe, Merdinoglu, Didier, Delledonne, Massimo, Pezzotti, Mario, Lecharny, Alain, Scarpelli, Claude, Artiguenave, Francois, Pe, M. Enrico, Valle, Giorgio, Morgante, Michele, Caboche, Michel, Adam-Blondon, Anne-Francoise, Weissenbach, Jean, Quetier, Francis, and Wincker, Patrick

Subjects
Grapes -- Genetic aspects, Genomes -- Identification and classification -- Genetic aspects, Angiosperms -- Natural history -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Identification and classification, Genetic aspects, Natural history
Abstract

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics [...]

Published
2007

6. Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.)

Author

Ravel, Catherine, Praud, Sebastien, Murigneux, Alain, Canaguier, Aurelie, Sapet, Frederic, Samson, Delphine, Balfourier, Francois, Dufour, Philippe, Chalhoub, Boulos, Brunel, Dominique, Beckert, Michel, and Charmet, Gilles

Subjects
Wheat -- Genetic aspects, Wheat -- Research, Genetic polymorphisms -- Research, Biological sciences
Abstract

Abstract: Information on single-nucleotide polymorphisms (SNPs) in hexaploid bread wheat is still scarce. The goal of this study was to detect SNPs in wheat and examine their frequency. Twenty-six bread [...]

Published
2006

8. A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance

Author

Scalabrin Simone, Le Clainche Isabelle, Brunaud Veronique, Guichard Cecile, De Berardinis Veronique, Cruaud Corinne, Canaguier Aurelie, Fabrice Legeai, Marconi Raffaella, Paillard Sophie, Moroldo Marco, Testolin Raffaele, Di Gaspero Gabriele, Morgante Michele, and Adam-Blondon Anne-Francoise

Subjects
Botany, QK1-989
Abstract

Abstract Background Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed. Results The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome. Conclusion Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.

Published
2008
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9. BSA-Seq : an efficient method to decipher a complex trait on Poplar, a highly heterozygous diploid genome

Author

Canaguier, Aurelie, Jorge, Véronique, Guérin, Vanina, Rogier, Odile, Segura, Vincent, Chauveau, Aurelie, Marquand, Elodie, Berard, Aurélie, Le Paslier, Marie-Christine, Bastien, Catherine, Faivre-Rampant, Patricia, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Biologie intégrée pour la valorisation de la diversité des arbres et de la forêt (BioForA), Institut National de la Recherche Agronomique (INRA)-Office National des Forêts (ONF), Département Ecologie des Forêts, Prairies et milieux Aquatiques (DEPT EFPA), and AIP Bio-ressources

Subjects
BSA-Seq, resistance, leaf rust, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Bioinformatics, fungi, Bio-informatique, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Poplar, Autre (Sciences du Vivant)
Abstract

International audience; The efficiency of the Bulk Segregant Analysis (BSA) had clearly been demonstrated to detect genomic regions and genes involved in diverse traits. It allows large experiments reducing the cost and time and preserving the power of full individual's population analysis. These past few years the combination of BSA and New Generation Sequence (NGS) data (BSA-Seq) gave a new accuracy and depth to the discovery on many traits of interest, mainly on crop and model species. In our study, we applied the BSA-Seq in a heterozygous and diploid genome context. We worked on the progenies derived from an interspecific cross Populus deltoides x Populus trichocarpa in which segregates the resistance to Melampsora larici populina (Mlp) leaf rust. We detected DNA variations with freebayes/0.9.21 and the soft masked genome of Populus trichocarpa Nisqually v3.0 as reference. Comparing DNA variations in between parents and bulks we obtained 27 regions or Quantitative Trait Loci based on NGS analysis (QTL-Seq) which could explain the resistance to Mlp. We first evaluated the strategy retrieving a previously cloned Mlp resistance gene governing the uredinia size in Populus trichocarpa clone 101-74 (RUS). Then we identified genomic markers which should better characterize this locus. So we demonstrated that, in our context, BSA-Seq allows us to improve the fine mapping of a major gene. We think it can be a promising method on a high heterozygous diploid genome as Poplar, to decipher complex trait. Next step is to proceed with it to fine map the other QTL-Seq.

Published
2018

10. BSA-Seq : An efficient tool to characterize loci involved in the Poplar leaf rust resistance

Author

Canaguier, Aurelie, Guérin, Vanina, Rogier, Odile, Le Clainche, Isabelle, Chauveau, Aurelie, MARQUAND, ELODIE, Berard, Aurélie, Le Paslier, Marie-Christine, Bastien, Catherine, Faivre-Rampant, Patricia, Jorge, Véronique, and Segura, Vincent

Subjects
BSA, NGS, rust, Poplar, Autre (Sciences du Vivant)
Abstract

The efficiency of the Bulk Segregant Analysis (BSA) had clearly been demonstrated to detect genomic regions and genes involved in diverse traits. It allows large experiments reducing the cost and time and preserving the power of full individual's population analysis. These past few years the combination of BSA and New Generation Sequence (NGS) data (BSA-Seq) gave a new accuracy and depth to the discovery on many traits of interest, mainly on crop and model species. In our study, we applied the BSA-Seq to narrow down Populus genomic regions involved in the resistance to Melampsora larici populina (Mlp) leaf rust. We worked on the 1417 progenies derived from an interspecific cross Populus deltoides clone 73028-62 (Pd) x Populus trichocarpa clone 101-74 (Pt) in which segregates qualitative and quantitative Mlp resistances. Four bulks were constituted based on (1) the phenotypes for uredinias size (bulk1: large, bulk2 and bulk3: intermediate, bulk4: small) and (2) the Pt genotypes at the RUS locus governing the uredinia size (bulk1 and bulk3 : [RUS], bulk2 and bulk4 : [rUS]). We used independently the soft masked genomes of Populus trichocarpa Nisqually v3.0 (Ptv3) and Populus deltoides v2.0 (Pdv2) as references to map parents and bulks Illumina reads with the BWAmem/0.7.15 suite and to detect DNA variations with Freebayes/0.9.21. For each common variant position between parents and bulks, we tracked the specific alleles of Pt and/or Pd in the bulks. Respectively from Ptv3 and Pdv2, we identified 13 and 11 regions. We first evaluated the strategy retrieving the previously finally mapped RUS gene, designed new genomic markers from Ptv3 to better characterize this locus and performed the in silico validation. Then we proceed with it to fine map the other regions. Most of them co-locate with QTL and could explain the resistance to Mlp. So we demonstrated that, in our context, even if the reference genome is different to the studied genomes, BSA-Seq allowed us to detect quickly and costly, regions which may be involved in a complex trait and improve the fine mapping of a major gene. We think it can be a promising method on a high heterozygous diploid genome as Poplar, to decipher complex trait. Next step is to identify candidate genes within the regions and better describe the mechanisms of resistance.

Published
2018

11. Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination 'hot spots'

Author

Drouaud, Jan, Camilleri, Christine, Bouruignon, Pierre-Yves, Canaguier, Aurelie, Vezon, Daniel, Giancola, Sandra, Brunel, Domonique, Colot, Vincent, Prum, Bernard, Quesneville, Hadi, and Mezard, Christine

Subjects
Arabidopsis -- Genetic aspects, Single nucleotide polymorphisms -- Research, Plant chromosomes -- Research, Health
Abstract

Single nucleotide polymorphisms are genotyped covering the entire chromosome 4 of Arabidopsis thaliana on 702 F2 plants, representing 1404 meioses to study CO localization in a higher plant. A variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals 'hot spots' of meiotic recombination contained in small fragments of few kilobases.

Published
2006

12. Improvement of the Grapevine genome assembly

Author

Canaguier, Aurelie, Scalabrin, Simone, Le Paslier, Marie-Christine, Duchêne, Eric, Mohellibi, Nacer, Berard, Aurélie, Chauveau, Aurelie, Boursiquot, Jean-Michel, Di Gaspero, Gabriele, HAUSMANN, Ludger, Martinez Zapater, José Miguel, Morgante, Michele, Adam-Blondon, Anne-Francoise, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Istituto di Genomica Applicata, Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université Louis Pasteur - Strasbourg I, Unité de Recherche Génomique Info (URGI), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Università degli Studi di Udine - University of Udine [Italie], Julius Kühn-Institut (JKI), Instituto de Ciencias de la Vid y el Vino - Institute of Grapevine and Wine Sciences, and Partenaires INRAE

Subjects
Vegetal Biology, Grapevine genome, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biologie végétale, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

13. BAC libraries for structural genomic development in oak

Author

Faivre-Rampant, Patricia, Lesur, Isabelle, Le Clainche, Isabelle, Canaguier, Aurelie, Boussardon, Clément, Martin-Magniette, Marie-Laure, Bodénès, Catherine, Salin, Franck, Le Provost, Grégoire, Berges, Helene, Kremer, Antoine, Plomion, Christophe, ProdInra, Migration, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), 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), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), and Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202).

Subjects
[SDV] Life Sciences [q-bio], Oak, [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, genome content, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS, BAC libraries
Abstract

Résumé du poster; National audience

Published
2012

14. Diversité moléculaire de la région chromosomique contrôlant la résistance à la rouille foliaire dans les collections de peupliers: Restitution appel à projets BRG 2007-2008

Author

Faivre-Rampant, Patricia, Bresson, Alois, Jorge, Véronique, Dowkiw, Arnaud, El-Malki, Redouane, Segura, Vincent, Guérin, Vanina, Bitton, Frederique, Le Clainche, Isabelle, Canaguier, Aurelie, Guichard, Cecile, Aluome, Christelle, Le Paslier, Marie-Christine, Bounon, Rémi, Berard, Aurélie, Brunel, Dominique, Vincent, S., Mohellibi, Nacer, Steinbach, Delphine, Chalhoub, Boulos, Bastien, Catherine, 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), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Etude du Polymorphisme des Génomes Végétaux (EPGV), Bayer Cropscience, and Unité de Recherche Génomique Info (URGI)

Subjects
PEUPLIER NOIR, polymorphisme nucléotidique, résistance à la rouille, génomique structurale, génome, [SDV]Life Sciences [q-bio], gène de résistance, séquençage, population naturelle, gène candidat, séquence de gènes, populus nigra, ComputingMilieux_MISCELLANEOUS, rouille foliaire
Abstract

National audience

Published
2011

15. Molecular linkage maps: strategies, resources and achievements

Author

Di Gaspero, Gabriele, Canaguier, Aurelie, Jusseaume, Julie, Tassin, Johan, Lemainque, Arnaud, Thareau, Vincent, Adam-Blondon, Anne-Francoise, Testolin, Raffaele, and Cipriani, Guido

Subjects
carte génétique, hétérozygotie, genetic map, SSR, SNP, integrated map, full-sib family, heterozygosity, vigne cultivée
Abstract

The development of genetic maps in grapevine started in the late 90s. It greatly benefi ted from the development of SSR markers by an international consortium, leading to the construction of integrated genetic maps. Software was improved for facilitating map construction in full sib families. A review of the different strategies that were developed for mapping in grapevine, including mapping populations, software and markers is provided here together with a discussion on their interest and limitations. Thanks to all these resources and experience, genetic mapping is now easy to handle in grapevine and is now widely used for QTL detection, map-based cloning, comparative mapping across species and genome sequence anchoring.

Published
2011

16. Molecular linkage maps: strategies, resources and achievements

Author

Cipriani, Guido, Di Gaspero, Gabriele, Canaguier, Aurelie, Jusseaume, Julie, Tassin, Johan, Lemainque, Arnaud, Thareau, Vincent, Adam-Blondon, Anne-Francoise, Testolin, Raffaele, Università degli Studi di Udine - University of Udine [Italie], Udine, 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 de Génomique, Université Paris-Sud - Paris 11 (UP11), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Istituto di Genomica Applicata, Anne-Francoise Adam-Blondon, and Jose-Miguel Martinez-Zapater

Subjects
[SDV]Life Sciences [q-bio], heterozygosity, SNP, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, genetic map, full-sib family, SSR, integrated map
Abstract

Chapitre 5; International audience; The development of genetic maps in grapevine started in the late 90s. It greatly benefi ted from the development of SSR markers by an international consortium, leading to the construction of integrated genetic maps. Software was improved for facilitating map construction in full sib families. A review of the different strategies that were developed for mapping in grapevine, including mapping populations, software and markers is provided here together with a discussion on their interest and limitations. Thanks to all these resources and experience, genetic mapping is now easy to handle in grapevine and is now widely used for QTL detection, map-based cloning, comparative mapping across species and genome sequence anchoring.

Published
2011

17. Allele mining in grape for the analysis of complex traits

Author

Roberto Bacilieri, Stéphane Nicolas, Richard Bounon, Alexis Dereeper, Marie-Christine Le Paslier, Guichard, Cecile C., Canaguier, Aurelie A., Vincent Thareau, Loic Le Cunff, Jean-Pierre Peros, Brunel, Dominique D., Agnès Doligez, Laucou, Valerie V., Thierry Lacombe, Jean-Michel Boursiquot, F Adam-Blondon, Anne-Francoise A., This, Patrice P., 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), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), 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), Université Paris-Sud - Paris 11 (UP11), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and 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)

Subjects
[SDV]Life Sciences [q-bio], Amériques
Abstract

International audience; In the past decade, thanks to an important international effort, our understanding of grape nuclear diversity greatly improved, in particular through European Programs such as GenRes81 and GrapeGen06 leading to the standardization of SSR analysis. Our knowledge of grape diversity in genes, is however still limited. A precise knowledge of gene diversity will be highly beneficial in order to improve our understanding of quantitative important traits. Since the publication of the grape sequence, we have now the possibility to study gene diversity in grape at a large scale. In the present work, SSR diversity in the INRA grape collection (2300 cultivars) enabled the definition of a highly diverse sample of 27 V. vinifera accessions. This set was completed by 7 accessions of V. vinifera subsp. sylvestris and several accessions of Vitis species from Asia or America. Analysis of gene diversity over this sample of 47 accessions was thus performed for a set of 900 genes scattered through the grape genome. Through bioinformatics developments, diversity maps of the grape genome have been drawn at different levels. This data will be very useful in order to select markers for mapping, for comparison of diversity between Vitis species and for the search of selective sweeps in grape. It will also be very useful in the assessment of DL in grape, a prerequisite for Whole Genome Association studies.

Published
2010

18. Physical mapping and re-sequencing of a set of resistance related genes in grapevine

Author

Moroldo, Marco, Paillard, Sophie, Marconi, R., Legeai, Fabrice, Canaguier, Aurelie, Cruaud, C., de Berardinis, Véronique, Guichard, Cecile, Brunaud, Veronique, Le Clainche, Isabelle, Bounon, Rémi, Chauveau, Aurelie, Berard, Aurélie, Scalabrin, S., de Paoli, E., Bacilieri, Roberto, Le Paslier, Marie-Christine, Brunel, Dominique, Testolin, R., Di Gaspero, G., Morgante, M., Adam-Blondon, Anne-Francoise, 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 de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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), Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Udine - University of Udine [Italie], Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), 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), Etude du Polymorphisme des Génomes Végétaux (EPGV), Dipartimento di Scienze matematiche, Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware [Newark], Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Applied Genomics Institute (IGA), Génétique de la Vigne, Labo/service de l'auteur, Ville service, Pays service., Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), ProdInra, Archive Ouverte, Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
[SDV] Life Sciences [q-bio], resistance, [SDV]Life Sciences [q-bio], food and beverages, mapping, grapevine
Abstract

Physical mapping and re-sequencing of a set of resistance related genes in grapevine. 17. Conference Plant and Animal Genomes

Published
2009

19. High throughput SNPs discovery in grapevine, poplar and tomato

Author

Le Paslier, Marie-Christine, Bounon, Rémi, Chauveau, Aurelie, Thareau, Vincent, Canaguier, Aurelie, Clainche, Isabelle, Houel, Cléa, Moroldo, Marco, Rolland, Sophie, Ranc, Nicolas, Bresson, Alois, Paolucci, Isabella, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), 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), Université Paris-Sud - Paris 11 (UP11), and Génétique et Amélioration des Fruits et Légumes (GAFL)

Subjects
SINGLE NUCLEOTIDE POLYMORPHISM, CDNA SEQUENCE, [SDV]Life Sciences [q-bio], PEUPLIER, SPADS ALGORITHM, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2009

20. A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance

Author

Moroldo, Marco, primary, Paillard, Sophie, additional, Marconi, Raffaella, additional, Fabrice, Legeai, additional, Canaguier, Aurelie, additional, Cruaud, Corinne, additional, De Berardinis, Veronique, additional, Guichard, Cecile, additional, Brunaud, Veronique, additional, Le Clainche, Isabelle, additional, Scalabrin, Simone, additional, Testolin, Raffaele, additional, Di Gaspero, Gabriele, additional, Morgante, Michele, additional, and Adam-Blondon, Anne-Francoise, additional

Published
2008
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21. Association genetics in relation with berry size variation in grapevine (Vitis vinifera)

Author

Cléa Houel, Le Clainche, Isabelle I., Canaguier, Aurelie A., F Adam-Blondon, Anne-Francoise A., Rémi Bounon, Berard, A., Marie-Christine Le Paslier, Brunel, Dominique D., Laurent Torregrosa, Roberto Bacilieri, Stéphane Nicolas, Thierry Lacombe, Alexis Dereeper, Jean-Pierre Peros, Chaïb, J., Thomas, M., Marie-Stéphanie Vernerey, Coriton, Olivier O., 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), Diversité et adaptation des plantes cultivées (UMR DIAPC), 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), Plant Industry, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Amélioration des Plantes et Biotechnologies Végétales (APBV), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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), and 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)

Subjects
[SDV]Life Sciences [q-bio], taille des baies, Solanacées
Abstract

Corresponding author: houel@evry.inra.fr; International audience; Berry size is an important trait both for yield (table grapes) and in relation to quality (wine grapes). The final size of an organ is dependent on cell number, cell size and/or number of carpel. Indeed it has been shown that cell number is a major determinant of fruit size variability in Solanaceae and Prunus, whereas a preliminary study on a small sample of grapevine genotypes suggested that the variability of berry size resulted from cell volume enlargement. At present only few genes involved in fruit size variation have been identified, mainly in Solanaceae and none in grapevine. Our aims are: (1) to check, in a large sample of grapevine genotypes, the relative importance of cell volume enlargement, number of cell and carpel in berry size variation, (2) to develop association genetics approaches with candidate genes for berry size and (3) to study the DNA polymorphism along the region carrying the fleshless berry locus (flb) in order to detect possible selection pressures in cultivated varieties. The flb locus was identified in a grapevine natural mutant which present berries with a size reduced by 20 times and circular seeds similar to wild grapevine berries. The ovaries and the berries of 3 subpopulations of cultivated Vitis vinifera genotypes (279), which represent the genetic and phenotypic variability of berry size, have been phenotyped. Preliminary results on a small sample of individual (27) suggested that the final berry size was determined at early stage of berry development. The ovarian size just before fertilization was variable and proportional to the final berry size. However the ovarian cell number or size seemed to explain the final berry size differently according to sub-populations. Several mechanisms and probably several genes would be involved in the variation of the berry size in these sub-populations. These data are currently under validation on the whole set of 279 individuals. In parallel, 44 candidate genes, orthologous to genes known to be involved in flower or fruit development and/or co-localizing with berry size QTLs (Quantitative Trait Locus) and/or expressed during grapevine berry development, have been partially or totally sequenced in 47 genotypes which reflect all the genetic diversity of grapevine. Several thousands of SNPs (Single Nucleotide Polymorphims) have been identified. A subset of these SNPs will be used for genotyping the 3 sub-populations using the SNPlex technology, in order to detect a possible correlation between genotypic and phenotypic variation. Finally, in order to test the hypothesis that flb is one of the genes selected during grapevine domestication, 69 gene fragments along flb locus (1Mbp) were sequenced in a sample of wild and cultivated Vitis vinifera. Our results revealed a small zone showing more polymorphism in wild genotypes than in cultivated genotypes and a large zone of 171Kb showing either more polymorphism in cultivated genotypes than in wild genotypes. These intervals will be studied more in details using two approaches: gene expression studies and an improvement of the genotype sampling for the DNA polymorphism studies.

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