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Anne Ricard - One of the best experts on this subject based on the ideXlab platform.

  • genomic analysis of gaits and racing performance of the French Trotter
    Journal of Animal Breeding and Genetics, 2021
    Co-Authors: Anne Ricard, Arnaud Duluard
    Abstract:

    The aim was to disentangle gait characteristics from other qualities needed for racing performances with a genomic analysis of French Trotters (FT). A sample of 1,390 horses were recruited, from which 46% were genotyped with Illumina chip of 54,602 SNPs, 49% with Affymetrix chip of 670,806 SNPs and 586 had a completed questionnaire on trotting technique. Racing performances cover the period 1996 to 2018. There were 252,368 FT-born; 96,617 qualified and 83,962 which participated in a race. After quality control, 377,611 SNPs were retained and imputed. Questionnaire described trotting technique over 13 questions which were summarized, after principal component analysis in 3 traits: pacer, heavy trot/gallop and other defects. GWAS and genomic evaluation were performed using single-step approach. We found 25 QTL for racing performances and 9 for trotting technique. Only DMRT3 mutation was significant for both traits. To tend to pace avoid the defect at gallop and lead to a better early career for earnings, less percentage of disqualified races at all ages and more harness than under saddle career. This is the portrait of AA genotype at DMRT3. We found 5 other QTL, not linked to gait traits, which might improve selection of genetically independent performance traits of earnings per races and percentage of finished races. For only earnings at different ages and in under saddle or harness races, genomic evaluation remains the best way to predict performances.

  • should we use the single nucleotide polymorphism linked to in genomic evaluation of French Trotter
    Journal of Animal Science, 2015
    Co-Authors: S Brard, Anne Ricard
    Abstract:

    An A/C mutation responsible for the ability to pace in horses was recently discovered in the gene. It has also been proven that allele C has a negative effect on Trotters' performances. However, in French Trotters (FT), the frequency of allele A is only 77% due to an unexpected positive effect of allele C in late-career FT performances. Here we set out to ascertain whether the genotype at SNP (linked to ) should be used to compute EBV for FT. We used the genotypes of 630 horses, with 41,711 SNP retained. The pedigree comprised 5,699 horses. Qualification status (Trotters need to complete a 2,000-m race within a limited time to begin their career) and earnings at different ages were precorrected for fixed effects and evaluated with a multitrait model. Estimated breeding values were computed with and without the genotype at SNP as a fixed effect in the model. The analyses were performed using pedigree only via BLUP and using the genotypes via genomic BLUP (GBLUP). The genotype at SNP was removed from the file of genotypes when already taken into account as a fixed effect. Alternatively, 3 groups of 100 candidates were used for validation. Validations were also performed on 50 random-clustered groups of 126 candidates and compared against the results of the 3 disjoint sets. For performances on which has a minor effect, the coefficients of correlation were not improved when the genotype at SNP was a fixed effect in the model (earnings at 3 and 4 yr). However, for traits proven strongly related to , the accuracy of evaluation was improved, increasing +0.17 for earnings at 2 yr, +0.04 for earnings at 5 yr and older, and +0.09 for qualification status (with the GBLUP method). For all traits, the bias was reduced when the SNP linked to was a fixed effect in the model. This work finds a clear rationale for using the genotype at for this multitrait evaluation. Genomic selection seemed to achieve better results than classic selection.

  • Does heterozygosity at the DMRT3 gene make French Trotters better racers?
    Genetics Selection Evolution, 2015
    Co-Authors: Anne Ricard
    Abstract:

    Background Recently, a mutation was discovered in the DMRT3 gene that controls pacing in horses. The mutant allele A is fixed in the American Standardbred Trotter breed, while in the French Trotter breed, the frequency of the wild-type allele C is still 24%. This study aimed at measuring the effect of DMRT3 genotypes on the performance of French Trotters and explaining why the polymorphism still occurs in this breed. Using a mixed animal model, genetic parameters and environmental effects on performance traits were estimated from data on 173 176 French Trotter races. The effect of the DMRT3 gene was then estimated by the effect of genotype at the highly linked SNP BIEC2-620109 (C-C, A-T) for 630 horses. A selection scheme that included qualification and racing performances was modeled to (1) verify if the observed superiority of heterozygous CT horses at this SNP could be explained only by selection and (2) understand why allele C has not disappeared in French Trotters. Results Heritability of racing performance traits was high for qualification test (0.56), moderate for annual earnings per finished race (0.26 to 0.31) and low for proportion of disqualified races (0.06 to 0.09). Genotype CC was always unfavorable compared to genotype TT for qualification: the probability to be qualified was 20% for CC vs. 48% for TT and earnings were -0.96 σ _ y lower for CC than for TT. Genotype CT was also unfavorable for qualification (40%) and earnings at 3 years (-0.21 σ _ y ), but favorable for earnings at ages greater than 5 years: +0.41 σ _ y ( P  = 7.10^−4). Selection on qualification could not explain more than 19% of the difference between genotypes CC and CT in earnings at ages greater than 5 years. Only a scenario for which genotype CT has a favorable effect on the performance of horses older than 5 years could explain that the polymorphism at the DMRT3 gene still exists in the French Trotter breed. Conclusions The use of mature horses in the French racing circuit can explain that the CA genotype is still present in the French Trotter horses.

  • Genome-wide association studies for osteochondrosis in French Trotter horses
    Journal of Animal Science, 2012
    Co-Authors: Simon Teyssèdre, M.c. Dupuis, Gerard Guérin, Laurent Schibler, J.m. Denoix, Jean Michel Elsen, Anne Ricard
    Abstract:

    A genome-wide association study for osteochondrosis (OC) in French Trotter horses was carried out to detect QTL using genotype data from the Illumina EquineSNP50 BeadChip assay. Analysis data came from 161 sire families of French Trotter horses with 525 progeny and family sizes ranging from 1 to 20. Genotypes were available for progeny (n = 525) and sires with at least 2 progeny (n = 98). Radiographic data were obtained from progeny using at least 10 views to reveal OC. All radiographic findings were described by at least 2 veterinary experts in equine orthopedics, and severity indices (scores) were assigned based on the size and location of the lesion. Traits used were a global score, the sum of all severity scores lesions (GM, quantitative measurement), and the presence or absence of OC on the fetlock (FM), hock (HM), and other sites (other). Data were analyzed using 2 mixed models including fixed effects, polygenic effects, and SNP or haplotype cluster effects. By combining results with both methods at moderate evidence of association threshold P < 5 × 10−5, this genome-wide association study displayed 1 region for GM on the Equus caballus chromosome (ECA) 13, 2 for HM on ECA 3 and 14, and 1 for other on ECA 15. One region on ECA 3 for HM represented the most significant hit (P = 3 × 10−6). By comparing QTL between traits at a decreased threshold (P < 5 × 10−4), the 4 QTL detected for GM were associated to a QTL detected for FM or HM but never both. Another interesting result was that no QTL were found in common between HM and FM.

Račkauskaitė Alma - One of the best experts on this subject based on the ideXlab platform.

  • A comparative analysis of French Trotters blood parameters
    Institutional Repository of Lithuanian University of Health Sciences, 2013
    Co-Authors: Račkauskaitė Alma
    Abstract:

    French Trotter come from crossed Norman horses, Thoroughbred, Haknio horses, American Trotters Breeding started about 1800 years. French Trotter become pupular horse breed in Lithuania, but the data about specific characteristics of this breed is almost nonexistent. So aim of study was to investigate the specific French Trotter blood morphological and biochemical properties, and comparison with literature about blood rates of Trotter. The study was carried out in October 2012. Blood samples were taken from horses kept in the X stud. For study was selected only clinically healthy horses. Total 20 of French Trotter horses were included in study, them age ranged from 2 to 10 years, 13 females and 7 males Trotters. Blood serum biochemical parameters (total protein, albumin, magnesium, calcium, creatinine, urea, alanine aminotransferase, aspartame aminotransferase) was used to measure specific chemical parameters of the device analyzes Hitachi 705 (Fig. 3)., use Diasyn reagents (Fig. 4). Test tubes with blood was first centrifuged for 15 min. 1500 rev. / Sec speeds, before blood test on this device. In the obtained results morphological blood parameters (WBC, RBC, HGB, HCT, MCV, MCH, MCHC, and PLT) was not deviations from the physiological rate. But by monitoring each parameter values were found devations from physiological rate. The results of blood biochemical parameters changed very little. After analysis of the literature and comparison with the results obtained during the investigation was noted the feeding have importance affect for blood parameters

Guerin Gérard - One of the best experts on this subject based on the ideXlab platform.

  • Recherche de gènes de prédisposition à des maladies génétiques équines (exemple de l'ostéochondrose)
    2005
    Co-Authors: Perrocheau, Maëlle Michèle Pierrette, Guerin Gérard
    Abstract:

    A strategy based on the analysis of an association between polymorphic microsatellites and osteochondrosis was chosen to identify osteochondrosis predisposition markers in horses. On the one hand, it requires a panel of horses with and without osteochondrosis and, on the other hand, it is necessary to produce a set of polymorphic microsatellites uniformly distributed on the equine genome and then to genotype these animals with these markers. Two hundred and seventy-three horse BAC clones were retrieved and gene identities were identified and were localized on the RH and cytogenetic maps. The equine RH and cytogenetic maps were enriched by 65% (167 genes) and 33% (120 genes), respectively and one hundred and one of the genes are localized on both maps. It has also led to the enrichment of the horse-human comparative map by 39% (186 gene localizations). At present, this map contains 670 genes and is composed of 58 homologous segments and 128 conserved segments. We have also shown that many equine chromosomes or chromosome regions have a conserved gene order when compared with that in man, whereas some regions have been rearranged. In parallel, a sample of more than 2100 French Trotter horses, affected or not by osteochondrosis were collected. The phenotype of these horses was defined by radiographic analysis of their feet, fetlocks, hocks and stifles performed by veterinaries. The incidence of osteochondrosis lesions (41%) and its heritability (0,18) were deduced. Blood samples could be obtained for 587 of these horses. These animals were born from 71 stallions and the average number of progeny per sire was seven. These 71 families include at least one progeny affected by osteochondrosis and one healthy progeny. The genotyping of these animals with microsatellites should lead to the identification of some chromosome regions, which might be associated with osteochondrosis predisposition in French Trotters.Afin de mettre en évidence les marqueurs de prédisposition à l'ostéochondrose chez le Cheval, une stratégie fondée sur une analyse d'association entre des séquences d'ADN polymorphes et le caractère ostéochondrose a été adoptée. Cette stratégie repose d'une part, sur la constitution d'un échantillon de chevaux sains et atteints d'ostéochondrose, d'autre part, sur la production d'un panel de marqueurs polymorphes répartis uniformément sur l'ensemble du génome équin puis le typage de ces animaux par ce panel de marqueurs. Dans ce but, les BAC correspondant à 273 gènes différents ont été identifiés et cherché à être localisés sur la carte d'hybrides d'irradiation et sur la carte cytogénétique. Ainsi, les cartes équines RH et cytogénétique ont été enrichies respectivement avec 167 (+65%) et 120 (+33%) gènes supplémentaires, 101 d'entre eux étant localisés simultanément sur les 2 cartes. D'autre part, ce travail a enrichi la carte comparée Homme-Cheval avec 186 localisations de gènes supplémentaires (+39%). Elle dénombre désormais 670 gènes et est constituée de 58 segments homologues au sein desquels figurent 128 segments conservés. On peut ainsi observer que certaines régions chromosomiques ou chromosomes équins sont fortement conservés par rapport à l'ordre des gènes sur les chromosomes homologues humains, alors que d'autres régions sont, au contraire, très remaniées. En parallèle, un échantillon de plus de 2100 chevaux de race Trotteur français, sains et atteints d'ostéochondrose a été constitué. Le phénotype de ces individus a été établi à partir de bilans radiographiques constitués d'un ensemble de clichés des pieds, boulets, jarrets et grassets, réalisés par des praticiens vétérinaires. Des paramètres génétiques des lésions d'ostéochondrose comme la prévalence (41%) et l'héritabilité (0,18) ont été estimés sur cet effectif de Trotteurs français. Des prélèvements sanguins pour 587 individus ont pu être recueillis. Ces chevaux appartiennent à 71 familles d'étalons différents, avec 7 descendants en moyenne par étalon parmi lesquels figurent au moins un individu sain et un atteint d'ostéochondrose. Le typage de ces familles ressources par des microsatellites devrait permettre d'identifier des régions chromosomiques impliquées dans la prédisposition à l'ostéochondrose chez le Trotteur françaisVERSAILLES-BU Sciences et IUT (786462101) / SudocSudocFranceF

Brard Sophie - One of the best experts on this subject based on the ideXlab platform.

  • Which theoretical and practical framework for the use of genomic selection in genetic evaluation of horses?
    2015
    Co-Authors: Brard Sophie
    Abstract:

    La sélection génomique substitue à la connaissance de la généalogie celle des séquences d’ADN et connait un succès spectaculaire dans la sélection des bovins laitiers. En équin, le gain de précision pour les valeurs génétiques en CSO a été estimé faible entre la généalogie et la génomique, éventuellement à cause des particularités des populations d’apprentissage et de validation. L’objectif est de définir pour les races équines les conditions d’efficacité et de fonctionnement de la sélection génomique. La partie théorique de la thèse a consisté en une méta-analyse afin de comprendre le lien entre précision théorique et observée en fonction des paramètres des populations. L’étude a montré l’importance du nombre efficace de marqueurs Me. Ce paramètre spécifique de la population, de la structure génomique et de la parenté doit être évalué, au même titre que l’héritabilité en génétique classique. D’un point de vue pratique, la 1ère voie d’amélioration était de rechercher des gènes à effet majeur sur l’aptitude au concours de saut d’obstacles (CSO) ou au concours complet. Aucun gène majeur n’a été localisé malgré des détections significatives. Le 2nd levier pour améliorer l’estimation des valeurs génétiques en CSO était d’utiliser le Single-Step, méthode qui combine l’information génomique des étalons génotypés et la généalogie de l’ensemble des chevaux non génotypés utilisés pour l’indexation. L’évaluation pour le CSO a donc été revisitée. Malgré le re-calcul de l’héritabilité et l’application des points sur toute la période, le gain en précision reste faible. La sélection génomique a également été testée sur des chevaux d’endurance, mais comme pour le CSO les précisions obtenues pour le moment ne sont pas assez élevées pour justifier une utilisation de la sélection génomique. Récemment, un gène majeur agissant sur l’aptitude à Trotter (DMRT3) a été identifié. Malgré l’effet très négatif d’un allèle sur la qualification et les performances précoces, le Trotteur français (TF) est polymorphe pour le gène à cause d’un effet positif de ce même allèle sur les performances tardives. La sélection classique et la sélection génomique ont été comparées en incluant ou non dans le modèle un marqueur lié à DMRT3, nous permettant d’identifier la meilleure combinaison de modèle et de méthode à utiliser pour estimer les valeurs génétiques du TF. Enfin, le paramètre Me a été estimé dans les populations de chevaux utilisées au cours de la thèse, et les résultats des évaluations génomiques ont été comparés en fonction de Me et des autres paramètres influant sur la précision de la sélection génomique. Deux nouveaux projets prévoyant de génotyper des chevaux de CSO d’une part et des TF d’autre part devraient permettre respectivement d’améliorer la précision de l’évaluation génomique en CSO et de confirmer l’intérêt de la prise en compte de DMRT3 dans l’évaluation génomique des TF.Genomic selection uses genotypes information instead of pedigree information for the estimation of breeding values. In dairy cattle, the selection schemes were greatly improved with this method. In horses, a first attempt of genomic selection showed that the evaluation accuracy was not much improved when using genotypes information compared to classic evaluation, possibly because of the structure of the reference and validation populations. The objective of the thesis was to define the theoretical and practical conditions for the use of genomic selection in horses. The theoretical work of the thesis consisted in a meta-analysis to understand the relation between observed and theoretical accuracy depending on the parameters of the population. We proved the importance of the effective number of independent segments in the genome Me. This parameter is specific of the population and of the genomic structure and relationship structure. We recommend to estimate this parameter before genomic evaluation, just like heritability that is estimated before genetic evaluation. Regarding practical tasks of the thesis, the first solution to improve the breeding values estimation for jumping performances was to look for genes having a major effect on performances in jumping competitions and three-day’s events, but no major gene was evidence in spite of significant detections. The 2nd solution was to perform a single-step evaluation. This method combines information from genotyped stallions and from the pedigree of the whole population. Even if the heritability was re-estimated and points distributed to all horses to have a homogeneous criteria, the accuracy of genomic evaluation was not much improved. Genomic selection was also tested on horses running endurance races, but as for jumping the accuracy was not high enough. Recently, a major gene having a huge effect on the ability of horses to trot was evidenced (DMRT3). Even if one allele has a negative effect on qualification and early earnings, French Trotter (FT) is still heterozygote because of a positive effect of this allele on late performances. Genetic and genomic evaluations were compared with or without using in the model a SNP linked to DMRT3 as a fixed effect. This study allowed identifying the best combination of model and method to use for estimation of FT breeding values. Finally, the parameter Me was estimated in the populations of horses used in the thesis. The results of genomic evaluations were compared according to Me and the other parameters having an influence on the accuracy of genomic evaluations. Two new projects will genotype more jumping horses and FT, they should allow to improve the accuracy of genomic evaluation for jumping horses and to acknowledge the interest of using DMRT3 in the genomic evaluation of FT

Perrocheau, Maëlle Michèle Pierrette - One of the best experts on this subject based on the ideXlab platform.

  • Recherche de gènes de prédisposition à des maladies génétiques équines (exemple de l'ostéochondrose)
    2005
    Co-Authors: Perrocheau, Maëlle Michèle Pierrette, Guerin Gérard
    Abstract:

    A strategy based on the analysis of an association between polymorphic microsatellites and osteochondrosis was chosen to identify osteochondrosis predisposition markers in horses. On the one hand, it requires a panel of horses with and without osteochondrosis and, on the other hand, it is necessary to produce a set of polymorphic microsatellites uniformly distributed on the equine genome and then to genotype these animals with these markers. Two hundred and seventy-three horse BAC clones were retrieved and gene identities were identified and were localized on the RH and cytogenetic maps. The equine RH and cytogenetic maps were enriched by 65% (167 genes) and 33% (120 genes), respectively and one hundred and one of the genes are localized on both maps. It has also led to the enrichment of the horse-human comparative map by 39% (186 gene localizations). At present, this map contains 670 genes and is composed of 58 homologous segments and 128 conserved segments. We have also shown that many equine chromosomes or chromosome regions have a conserved gene order when compared with that in man, whereas some regions have been rearranged. In parallel, a sample of more than 2100 French Trotter horses, affected or not by osteochondrosis were collected. The phenotype of these horses was defined by radiographic analysis of their feet, fetlocks, hocks and stifles performed by veterinaries. The incidence of osteochondrosis lesions (41%) and its heritability (0,18) were deduced. Blood samples could be obtained for 587 of these horses. These animals were born from 71 stallions and the average number of progeny per sire was seven. These 71 families include at least one progeny affected by osteochondrosis and one healthy progeny. The genotyping of these animals with microsatellites should lead to the identification of some chromosome regions, which might be associated with osteochondrosis predisposition in French Trotters.Afin de mettre en évidence les marqueurs de prédisposition à l'ostéochondrose chez le Cheval, une stratégie fondée sur une analyse d'association entre des séquences d'ADN polymorphes et le caractère ostéochondrose a été adoptée. Cette stratégie repose d'une part, sur la constitution d'un échantillon de chevaux sains et atteints d'ostéochondrose, d'autre part, sur la production d'un panel de marqueurs polymorphes répartis uniformément sur l'ensemble du génome équin puis le typage de ces animaux par ce panel de marqueurs. Dans ce but, les BAC correspondant à 273 gènes différents ont été identifiés et cherché à être localisés sur la carte d'hybrides d'irradiation et sur la carte cytogénétique. Ainsi, les cartes équines RH et cytogénétique ont été enrichies respectivement avec 167 (+65%) et 120 (+33%) gènes supplémentaires, 101 d'entre eux étant localisés simultanément sur les 2 cartes. D'autre part, ce travail a enrichi la carte comparée Homme-Cheval avec 186 localisations de gènes supplémentaires (+39%). Elle dénombre désormais 670 gènes et est constituée de 58 segments homologues au sein desquels figurent 128 segments conservés. On peut ainsi observer que certaines régions chromosomiques ou chromosomes équins sont fortement conservés par rapport à l'ordre des gènes sur les chromosomes homologues humains, alors que d'autres régions sont, au contraire, très remaniées. En parallèle, un échantillon de plus de 2100 chevaux de race Trotteur français, sains et atteints d'ostéochondrose a été constitué. Le phénotype de ces individus a été établi à partir de bilans radiographiques constitués d'un ensemble de clichés des pieds, boulets, jarrets et grassets, réalisés par des praticiens vétérinaires. Des paramètres génétiques des lésions d'ostéochondrose comme la prévalence (41%) et l'héritabilité (0,18) ont été estimés sur cet effectif de Trotteurs français. Des prélèvements sanguins pour 587 individus ont pu être recueillis. Ces chevaux appartiennent à 71 familles d'étalons différents, avec 7 descendants en moyenne par étalon parmi lesquels figurent au moins un individu sain et un atteint d'ostéochondrose. Le typage de ces familles ressources par des microsatellites devrait permettre d'identifier des régions chromosomiques impliquées dans la prédisposition à l'ostéochondrose chez le Trotteur françaisVERSAILLES-BU Sciences et IUT (786462101) / SudocSudocFranceF