416 results on '"Le Roy, Pascale"'
Search Results
2. Nest preference and laying duration traits to select against floor eggs in laying hens
- Author
-
Bécot, Lorry, Bédère, Nicolas, Coton, Jenna, Burlot, Thierry, and Le Roy, Pascale
- Published
- 2023
- Full Text
- View/download PDF
3. Reliability of genomic evaluation for egg quality traits in layers
- Author
-
Picard Druet, David, Varenne, Amandine, Herry, Florian, Hérault, Frédéric, Allais, Sophie, Burlot, Thierry, and Le Roy, Pascale
- Published
- 2020
- Full Text
- View/download PDF
4. A Mutation in PRKAG3 Associated with Excess Glycogen Content in Pig Skeletal Muscle
- Author
-
Milan, Denis, Jeon, Jin-Tae, Looft, Christian, Amarger, Valerie, Robic, Annie, Thelander, Mattias, Rogel-Gaillard, Claire, Paul, Sven, Iannuccelli, Nathalie, Rask, Lars, Ronne, Hans, Lundström, Kerstin, Reinsch, Norbert, Gellin, Joel, Kalm, Ernst, Le Roy, Pascale, Chardon, Patrick, and Andersson, Leif
- Published
- 2000
5. Additional file 1 of Nest preference and laying duration traits to select against floor eggs in laying hens
- Author
-
Bécot, Lorry, Bédère, Nicolas, Coton, Jenna, Burlot, Thierry, and Le Roy, Pascale
- Abstract
Additional file 1: Table S1. Summary statistics of phenotypic data for the mean time of entry (MTE) for nest visits with oviposition for the entire recording period (24–64 weeks of age). Table S2. Genetic ( $${\sigma }_{a}^{2}$$ σ a 2 ), common environment ( $${\sigma }_{c}^{2}$$ σ c 2 ), and residual ( $${\sigma }_{e}^{2}$$ σ e 2 ) variances of laying duration traits. Variance components estimated from the model used to calculate least-square means of laying duration traits. Table S3. Genetic correlations between 28-day periods for mean laying duration. Table S4. Genetic correlations between 28-day periods for mean duration in the nest before laying. Table S5. Genetic correlations between 28-day periods for mean duration in the nest after laying.
- Published
- 2023
- Full Text
- View/download PDF
6. Design of low density SNP chips for genotype imputation in layer chicken
- Author
-
Herry, Florian, Hérault, Frédéric, Picard Druet, David, Varenne, Amandine, Burlot, Thierry, Le Roy, Pascale, and Allais, Sophie
- Published
- 2018
- Full Text
- View/download PDF
7. Implementation of genomic selection on production and quality traits and linkage disequilibrium in Crassostrea gigas
- Author
-
Jourdan, Antoine, Boudry, P, Enez, Florian, Haffray, Pierrick, Chenier, F, Vetois, E, Allal, François, Le Roy, Pascale, Phocas, Florence, Bugeon, Jérôme, Dégremont, Lionel, Morvezen, Romain, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), NAISSAIN, SATMAR, Laboratoire Service d' Experimentations Aquacoles [Palavas les Flots] (LSEA MARBEC), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), R.F. Veerkamp, and Y. de Haas
- Subjects
[SDV]Life Sciences [q-bio] - Abstract
International audience; The recent progress and cost reduction of genotyping technologies allows for the implementation of genomic selection (GS) on more and more cultivated species. In this study, we explore the genomic determinism of commercial traits and test the effectiveness and the possible cost reduction of GS in breeding programs of the cupped oyster Crassostrea gigas. Two populations of more than 1000 individuals have been phenotyped and genotyped for 40,000 SNP (Guitierez et al., 2017). Heritability was estimated to be moderate for commercial traits of interest (between 0.19 and 0.34). The accuracy of the genomic prediction models outperformed the classical selection on pedigree by 22 to 55%. A limited linkage disequilibrium (LD) level (less than 0.1) was observed. These results suggest that the use of GS in oyster breeding can improve the selection of breeding candidates to enhance commercial traits but need a specific account and exploration of the very low LD.
- Published
- 2022
8. Laying hens tweet. They also lead and follow! Implications for genetic selection against gregarious nesting
- Author
-
Bécot, Lorry, Bédère, Nicolas, Burlot, Thierry, Le Roy, Pascale, and Bernard, Emilie
- Subjects
[SDV.SA.SPA] Life Sciences [q-bio]/Agricultural sciences/Animal production studies ,[SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics - Abstract
Gregarious nesting occurs when a hen chooses a nest already occupied while other nests are vacant, increasing welfare and production problems. This study aims to propose two predictors of gregarious nesting: weighted indegree (WID) and weighted outdegree (WOD), which are the number of times a hen entered an individual nest next to a vacant nest or an occupied nest , respectively. Nesting behaviour was recorded using individual electronic nests for 210 days. Genetic parameters for WID, WOD and nesting behaviour traits were estimated for 1,268 and 1,080 Rhode Island Red and White Leghorn respectively. For both lines, heritability estimates were high for WID (0.40/0.53) and low for WOD (0.12/0.15). Moderate genetic correlations were estimated between WID and WOD (+0.26/-0.35) and strong genetic correlations with some nesting behaviour traits. WID and WOD could help to select against gregarious nesting but the effects for hens using collective nests remain to be evaluated.
- Published
- 2022
9. Genetic parameters for the oviposition time using high-throughput phenotyping from individual electronic nests in laying hens
- Author
-
Bécot, Lorry, Bédère, Nicolas, Coton, Jenna, Burlot, Thierry, Le Roy, Pascale, and BEDERE, Nicolas
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV.BA] Life Sciences [q-bio]/Animal biology ,[SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics - Abstract
Oviposition time is a predictor of the laying rhythm. Drift in oviposition time (i.e. more than 24h between 2 oviposition times) can lead the hen to make a pause day. The recent availability of an individual electronic nest enables high-throughput phenotyping of laying behavior like the record of Daily Oviposition Time (DOT). In this study, the genetic background of DOT along the production time was investigated through the estimation of heritability coefficients for 10 successive periods. For the genetic evaluation purpose, the use of the mean or the variance of DOT per hen, instead of the repeated data, to estimate the breeding values of hens was then considered.Data were continuously recorded on laying hens raised in a barn thanks to individual electronic nests, which use radio-frequency identification of hens. The oviposition time was recorded on 1,180 Rhode Island Red hens (RIR) and 932 White Leghorn hens (WL) between 24 and 64 weeks of age. Heritability coefficients of DOT were estimated for 10 periods of 28-days between 24 and 64 weeks of age, using REML methodology applied to an animal model. Heritability coefficients of DOT, of the mean of DOT per hen (MOT) and the Logarithm of the DOT Variance per hen (LVOT) were estimated for the whole period (24 to 64 weeks of age) and the Estimated Breeding Values (EBVs) of hens for DOT, MOT and LVOT were compared.Earliest recorded DOT was 2h05 and 3h07 after turning on the light for RIR and WL respectively. According to the period of 28-days, low to moderate heritability was estimated for DOT with values ranging from 0.28 ± 0.06 and 0.42 ± 0.07 for RIR, and 0.13 ± 0.03 and 0.24 ± 0.05 for WL. For the whole period, moderate to high heritability was estimated for MOT (0.73 ± 0.08 for RIR and 0.56 ± 0.08 for WL), and LVOT (0.42 ± 0.07 for RIR and 0.45 ± 0.08 for WL). The Spearman correlations between the EBVs of hens for DOT and MOT were 0.99 in both lines. The Spearman correlations between the EBVs of hens for DOT and LVOT were 0.87 and 0.65 for RIR and WL respectively.These results indicate that DOT captures genetic information closer to MOT than LVOT. The rankings of candidates are the same for MOT and DOT. However, the calculation time of EBVs is faster for MOT than for DOT, suggesting that MOT is more interesting for the genetic evaluations. The existence of genetic background for the oviposition time is promising to identify candidate genes implicated in the expression of the laying rhythm.
- Published
- 2022
10. No G×E on egg qualities and body weight between cage and floor systems, implications for breeding programmes in laying hens
- Author
-
Bédère, Nicolas, Bécot, Lorry, Burlot, Thierry, Le Roy, Pascale, and Bernard, Emilie
- Subjects
[SDV.SA.SPA] Life Sciences [q-bio]/Agricultural sciences/Animal production studies ,[SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics - Abstract
The main objective of this study was to quantify genotype-by-environment interactions for egg quality traits and body weight in laying hens between cage and cage -free systems. Records of 18,524 eggs for quality traits and 10,266 hens for body weight from a pedigreed Rhode Island Red line were used. Hens were hatched across 5 batches from 2018 to 2020, siblings are housed in two systems: a cage and a floor system. Random regressions were modelled to estimate variance components. Heritability estimates were moderate to high in both systems(0.29-0.77). Genetic correlations between the cage and the floor system were high (≥0.79), and genetic correlations between the intercept and the slope of the reaction norm ranged from -0.69 to 0.27. The results indicate that there is no need to maintain a dedicated breeding programme per system, if the breeding goals are identical, which is unlikely.
- Published
- 2022
11. Detection of quantitative trait loci for reproduction and production traits in Large White and French Landrace pig populations (Open Access publication)
- Author
-
Bidanel Jean-Pierre, Mercat Marie-José, Ronan Gueblez, Juliette Riquet, Gilbert Hélène, Druet Tom, Iannuccelli Nathalie, Tribout Thierry, Milan Denis, and Le Roy Pascale
- Subjects
quantitative trait locus ,pig ,commercial population ,production trait ,reproduction trait ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract A genome-wide scan was performed in Large White and French Landrace pig populations in order to identify QTL affecting reproduction and production traits. The experiment was based on a granddaughter design, including five Large White and three French Landrace half-sib families identified in the French porcine national database. A total of 239 animals (166 sons and 73 daughters of the eight male founders) distributed in eight families were genotyped for 144 microsatellite markers. The design included 51 262 animals recorded for production traits, and 53 205 litter size records were considered. Three production and three reproduction traits were analysed: average backfat thickness (US_M) and live weight (LWGT) at the end of the on-farm test, age of candidates adjusted at 100 kg live weight, total number of piglets born per litter, and numbers of stillborn (STILLp) and born alive (LIVp) piglets per litter. Ten QTL with medium to large effects were detected at a chromosome-wide significance level of 5% affecting traits US_M (on SSC2, SSC3 and SSC17), LWGT (on SSC4), STILLp (on SSC6, SSC11 and SSC14) and LIVp (on SSC7, SSC16 and SSC18). The number of heterozygous male founders varied from 1 to 3 depending on the QTL.
- Published
- 2008
- Full Text
- View/download PDF
12. Methods for the detection of multiple linked QTL applied to a mixture of full and half sib families
- Author
-
Le Roy Pascale and Gilbert Hélène
- Subjects
QTL detection ,linked QTL ,multiple trait ,sib families ,simulations ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract A new multiple trait strategy based on discriminant analysis was studied for efficient detection of linked QTL in outbred sib families, in comparison with a multivariate likelihood technique. The discriminant analysis technique describes the segregation of a linear combination of the traits in a univariate likelihood. This combination is calculated for each pair of positions depending on the inheritance of the pairs of QTL haplotypes in the progeny. The gains in power and accuracy for position estimations of multiple trait methods in grid searches were evaluated in reference to single trait detections of linked QTL. The methods were applied to simulated designs with two correlated traits submitted to various effects from the linked QTL. Multiple trait strategies were generally more powerful and accurate than the single trait technique. Linked QTL were distinguished when they were separated enough to identify informative recombinations: at least two genetic markers and 25 cM between the QTL under the simulated conditions. Except in a particular case, discriminant analysis was at least as powerful as the multivariate technique and its implementation was five times faster. Combining the advantages from both methodologies, we finally propose a complete strategy for rapid and efficient systematic multivariate detections in outbred populations.
- Published
- 2007
- Full Text
- View/download PDF
13. Fatness QTL on chicken chromosome 5 and interaction with sex
- Author
-
Vignal Alain, Aggrey Sammy, Cogburn Larry, Simon Jean, Vignoles Florence, Demeure Olivier, Le Roy Pascale, Le Bihan-Duval Elisabeth, Lagarrigue Sandrine, Pitel Frédérique, Abasht Behnam, and Douaire Madeleine
- Subjects
meat-type chickens ,quantitative trait loci ,fatness QTL ,QTL × sex interaction ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Quantitative trait loci (QTL) affecting fatness in male chickens were previously identified on chromosome 5 (GGA5) in a three-generation design derived from two experimental chicken lines divergently selected for abdominal fat weight. A new design, established from the same pure lines, produced 407 F2 progenies (males and females) from 4 F1-sire families. Body weight and abdominal fat were measured on the F2 at 9 wk of age. In each sire family, selective genotyping was carried out for 48 extreme individuals for abdominal fat using seven microsatellite markers from GGA5. QTL analyses confirmed the presence of QTL for fatness on GGA5 and identified a QTL by sex interaction. By crossing one F1 sire heterozygous at the QTL with lean line dams, three recombinant backcross 1 (BC1) males were produced and their QTL genotypes were assessed in backcross 2 (BC2) progenies. These results confirmed the QTL by sex interaction identified in the F2 generation and they allow mapping of the female QTL to less than 8 Mb at the distal part of the GGA5. They also indicate that fat QTL alleles were segregating in both fat and lean lines.
- Published
- 2006
- Full Text
- View/download PDF
14. Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness
- Author
-
Neau André, Pitel Frédérique, Vignal Alain, Simon Jean, Leclercq Bernard, Carré Wilfrid, Cogburn Larry, Aggrey Sammy, Amigues Yves, Lagarrigue Sandrine, Abasht Behnam, Le Roy Pascale, Sourdioux Michel, and Douaire Madeleine
- Subjects
quantitative trait locus ,abdominal fat ,breast muscle ,chicken ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Quantitative trait loci (QTL) for abdominal fatness and breast muscle weight were investigated in a three-generation design performed by inter-crossing two experimental meat-type chicken lines that were divergently selected on abdominal fatness. A total of 585 F2 male offspring from 5 F1 sires and 38 F1 dams were recorded at 8 weeks of age for live body, abdominal fat and breast muscle weights. One hundred-twenty nine microsatellite markers, evenly located throughout the genome and heterozygous for most of the F1 sires, were used for genotyping the F2 birds. In each sire family, those offspring exhibiting the most extreme values for each trait were genotyped. Multipoint QTL analyses using maximum likelihood methods were performed for abdominal fat and breast muscle weights, which were corrected for the effects of 8-week body weight, dam and hatching group. Isolated markers were assessed by analyses of variance. Two significant QTL were identified on chromosomes 1 and 5 with effects of about one within-family residual standard deviation. One breast muscle QTL was identified on GGA1 with an effect of 2.0 within-family residual standard deviation.
- Published
- 2006
15. Power of three multitrait methods for QTL detection in crossbred populations
- Author
-
Le Roy Pascale and Gilbert Hélène
- Subjects
multitrait ,QTL ,sib families ,simulations ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract The multitrait detections of QTL applied to a mixture of full- and half-sib families require specific strategies. Indeed, the number of parameters estimated by the multivariate methods is excessive compared with the size of the population. Thus, only multitrait methods based on a univariate analysis of a linear combination (LC) of the traits can be extensively performed. We compared three strategies to obtain the LC of the traits. Two linear transformations were performed on the overall population. The last one was performed within each half-sib family. Their powers were compared on simulated data depending on the frequency of the two QTL alleles in each of the grand parental populations of an intercross design. The transformations from the whole population did not lead to a large loss of power even though the frequency of the QTL alleles was similar in the two grand parental populations. In these cases, applying the within-sire family transformation improved the detection when the number of progeny per sire was greater than 100.
- Published
- 2004
- Full Text
- View/download PDF
16. 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
-
Le Roy Pascale, Burlot Thierry, Naveau Jean, Zhang Siqing, Bidanel Jean-Pierre, and Marie-Pierre Sanchez
- Subjects
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.
- Published
- 2003
- Full Text
- View/download PDF
17. Comparison of three multitrait methods for QTL detection
- Author
-
Le Roy Pascale and Gilbert Hélène
- Subjects
multitrait ,QTL ,sib families ,simulations ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract A comparison of power and accuracy of estimation of position and QTL effects of three multitrait methods and one single trait method for QTL detection was carried out on simulated data, taking into account the mixture of full and half-sib families. One multitrait method was based on a multivariate function as the penetrance function (MV). The two other multitrait methods were based on univariate analysis of linear combination(s) (LC) of the traits. One was obtained by a principal component analysis (PCA) performed on the phenotypic data. The second was based on a discriminate analysis (DA). It calculates a LC of the traits at each position, maximising the ratio between the genetic and the residual variabilities due to the putative QTL. Due to its number of parameters, MV was less powerful and accurate than the other methods. In general, DA better detected QTL, but it had lower accuracy for the QTL effect estimation when the detection power was low, due to higher bias than the other methods. In this case, PCA was better. Otherwise, PCA was slightly less powerful and accurate than DA. Compared to the single trait method, power can be improved by 30% to 100% with multitrait methods.
- Published
- 2003
- Full Text
- View/download PDF
18. Detection of quantitative trait loci for carcass composition traits in pigs
- Author
-
Renard Christine, Le Roy Pascale, Gruand Joseph, Amigues Yves, Riquet Juliette, Iannuccelli Nathalie, Bidanel Jean-Pierre, Milan Denis, and Chevalet Claude
- Subjects
pig ,gene mapping ,quantitative trait locus ,carcass composition ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract A quantitative trait locus (QTL) analysis of carcass composition data from a three-generation experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. A total of 488 F2 males issued from six F1 boars and 23 F1 sows, the progeny of six LW boars and six MS sows, were slaughtered at approximately 80 kg live weight and were submitted to a standardised cutting of the carcass. Fifteen traits, i.e. dressing percentage, loin, ham, shoulder, belly, backfat, leaf fat, feet and head weights, two backfat thickness and one muscle depth measurements, ham + loin and back + leaf fat percentages and estimated carcass lean content were analysed. Animals were typed for a total of 137 markers covering the entire porcine genome. Analyses were performed using a line-cross (LC) regression method where founder lines were assumed to be fixed for different QTL alleles and a half/full sib (HFS) maximum likelihood method where allele substitution effects were estimated within each half-/full-sib family. Additional analyses were performed to search for multiple linked QTL and imprinting effects. Significant gene effects were evidenced for both leanness and fatness traits in the telomeric regions of SSC 1q and SSC 2p, on SSC 4, SSC 7 and SSC X. Additional significant QTL were identified for ham weight on SSC 5, for head weight on SSC 1 and SSC 7, for feet weight on SSC 7 and for dressing percentage on SSC X. LW alleles were associated with a higher lean content and a lower fat content of the carcass, except for the fatness trait on SSC 7. Suggestive evidence of linked QTL on SSC 7 and of imprinting effects on SSC 6, SSC 7, SSC 9 and SSC 17 were also obtained.
- Published
- 2002
- Full Text
- View/download PDF
19. Detection of quantitative trait loci for growth and fatness in pigs
- Author
-
Gellin Joël, Renard Christine, Quintanilla Raquel, Lagant Hervé, Le Roy Pascale, Gruand Joseph, Caritez Jean-Claude, Boscher Marie-Yvonne, Bourgeois Florence, Amigues Yves, Iannuccelli Nathalie, Milan Denis, Bidanel Jean-Pierre, Ollivier Louis, and Chevalet Claude
- Subjects
pig ,gene mapping ,quantitative trait locus ,growth ,fatness ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract A quantitative trait locus (QTL) analysis of growth and fatness data from a three-generation experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. Six boars and 23 F1 sows, the progeny of six LW boars and six MS sows, produced 530 F2 males and 573 F2 females. Nine growth traits, i.e. body weight at birth and at 3, 10, 13, 17 and 22 weeks of age, average daily gain from birth to 3 weeks, from 3 to 10 weeks and from 10 to 22 weeks of age, as well as backfat thickness at 13, 17 and 22 weeks of age and at 40 and 60 kg live weight were analysed. Animals were typed for a total of 137 markers covering the entire porcine genome. Analyses were performed using two interval mapping methods: a line-cross (LC) regression method where founder lines were assumed to be fixed for different QTL alleles and a half-/full-sib (HFS) maximum likelihood method where allele substitution effects were estimated within each half-/full-sib family. Both methods revealed highly significant gene effects for growth on chromosomes 1, 4 and 7 and for backfat thickness on chromosomes 1, 4, 5, 7 and X, and significant gene effects on chromosome 6 for growth and backfat thickness. Suggestive QTLs were also revealed by both methods on chromosomes 2 and 3 for growth and 2 for backfat thickness. Significant gene effects were detected for growth on chromosomes 11, 13, 14, 16 and 18 and for backfat thickness on chromosome 8, 10, 13 and 14. LW alleles were associated with high growth rate and low backfat thickness, except for those of chromosome 7 and to a lesser extent early-growth alleles on chromosomes 1 and 2 and backfat thickness alleles on chromosome 6.
- Published
- 2001
- Full Text
- View/download PDF
20. Genetic variability of nesting behavior and egg production traits for laying hens raised in a cage-free system
- Author
-
BÉCOT, Lorry, Bédère, Nicolas, Coton, Jenna, Burlot, Thierry, Le Roy, Pascale, Bernard, Emilie, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), NOVOGEN, and Groupe Grimaud
- Subjects
[SDV] Life Sciences [q-bio] ,Quantitative genetics ,[SDV]Life Sciences [q-bio] ,Laying hens ,Agronomy - Abstract
National audience; In laying hens, the importance of cage-free systems (barn, free-range and organic) has increased in recent years. These systems require that laying hens lay their eggs in nests. Indeed, off-nest laid eggs impair the production performance of the flock because they are most of the time down graded or lost. Consequently, select laying hens on nesting behavior would be a good opportunity to reduce off-nest laid eggs and improve egg production. However, little is known about such traits. Our study aimed at estimating genetic parameters of nesting behavior traits and their genetic correlations with a production trait, in order to evaluate their potential inclusion in breeding programs. Data were continuously recorded on laying hens raised in a barn thanks to individual electronic nests, which use radio-frequency identification of hens. Nesting behavior and production traits were recorded between 24 (peak of egg production) and 64 (middle of egg production) weeks of age on two pure lines: 1,430 Rhode Island Red hens (RIR) and 1,008 White Leghorn hens (WL). The nesting behavior traits studied were the mean laying duration (MLD), i.e. the mean time spent in the nests to lay, the mean distance between nests of laying (MDN) and the rhythm of lay, like clutch number and the mean oviposition time (MOT). The egg production trait studied was the laying rate in the nests (LRN). Genetic parameters were estimated by applying there stricted maximum like lihood method to an animal model. High (0.55 and 0.68) and moderate (0.32 and 0.37) heritability estimates were found for MLD and MDN respectively. For these two traits, null or favorable genetic correlations with LRN were estimated. Select laying hens with a low MLD and high MDN, i.e. high exploratory behavior, could help to reduce off-nest laid eggs. In the two lines, high heritability estimateswere found for clutch number and MOT with values between 0.40 and 0.66. For LRN, heritability estimates were 0.09 and 0.25 for RIR and WL respectively. Strong negative genetic correlations (-0.72 and -0.61) were estimated between clutch number and LRN, indicating that select laying hens with a low clutch number could increase LRN. Genetic correlations between MOT and LRN were lower with estimates values from -0.04 and -0.44 for RIR and WL respectively. The existence of a genetic background for nesting behavior traits is promising to identify quantitative traits locus and candidate genes implicated in the expression of such traits.
- Published
- 2021
21. Identification of polymorphisms in Protein Coding Genes which affect eggshell quality traits in layers
- Author
-
Herault, Frédéric, Diot, Christian, Burlot, Thierry, Gautron, Joël, Moreau, Thierry, Le Roy, Pascale, Hérault, Frédéric, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), NOVOGEN, Groupe Grimaud, Biologie des Oiseaux et Aviculture (BOA), Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,[SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2021
22. Sélection sur la ponte des poules en systèmes alternatifs à la cage
- Author
-
BÉCOT, Lorry, Bédère, Nicolas, Le Roy, Pascale, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), NOVOGEN, and Groupe Grimaud
- Subjects
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,[SDV]Life Sciences [q-bio] - Abstract
International audience; The number of laying hens raised in cage-free systems has increased in Europe. In these breeding systems, hens live freely in large groups and must lay eggs in nests. Breeders need to measure the individual laying performance of hens under these very different cage conditions. To do so, electronic nests have been developed. These nests enable to measure regular selection criteria, i.e. egg production and egg quality traits, but also provide access to new egg-laying traits, related to pre-laying behavior and nesting behavior. Reproductive rhythm traits can also be measured precisely by recording the laying time. Although there is little knowledge of the genetic background of these egg-laying traits, there are already selection opportunities for increasing egg-laying performance in these breeding systems as well as improved adaptation capacity and welfare.; Les effectifs de poules pondeuses élevées dans des systèmes alternatifs à la cage augmentent en Europe. Dans ces systèmes, les poules évoluent librement dans des groupes de grande taille et doivent pondre dans des nids. Les sélectionneurs ont besoin de mesurer les performances de ponte individuelles des poules dans ces conditions très différentes de la cage. Pour cela, des nids électroniques ont été développés. Ces nids permettent de mesurer les critères de sélection classiques de production d’œufs et de qualité d’œuf, mais également de nouveaux caractères de ponte liés au comportement précédant la ponte et au comportement au nid. Les caractères de rythme de ponte des poules peuvent aussi être mesurés précisément grâce à l’enregistrement de l’heure de ponte. Les connaissances sur le déterminisme génétique de ces caractères de ponte, encore partielles, offrent d’ores et déjà des perspectives de sélection pour améliorer les performances de ponte dans ces systèmes d’élevage ainsi que la capacité d’adaptation des animaux et leur bien-être.
- Published
- 2021
23. Comparison between the three porcine RN genotypes for growth, carcass composition and meat quality traits
- Author
-
Monin Gabriel, Juin Hervé, Sellier Pierre, Talmant André, Caritez Jean-Claude, Elsen Jean-Michel, and Le Roy Pascale
- Subjects
pig ,major gene ,RN gene ,meat quality ,carcass composition ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract A three-step experimental design has been carried out to add evidence about the existence of the RN gene, with two segregating alleles RN- and rn+, having major effects on meat quality in pigs, to estimate its effects on production traits and to map the RN locus. In the present article, the experimental population and sampling procedures are described and discussed, and effects of the three RN genotypes on growth and carcass traits are presented. The RN genotype had no major effect on growth performance and killing out percentage. Variables pertaining to carcass tissue composition showed that the RN- allele is associated with leaner carcasses (about 1 s.d. effect without dominance for back fat thickness, 0.5 s.d. effect with dominance for weights of joints). Muscle glycolytic potential (GP) was considerably higher in RN- carriers, with a maximum of a 6.85 s.d. effect for the live longissimus muscle GP. Physico-chemical characteristics of meat were also influenced by the RN genotype in a dominant way, ultimate pH differing by about 2 s.d. between homozygous genotypes and meat colour by about 1 s.d. Technological quality was also affected, with a 1 s.d. decrease in technological yield for RN- carriers. The RN genotype had a more limited effect on eating quality. On the whole, the identity between the acid meat condition and the RN- allele effect is clearly demonstrated (higher muscle GP, lower ultimate pH, paler meat and lower protein content), and the unfavourable relationship between GP and carcass lean to fat ratio is confirmed.
- Published
- 2000
- Full Text
- View/download PDF
24. Nest acceptance, clutch, and oviposition traits are promising selection criteria to improve egg production in cage-free system
- Author
-
Becot, Lorry, primary, Bedere, Nicolas, additional, Burlot, Thierry, additional, Coton, Jenna, additional, and Le Roy, Pascale, additional
- Published
- 2021
- Full Text
- View/download PDF
25. Alternative models for QTL detection in livestock. III. Heteroskedastic model and models corresponding to several distributions of the QTL effect
- Author
-
Elsen Jean, Boichard Didier, Le Roy Pascale, Goffinet Bruno, and Mangin Brigitte
- Subjects
Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Published
- 1999
- Full Text
- View/download PDF
26. Alternative models for QTL detection in livestock. II. Likelihood approximations and sire marker genotype estimations
- Author
-
Elsen Jean-Michel, Boichard Didier, Le Roy Pascale, Goffinet Bruno, and Mangin Brigitte
- Subjects
Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Published
- 1999
- Full Text
- View/download PDF
27. Alternative models for QTL detection in livestock. I. General introduction
- Author
-
Boichard Didier, Goffinet Bruno, Mangin Brigitte, Elsen Jean-Michel, and Le Roy Pascale
- Subjects
Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Published
- 1999
- Full Text
- View/download PDF
28. Selection for reduced muscle glycolytic potential in Large White pigs. III. Correlated responses in growth rate, carcass composition and reproductive traits
- Author
-
Sellier Pierre, Monin Gabriel, Talmant André, Gogué Jean, Le Roy Pascale, and Larzul Catherine
- Subjects
Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Published
- 1999
- Full Text
- View/download PDF
29. Selection for reduced muscle glycolytic potential in Large White pigs. II. Correlated responses in meat quality and muscle compositional traits
- Author
-
Monin Gabriel, Sellier Pierre, Ecolan Patrick, Lefaucheur Louis, Jacquet Bernard, Talmant André, Gogué Jean, Le Roy Pascale, and Larzul Catherine
- Subjects
Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Published
- 1999
- Full Text
- View/download PDF
30. Selection for reduced muscle glycolytic potential in Large White pigs I. Direct responses
- Author
-
Sellier Pierre, Monin Gabriel, Talmant André, Gogué Jean, Larzul Catherine, and Le Roy Pascale
- Subjects
Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Published
- 1998
- Full Text
- View/download PDF
31. Comparison of analyses of the XVth QTLMAS common dataset III: Genomic Estimations of Breeding Values
- Author
-
Demeure Olivier, Le Roy Pascale, Filangi Olivier, and Elsen Jean-Michel
- Subjects
Medicine ,Science - Abstract
Abstract Background The QTLMAS XVth dataset consisted of pedigree, marker genotypes and quantitative trait performances of animals with a sib family structure. Pedigree and genotypes concerned 3,000 progenies among those 2,000 were phenotyped. The trait was regulated by 8 QTLs which displayed additive, imprinting or epistatic effects. The 1,000 unphenotyped progenies were considered as candidates to selection and their Genomic Estimated Breeding Values (GEBV) were evaluated by participants of the XVth QTLMAS workshop. This paper aims at comparing the GEBV estimation results obtained by seven participants to the workshop. Methods From the known QTL genotypes of each candidate, two "true" genomic values (TV) were estimated by organizers: the genotypic value of the candidate (TGV) and the expectation of its progeny genotypic values (TBV). GEBV were computed by the participants following different statistical methods: random linear models (including BLUP and Ridge Regression), selection variable techniques (LASSO, Elastic Net) and Bayesian methods. Accuracy was evaluated by the correlation between TV (TGV or TBV) and GEBV presented by participants. Rank correlation of the best 10% of individuals and error in predictions were also evaluated. Bias was tested by regression of TV on GEBV. Results Large differences between methods were found for all criteria and type of genetic values (TGV, TBV). In general, the criteria ranked consistently methods belonging to the same family. Conclusions Bayesian methods - A
- Published
- 2012
- Full Text
- View/download PDF
32. Estimation of additive and dominant variance of egg quality traits in pure-line layers
- Author
-
Picard Druet, David, Tusell, Llibertat, Herault, Frédéric, Herry, Florian, Allais, Sophie, Varenne, Amandine, Burlot, Thierry, Le Roy, Pascale, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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], Novogen, 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), 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, and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
- Subjects
Genomic selection ,Dominance genetic variance ,Pure-line layers ,Egg quality ,qualité des oeufs ,[SDV]Life Sciences [q-bio] ,variance génétique ,laying hen ,poule pondeuse ,sélection génomique ,genomic selection - Abstract
Improved performances are partly due to heterosis effects. One of the basis of heterosis is dominance, which cannot be inherited.However, it can be exploited to boost the total genetic merit of the animals. This has a special interest in avian selection schemeswhere commercial animals are crossbred. In this study, we have estimated additive and dominance genetic variances for severalegg quality traits in pure-line layers.Around 10,500 egg quality performances were used, collected from 1,148 female Rhode Island layers, phenotyped at 70 weeksold and genotyped using a 600K high density SNP chip. Five egg quality traits were analysed: egg weight (EW), egg shell color(ESC), egg shell strength (ESS), albumen height (AH) and egg shell shape (ESShape). Additive and dominance genetic varianceswere estimated via EM-REML with univariate models. That included an inbreeding coefficient and an additive and a dominancerandom effect. Dominance variance explained a small fraction of the phenotypic variance (between 2 to 4 % across all traits).However, it represented a relevant fraction of the total genetic variance for some of the traits (16%, 10%, 35%, 2.4% and 15% ofthe total genetic variance for EW, ESC, ESS, AH, ESShape, respectively).Further research will estimate additive and dominance genetic correlations between the traits to maximize the total genetic gainof these traits simultaneously. In addition, a genomic BLUP with dominance effects is envisaged for the joint analyses of purebredand crossbred performances, to evaluate the potential to generate superior crossbred performances.
- Published
- 2019
33. Use of data from crossbred animals for a genomic evaluation of pure line layer
- Author
-
Picard Druet, David, Varenne, Amandine, Herault, Frédéric, Burlot, Thierry, Allais, Sophie, Le Roy, Pascale, 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, and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
- Subjects
qualité des oeufs ,[SDV]Life Sciences [q-bio] ,education ,laying hen ,évaluation génomique ,poule pondeuse ,humanities ,Crossbred ,Laying hen ,Egg quality ,Genomic evaluation ,Accuracy ,hybridization ,hybridation ,reproductive and urinary physiology ,health care economics and organizations ,précision de sélection - Abstract
Use of data from crossbred animals for a genomic evaluation of pure line layer. XIth European symposium on poultry genetics (ESPG)
- Published
- 2019
34. Interest of Genotyping-by-Sequencing technologies as an alternative to low density SNP chips for genomic selection in layer chicken
- Author
-
Herry, Florian, Herault, Frédéric, Picard Druet, David, Bardou, Philippe, Eché, Camille, Varenne, Amandine, Burlot, Thierry, Le Roy, Pascale, Allais, Sophie, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Novogen, 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, GeT PlaGe, Genotoul, 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)-Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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], Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
- Subjects
Imputation accuracy ,génotypage ,[SDV]Life Sciences [q-bio] ,Genotyping-by-Sequencing ,Genomic selection ,Low density panel ,Genomic evaluation accuracy ,laying hen ,évaluation génomique ,sélection génomique ,poule pondeuse ,précision de sélection ,genomic selection - Abstract
To reduce the cost of genomic selection, low density SNP chip can be used in combination with imputation for genotyping the selection candidates instead of using high density (HD) SNP chip. Concurrently, next-generation sequencing (NGS) techniques has been increasingly used in livestock species but remain expensive to be routinely used in selection. An alternative and costefficient solution is the Genotyping by Genome Reducing and Sequencing (GGRS) techniques to sequence only a fraction of the genome by using restriction enzymes. This approach was simulated from sequences of 1027 individuals in a pure layer line, using four enzymes (EcoRI, TaqI, AvaII and PstI). Imputation accuracy on HD genotypes was assessed as the mean correlation between true and imputed genotypes. Egg weight, egg shell color, egg shell strength and albumen height were evaluated with single-step GBLUP methodology. The impact of imputation errors on the genomic estimated breeding values (GEBV) was also investigated.AvaII or PstI led to the detection of more than 10K SNPs in common with the HD SNP chip resulting in imputation accuracy higher than 0.97. The impact of imputation errors on the ranking of the selection candidates was reduced with Spearman correlation (between GEBV calculated on true and imputed genotypes) higher than 0.97 for AvaII and PstI. Finally, the GGRS approach can be an interesting alternative to low density SNP chip for genomic selection. However, with real data, heterogeneity between individuals with missing data has to be taken into account.
- Published
- 2019
35. Accuracy of whole-genome sequence genotype imputation in a layer line
- Author
-
Allais, Sophie, Herry, Florian, Herault, Frédéric, Picard Druet, David, Bardou, Philippe, Eche, Camille, Varenne, Amandine, Burlot, Thierry, 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, 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, US 1426 Génome et Transcriptome - Plateforme Génomique, Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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], 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), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
- Subjects
Layer line ,NGS ,[SDV]Life Sciences [q-bio] ,GWAS ,SNP beadchip ,Imputation - Abstract
Over the past several years, high-density genotyping has led to major advances in genomic selection and understanding of genomes. This is also the case in laying hens with the availability of the Affymetrix HD 600K chip since 2013. Nowadays, NGS costs are becoming more and more affordable. Based on the HD SNP chip, the use of imputation to go back to the sequence level then makes it possible to obtain information on millions of polymorphisms for a large number of individuals. In this study, we analyzed the quality of the imputation of the HD chip genotypes on sequence genotypes for 90 individuals of a layer line presenting the 2 types of information. After quality control, these individuals presented genotypes for 290K and more than 6 million SNPs respectively with 600K genotyping and 20X sequencing. We carried out a cross-validation with 8 draws of 5 individuals. The correlation between true and imputed genotypes was between 0.96 and 0.99 depending on the individual.Correlations were greater than 0.90 for all chromosomes except chromosomes 16 and 25. After this validation work, we imputed an additional set of 95 individuals to perform GWAS. These analyses confirmed some QTLs of interest as a QTL of egg shell color on chromosome 7 and a QTL of egg shell strength on chromosome 1.
- Published
- 2019
36. Interest of using imputation for genomic evaluation in layer chicken
- Author
-
Herry, Florian, primary, Druet, David Picard, additional, Hérault, Frédéric, additional, Varenne, Amandine, additional, Burlot, Thierry, additional, Le Roy, Pascale, additional, and Allais, Sophie, additional
- Published
- 2020
- Full Text
- View/download PDF
37. Apport des informations sur des croisées dans le cadre de l’évaluation génomique sur la qualité des œufs chez la poule
- Author
-
Picard--Druet, David, Varenne, Amandine, Hérault, Frédéric, Herry, Florian, Allais, Sophie, Burlot, Thierry, Le Roy, Pascale, 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), and Novogen
- 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] - Abstract
National audience; Avian breeders are currently putting in place genomic selection in their selection schemes. One key parameter to optimize selection schemes, and so genetic gain of selected populations, is to correctly predict the accuracy of genomic evaluation. In a previous study, it has been shown that genomic selection at birth was a very promising strategy for breeders selection in purebred. As crossbred between pure lines is commonly used in avian selection schemes, raises the question about the use of crossbred offspring in breeders evaluation, and their impact on evaluation accuracy. In this study, we had 2 goals. First, estimation of genetic correlation, for the same egg quality trait, between performance from pure line, and cross line layers. Then, estimation of the differences in evaluation accuracy, by adding crossbred information to pure line evaluation. Results shown that genetic correlation between purebred and crossbred trait is strong, but did not allow to consider that it is the same trait. Adding crossbred performances into evaluations allowed to obtain better results, globally, than in separated evaluations.; Depuis quelques années, la sélection génomique commence à se mettre en place dans la filière avicole. Dans le but d’optimiser les schémas de sélection, et donc le progrès génétique des populations sélectionnées, il est important de connaître la précision de l’évaluation génomique, comparativement à l’évaluation génétique. Dans une étude précédente, il avait été observé que l’usage de la sélection génomique à la naissance était une stratégie très prometteuse pour la sélection des reproducteurs en race pure. Le croisement entre lignées pures étant utilisé à large échelle par les schémas de sélection avicoles, il s’est posé la question de l’utilisation des données des descendantes croisées sur l’évaluation des reproducteurs, et de leur influence sur la précision de l’évaluation. Dans le cadre de cette étude, 2 objectifs ont été poursuivis. Tout d’abord, estimer la corrélation génétique, pour un même caractère de qualité d’œuf, entre la performance exprimée par des poules de lignée pure, et celle des poules croisées. Ensuite, estimer les différences de précision apportées par l’intégration des données des croisées à l’évaluation en lignée pure. Les résultats ont montré que la corrélation génétique entre caractère pur et croisé est forte, mais ne permet pas de considérer qu’il s’agit du même caractère. L’ajout des performances de croisées aux évaluations a permis d’obtenir des résultats globalement meilleurs qu’en évaluations séparées.
- Published
- 2019
38. Étude du déséquilibre de liaison dans des lignées de poules de types génétiques 'ponte' et 'chair'
- Author
-
Hérault, Frédéric, Varenne, Amandine, Burlot, Thierry, Recoquillay, Julien, Macé, Camille, Fagnoul, Frédéric, Picard Druet, David, Herry, Florian, Allais, Sophie, Le Roy, Pascale, 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, Hubbard SAS, Partenaires INRAE, NOVOGEN, Groupe Grimaud, Hubbard, and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
- Subjects
volaille ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,cartographie fine ,qtl ,[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,poule ,évaluation génomique ,génotype ,déséquilibre de liaison - Abstract
La structure du déséquilibre de liaison (DL) au sein des populations en sélection impacte fortement la précision obtenue lors des études de cartographie de QTL ou lors de l’évaluation génomique des reproducteurs. Chez les oiseaux, la structure hétérogène du génome nécessite de décrire précisément le DL pour optimiser la sélection. L’utilisation des puces SNP haute densité pour le génotypage des populations de volailles est une opportunité pour approfondir notre connaissance de la structure du DL de ces populations. L’objectif de cette étude est d’acquérir une connaissance haute résolution de la structure du DL au sein de populations de poules de types ponte et chair. Nous avons analysé les génotypes (puce 600 K Affymetrix® Axiom® HD SNP) de 1541 animaux issus de 3 populations. L’étendue et le niveau du DL ont été estimés par le r2 moyen à distance physique donnée entre SNP. Cette étude met en évidence des différences importantes de structure du DL entre lignées et entre chromosomes. L’étendue et le niveau du DL sont plus importants dans les lignées de type ponte ou pour les macro-chromosomes et le chromosome Z. Ce niveau important de DL peut faciliter la détection de QTL sur ces chromosomes, mais peut également compliquer la localisation fine de polymorphismes causaux. A l’inverse, le faible niveau de DL observé sur les micro-chromosomes nécessite l’utilisation d’une forte densité de SNP pour détecter une association avec un phénotype, mais devrait permettre la cartographie fine d’un polymorphisme causal. Ces différences sont à prendre en considération pour définir une stratégie de génotypage économique et efficace pour la cartographie fine de QTL ou l’évaluation génomique., Knowledge of the linkage disequilibrium (LD) pattern is useful in animal genetic studies as it underlies mapping studies and genomic selection. This is all the more important in birds given the heterogeneous structure of the avian karyotype. Recently, the availability of the high density 600 K Affymetrix® Axiom® HD SNP genotyping array allowed to assess an in-depth knowledge of the LD pattern in chicken genome. The aim of the present study was to assess a higher resolution of the LD pattern in chicken genome in layer and broiler lines. In this study, we analyzed genotypes of 1541 animals from layers and broiler commercial populations to characterize their LD pattern. LD was measured by the average r2 value at a given physical distance between SNP. LD extended over a larger region for layer lines than for broiler line. Most differences between lines appeared at small interval distances (< 0.5Mb). LD extent and decay differed considerably between chromosomes categories. Average r2 values were higher for Z chromosome than for macro, intermediates and microchromosomes. The extent of useful LD observed for autosomal chromosomes was at least ten-fold longer for layer lines than for broiler. Finally, this study shed light on high LD for Z chromosome. The differences in LD pattern observed between chromosomes and chicken lines should be taken into account to define an economically efficient genotyping strategy.
- Published
- 2019
39. Quelles performances pour les animaux de demain ? Objectifs et méthodes de sélection
- Author
-
Le Roy, Pascale, Ducos, Alain, Phocas, Florence, 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), 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, Génétique Animale et Biologie Intégrative (GABI), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
- Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT] ,sélection ,production ,génétique ,environnement - Abstract
National audience; Meeting the issues related to sustainable development of livestock farming requires innovations in genetics. In every sector, this is all about improving the robustness of animals by enhancing their abilities to adapt by including numerous efficiency traits in the breeding goals of selection programs particularly regarding health and adaptability to less standardized feed resources and of fluctuating nutritional value, changing and varied environments, and climate change. This leads to consider genotype-by-environment interactions within genetic evaluation procedures and to assess the performances of animals in low input systems, especially regarding feed and drug use. Since the end of the 2000s, the method that has been progressively used in all livestock breeding sectors is genomic selection, which, by disconnecting the computation of genetic values of selection candidates from phenotype recordings, makes it easier to select new traits and to take into account genotype-by-environment interactions. In the relatively near future, it will be technically possible to use strategies of targeted modification and selection of genomes that could substantially increase genetic gains, in comparison with those obtained with current genomic selection programs. However, the use of these new breeding techniques raises numerous issues on scientific, operational, ethical, and political levels.; Les objectifs et méthodes d’amélioration génétique doivent évoluer pour répondre aux enjeux du développement durable des filières d’élevage. Dans toutes les espèces, il s’agit désormais d’améliorer la robustesse des animaux en promouvant leurs capacités d’adaptation, en intégrant dans les objectifs des programmes de sélection de nombreux caractères d’efficience, en particulier de santé et d’adaptation à des ressources alimentaires moins standardisées et de qualité fluctuante, à des environnements changeants et variés, et au changement climatique. Cela amène à considérer les interactions génotype x environnement dans la prédiction des valeurs génétiques et à évaluer les performances des animaux dans des systèmes à moindres intrants, notamment alimentaires et médicamenteux. Depuis la fin des années 2000, la méthode mise en oeuvre progressivement dans toutes les filières est la sélection génomique qui, en déconnectant le calcul des valeurs génétiques des candidats à la sélection de l’obtention de phénotypes, facilite la sélection de nouveaux caractères et la prise en compte des interactions génotype x environnement. Dans un futur relativement proche, il sera techniquement possible de mettre en oeuvre des stratégies de modification et sélection ciblées des génomes qui pourraient substantiellement accroitre les gains de progrès génétique en comparaison avec ceux obtenus dans les programmes actuels de sélection génomique. Toutefois, l’utilisation de ces nouvelles techniques de sélection animale pose de nombreuses questions, tant sur le plan scientifique, qu’opérationnel, éthique ou politique.
- Published
- 2019
40. Simple test statistics for major gene detection: a numerical comparison
- Author
-
Le Roy, Pascale and Elsen, J. M.
- Published
- 1992
- Full Text
- View/download PDF
41. Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses
- Author
-
Wang Xiaoqiang, Gilbert Hélène, Moreno Carole, Filangi Olivier, Elsen Jean-Michel, and Le Roy Pascale
- Subjects
QTL ,linkage analysis ,QTL location ,bias ,Genetics ,QH426-470 - Abstract
Abstract Background Quantitative trait loci (QTL) detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations. The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location. Results A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i.e. designs with low power. Practical recommendations for experimental designs for QTL detection in outbred populations are given on the basis of this bias quantification. Furthermore, an original algorithm is proposed to adjust the location of a QTL, obtained with interval mapping, which co located with a marker. Conclusions Therefore, one should be attentive when one QTL is mapped at the location of one marker, especially under low power conditions.
- Published
- 2012
- Full Text
- View/download PDF
42. Accuracy of genomic evaluation in pure line layers
- Author
-
Picard--Druet, David, HERRY, Florian, Varenne, Amandine, Herault, Frédéric, Allais, Sophie, Burlot, Thierry, Le Roy, Pascale, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Novogen, ANR-10-GENOM BTV-015 UtOpIGe, ANR-10-GENM-0015,UtOpIGe,Vers une Utilisation Optimale de l'Information Génomique dans les schémas pyramidaux(2010), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-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)
- Subjects
Animal biology ,héritabilité ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,laying hen ,évaluation génomique ,heritability ,évaluation génétique ,poule pondeuse ,genetic correlation ,corrélation génétique ,accuracy of measurement ,Single step ,phénotypage ,génotypage ,Biologie animale ,précision de la mesure ,Genomic evaluation ,Laying hens ,Accuracy - Abstract
Avian breeders are actually putting in place genomic selection in their selection schemes. One key parameter to optimize selection schemes is to correctly predict the accuracy of genomic evaluation. This paper presents results obtained by comparing accuracy of genetic and genomic evaluations on multiple traits, using several reference populations with different amount of phenotypic informations. Genetic parameters (heritability and genetic correlations) were observed, and found very stable. EBVs and GEBVs accuracies showed that genomic evaluation was each time more accurate than genetic evaluation, especially when phenotypic information was restreint. It was also found that the use of sexual chromosome genotype had a negative impact on traits evaluation for dams (no effect found on sires). In any case, genomic evaluation of breeding birds at birth seems to be a promising strategy for layers.
- Published
- 2018
43. Design of a low density SNP chip for genotype imputation in layer chickens
- Author
-
HERRY, Florian, Hérault, Frédéric, Picard--Druet, David, Varenne, Amandine, Burlot, Thierry, Le Roy, Pascale, Allais, Sophie, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Novogen, ANR-10-GENOM_BTV-015 UtOpIGe, Institut National de la Recherche Agronomique (INRA)-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)
- Subjects
Animal biology ,Imputation accuracy ,Layer chickens ,Low density SNP panel ,Linkage disequilibrium ,polymorphisme nucléotidique simple (SNP) ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,laying hen ,évaluation génomique ,poule pondeuse ,génotypage ,Biologie animale ,déséquilibre de liaison ,précision de sélection - Abstract
The main goal of selection is to choose breeders of the next generation among a set of selection candidates. In genomic selection, the choice of breeders is based on the use of information on DNA polymorphisms, in particular SNP, in addition of performance measures. Since 2013, a commercial high density genotyping chip (600,000 markers) for chicken allowed the implementation of genomic selection in layer and broiler breeding. However, genotyping costs with this chip still remain high for a routine use on a large number of selection candidates. Consequently, it is interesting to develop, at a lower cost, low density genotyping chips. To do so, a set of SNP markers has to be selected to enable an imputation (prediction) of missing genotypes with high accuracy on a high density chip (HD chip). In this perspective, we conducted various simulation studies to choose the optimal strategy for low density genotyping of two different lines of laying hen. Different low density genotyping chips were designed according to two methodologies: a choice of SNP depending on a clustering of SNP based on linkage disequilibrium threshold or a choice of SNP at regular intervals (kb) along each chromosome. Imputation accuracy was assessed as the mean correlation between true and imputed genotypes. Results showed that correlations were more sensitive to false imputation of SNPs with low Minor Allele Frequency (MAF) with the equidistant methodology. Imputation accuracy improved with SNP density and when a higher LD threshold is used for SNP selection. Given the particular structure of the avian genome with chromosomes of very heterogeneous sizes and extents of LD, imputation accuracy differed according to the type of chromosome. All the simulation studies showed that linkage disequilibrium methodology enabled to get better results of imputation than with equidistant methodology.
- Published
- 2018
44. Impact of the size of the reference population and kinship degree on low density genotyping strategies for genotype imputation in layer chickens
- Author
-
Burlot, Thierry, Herry, Florian, Hérault, Frédéric, Picard--Druet, David, Varenne, Amandine, Le Roy, Pascale, Allais, Sophie, Novogen, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), ANR-10-GENOM_BTV-015 UtOpIGe, 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), 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
Animal biology ,polymorphisme nucléotidique simple (SNP) ,Imputation accuracy ,Layer chickens ,Reference population ,Kinship degree ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,laying hen ,évaluation génomique ,poule pondeuse ,génotypage ,Biologie animale ,déséquilibre de liaison ,précision de sélection - Abstract
The main goal of selection is to choose breeders of the next generation among a set of selection candidates. In genomic selection, the choice of breeders rests on the use of information on DNA polymorphisms, in particular SNP, in addition of performance measures. Since 2013, a commercial high density genotyping chip (600,000 markers) for chicken allowed the implementation of genomic selection in layer and broiler breeding. However, genotyping costs with this chip still remain high for a routine use on a large number of selection candidates. Consequently, it is interesting to develop, at a lower cost, low density genotyping chips. To do so, a set of SNP markers has to be selected to enable an imputation (prediction) of missing genotypes on a high density chip (HD chip). This imputation enables to predict missing genotypes of all selection candidates from high density genotyping of a reference population with phenotypes. In this perspective, according to the reference population, various simulation studies were conducted to choose the best strategy for low density genotyping of laying hen lines. Two different low density genotyping chips of 10K SNP were designed according to two methodologies: a choice of SNP depending on a clustering based on linkage disequilibrium threshold or a choice of SNP at regular intervals (kb) along each chromosome. Imputation accuracy was assessed as the mean correlation between true and imputed genotypes. Focusing on populationnal factors that can influence imputation accuracy, it is shown that imputation accuracy improves with an increase in the size of the reference population. By decreasing the kinship degree between reference and candidate population, it is seen that imputation accuracy decreases. Most importantly, results show that a key point in getting good imputations is to have the direct parents in the reference population. Finally, all different genotyping strategies focused on population factors show that linkage disequilibrium methodology enables to get better results of imputation than with equidistant methodology.
- Published
- 2018
45. A linkage disequilibrium study in layers and broiler commercial chicken populations
- Author
-
Hérault, Frédéric, HERRY, Florian, Varenne, Amandine, Burlot, Thierry, Picard--Druet, David, Recoquillay, Julien, Macé, Camille, Fagnoul, Frédéric, Allais, Sophie, 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, Hubbard, ANR-10-GENOM_BTV-015 UtOpIGe, ANR-10-GENM-0015,UtOpIGe,Vers une Utilisation Optimale de l'Information Génomique dans les schémas pyramidaux(2010), 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), 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
Animal biology ,polymorphisme nucléotidique simple (SNP) ,broilers ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,layer ,broiler ,linkage disequilibrium ,génome ,Biologie animale ,déséquilibre de liaison ,poulet de chair - Abstract
Knowledge of the linkage disequilibrium (LD) pattern is useful in animal genetic studies as it underlies mapping studies and genomic selection. Recently, the availability of the high density 600K Affymetrix® Axiom® HD SNP genotyping array allows to asses a higher resolution of the LD structure in chicken genome. In this study, we analysed genotypes of 1541 animals from layers and broiler commercial populations to characterize their LD pattern. LD was measured by the average r2 value at a given physical distance between SNP. LD extends over a larger region for layers line than for broiler line. Most differences between lines appeared at small interval distance (< 0.5Mb). LD extent and decay differed considerably between chromosome categories. Average r2 values were higher for Z chromosome than for macro, intermediates and microchromosomes. The extent of useful LD observed for autosomal chromosomes is at least tenfold longer for layers line than for broiler. Finally, this study shed light on high LD for the Z chromosome. The differences in LD pattern observed between chromosomes and chicken lines should be taken into account to define an economically efficient genotyping strategy.
- Published
- 2018
46. Deterministic modelling of a poultry breeding scheme
- Author
-
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
47. Relevance of genomic evaluation for egg quality traits in layers
- Author
-
Picard Druet, David, primary, Varenne, Amandine, additional, Herry, Florian, additional, Hérault, Frédéric, additional, Allais, Sophie, additional, Burlot, Thierry, additional, and Le Roy, Pascale, additional
- Published
- 2019
- Full Text
- View/download PDF
48. Quelles performances pour les animaux de demain ? Objectifs et méthodes de sélection
- Author
-
LE ROY, Pascale, primary, DUCOS, Alain, additional, and PHOCAS, Florence, additional
- Published
- 2019
- Full Text
- View/download PDF
49. Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken
- Author
-
Blum Yuna, Le Mignon Guillaume, Causeur David, Filangi Olivier, Désert Colette, Demeure Olivier, Le Roy Pascale, and Lagarrigue Sandrine
- Subjects
Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Integrative genomics approaches that combine genotyping and transcriptome profiling in segregating populations have been developed to dissect complex traits. The most common approach is to identify genes whose eQTL colocalize with QTL of interest, providing new functional hypothesis about the causative mutation. Another approach includes defining subtypes for a complex trait using transcriptome profiles and then performing QTL mapping using some of these subtypes. This approach can refine some QTL and reveal new ones. In this paper we introduce Factor Analysis for Multiple Testing (FAMT) to define subtypes more accurately and reveal interaction between QTL affecting the same trait. The data used concern hepatic transcriptome profiles for 45 half sib male chicken of a sire known to be heterozygous for a QTL affecting abdominal fatness (AF) on chromosome 5 distal region around 168 cM. Results Using this methodology which accounts for hidden dependence structure among phenotypes, we identified 688 genes that are significantly correlated to the AF trait and we distinguished 5 subtypes for AF trait, which are not observed with gene lists obtained by classical approaches. After exclusion of one of the two lean bird subtypes, linkage analysis revealed a previously undetected QTL on chromosome 5 around 100 cM. Interestingly, the animals of this subtype presented the same q paternal haplotype at the 168 cM QTL. This result strongly suggests that the two QTL are in interaction. In other words, the "q configuration" at the 168 cM QTL could hide the QTL existence in the proximal region at 100 cM. We further show that the proximal QTL interacts with the previous one detected on the chromosome 5 distal region. Conclusion Our results demonstrate that stratifying genetic population by molecular phenotypes followed by QTL analysis on various subtypes can lead to identification of novel and interacting QTL.
- Published
- 2011
- Full Text
- View/download PDF
50. Genetic variability of transcript abundance in pig peri-mortem skeletal muscle: eQTL localized genes involved in stress response, cell death, muscle disorders and metabolism
- Author
-
Liaubet Laurence, Lobjois Valérie, Faraut Thomas, Tircazes Aurélie, Benne Francis, Iannuccelli Nathalie, Pires José, Glénisson Jérome, Robic Annie, Le Roy Pascale, SanCristobal Magali, and Cherel Pierre
- Subjects
eQTL ,muscle ,transcriptome ,genetical genomics ,systems biology ,pig ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Genetical genomics studies have mainly focused on cell lines, blood cells or adipose tissues, from human clinical samples or mice inbred lines. Few eQTL studies have focused on animal tissues sampled from outbred populations to reflect natural genetic variation of gene expression levels in animals. In this work, we analyzed gene expression in a whole tissue, pig skeletal muscle sampled from individuals from a half sib F2 family shortly after slaughtering. Results QTL detection on transcriptome measurements was performed on a family structured population. The analysis identified 335 eQTLs affecting the expression of 272 transcripts. The ontologic annotation of these eQTLs revealed an over-representation of genes encoding proteins involved in processes that are expected to be induced during muscle development and metabolism, cell morphology, assembly and organization and also in stress response and apoptosis. A gene functional network approach was used to evidence existing biological relationships between all the genes whose expression levels are influenced by eQTLs. eQTLs localization revealed a significant clustered organization of about half the genes located on segments of chromosome 1, 2, 10, 13, 16, and 18. Finally, the combined expression and genetic approaches pointed to putative cis-drivers of gene expression programs in skeletal muscle as COQ4 (SSC1), LOC100513192 (SSC18) where both the gene transcription unit and the eQTL affecting its expression level were shown to be localized in the same genomic region. This suggests cis-causing genetic polymorphims affecting gene expression levels, with (e.g. COQ4) or without (e.g. LOC100513192) potential pleiotropic effects that affect the expression of other genes (cluster of trans-eQTLs). Conclusion Genetic analysis of transcription levels revealed dependence among molecular phenotypes as being affected by variation at the same loci. We observed the genetic variation of molecular phenotypes in a specific situation of cellular stress thus contributing to a better description of muscle physiologic response. In turn, this suggests that large amounts of genetic variation, mediated through transcriptional networks, can drive transient cell response phenotypes and contribute to organismal adaptative potential.
- Published
- 2011
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.