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2. Epigenetics at the interface between environment and DNA: what importance for breeding practices and selection methods?

Author

Coustham, V., primary, Andrieux, C., additional, Collin, A., additional, David, I., additional, Demars, J., additional, Houssier, M., additional, Lagarrigue, S., additional, Métayer-Coustard, S., additional, Mignon-Grasteau, S., additional, Petit, A., additional, Vitorino Carvalho, A., additional, Zerjal, T., additional, and Pitel, F., additional

Published
2022
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18. Dietary methionine deficiency reduces laying performances of female common ducks and impacts traits of interest of their mule ducklings

Author

Bodin, L, primary, Sécula, A, additional, Chapuis, H, additional, Cornuez, A, additional, Lessire, M, additional, Cobo, E, additional, Marie-Louise, S, additional, Bonnefont, C M D, additional, Barrieu, J, additional, Mercerand, F, additional, Bravo, C, additional, Manse, H, additional, Le Bourhis, M C, additional, Martin, X, additional, Pitel, F, additional, Brun, J M, additional, and Morisson, M, additional

Published
2019
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25. Comparative genomics reveals insights into avian genome evolution and adaptation

Author

Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., Odeen, A., Cui, J., Zhou, Q., Xu, L., Pan, H., Wang, Z., Jin, L., Zhang, P., Hu, H., Yang, W., Hu, J., Xiao, J., Yang, Z., Liu, Y., Xie, Q., Yu, H., Lian, J., Wen, P., Zhang, F., Li, H., Zeng, Y., Xiong, Z., Liu, S., Zhou, L., Huang, Z., An, N., Wang, J., Zheng, Q., Xiong, Y., Wang, G., Wang, B., Fan, Y., da Fonseca, R. R., Alfaro-Nunez, A., Schubert, M., Orlando, L., Mourier, T., Howard, J. T., Ganapathy, G., Pfenning, A., Whitney, O., Rivas, M. V., Hara, E., Smith, J., Farre, M., Narayan, J., Slavov, G., Romanov, M. N., Borges, R., Machado, J. P., Khan, I., Springer, M. S., Gatesy, J., Hoffmann, F. G., Opazo, J. C., Hastad, O., Sawyer, R. H., Kim, H., Kim, K.-W., Kim, H. J., Cho, S., Li, N., Huang, Y., Bruford, M. W., Zhan, X., Dixon, A., Bertelsen, M. F., Derryberry, E., Warren, W., Wilson, R. K., Li, S., Ray, D. A., Green, R. E., O'Brien, S. J., Griffin, D., Johnson, W. E., Haussler, D., Ryder, O. A., Willerslev, E., Graves, G. R., Alstrom, P., Fjeldsa, J., Mindell, D. P., Edwards, S. V., Braun, E. L., Rahbek, C., Burt, D. W., Houde, P., Zhang, Y., Yang, H., Jarvis, E. D., Gilbert, M. T. P., Ye, C., Liang, S., Yan, Z., Zepeda, M. L., Campos, P. F., Velazquez, A. M. V., Samaniego, J. A., Avila-Arcos, M., Martin, M. D., Barnett, R., Ribeiro, A. M., Mello, C. V., Lovell, P. V., Almeida, D., Maldonado, E., Pereira, J., Sunagar, K., Philip, S., Dominguez-Bello, M. G., Bunce, M., Lambert, D., Brumfield, R. T., Sheldon, F. H., Holmes, E. C., Gardner, P. P., Steeves, T. E., Stadler, P. F., Burge, S. W., Lyons, E., McCarthy, F., Pitel, F., Rhoads, D., and Froman, D. P.

Abstract

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

Published
2014

28. Transcriptome profiling reveals interaction between two QTL for fatness in chicken

Author

Blum, Yuna, Le Mignon, Guillaume, Pitel, F., Causeur, David, Demeure, Olivier, Le Roy, P., Lagarrigue, Sandrine, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche Mathématique de Rennes (IRMAR), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Génétique Animale (GARen), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Ecole Nationale Supérieure Agronomique de Rennes, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), IFR140-Ecole Nationale Supérieure Agronomique de Rennes-AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Ecole Nationale Supérieure Agronomique de Rennes, Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Génétique Animale ( GARen ), and Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST-Ecole Nationale Supérieure Agronomique de Rennes-IFR140

Subjects
animal structures, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], embryonic structures, food and beverages, [ MATH.MATH-ST ] Mathematics [math]/Statistics [math.ST], [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH], [ STAT.TH ] Statistics [stat]/Statistics Theory [stat.TH]
Abstract

Transcriptome profiling reveals interaction between two QTL for fatness in chicken

Published
2011

29. The first chicken non-official comparison test

Author

Lasagna, Emiliano, Monteagudo Ibáñez, L. V., Rhoads, D., Gil, M. G., Landi, V., Guémené, D., Pitel, F., Cassandro, M., Bagnato, A., and Weigend, S.

Subjects
chicken, comparison test, microsatellite marker
Published
2011

31. A la croisée de la génomique positionnelle et fonctionnelle : application à l'identification d'une mutation chez le poulet et perspectives de recherches en qualité de la viande

Author

Le Bihan-Duval, E., Berri, C., Pitel, F., Nadaf, J., Sibut, V., Lagarrigue, Sandrine, Duclos, M.J., Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, ITAVI, Génétique Animale (GARen), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Ecole Nationale Supérieure Agronomique de Rennes, IFR140-Ecole Nationale Supérieure Agronomique de Rennes-AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, VIANDE, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, POULET, GENOMIQUE FONCTIONNELLE, GALLUS GALLUS, QTL, SELECTION GENOMIQUE, QUALITE TECHNOLOGIQUE, transcriptome, ComputingMilieux_MISCELLANEOUS, PROTEOME
Abstract

A la croisée de la génomique positionnelle et fonctionnelle : application à l'identification d'une mutation chez le poulet et perspectives de recherches en qualité de la viande

Published
2010

32. eQTL Mapping allows to refine abdominal fatness QTL in chicken

Author

Le Mignon, G., Pitel, F., Demeure, O., Leroux, S., Douaire, M., Abasht, B., Diot, C., Le Roy, P., Lagarrigue, Sandrine, Génétique Animale (GARen), IFR140-Ecole Nationale Supérieure Agronomique de Rennes-AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Ecole Nationale Supérieure Agronomique de Rennes, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, POULET, FATNESS, CHICKENS, [SDV]Life Sciences [q-bio], food and beverages, EQTL, ENGRAISSEMENT
Abstract

Whereas many QTL for various traits were mapped in livestock, the identification of causal mutations remains laborious. In this study, we propose to combine transcriptomic data and linkage analysis for refining a chicken QTL region previously detected on GGA5 with a strong effect on abdominal fatness. Transcriptome profiles for 46 offspring of a sire heterozygous for the QTL were obtained using a chicken 20K oligochips (ARK-genomics). Two groups among the 46 offspring were defined according to the phenotype. 113 genes among the 20460 oligo-genes were differentially expressed between these two groups on the basis of Anova analyses (p

Published
2008

34. Génomique des canards

Author

VIGNAL, A., primary, DIOT, C., additional, MOLETTE, C., additional, MORISSON, M., additional, FARAUT, T., additional, RAO, M., additional, PITEL, F., additional, FILLON, V., additional, and MARIE-ETANCELIN, C., additional

Published
2013
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35. Effects on resistance to Salmonella carrier-state to two candidate gene in fowls

Author

Beaumont, Catherine, Protais, J., Colin, P., Salvar, G., Pitel, F., Plisson-Petit, F., Vignal, Alain, Le Roy, P., Malo, D., Leveque, G., and Elsen, Jean-Michel

Subjects
Modèle, Salmonella, L10 - Génétique et amélioration des animaux, Infection, Résistance aux maladies
Abstract

As significant heritabilities were estimated for resistance to Salmonella carrier-state (defined as the persistency of the bacteria four weeks after inoculation) selection could reduce the risk for the consumer of food toxi-infections but identifying the genes underlying resistance would avoid expensive and extensive measurements. Two genes, Nramp1 (Natural Resistance Associated Macrophage Protein 1) renamed SIc11a1 for Solute carrier family 11, member 1 and TIr4 (Toll-like Receptor 4) have recently been identified in a mouse model of Salmonella infection and the implications of the regions carrying these genes in the resistance of 1 day-old chicks demonstrated. The goal of this work was thus to test the hypothesis of an implication of SLC11A1 and TLR4 in resistance to Salmonella carrier-state. A total of 345 hens issued of 20 sires and 51 dams were therefore orally inoculated at peak of lay with 1,5 x 109 c.f.u. of a PT4 strain of Salmonella enteritidis and slaughtered 4 weeks later. Colonisation of spleen, liver, caeca and ovary was investigated, both with and without enrichment, to distinguish between low and high levels of contamination. Resistance was assessed by five all-or-none traits, discriminating between contaminated (whether after enrichment or not) and uncontaminated animals for each organ and for all of them (discriminating between animals whose all four organs were found free from Salmonella versus those with at least one contaminated organ). For the analysis of data with extreme incidences (close to 0 or 100%), that is ovary and animal contamination, data of family with no positive organs, i.e. no information, were discarded. Five microsatellites from each region were used for genotyping. Association between the markers and the resistance to carrier-state, was analysed with the QTLMAP program using the principles of interval mapping and maximum likelihood. The model of analysis took into account the structure of the population, i.e. a mixture of full and half sib families. The significance thresholds were estimated from the 5% empirical quantiles of the test statistic distribution. A significant effect on chromosome 7 could be observed on the rate of spleen contamination (P

Published
2002

36. First report on chicken genes and chromosomes 2000

Author

Schmid, M., Nanda, I., Guttenbach, M., Steinlein, C., Hoehn, H., Schartl, M., Haaf, T., Weigend, S., Fries, R., Buerstedde, J.M., Wimmers, K., Burt, D.W., Smith, J., A'hara, S., Law, A., Griffin, D.K., Bumstead, N., Kaufman, J., Thomson, P.A., Burke, T., Groenen, M.A.M., Crooijmans, R.P.M.A., Vignal, A., Fillon, V., Morisson, M., Pitel, F., Tixier-Boichard, M., Ladjali-Mohammedi, K., Hillel, J., and Maki-Tanila, A.

Subjects
WIAS, Life Science, Fokkerij en Genomica, Animal Breeding and Genomics
Published
2000

37. Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines

Author

Loywyck, V., Bed'hom, B., Pinard-van der Laan, M.H., Pitel, F., Verrier, E., Bijma, P., Loywyck, V., Bed'hom, B., Pinard-van der Laan, M.H., Pitel, F., Verrier, E., and Bijma, P.

Abstract

We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL) regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed values greater than 0.15. However, the non-significant difference (P > 0.05) between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm thatmarkers located inQTL regions on chromosomes 1, 7 and 14 were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone

Published
2008

38. Linkage mapping of quantitative trait loci for phosphorus utilization and growth related traits in an F2-cross of Japanese quail (Coturnix japonica).

Author

Beck, P., Stratz, P., Preuß, S., Pitel, F., Recoquillay, J., Duval, E., Rodehutscord, M., and Bennewitz, J.

Subjects
JAPANESE quail, CHROMOSOMES, BODY weight
Abstract

Copyright of European Poultry Science / Archiv für Geflügelkunde is the property of Verlag Eugen Ulmer and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2016
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39. A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes

Author

Pitel, F., Abasht, B., Morrison, M., Crooijmans, R.P.M.A., Vignoles, F., Leroux, S., Feve, K., Bardes, S., Milan, D., Lagarrigue, S., Groenen, M.A.M., Douaire, M., Vignal, A., Pitel, F., Abasht, B., Morrison, M., Crooijmans, R.P.M.A., Vignoles, F., Leroux, S., Feve, K., Bardes, S., Milan, D., Lagarrigue, S., Groenen, M.A.M., Douaire, M., and Vignal, A.

Abstract

Background - The resolution of radiation hybrid (RH) maps is intermediate between that of the genetic and BAC (Bacterial Artificial Chromosome) contig maps. Moreover, once framework RH maps of a genome have been constructed, a quick location of markers by simple PCR on the RH panel is possible. The chicken ChickRH6 panel recently produced was used here to construct a high resolution RH map of chicken GGA5. To confirm the validity of the map and to provide valuable comparative mapping information, both markers from the genetic map and a high number of ESTs (Expressed Sequence Tags) were used. Finally, this RH map was used for testing the accuracy of the chicken genome assembly for chromosome 5. Results - A total of 169 markers (21 microsatellites and 148 ESTs) were typed on the ChickRH6 RH panel, of which 134 were assigned to GGA5. The final map is composed of 73 framework markers extending over a 1315.6 cR distance. The remaining 61 markers were placed alongside the framework markers within confidence intervals. Conclusion - The high resolution framework map obtained in this study has markers covering the entire chicken chromosome 5 and reveals the existence of a high number of rearrangements when compared to the human genome. Only two discrepancies were observed in relation to the sequence assembly recently reported for this chromosome.

Published
2004

45. 2003 Spring meeting of the WPSA French Branch

Author

Fillon, V., primary, Vignoles, M., additional, Garrigues, A., additional, Pitel, F., additional, Morisson, M., additional, Crooijmans, R.P.M.A., additional, Groenen, M.A.M., additional, Gellin, J., additional, and Vignal, A., additional

Published
2003
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46. Effect of two candidate genes on the Salmonella carrier state in fowl

Author

Beaumont, C, primary, Protais, J, additional, Pitel, F, additional, Leveque, G, additional, Malo, D, additional, Lantier, F, additional, Plisson-Petit, F, additional, Colin, P, additional, Protais, M, additional, Le Roy, P, additional, Elsen, JM, additional, Milan, D, additional, Lantier, I, additional, Neau, A, additional, Salvat, G, additional, and Vignal, A, additional

Published
2003
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