47 results on '"Burlot T"'
Search Results
2. Egg production in nests and nesting behaviour: genetic correlations with egg quality and body weight for laying hens on the floor
- Author
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Bécot, L., primary, Bédère, N., additional, Ferry, A., additional, Burlot, T., additional, and Le Roy, P., additional
- Published
- 2023
- Full Text
- View/download PDF
3. Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach
- Author
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Jehl, F., Désert, C., Klopp, C., Brenet, M., Rau, A., Leroux, S., Boutin, M., Lagoutte, L., Muret, K., Blum, Y., Esquerré, D., Gourichon, D., Burlot, T., Collin, A., Pitel, F., Benani, A., Zerjal, T., and Lagarrigue, S.
- Published
- 2019
- Full Text
- View/download PDF
4. 600. No G×E on egg qualities and body weight between cage and floor systems, implications for breeding programmes in laying hens
- Author
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Bédère, N., primary, Bécot, L., additional, Burlot, T., additional, and Le Roy, P., additional
- Published
- 2022
- Full Text
- View/download PDF
5. 116. Laying hens tweet: they also lead and follow – implications for genetic selection against gregarious nesting
- Author
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Bécot, L., primary, Bédère, N., additional, Burlot, T., additional, and Le Roy, P., additional
- Published
- 2022
- Full Text
- View/download PDF
6. 98. Combined effect of genetics and gut microbiota on variations in vaccine response in hens
- Author
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Lecoeur, A., primary, Blanc, F., additional, Gourichon, D., additional, Bruneau, N., additional, Burlot, T., additional, Calenge, F., additional, and Pinard-van der Laan, M.H., additional
- Published
- 2022
- Full Text
- View/download PDF
7. Combined effects of genetics and gut microbiota on vaccine response in laying hens
- Author
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Lecoeur, A., primary, Blanc, F., additional, Gourichon, D., additional, Bruneau, N., additional, Burlot, T., additional, Calenge, F., additional, and Pinard-van der Laan, M-H., additional
- Published
- 2022
- Full Text
- View/download PDF
8. Select on nesting behavior to improve egg production for hens in cage-free systems
- Author
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Bécot, L., primary, Bédère, N., additional, Coton, J., additional, Burlot, T., additional, and Le Roy, P., additional
- Published
- 2022
- Full Text
- View/download PDF
9. An Integrated Approach of Genetic Resistance to Salmonella Carrier State in Fowls: from Genetics to Genomics and Modelling
- Author
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Beaumont, C., primary, Lecerf, F., additional, Protais, J., additional, Calenge, F., additional, Prevost, K., additional, Lalmanach, A.C., additional, Chapuis, H., additional, Pitel, F., additional, Burlot, T., additional, Sellier, N., additional, Fravalo, P., additional, Vignal, A., additional, and Velge, P., additional
- Published
- 2008
- Full Text
- View/download PDF
10. Deterministic modelling of a poultry breeding scheme
- Author
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François, Yoannah, Alnahhas, N., Brard-Fudulea, S., Varenne, A., Burlot, T., Chapuis, Herve, Elsen, Jean Michel, Le Roy, Pascale, ProdInra, Migration, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-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, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,[SDV.GEN] Life Sciences [q-bio]/Genetics ,[SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics ,[INFO] Computer Science [cs] ,poultry selection scheme ,deterministic modelling ,genomic selection - Abstract
International audience; Deterministic modelling of a poultry breeding scheme Deterministic modeling of selection schemes consists of calculating the expected genetic gain after a selection process. Consequences of selection on the genetic trend are calculated using equations based on estimated breeding values and on parameters describing the population and the selection process. Professionals could use this tool to compare different strategies for the improvement of their selection schemes. In this study, the model is based on a layer chicken breeding scheme. Breeding goal includes numerous traits such as laying performances, egg quality and body weight. This is a two steps model combining a familial selection process and an individual one. Within selected families, candidates from the good families are undergoing a mass selection whereas candidates from medium families are undergoing a within family selection of a fixed number of candidates. The model requires a large number of parameters: number of candidates, proportions of selected families and selected candidates per family, accuracy of breeding values, genetic correlations between traits, weights of traits in the selection index. The variability of the parameters composing the model enables comparing a large diversity of scenarios, including the use of genomic evaluations. In order to illustrate the usefulness of the model, we simulated 3 selection strategies using classic breeding values and/or genomic breeding values. The genetic gain predictions obtained were then compared. The model included two traits T1 (h² = 0.13) and T2 (h² = 0.33), with a genetic correlation varying between 0 and 0.70 and a weight in the index of 40% and 60% respectively. Results show an increase of predicted gain for both traits with genomic evaluation. Improvement is constant for T2, whereas for T1 the increase of predicted gain is much better when genetic correlation between T1 and T2 is high. The genomic breeding scheme model seems more sensitive than the classic breeding scheme to parameters like the between traits correlation and their weight in the index.
- Published
- 2018
11. Evaluation génomique du poids d'oeuf chez des poules pondeuses soumises à différents régimes alimentaires
- Author
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Chapuis, Herve, Herault, Frédéric, Varenne, A, Romé, Hélène, Ruer, Typhanie, Alleno, C., Dehais, Patrice, Vignal, Alain, Burlot, T, Le Roy, Pascale, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Novogen, Zootests, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-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, ANR UtOpIGe, Syndicats des sélectionneurs avicoles et aquacoles français (SYSAAF), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], and ProdInra, Archive Ouverte
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] - Abstract
The ANR UtOplGe project aims at assessing the value of genomic selection in pyramidal selection schemes, wherethe selection is conducted on a small size nucleus, before the wide dissemination of genetic progress throughsuccessive stages of multiplication and production. We present preliminary results in a selection scheme of layinghens and we also analyze possible interactions genotype x environment (G x E) through two diets differentiated onthe given energy leve! (Low Energy, BE with 2455 kea! vs. High Energy, HE with 2881 kea!). The referencepopulation consisted of 453 roosters of a pure li ne, genotyped with a high density chip (Aft)m etrix® Axiom® HD600k SNPs chip). Associated phenotypes were those of3 1,38ldaughters ofthese males, obtained by crossing withanother line, housed in multiple cages and equally allocated to one or the other of the two diets. The val idation wasbased on the genetic evaluation and selection within 551 males candidates, sons of the preceding ones. Thesecandidates were simply genotyped when selected and performance oftheir sisters were not yet available. Genomicindices were estimated according to the "Single Step" procedure. This analysis focused on egg weight at 65 weeksof age. While genetic parameters estimated with the markers information were quite similar to those obtained withthe conventional pedigree information in pure Iine, calculated genomic indices were significantly more accuratethan pedigree index, with a reliability (CD) twice as high for candidates known only on genotype. Moreover, foregg weight, no significant G x E interaction (estimated genetic correlation> 0.90) between diets was observed.These encouraging results support the establishment of a routine genomic selection in laying hens., Le programme ANR UtOplGe vise à évaluer l' intérêt de la sélection génomique dans des filières pyramidales, où lasélection est menée sur un noyau de taille restreinte, avant une large diffusion du progrès génétique via les étagessuccessifs de multiplication et production. Nous présentons ici les résultats préliminaires dans un schéma desélection de poules pondeuses, où nous analysons également d'éventuelles interactions Génotype x Environnement(GxE), au travers de deux régimes alimentaires différenciés sur le niveau d'énergie apporté (régime Basse Energie,BE, à 2455 kea! vs. régime Haute Energie, HE, à 2881 kea!). La population de référence est constituée par 453 coqsd'une lignée pure commerciale, génotypés avec une puce haute densité (la puce AffYmetrix® Axiom® HD 600kSNP). Les phénotypes associés sont ceux de 3 13 81 filles de ces coqs, obtenues par croisement avec une autrelignée, élevées en cages multiples et soumises pour moitié à l'un ou l'autre des deux régimes alimentaires. Lavalidation consiste à évaluer puis sélectionner parmi 551 coqs candidats. fils des précédents. Les coqs candidatssont simplement génotypés au moment du choix et les performances de leurs soeurs ne sont pas encore disponibles.Un index génomique est estimé, selon la procédure« Single Step ». La présente analyse porte sur le poids des oeufsà 65 semaines. Alors que les paramètres génétiques obtenus avec l' information des marqueurs sont assezsemblables à ceux obtenus en lignée pure avec l'évaluation classique, les indices génomiques calculés sontnettement plus précis que des indices sur ascendance, avec un CD deux fo is plus élevé pour les candidats connusuniquement sur génotype. Par ailleurs, pour le poids d'oeuf on ne constate pas d'interaction GxE notable(corrélation génétique estimée >0.90) entre les régimes. Ces résultats encourageants plaident en faveur de la miseen place d 'une sélection génomique de routine chez la poule pondeuse.
- Published
- 2015
12. Détection de QTL chez la poule pondeuse dans un contexte alimentaire changeant
- Author
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Romé, Hélène, Varenne, A, Herault, Frédéric, Chapuis, Herve, Alleno, C., Dehais, Patrice, Vignal, Alain, Burlot, T, Le Roy, Pascale, ProdInra, Archive Ouverte, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Novogen, Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA), Syndicats des sélectionneurs avicoles et aquacoles français (SYSAAF), Zootests, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), 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-École nationale supérieure agronomique de Toulouse [ENSAT], École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, 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), Unité de Recherches Avicoles (URA), and Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF)
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] - Abstract
absent
- Published
- 2015
13. Genomic evaluation for egg weight in crossbred layers receiving various diets
- Author
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Chapuis, Herve, Herault, Frédéric, Varenne, Amandine, Romé, Hélène, Alleno, C., Dehais, Patrice, Vignal, Alain, Burlot, T, Le Roy, Pascale, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Novogen, Zootests, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-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, Syndicats des sélectionneurs avicoles et aquacoles français (SYSAAF), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
- Subjects
[SDV]Life Sciences [q-bio] - Abstract
This paper presents the preliminary results obtained during the implementation of a genomic evaluation for egg weight in laying hens. One originality of the project is to have used a population of crossbred hens to estimate GEBV of purebred sires. Moreover, hens were divided in 2 groups fed with 2 diets of Low Energy and High Energy. The genomic evaluation from performance of crossbred daughters is more accurate than traditional genetic evaluation in purebred. The interaction genotype x diet seems to be low.
- Published
- 2014
14. Yolk hormones influence in ovo olfactory learning and feeding behaviour in domestic chicks
- Author
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BERTIN, Aline, Burlot, T., Bernard, Barbara, Meurisse, Maryse, Vaudin, Pascal, Calandreau, Ludovic, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Novogen, European Societies for Behavioural Biology. CZE., ProdInra, Migration, and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT] ,[SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2014
15. Detection of QTL influencing egg production in layers receiving various diets
- Author
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Romé, Hélène, Varenne, A., Herault, Frédéric, Chapuis, Herve, Alleno, C., Vignal, Alain, Burlot, T., Le Roy, Pascale, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Novogen, Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA), Syndicats des sélectionneurs avicoles et aquacoles français (SYSAAF), Zootests, Laboratoire de Génétique Cellulaire (LGC), 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-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), Unité de Recherches Avicoles (URA), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and ProdInra, Archive Ouverte
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] - Abstract
Session 25. Free communications – molecular genetics; absent
- Published
- 2013
16. Quality of eggs : any better, any worse?
- Author
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Nys, Yves, Burlot, T., Dunn, I.C., Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA), Institut de Sélection Animale - Hendrix genetics company (ISA), and Roslin Institute
- Subjects
[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2008
17. Internal quality of eggs : any better, any worse?
- Author
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Nys, Yves, Burlot, T., Dunn, I.C., Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA), Institut de Sélection Animale - Hendrix genetics company (ISA), BBSRC Roslin Institute, and Partenaires INRAE
- Subjects
[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2008
18. Résistance au portage de salmonelles : faisabilité d'une sélection en aviculture
- Author
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Sellier, Nadine, Beaumont, Catherine, Chapuis, Herve, Velge, Philippe, MARIE-ETANCELIN, Christel, Burlot, T., ProdInra, Migration, Unité de Recherches Avicoles (URA), and Institut National de la Recherche Agronomique (INRA)
- Subjects
[SDV] Life Sciences [q-bio] ,CHICKENS ,[SDV]Life Sciences [q-bio] ,DISEASE RESISTANCE ,[INFO]Computer Science [cs] ,[INFO] Computer Science [cs] ,SALMONELLA - Published
- 2008
19. An integrated approach of genetic resistance to Salmonella carrier state in fowls : from genetics to genomics and modelization
- Author
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Beaumont, Catherine, Lecerf, Frédéric, Protais, J, Prevost, K, Lalmanach, Anne-Christine, Chapuis, Herve, Pitel, Frédérique, Burlot, T, Sellier, Nadine, Fravalo, P, Vignal, Alain, Velge, Philippe, Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA), 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, Infectiologie Animale et Santé Publique (UR IASP), and Inconnu
- Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,ComputingMilieux_MISCELLANEOUS - Abstract
National audience
- Published
- 2007
20. Likelihood and Bayesian analyses reveal major genes affecting body composition, carcass, meat quality and number of false teats in a Chinese european pig line
- Author
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Sanchez, Marie Pierre, Bidanel, Jean Pierre, ZHANG, S., NAVEAU, J., BURLOT, T., Le Roy, Pascale, Station de Génétique Quantitative et Appliquée (SGQA), and Institut National de la Recherche Agronomique (INRA)
- Subjects
maximum de vraisemblance ,MAJOR GENES ,SEGREGATION ANALYSIS ,MAXIMUM LIKELIHOOD ,BAYESIAN METHODS ,PIGS ,METHODES BAYESIENNES ,[SDV]Life Sciences [q-bio] ,porcin ,gène majeur ,analyse de ségrégation ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2003
21. Likelihood and bayesian approaches for the detection of major genes affecting body composition, carcass, meat quality and reproduction traits in a Chinese European pig line
- Author
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Sanchez, Marie Pierre, Bidanel, Jean Pierre, Zhang, S., NAVEAU, J., Burlot, T., Le Roy, Pascale, Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
- Subjects
[SDV] Life Sciences [q-bio] ,LIKELIHOOD ,SECREGATION ANALYSIS ,MAJOR GENES ,[SDV]Life Sciences [q-bio] ,BAYESIAN ANALYSIS ,PIGS ,VRAISEMBLANCE - Published
- 2001
22. Mise en évidence de gènes à effets majeurs sur la composition corporelle, le rendement technologique Napole et le nombre de tétines dans la lignée porcine sino-européenne Tiameslan
- Author
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Sanchez, Marie Pierre, Bidanel, Jean Pierre, Zhang, S., NAVEAU, J., Burlot, T., Le Roy, Pascale, Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
- Subjects
[SDV] Life Sciences [q-bio] ,BODY COMPOSITION ,MAJOR GENES ,NOMBRE DE TETINES ,[SDV]Life Sciences [q-bio] ,NAPOLE TECHNOLOGICAL YIELD ,PIGS ,RENDEMENT TECHNOLOGIQUE NAPOLE ,TEATS NUMBER ,ComputingMilieux_MISCELLANEOUS - Abstract
National audience
- Published
- 2001
23. Genetic parameters and genetic trends in the Chinese- European Tiameslan composite pig line. I. Genetic parameters (performance trait, reproductive trait, Chinese breed)
- Author
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Zhang, S., Bidanel, Jean Pierre, Burlot, T., Legault, C., and Naveau, J.
- Subjects
performance de reproduction ,porcin ,amélioration des animaux ,performance animale ,paramètre génétique ,race animale - Published
- 2000
24. Genetic parameters and genetic trends in the Chinese-European Tiameslan composite pig line. 2. genetic trends (performance trait, reproductive trait, Chinese breed)
- Author
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Zhang, S., Bidanel, Jean Pierre, Burlot, T., Legault, C., and Naveau, J.
- Subjects
performance de reproduction ,porcin ,amélioration des animaux ,performance animale ,race animale - Published
- 2000
25. Paramètres génétiques et évolutions génétiques dans la lignée composite sino-européenne Tiameslan. 2. Evolutions génétiques (caractère de production, caractère de reproduction, race chinoise)
- Author
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Zhang, S., Bidanel, Jean Pierre, Burlot, T., Legault, Christian, NAVEAU, J., Station de Génétique Quantitative et Appliquée (SGQA), and Institut National de la Recherche Agronomique (INRA)
- Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2000
26. Paramètres génétiques et évolutions génétiques dans la lignée composite sino-européenne Tiameslan. 1. Paramétres génétiques (caractère de production, caractère de reproduction, race chinoise)
- Author
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Zhang, S., Bidanel, Jean Pierre, Burlot, T., Legault, Christian, NAVEAU, J., Station de Génétique Quantitative et Appliquée (SGQA), and Institut National de la Recherche Agronomique (INRA)
- Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2000
27. Genetic parameters and genetic trends in the sino-european tia meslan composite line
- Author
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Burlot, T., Zhang Siqing,, NAVEAU, J., Legault, Christian, Bidanel, Jean Pierre, ProdInra, Migration, Station de Génétique Quantitative et Appliquée (SGQA), and Institut National de la Recherche Agronomique (INRA)
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 1998
28. Genetic parameters and genetic trends in the Sino-European Tiameslan composite line
- Author
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Zhang Siqing,, Burlot, T., Naveau, J., Legault, Christian, Bidanel, Jean Pierre, Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), ProdInra, Migration, PEN AR LAN France, and Partenaires INRAE
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 1998
29. Etude des relations entre le potentiel glycolytique du muscle et les caracteres de production dans les lignees Laconie et Penshire
- Author
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Le Roy, Pascale, Przybylski , W., Burlot, T., Bazin, C., Lagant, Herve, Monin, Gabriel, Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), and Station de recherches sur la viande
- Subjects
[SDV.IDA]Life Sciences [q-bio]/Food engineering ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,ComputingMilieux_MISCELLANEOUS - Abstract
National audience
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- 1994
30. An integrated approach of genetic resistance to salmonella carrier-state in fowls: from genetics to genomics and modelization
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Catherine Beaumont, Frédéric Lecerf, Protais, J., Kevin Prevost, Anne-Christine Lalmanach, Herve Chapuis, Frédérique Pitel, Burlot, T., Nadine Sellier, Fravalo, P., Alain Vignal, Philippe Velge, 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, and ProdInra, Migration
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[SDV] Life Sciences [q-bio] ,CHICKENS ,[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,[INFO] Computer Science [cs] ,SALMONELLA ,RESISTANCE ,SALMONELLES
31. Likelihood and Bayesian analyses reveal major genes affecting body composition, carcass, meat quality and the number of false teats in a Chinese European pig line
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Le Roy Pascale, Burlot Thierry, Naveau Jean, Zhang Siqing, Bidanel Jean-Pierre, and Marie-Pierre Sanchez
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segregation analysis ,likelihood ,Bayesian ,major gene ,pig ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Segregation analyses were performed using both maximum likelihood – via a Quasi Newton algorithm – (ML-QN) and Bayesian – via Gibbs sampling – (Bayesian-GS) approaches in the Chinese European Tiameslan pig line. Major genes were searched for average ultrasonic backfat thickness (ABT), carcass fat (X2 and X4) and lean (X5) depths, days from 20 to 100 kg (D20100), Napole technological yield (NTY), number of false (FTN) and good (GTN) teats, as well as total teat number (TTN). The discrete nature of FTN was additionally considered using a threshold model under ML methodology. The results obtained with both methods consistently suggested the presence of major genes affecting ABT, X2, NTY, GTN and FTN. Major genes were also suggested for X4 and X5 using ML-QN, but not the Bayesian-GS, approach. The major gene affecting FTN was confirmed using the threshold model. Genetic correlations as well as gene effect and genotype frequency estimates suggested the presence of four different major genes. The first gene would affect fatness traits (ABT, X2 and X4), the second one a leanness trait (X5), the third one NTY and the last one GTN and FTN. Genotype frequencies of breeding animals and their evolution over time were consistent with the selection performed in the Tiameslan line.
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- 2003
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32. Genetic parameters and genetic trends in the Chinese × European Tiameslan composite pig line. II. Genetic trends
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Legault Christian, Burlot Thierry, Bidanel Jean-Pierre, Zhang Siqing, and Naveau Jean
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pigs ,genetic trend ,performance trait ,reproductive trait ,Chinese breed ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract The Tiameslan line was created between 1983 and 1985 by mating Meishan × Jiaxing crossbred Chinese boars with sows from the Laconie composite male line. The Tiameslan line has been selected since then on an index combining average backfat thickness (ABT) and days from 20 to 100 kg (DT). Direct and correlated responses to 11 years of selection were estimated using BLUP methodology applied to a multiple trait animal model. A total of 11 traits were considered, i.e.: ABT, DT, body weight at 4 (W4w), 8 (W8w) and 22 (W22w) weeks of age, teat number (TEAT), number of good teats (GTEAT), total number of piglets born (TNB), born alive (NBA) and weaned (NW) per litter, and birth to weaning survival rate (SURV). Performance data from a total of 4 881 males and 4 799 females from 1 341 litters were analysed. The models included both direct and maternal effects for ABT, W4w and W8w. Male and female performances were considered as different traits for W22w, DT and ABT. Genetic parameters estimated in another paper (Zhang et al., Genet. Sel. Evol. 32 (2000) 41-56) were used to perform the analyses. Favourable phenotypic (ΔP) and direct genetic trends (ΔGd) were obtained for post-weaning growth traits and ABT. Trends for maternal effects were limited. Phenotypic and genetic trends were larger in females than in males for ABT (e.g. ΔGd = -0.48 vs. -0.38 mm/year), were larger in males for W22w (ΔGd = 0.90 vs. 0.58 kg/year) and were similar in both sexes for DT (ΔGd = -0.54 vs. -0.55 day/year). Phenotypic and genetic trends were slightly favourable for W4w, W8w, TEAT and GTEAT and close to zero for reproductive traits.
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- 2000
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33. Genetic parameters and genetic trends in the Chinese × European Tiameslan composite pig line. I. Genetic parameters
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Legault Christian, Burlot Thierry, Bidanel Jean-Pierre, Zhang Siqing, and Naveau Jean
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pigs ,genetic parameters ,performance trait ,reproductive trait ,Chinese breed ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Genetic parameters of body weight at 4 (W4 w), 8 (W8 w) and 22 (W22 w) weeks of age, days from 20 to 100 kg (DT), average backfat thickness at 100 kg (ABT), teat number (TEAT), number of good teats (GTEAT), total number of piglets born (TNB), born alive (NBA) and weaned (NW) per litter, and birth to weaning survival rate (SURV) were estimated in the Chinese × European Tiameslan composite line using restricted maximum likelihood methodology applied to a multiple trait animal model. Performance data from a total of 4 881 males and 4 799 females from 1 341 litters were analysed. Different models were fitted to the data in order to estimate the importance of maternal effects on production traits, as well as genetic correlations between male and female performance. The results showed the existence of significant maternal effects on W4w, W8w and ABT and of variance heterogeneity between sexes for W22w, DT, ABT and GTEAT. Genetic correlations between sexes were 0.79, 0.71 and 0.82, respectively, for W22w, DT and ABT and above 0.90 for the other traits. Heritability estimates were larger than (ABT and TEAT) or similar to (other traits) average literature values. Some genetic antagonism was evidenced between production traits, particularly W4w, W8w and ABT, and reproductive traits.
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- 2000
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34. Host genetics drives differences in cecal microbiota composition and immune traits of laying hens raised in the same environment.
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Lecoeur A, Blanc F, Gourichon D, Bruneau N, Burlot T, Pinard-van der Laan MH, and Calenge F
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- Animals, Female, Poultry Diseases microbiology, Poultry Diseases immunology, Newcastle Disease immunology, Vaccination veterinary, RNA, Ribosomal, 16S analysis, RNA, Ribosomal, 16S genetics, Chickens immunology, Chickens genetics, Chickens microbiology, Gastrointestinal Microbiome, Newcastle disease virus immunology, Viral Vaccines immunology, Cecum microbiology, Cecum immunology
- Abstract
Vaccination is one of the most effective strategies for preventing infectious diseases but individual vaccine responses are highly heterogeneous. Host genetics and gut microbiota composition are 2 likely drivers of this heterogeneity. We studied 94 animals belonging to 4 lines of laying hens: a White Leghorn experimental line genetically selected for a high antibody response against the Newcastle Disease Virus (NDV) vaccine (ND3) and its unselected control line (CTR), and 2 commercial lines (White Leghorn [LEG] and Rhode Island Red [RIR]). Animals were reared in the same conditions from hatching to 42 d of age, and animals from different genetic lines were mixed. Animals were vaccinated at 22 d of age and their humoral vaccine response against NDV was assessed by hemagglutination inhibition assay and ELISA from blood samples collected at 15, 19, and 21 d after vaccination. The immune parameters studied were the 3 immunoglobulins subtypes A, M, and Y and the blood cell composition was assessed by flow cytometry. The composition of the cecal microbiota was assessed at the end of the experiment by analyzing amplified 16S rRNA gene sequences to obtain amplicon sequence variants (ASV). The 4 lines showed significantly different levels of NDV vaccine response at the 3 measured points, with, logically, a higher response of the genetically selected ND3 line, and intermediate and low responses for the unselected CTR control line and for the 2 commercial lines, respectively. The ND3 line displayed also a higher proportion of immunoglobulins (IgA, IgM, and IgY). The RIR line showed the most different blood cell composition. The 4 lines showed significantly different microbiota characteristics: composition, abundances at all taxonomic levels, and correlations between genera and vaccine response. The tested genetic lines differ for immune parameters and gut microbiota composition and functions. These phenotypic differences can be attributed to genetic differences between lines. Causal relationships between both types of parameters are discussed and will be investigated in further studies., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2024
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35. Restriction site-associated DNA sequencing technologies as an alternative to low-density SNP chips for genomic selection: a simulation study in layer chickens.
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Herry F, Hérault F, Lecerf F, Lagoutte L, Doublet M, Picard-Druet D, Bardou P, Varenne A, Burlot T, Le Roy P, and Allais S
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- Animals, Genome, Genomics methods, Genotype, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Chickens genetics
- Abstract
Background: To reduce the cost of genomic selection, a low-density (LD) single nucleotide polymorphism (SNP) chip can be used in combination with imputation for genotyping selection candidates instead of using a high-density (HD) SNP chip. Next-generation sequencing (NGS) techniques have been increasingly used in livestock species but remain expensive for routine use for genomic selection. An alternative and cost-efficient solution is to use restriction site-associated DNA sequencing (RADseq) techniques to sequence only a fraction of the genome using restriction enzymes. From this perspective, use of RADseq techniques followed by an imputation step on HD chip as alternatives to LD chips for genomic selection was studied in a pure layer line., Results: Genome reduction and sequencing fragments were identified on reference genome using four restriction enzymes (EcoRI, TaqI, AvaII and PstI) and a double-digest RADseq (ddRADseq) method (TaqI-PstI). The SNPs contained in these fragments were detected from the 20X sequence data of the individuals in our population. Imputation accuracy on HD chip with these genotypes was assessed as the mean correlation between true and imputed genotypes. Several production traits were evaluated using single-step GBLUP methodology. The impact of imputation errors on the ranking of the selection candidates was assessed by comparing a genomic evaluation based on ancestry using true HD or imputed HD genotyping. The relative accuracy of genomic estimated breeding values (GEBVs) was investigated by considering the GEBVs estimated on offspring as a reference. With AvaII or PstI and ddRADseq with TaqI and PstI, more than 10 K SNPs were detected in common with the HD SNP chip, resulting in an imputation accuracy greater than 0.97. The impact of imputation errors on genomic evaluation of the breeders was reduced, with a Spearman correlation greater than 0.99. Finally, the relative accuracy of GEBVs was equivalent., Conclusions: RADseq approaches can be interesting alternatives to low-density SNP chips for genomic selection. With more than 10 K SNPs in common with the SNPs of the HD SNP chip, good imputation and genomic evaluation results can be obtained. However, with real data, heterogeneity between individuals with missing data must be considered., (© 2023. The Author(s).)
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- 2023
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36. Nest preference and laying duration traits to select against floor eggs in laying hens.
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Bécot L, Bédère N, Coton J, Burlot T, and Le Roy P
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- Animals, Female, Housing, Animal, Oviposition genetics, Eggs, Chickens genetics, Animal Husbandry methods
- Abstract
Background: Floor eggs, which are defined as eggs that hens lay off-nest, are a major issue in cage-free layer poultry systems. They create additional work for farmers because they must be collected by hand. They are also usually soiled or broken, which results in economic losses. Nonetheless, knowledge about the genetics of nesting behavior is limited. The aim of this study was to estimate genetic parameters for traits related to nest preference for laying and to time spent in the nests used for laying (laying duration)., Methods: Two pure lines of laying hens were studied: 927 Rhode Island Red and 980 White Leghorn. Electronic nests were used to record the nesting behavior of these hens in floor pens from 24 to 64 weeks of age. Nest preference was studied based on the mean distance between nests used for laying and the percentage of nests used for laying. Laying duration was studied based on mean laying duration, mean duration in the nest before laying, and mean duration in the nest after laying. Genetic parameters were estimated for each line using a restricted maximum-likelihood method applied to a pedigree-based multi-trait animal model., Results: Estimates of genetic parameters were similar for the two lines. Estimates of heritability ranged from 0.18 to 0.37 for nest preference traits and from 0.54 to 0.70 for laying duration traits. Estimates of genetic correlations of these traits with clutch number or mean oviposition time were favorable. Positive genetic correlations were estimated between nest preference and laying rate in the nests or nest acceptance for laying (+ 0.06 to + 0.37)., Conclusions: These results show that genetics influences traits related to nest preference and laying duration. Selecting hens that have no preference for particular nests and spend little time laying in the nests could help optimize nest use, reduce their occupation rate, and thus decrease the incidence of floor eggs in cage-free systems. Genetic correlations of these traits with other traits of interest related to hen welfare and egg quality have yet to be estimated., (© 2023. The Author(s).)
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- 2023
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37. RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis -Regulation Analysis by Allele-Specific Expression in Livestock Species.
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Jehl F, Degalez F, Bernard M, Lecerf F, Lagoutte L, Désert C, Coulée M, Bouchez O, Leroux S, Abasht B, Tixier-Boichard M, Bed'hom B, Burlot T, Gourichon D, Bardou P, Acloque H, Foissac S, Djebali S, Giuffra E, Zerjal T, Pitel F, Klopp C, and Lagarrigue S
- Abstract
In addition to their common usages to study gene expression, RNA-seq data accumulated over the last 10 years are a yet-unexploited resource of SNPs in numerous individuals from different populations. SNP detection by RNA-seq is particularly interesting for livestock species since whole genome sequencing is expensive and exome sequencing tools are unavailable. These SNPs detected in expressed regions can be used to characterize variants affecting protein functions, and to study cis -regulated genes by analyzing allele-specific expression (ASE) in the tissue of interest. However, gene expression can be highly variable, and filters for SNP detection using the popular GATK toolkit are not yet standardized, making SNP detection and genotype calling by RNA-seq a challenging endeavor. We compared SNP calling results using GATK suggested filters, on two chicken populations for which both RNA-seq and DNA-seq data were available for the same samples of the same tissue. We showed, in expressed regions, a RNA-seq precision of 91% (SNPs detected by RNA-seq and shared by DNA-seq) and we characterized the remaining 9% of SNPs. We then studied the genotype (GT) obtained by RNA-seq and the impact of two factors (GT call-rate and read number per GT) on the concordance of GT with DNA-seq; we proposed thresholds for them leading to a 95% concordance. Applying these thresholds to 767 multi-tissue RNA-seq of 382 birds of 11 chicken populations, we found 9.5 M SNPs in total, of which ∼550,000 SNPs per tissue and population with a reliable GT (call rate ≥ 50%) and among them, ∼340,000 with a MAF ≥ 10%. We showed that such RNA-seq data from one tissue can be used to ( i ) detect SNPs with a strong predicted impact on proteins, despite their scarcity in each population (16,307 SIFT deleterious missenses and 590 stop-gained), ( ii ) study, on a large scale, cis -regulations of gene expression, with ∼81% of protein-coding and 68% of long non-coding genes (TPM ≥ 1) that can be analyzed for ASE, and with ∼29% of them that were cis -regulated, and ( iii ) analyze population genetic using such SNPs located in expressed regions. This work shows that RNA-seq data can be used with good confidence to detect SNPs and associated GT within various populations and used them for different analyses as GTEx studies., Competing Interests: The 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 © 2021 Jehl, Degalez, Bernard, Lecerf, Lagoutte, Désert, Coulée, Bouchez, Leroux, Abasht, Tixier-Boichard, Bed’hom, Burlot, Gourichon, Bardou, Acloque, Foissac, Djebali, Giuffra, Zerjal, Pitel, Klopp and Lagarrigue.)
- Published
- 2021
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38. Nest acceptance, clutch, and oviposition traits are promising selection criteria to improve egg production in cage-free system.
- Author
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Becot L, Bedere N, Burlot T, Coton J, and Le Roy P
- Subjects
- Animals, Biomarkers, Chickens, Eggs, Female, Housing, Animal trends, Oviposition genetics, Phenotype, Selective Breeding genetics, Animal Husbandry methods, Breeding methods, Nesting Behavior physiology
- Abstract
In cage-free systems, laying hens must lay their eggs in the nests. Selecting layers based on nesting behavior would be a good strategy for improving egg production in these breeding systems. However, little is known about the genetic determinism of nest-related traits. Laying rate in the nests (LRN), clutch number (CN), oviposition traits (OT), and nest acceptance for laying (NAL) of 1,430 Rhode Island Red (RIR) hens and 1,008 White Leghorn (WL) hens were recorded in floor pens provided with individual electronic nests. Heritability and genetic and phenotypic correlations of all traits were estimated over two recording periods-the peak (24-43 weeks of age) and the middle (44-64 weeks of age) of production-by applying the restricted maximum likelihood method to an animal model. The mean oviposition time (MOT) ranged from 2 h 5 min to 3 h and from 3 h 35 min to 3 h 44 min after turning on the lights for RIR and WL hens, respectively. The mean oviposition interval ranged from 24 h 3 min to 24 h 16 min. All heritability and correlation estimates were similar for RIR and WL. Low to moderate heritability coefficients were estimated for LRN (0.04-0.25) and moderate to high heritability coefficients for CN and OT (0.27-0.68). CN and OT were negatively genetically correlated with LRN (-0.92 to -0.39) except during peak production for RIR (-0.30 to +0.43). NAL was weakly to moderately heritable (0.13-0.26). Genetic correlations between NAL and other traits were low to moderate (-0.41 to +0.44). In conclusion, CN and OT are promising selection criteria to improve egg production in cage-free systems. NAL can be also used to reduce the number of eggs laid off-nest in these breeding systems. However, variability in MOT must be maintained to limit competition for the nests., Competing Interests: The authors have read the journal’s policy, and the authors of this study have the following competing interests to declare: TB and JC are employed by Novogen, a laying hens breeding company. The data are of commercial interest for Novogen but this interest did not influence the results in this manuscript in any matter. This does not alter our adherence to PLOS ONE policies on sharing data and materials. There are no patents, products in development or marketed products associated with this research to declare. LB, NB, and PLR declare that they have no competing interests.
- Published
- 2021
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39. Interest of using imputation for genomic evaluation in layer chicken.
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Herry F, Druet DP, Hérault F, Varenne A, Burlot T, Le Roy P, and Allais S
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- Animals, Breeding, Genetic Markers, Genome, Oligonucleotide Array Sequence Analysis economics, Oligonucleotide Array Sequence Analysis methods, Sensitivity and Specificity, Chickens genetics, Genomics methods, Oligonucleotide Array Sequence Analysis veterinary, Polymorphism, Single Nucleotide
- Abstract
With the availability of the 600K Affymetrix Axiom high-density (HD) single nucleotide polymorphism (SNP) chip, genomic selection has been implemented in broiler and layer chicken. However, the cost of this SNP chip is too high to genotype all selection candidates. A solution is to develop a low-density SNP chip, at a lower price, and to impute all missing markers. But to routinely implement this solution, the impact of imputation on genomic evaluation accuracy must be studied. It is also interesting to study the consequences of the use of low-density SNP chips in genomic evaluation accuracy. In this perspective, the interest of using imputation in genomic selection was studied in a pure layer line. Two low-density SNP chip designs were compared: an equidistant methodology and a methodology based on linkage disequilibrium. Egg weight, egg shell color, egg shell strength, and albumen height were evaluated with single-step genomic best linear unbiased prediction methodology. The impact of imputation errors or the absence of imputation on the ranking of the male selection candidates was assessed with a genomic evaluation based on ancestry. Thus, genomic estimated breeding values (GEBV) obtained with imputed HD genotypes or low-density genotypes were compared with GEBV obtained with the HD SNP chip. The relative accuracy of GEBV was also investigated by considering as reference GEBV estimated on the offspring. A limited reordering of the breeders, selected on a multitrait index, was observed. Spearman correlations between GEBV on HD genotypes and GEBV on low-density genotypes (with or without imputation) were always higher than 0.94 with more than 3K SNP. For the genetically closer, top 150 individuals for a specific trait, with imputation, the reordering was reduced with correlation higher than 0.94 with more than 3K SNP. Without imputation, the correlations remained lower than 0.85 with less than 3K and 16K SNP for equidistant and linkage disequilibrium methodology, respectively. The differences in GEBV correlations between both methodologies were never significant. The conclusions were the same for all studied traits., (Copyright © 2020. Published by Elsevier Inc.)
- Published
- 2020
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40. Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species.
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Piégu B, Arensburger P, Beauclair L, Chabault M, Raynaud E, Coustham V, Brard S, Guizard S, Burlot T, Le Bihan-Duval E, and Bigot Y
- Subjects
- Animals, Centromere genetics, Gene Duplication, RNA, Ribosomal genetics, Tandem Repeat Sequences, Telomere genetics, Breeding, Chickens genetics, Domestication, Genome Size, Polymorphism, Genetic
- Abstract
Efforts to elucidate the causes of biological differences between wild fowls and their domesticated relatives, the chicken, have to date mainly focused on the identification of single nucleotide mutations. Other types of genomic variations have however been demonstrated to be important in avian evolution and associated to variations in phenotype. They include several types of sequences duplicated in tandem that can vary in their repetition number. Here we report on genome size differences between the red jungle fowl and several domestic chicken breeds and selected lines. Sequences duplicated in tandem such as rDNA, telomere repeats, satellite DNA and segmental duplications were found to have been significantly re-shaped during domestication and subsequently by human-mediated selection. We discuss the extent to which changes in genome organization that occurred during domestication agree with the hypothesis that domesticated animal genomes have been shaped by evolutionary forces aiming to adapt them to anthropized environments., (Copyright © 2019 Elsevier Inc. All rights reserved.)
- Published
- 2020
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41. Reliability of genomic evaluation for egg quality traits in layers.
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Picard Druet D, Varenne A, Herry F, Hérault F, Allais S, Burlot T, and Le Roy P
- Subjects
- Animals, Cattle, Female, Genetic Association Studies, Genotype, Male, Phenotype, Eggs, Genome, Genomics methods, Quantitative Trait, Heritable
- Abstract
Background: Genomic evaluation, based on the use of thousands of genetic markers in addition to pedigree and phenotype information, has become the standard evaluation methodology in dairy cattle breeding programmes over the past several years. Despite the many differences between dairy cattle breeding and poultry breeding, genomic selection seems very promising for the avian sector, and studies are currently being conducted to optimize avian selection schemes. In this optimization perspective, one of the key parameters is to properly predict the accuracy of genomic evaluation in pure line layers., Results: It was observed that genomic evaluation, whether performed on males or females, always proved more accurate than genetic evaluation. The gain was higher when phenotypic information was narrowed, and an augmentation of the size of the reference population led to an increase in accuracy prediction with regard to genomic evaluation. By taking into account the increase of selection intensity and the decrease of the generation interval induced by genomic selection, the expected annual genetic gain would be higher with ancestry-based genomic evaluation of male candidates than with genetic evaluation based on collaterals. This advantage of genomic selection over genetic selection requires more detailed further study for female candidates., Conclusions: In conclusion, in the population studied, the genomic evaluation of egg quality traits of breeding birds at birth seems to be a promising strategy, at least for the selection of males.
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- 2020
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42. Design of low density SNP chips for genotype imputation in layer chicken.
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Herry F, Hérault F, Picard Druet D, Varenne A, Burlot T, Le Roy P, and Allais S
- Subjects
- Animals, Chickens growth & development, Chromosomes, Gene Frequency, Genotype, Linkage Disequilibrium, Chickens genetics, Oligonucleotide Array Sequence Analysis methods, Polymorphism, Single Nucleotide
- Abstract
Background: The main goal of selection is to achieve genetic gain for a population by choosing the best breeders among a set of selection candidates. Since 2013, the use of a high density genotyping chip (600K Affymetrix® Axiom® HD genotyping array) for chicken has enabled the implementation of genomic selection in layer and broiler breeding, but the genotyping costs remain high for a routine use on a large number of selection candidates. It has thus been deemed interesting to develop a low density genotyping chip that would induce lower costs. In this perspective, various simulation studies have been conducted to find the best way to select a set of SNPs for low density genotyping of two laying hen lines., Results: To design low density SNP chips, two methodologies, based on equidistance (EQ) or on linkage disequilibrium (LD) were compared. Imputation accuracy was assessed as the mean correlation between true and imputed genotypes. The results showed correlations more sensitive to false imputation of SNPs having low Minor Allele Frequency (MAF) when the EQ methodology was used. An increase in imputation accuracy was obtained when SNP density was increased, either through an increase in the number of selected windows on a chromosome or through the rise of the LD threshold. Moreover, the results varied depending on the type of chromosome (macro or micro-chromosome). The LD methodology enabled to optimize the number of SNPs, by reducing the SNP density on macro-chromosomes and by increasing it on micro-chromosomes. Imputation accuracy also increased when the size of the reference population was increased. Conversely, imputation accuracy decreased when the degree of kinship between reference and candidate populations was reduced. Finally, adding selection candidates' dams in the reference population, in addition to their sire, enabled to get better imputation results., Conclusions: Whichever the SNP chip, the methodology, and the scenario studied, highly accurate imputations were obtained, with mean correlations higher than 0.83. The key point to achieve good imputation results is to take into account chicken lines' LD when designing a low density SNP chip, and to include the candidates' direct parents in the reference population.
- Published
- 2018
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43. Yolk hormones influence in ovo chemosensory learning, growth, and feeding behavior in domestic chicks.
- Author
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Bertin A, Meurisse M, Arnould C, Leterrier C, Constantin P, Cornilleau F, Vaudin P, Burlot T, Delaveau J, Rat C, and Calandreau L
- Subjects
- Androgens pharmacology, Animals, Animals, Newborn, Chick Embryo, Egg Yolk chemistry, Estrogens pharmacology, Female, Fish Oils, Food Preferences drug effects, Odorants, Pregnancy, Progestins pharmacology, Behavior, Animal drug effects, Chickens growth & development, Estradiol pharmacology, Feeding Behavior drug effects, Hormones pharmacology, Learning drug effects, Progesterone pharmacology, Testosterone pharmacology
- Abstract
In this study, we assessed whether prenatal exposure to elevated yolk steroid hormones can influence in ovo chemosensory learning and the behavior of domestic chicks. We simulated a maternal environmental challenge by experimentally enhancing yolk progesterone, testosterone, and estradiol concentrations in hen eggs prior to incubation. The embryos from these hormones-treated eggs (HO) as well as sham embryos (O) that had received the vehicle-only were exposed to the odor of fish oil (menhaden) between embryonic Days 11 and 20. An additional group of control embryos (C) was not exposed to the odor. All chicks were tested following hatching for their feeding preferences between foods that were or were not odorized with the menhaden odor. In the 3-min choice tests, the behavior of O chicks differed significantly according to the type of food whereas C and HO chicks showed no preference between odorized and non-odorized food. Our result suggests weaker response in HO chicks. In addition, HO chicks showed impaired growth and reduced intake of an unfamiliar food on the 24-h time scale compared to controls. Our data suggest that embryonic exposure to increased yolk hormone levels can alter growth, chemosensory learning, and the development of feeding behaviors., (© 2015 Wiley Periodicals, Inc.)
- Published
- 2016
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44. GWAS analyses reveal QTL in egg layers that differ in response to diet differences.
- Author
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Romé H, Varenne A, Hérault F, Chapuis H, Alleno C, Dehais P, Vignal A, Burlot T, and Le Roy P
- Subjects
- Animals, Chickens genetics, Chromosome Mapping, Diet, Female, Gene-Environment Interaction, Genome-Wide Association Study, Polymorphism, Single Nucleotide, Chickens physiology, Oviparity, Quantitative Trait Loci
- Abstract
Background: The genetic architecture of egg production and egg quality traits, i.e. the quantitative trait loci (QTL) that influence these traits, is still poorly known. To date, 33 studies have focused on the detection of QTL for laying traits in chickens, but less than 10 genes have been identified. The availability of a high-density SNP (single nucleotide polymorphism) chicken array developed by Affymetrix, i.e. the 600K Affymetrix(®) Axiom(®) HD genotyping array offers the possibility to narrow down the localization of previously detected QTL and to detect new QTL. This high-density array is also anticipated to take research beyond the classical hypothesis of additivity of QTL effects or of QTL and environmental effects. The aim of our study was to search for QTL that influence laying traits using the 600K SNP chip and to investigate whether the effects of these QTL differed between diets and age at egg collection., Results: One hundred and thirty-one QTL were detected for 16 laying traits and were spread across all marked chromosomes, except chromosomes 16 and 25. The percentage of variance explained by a QTL varied from 2 to 10 % for the various traits, depending on diet and age at egg collection. Chromosomes 3, 9, 10 and Z were overrepresented, with more than eight QTL on each one. Among the 131 QTL, 60 had a significantly different effect, depending on diet or age at egg collection. For egg production traits, when the QTL × environment interaction was significant, numerous inversions of sign of the SNP effects were observed, whereas for egg quality traits, the QTL × environment interaction was mostly due to a difference of magnitude of the SNP effects., Conclusions: Our results show that numerous QTL influence egg production and egg quality traits and that the genomic regions, which are involved in shaping the ability of layer chickens to adapt to their environment for egg production, vary depending on the environmental conditions. The next question will be to address what the impact of these genotype × environment interactions is on selection.
- Published
- 2015
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45. Likelihood and Bayesian analyses reveal major genes affecting body composition, carcass, meat quality and the number of false teats in a Chinese European pig line.
- Author
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Sanchez MP, Bidanel JP, Zhang S, Naveau J, Burlot T, and Le Roy P
- Subjects
- Animals, Bayes Theorem, Genetic Markers genetics, Inheritance Patterns genetics, Likelihood Functions, Models, Genetic, Quantitative Trait Loci, Body Composition genetics, Meat, Swine genetics
- Abstract
Segregation analyses were performed using both maximum likelihood--via a Quasi Newton algorithm--(ML-QN) and Bayesian--via Gibbs sampling--(Bayesian-GS) approaches in the Chinese European Tiameslan pig line. Major genes were searched for average ultrasonic backfat thickness (ABT), carcass fat (X2 and X4) and lean (X5) depths, days from 20 to 100 kg (D20100), Napole technological yield (NTY), number of false (FTN) and good (GTN) teats, as well as total teat number (TTN). The discrete nature of FTN was additionally considered using a threshold model under ML methodology. The results obtained with both methods consistently suggested the presence of major genes affecting ABT, X2, NTY, GTN and FTN. Major genes were also suggested for X4 and X5 using ML-QN, but not the Bayesian-GS, approach. The major gene affecting FTN was confirmed using the threshold model. Genetic correlations as well as gene effect and genotype frequency estimates suggested the presence of four different major genes. The first gene would affect fatness traits (ABT, X2 and X4), the second one a leanness trait (X5), the third one NTY and the last one GTN and FTN. Genotype frequencies of breeding animals and their evolution over time were consistent with the selection performed in the Tiameslan line.
- Published
- 2003
- Full Text
- View/download PDF
46. Genetic parameters and genetic trends in the Chinese x European Tiameslan composite pig line. I. Genetic parameters.
- Author
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Zhang S, Bidanel JP, Burlot T, Legault C, and Naveau J
- Abstract
Genetic parameters of body weight at 4 (W4w), 8 (W8w) and 22 (W22w) weeks of age, days from 20 to 100 kg (DT), average backfat thickness at 100 kg (ABT), teat number (TEAT), number of good teats (GTEAT), total number of piglets born (TNB), born alive (NBA) and weaned (NW) per litter, and birth to weaning survival rate (SURV) were estimated in the Chinese x European Tiameslan composite line using restricted maximum likelihood methodology applied to a multiple trait animal model. Performance data from a total of 4 881 males and 4 799 females from 1 341 litters were analysed. Different models were fitted to the data in order to estimate the importance of maternal effects on production traits, as well as genetic correlations between male and female performance. The results showed the existence of significant maternal effects on W4w, W8w and ABT and of variance heterogeneity between sexes for W22w, DT, ABT and GTEAT. Genetic correlations between sexes were 0.79, 0.71 and 0.82, respectively, for W22w, DT and ABT and above 0.90 for the other traits. Heritability estimates were larger than (ABT and TEAT) or similar to (other traits) average literature values. Some genetic antagonism was evidenced between production traits, particularly W4w, W8w and ABT, and reproductive traits.
- Published
- 2000
- Full Text
- View/download PDF
47. Genetic parameters and genetic trends in the Chinese x European Tiameslan composite pig line. II. Genetic trends.
- Author
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Zhang S, Bidanel JP, Burlot T, Legault C, and Naveau J
- Abstract
The Tiameslan line was created between 1983 and 1985 by mating Meishan x Jiaxing crossbred Chinese boars with sows from the Laconie composite male line. The Tiameslan line has been selected since then on an index combining average backfat thickness (ABT) and days from 20 to 100 kg (DT). Direct and correlated responses to 11 years of selection were estimated using BLUP methodology applied to a multiple trait animal model. A total of 11 traits were considered, i.e.: ABT, DT, body weight at 4 (W4w), 8 (W8w) and 22 (W22w) weeks of age, teat number (TEAT), number of good teats (GTEAT), total number of piglets born (TNB), born alive (NBA) and weaned (NW) per litter, and birth to weaning survival rate (SURV). Performance data from a total of 4,881 males and 4,799 females from 1,341 litters were analysed. The models included both direct and maternal effects for ABT, W4w and W8w. Male and female performances were considered as different traits for W22w, DT and ABT. Genetic parameters estimated in another paper (Zhang et al., Genet. Sel. Evol. 32 (2000) 41-56) were used to perform the analyses. Favourable phenotypic (DeltaP) and direct genetic trends (DeltaG(d)) were obtained for post-weaning growth traits and ABT. Trends for maternal effects were limited. Phenotypic and genetic trends were larger in females than in males for ABT (e.g. DeltaG(d) = - 0.48 vs. -0.38 mm/year), were larger in males for W22w (DeltaG(d) = 0.90 vs. 0.58 kg/year) and were similar in both sexes for DT (DeltaG(d) = - 0.54 vs. - 0.55 day/year). Phenotypic and genetic trends were slightly favourable for W4w, W8w, TEAT and GTEAT and close to zero for reproductive traits.
- Published
- 2000
- Full Text
- View/download PDF
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