Population structure and genomic diversity of the Einsiedler horse.

The breeding history of the Einsiedler horse is closely connected with the Benedictine cloister Einsiedeln. In the mid-nineteenth century, it was decided to use European Warmblood stallions for cross-breeding and to abandon the selection of stallions. Since that time, it has only been possible to trace back the origin of Einsiedler horses using maternal ancestry information. Here, we collected high-density genotype data for European Warmblood horses (Selle Français, Swiss Warmblood and Einsiedler) and Franches-Montagnes horses, the last native Swiss horse breed, to unravel the current population structure of the Einsiedler horse. Using commonly applied methods to ascertain fine-scale population structures, it was not possible to clearly differentiate the Einsiedler from other European Warmblood horses. However, by means of runs of homozygosity (ROH) we were able to detect breed-specific ROH islands for the Einsiedler horse, including genes involved in domestication and adaptation to high altitude. Therefore, future breeding activities should involve the screening of these breed-specific ROH segments, the revival of cryopreserved sperm and the selection of Einsiedler stallions.

An improved transmissibility model to detect transgenerational transmitted environmental effects.

BACKGROUND: Evolutionary studies have reported that non-genetic information can be inherited across generations (epigenetic marks, microbiota, cultural inheritance). Non-genetic information is considered to be a key element to explain the adaptation of wild species to environmental constraints because it lies at the root of the transgenerational transmission of environmental effects. The "transmissibility model" was proposed several years ago to better predict the transmissible potential of each animal by taking these diverse sources of inheritance into account in a global transmissible potential. We propose to improve this model to account for the influence of the environment on the global transmissible potential as well. This extension of the transmissibility model is the "transmissibility model with environment" that considers a covariance between transmissibility samplings of animals sharing the same environment. The null hypothesis of "no transmitted environmental effect" can be tested by comparing the two models using a likelihood ratio test (LRT). RESULTS: We performed simulations that mimicked an experimental design consisting of two lines of animals with one exposed to a particular environment at a given generation. This enabled us to evaluate the performances of the transmissibility model with environment so as to detect and quantify transgenerational transmitted environmental effects. The power and the realized type I error of the LRT were compared to those of a T-test comparing the phenotype of the two lines, three generations after the environmental exposure for different sets of parameters. The power of the LRT ranged from 45 to 94%, whereas that of the T-test was always lower than 26%. In addition, the realized type I error of the T-test was 15% and that of the LRT was 5%, as expected. Variances, the covariance between transmissibility samplings, and path coefficients of transmission estimated with the transmissibility model with environment were close to their true values for all sets of parameters. CONCLUSIONS: The transmissibility model with environment is effective in modeling vertical transmission of environmental effects.

Genetic analysis of geometric morphometric 3D visuals of French jumping horses.

BACKGROUND: For centuries, morphology has been the most commonly selected trait in horses. A 3D video recording enabled us to obtain the coordinates of 43 anatomical landmarks of 2089 jumping horses. Generalized Procrustes analysis provided centered and scaled coordinates that were independent of volume, i.e., centroid size. Genetic analysis of these coordinates (mixed model; 17,994 horses in the pedigree) allowed us to estimate a variance-covariance matrix. New phenotypes were then defined: the "summarized shapes". They were obtained by linear combinations of Procrustes coordinates with, as coefficients, the eigenvectors of the genetic variance-covariance matrix. These new phenotypes were used in genome-wide association analyses (GWAS) and multitrait genetic analysis that included judges' scores and competition results of the horses. RESULTS: We defined ten shapes that represented 86% of the variance, with heritabilities ranging from 0.14 to 0.42. Only one of the shapes was found to be genetically correlated with competition success (rg = - 0.12, standard error = 0.07). Positive and negative genetic correlations between judges' scores and shapes were found. This means that the breeding objective defined by judges involves improvement of anatomical parts of the body that are negatively correlated with each other. Known single nucleotide polymorphisms (SNPs) on chromosomes 1 and 3 for height at withers were significant for centroid size but not for any of the shapes. As these SNPs were not associated with the shape that distinguished rectangular horses from square horses (with height at withers greater than body length), we hypothesize that these SNPs play a role in the overall development of horses, i.e. in height, width, and length but not in height at withers when standardized to unit centroid size. Several other SNPs were found significant for other shapes. CONCLUSIONS: The main application of 3D morphometric analysis is the ability to define the estimated breeding value (EBV) of a sire based on the shape of its potential progeny, which is easier for breeders to visualize in a single synthetic image than a full description based on linear profiling. However, the acceptance of these new phenotypes by breeders and the complex nature of summarized shapes may be challenging. Due to the low genetic correlations of the summarized shapes with jumping performance, the methodology did not allow indirect performance selection criteria to be defined.

Copula miss-specification in REML multivariate genetic animal model estimation.

BACKGROUND: In animal genetics, linear mixed models are used to deal with genetic and environmental effects. The variance and covariance terms of these models are usually estimated by restricted maximum likelihood (REML), which provides unbiased estimators. A strong hypothesis of REML estimation is the multi-normality of the response variables. However, in practice, even if the marginal distributions of each phenotype are normal, the multi-normality assumption may be violated by non-normality of the cross-sectional dependence structure, that is to say when the copula of the multivariate distribution is not Gaussian. This study uses simulations to evaluate the impact of copula miss-specification in a bivariate animal model on REML estimations of variance components. RESULT: Bivariate phenotypes were simulated for populations undergoing selection, considering different copulas for the dependence structure between the error components. Two multi-trait situations were considered: two phenotypes were measured on the selection candidates, or only one phenotype was measured on the selection candidates. Three generations with random selection and five generations with truncation selection based on estimated breeding values were simulated. When selection was performed at random, no significant differences were observed between the REML estimations of variance components and the true parameters even for the non-Gaussian distributions. For the truncation selections, when two phenotypes were measured on candidates, biases were systematically observed in the variance components for high residual dependence in the case of non-Gaussian distributions, especially in the case of a heavy-tailed or asymmetric distribution when the two traits were measured. Conversely, when only one phenotype was measured on candidates, no difference was observed between the Gaussian and non-Gaussian distributions in REML estimations. CONCLUSIONS: This study confirms that REML can be used by geneticists to evaluate breeding values in the multivariate case even if the multivariate phenotypes deviate from normality in the situation of random selection or if one trait is not measured for the candidate under selection. Nevertheless, when the two traits are measured, the violation of the normality assumption may lead to non-negligible biases in the REML estimations of the variance-covariance components.

Quality of breeding value predictions from longitudinal analyses, with application to residual feed intake in pigs.

BACKGROUND: An important goal in animal breeding is to improve longitudinal traits. The objective of this study was to explore for longitudinal residual feed intake (RFI) data, which estimated breeding value (EBV), or combination of EBV, to use in a breeding program. Linear combinations of EBV (summarized breeding values, SBV) or phenotypes (summarized phenotypes) derived from the eigenvectors of the genetic covariance matrix over time were considered, and the linear regression method (LR method) was used to facilitate the evaluation of their prediction accuracy. RESULTS: Weekly feed intake, average daily gain, metabolic body weight, and backfat thickness measured on 2435 growing French Large White pigs over a 10-week period were analysed using a random regression model. In this population, the 544 dams of the phenotyped animals were genotyped. These dams did not have own phenotypes. The quality of the predictions of SBV and breeding values from summarized phenotypes of these females was evaluated. On average, predictions of SBV at the time of selection were unbiased, slightly over-dispersed and less accurate than those obtained with additional phenotypic information. The use of genomic information did not improve the quality of predictions. The use of summarized instead of longitudinal phenotypes resulted in predictions of breeding values of similar quality. CONCLUSIONS: For practical selection on longitudinal data, the results obtained with this specific design suggest that the use of summarized phenotypes could facilitate routine genetic evaluation of longitudinal traits.

Equine vitiligo-like depigmentation in grey horses is related to genes involved in immune response and tumor metastasis.

BACKGROUND: In horses, the autoimmune disease vitiligo is characterized by the loss of melanocytes and results in patchy depigmentation of the skin around the eyes, muzzle and the perianal region. Vitiligo-like depigmentation occurs predominantly in horses displaying the grey coat colour and is observed at a prevalence level of 26.0-67.0% in grey horses compared with only 0.8-3.5% in non-grey horses. While the polygenetic background of this complex disease is well documented in humans, the underlying candidate genes for this skin disorder in horses remain unknown. In this study we aim to perform a genome-wide association study (GWAS) for identifying putative candidate loci for vitiligo-like depigmentation in horses. METHODS: In the current study, we performed a GWAS analysis using high-density 670 k single nucleotide polymorphism (SNP) data from 152 Lipizzan and 104 Noriker horses, which were phenotyped for vitiligo-like depigmentation by visual inspection. After quality control 376,219 SNPs remained for analyses, the genome-wide Bonferroni corrected significance level was p < 1.33e-7. RESULTS: We identified seven candidate genes on four chromosomes (ECA1, ECA13, ECA17, ECA20) putatively involved in vitiligo pathogenesis in grey horses. The highlighted genes PHF11, SETDB2, CARHSP1 and LITAFD, are associated with the innate immune system, while the genes RCBTB1, LITAFD, NUBPL, PTP4A1, play a role in tumor suppression and metastasis. The antagonistic pathogenesis of vitiligo in relation to cancer specific enhanced cell motility and/or metastasis on typical melanoma predilection sites underlines a plausible involvement of RCBTB1, LITAFD, NUBPL, and PTP4A1. CONCLUSIONS: The proposed candidate genes for equine vitiligo-like depigmentation, indicate an antagonistic relation between vitiligo and tumor metastasis in a horse population with higher incidence of melanoma. Further replication and expression studies should lead to a better understanding of this skin disorder in horses.

Genomic analysis of gaits and racing performance of the French trotter.

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.

Inclusive inheritance for residual feed intake in pigs and rabbits.

Non-genetic information (epigenetic, microbiota, behaviour) that results in different phenotypes in animals can be transmitted from one generation to the next and thus is potentially involved in the inheritance of traits. However, in livestock species, animals are selected based on genetic inheritance only. The objective of the present study was to determine whether non-genetic inherited effects play a role in the inheritance of residual feed intake (RFI) in two species: pigs and rabbits. If so, the path coefficients of the information transmitted from sire and dam to offspring would differ from the expected transmission factor of 0.5 that occurs if inherited information is of genetic origin only. Two pigs (pig1, pig2) and two rabbits (rabbit1, rabbit2) datasets were used in this study (1,603, 3,901, 5,213 and 4,584 records, respectively). The test of the path coefficients to 0.5 was performed for each dataset using likelihood ratio tests (null model: transmissibility model with both path coefficients equal to 0.5, full model: unconstrained transmissibility model). The path coefficients differed significantly from 0.5 for one of the pig datasets (pig2). Although not significant, we observed, as a general trend, that sire path coefficients of transmission were lower than dam path coefficients in three of the datasets (0.46 vs 0.53 for pig1, 0.39 vs 0.44 for pig2 and 0.38 vs 0.50 for rabbit1). These results suggest that phenomena other than genetic sources of inheritance explain the phenotypic resemblance between relatives for RFI, with a higher transmission from the dam's side than from the sire's side.

Population Networks Associated with Runs of Homozygosity Reveal New Insights into the Breeding History of the Haflinger Horse.

Within the scope of current genetic diversity analyses, population structure and homozygosity measures are independently analyzed and interpreted. To enhance analytical power, we combined the visualization of recently described high-resolution population networks with runs of homozygosity (ROH). In this study, we demonstrate that this approach enabled us to reveal important aspects of the breeding history of the Haflinger horse. We collected high-density genotype information of 531 horses originating from 7 populations which were involved in the formation of the Haflinger, namely 32 Italian Haflingers, 78 Austrian Haflingers, 190 Noriker, 23 Bosnian Mountain Horses, 20 Gidran, 33 Shagya Arabians, and 155 Purebred Arabians. Model-based cluster analysis identified substructures within Purebred Arabian, Haflinger, and Noriker that reflected distinct genealogy (Purebred Arabian), geographic origin (Haflinger), and coat color patterns (Noriker). Analysis of ROH revealed that the 2 Arabian populations (Purebred and Shagya Arabians), Gidran and the Bosnian Mountain Horse had the highest genome proportion covered by ROH segments (306-397 Mb). The Noriker and the Austrian Haflinger showed the lowest ROH coverage (228, 282 Mb). Our combined visualization approach made it feasible to clearly identify outbred (admixture) and inbred (ROH segments) horses. Genomic inbreeding coefficients (FROH) ranged from 10.1% (Noriker) to 17.7% (Purebred Arabian). Finally it could be demonstrated, that the Austrian Haflinger sample has a lack of longer ROH segments and a deviating ROH spectrum, which is associated with past bottleneck events and the recent mating strategy favoring out-crosses within the breed.

Genotype imputation accuracy in multiple equine breeds from medium- to high-density genotypes.

Genotype imputation is now a key component of genomic analyses as it increases the density of available genotypes within a population. However, many factors can influence imputation accuracy. The aim of this study was to assess and compare the accuracy of imputation of high-density genotypes (Affymetrix Axiom Equine genotyping array, 670,806 SNPs) from two moderate-density genotypes (Illumina Equine SNP50 BeadChip, 54,602 SNPs and Illumina Equine SNP70 BeadChip, 65,157 SNPs), using single-breed or multiple-breed reference sets. Genotypes were available from five groups of horse breeds: Arab (AR, 1,207 horses), Trotteur Français (TF, 979 horses), Selle Français (SF, 1,979 horses), Anglo-Arab (AA, 229 horses) and various foreign sport horses (FH, 209 horses). The proportions of horses genotyped with the high-density (HD) chip in each breed group were 10% in AA, 15% in AR and FH, 30% in TF and 57% in SF. A validation set consisting of one-third of the horses genotyped with the HD chip was formed and their genotypes deleted. Two imputation strategies were compared, one in which the reference population consisted only of horses from the same breed group as in the validation set, and another with horses from all breed groups. For the first strategy, concordance rates (CRs) ranged from 97.8% (AR) to 99.0% (TF) and correlations (r²) from 0.94 (AR) to 0.99 (TF). For the second strategy, CR ranged from 97.4% (AR) to 98.9% (TF) and r² from 0.93 (AR) to 0.99 (TF). Overall, the results show a small advantage of within-breed imputation compared with multi-breed imputation. Adding horses from different breed groups to the reference population does not improve the accuracy of imputation. Imputation provides an accurate means of combining data sets from different genotyping platforms, now necessary with the increasing use of the recently developed Affymetrix Axiom Equine genotyping array.

Does heterozygosity at the DMRT3 gene make French trotters better racers?

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 σy lower for CC than for TT. Genotype CT was also unfavorable for qualification (40%) and earnings at 3 years (-0.21 σy), but favorable for earnings at ages greater than 5 years: +0.41 σy (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.

A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species.

BACKGROUND: With dense genotyping, many choices exist for methods to detect quantitative trait loci (QTL) in livestock populations. However, no across-species study has been conducted on the performance of different methods using real data. We compared three methods that correct for relatedness either implicitly or explicitly: linkage and linkage disequilibrium haplotype-based analysis (LDLA), efficient mixed-model association (EMMA) analysis, and Bayesian whole-genome regression (BayesC). We analyzed one chromosome in each of five datasets (dairy cattle, beef cattle, sheep, horses, and pigs) using real genotypes based on dense single nucleotide polymorphisms and phenotypes. The P values corrected for multiple testing or Bayes factors greater than 150 were considered to be significant. To complete the real data study, we also simulated quantitative trait loci (QTL) for the same datasets based on the real genotypes. Several scenarios were chosen, with different QTL effects and linkage disequilibrium patterns. A pseudo-null statistical distribution was chosen to make the significance thresholds comparable across methods. RESULTS: For the real data, the three methods generally agreed within 1 or 2 cM for the locations of QTL regions and disagreed when no signals were significant (e.g. in pigs). For certain datasets, LDLA had more significant signals than EMMA or BayesC, but they were concentrated around the same peaks. Therefore, the three methods detected approximately the same number of QTL regions. For the simulated data, LDLA was slightly less powerful and accurate than either EMMA or BayesC but this depended strongly on how thresholds were set in the simulations. CONCLUSIONS: All three methods performed similarly for real and simulated data. No method was clearly superior across all datasets or for any particular dataset. For computational efficiency and ease of interpretation, EMMA is recommended, but using more than one method is suggested.

Surgical anatomy of the preauricular anteroparotid approach for mandibular condyle surgery.

PURPOSE: The different surgical approaches used to treat mandibular condyle fractures are carried out in the periparotid skin area and can lead to facial nerve injury. We conducted a preauricular and anteroparotid surgical approach. Our main aim was to show the anatomical relationship between this approach site and the facial nerve branches, and to define cutaneous landmarks to locate the extraparotid facial nerve branches. METHOD: A 2-step dissection of 13 fresh human cadaver semi-heads was performed: a preauricular approach followed by a superficial parotidectomy to visualize the facial nerve. Its course and ramifications were studied and compared to cutaneous landmarks. The proximity of the facial nerve branches with the surgical approach site was observed. RESULTS: The approach allowed systematically visualising the zygomatic and/or buccal branches. No facial nerve branches were sectioned. In three cases (23 %), a nerve branch was visualized during the approach. The buccal and zygomatic branches were ramified in 77 % of cases. CONCLUSIONS: During our preauricular anteroparotid approach, the buccal and zygomatic branches were visualized but none was sectioned. Most often the approach was carried out between these two branches (46 % of cases). Cutaneous landmarks used were reliable to define a safe and nerve-free area for dissection. The buccal and zygomatic branches are very interesting because their high number of ramifications and anastomoses could serve as nerve relays in case of surgical lesion.

Study of CCN3 (NOV) and DDR1 in normal melanocytes and vitiligo skin.

We have hypothesised that melanocytes disappear in vitiligo because they are weakly attached to the epidermal basal membrane (melanocytorrhagy). In the epidermis, attachment of melanocytes to collagen IV is mediated through DDR1, which is under the control of CCN3. DDR1 genetic variants have been associated with vitiligo in patients of different ethnic origin. In vitro studies have shown that inhibition of CCN3 induces the detachment of melanocytes. We have studied in parallel the expression of CCN3 and DDR1 in lesional and perilesional skin of patients with vitiligo and the impact of the silencing of CCN3 and DDR1 in normal human melanocytes on their behaviour in epidermal reconstructs. Our in vivo study provides evidence of a dysregulation of the DDR1-CCN3 interaction in vitiligo skin as melanocytes remaining in perilesional skin did not express CCN3. Expression of DDR1 was decreased in lesional versus perilesional vitiligo skin in the majority of patients, and the expression of collagen IV was found decreased in all patients. Silencing of CCN3 in melanocytes induced a significant inhibition of cell adhesion to collagen IV whereas melanocytes transduced with shDDR1 still adhered well on collagen IV and did not increase melanocyte loss in epidermal reconstructs as compared with normal melanocytes. Melanocyte detachment was observed but not in all reconstructs using CCN3 silenced melanocytes. Overall, our study confirms that a downregulation of CCN3 is implicated in melanocyte adhesion in part through DDR1. In vitiligo skin, the interaction of CCN3 with other molecules, such as TGFß and CCN2, needs to be addressed.

Statistical distributions of test statistics used for quantitative trait association mapping in structured populations.

BACKGROUND: Spurious associations between single nucleotide polymorphisms and phenotypes are a major issue in genome-wide association studies and have led to underestimation of type 1 error rate and overestimation of the number of quantitative trait loci found. Many authors have investigated the influence of population structure on the robustness of methods by simulation. This paper is aimed at developing further the algebraic formalization of power and type 1 error rate for some of the classical statistical methods used: simple regression, two approximate methods of mixed models involving the effect of a single nucleotide polymorphism (SNP) and a random polygenic effect (GRAMMAR and FASTA) and the transmission/disequilibrium test for quantitative traits and nuclear families. Analytical formulae were derived using matrix algebra for the first and second moments of the statistical tests, assuming a true mixed model with a polygenic effect and SNP effects. RESULTS: The expectation and variance of the test statistics and their marginal expectations and variances according to the distribution of genotypes and estimators of variance components are given as a function of the relationship matrix and of the heritability of the polygenic effect. These formulae were used to compute type 1 error rate and power for any kind of relationship matrix between phenotyped and genotyped individuals for any level of heritability. For the regression method, type 1 error rate increased with the variability of relationships and with heritability, but decreased with the GRAMMAR method and was not affected with the FASTA and quantitative transmission/disequilibrium test methods. CONCLUSIONS: The formulae can be easily used to provide the correct threshold of type 1 error rate and to calculate the power when designing experiments or data collection protocols. The results concerning the efficacy of each method agree with simulation results in the literature but were generalized in this work. The power of the GRAMMAR method was equal to the power of the FASTA method at the same type 1 error rate. The power of the quantitative transmission/disequilibrium test was low. In conclusion, the FASTA method, which is very close to the full mixed model, is recommended in association mapping studies.

DPF3, A Putative Candidate Gene For Melanoma Etiopathogenesis in Gray Horses.

Melanoma prevalence in gray horses reaches up to 50% and more. Several studies have documented a genetic melanoma predisposition which is referred to the 4.6 kb duplication in intron 6 of STX17 and its surrounding haplotype. However, the genetic background and mechanisms responsible for differences in etiopathogenesis of equine dermal melanomatosis still remain unknown. In the current study, we performed a genome wide association analysis in 141 Lipizzan horses and subsequently identified one candidate gene on chromosome 24 putatively involved in melanoma pathogenesis in gray horses. The associated SNP was located in the intronic region of DPF3, a gene which is involved in humans in cell growth, proliferation, apoptosis and motility of cancer cells. The replication study in 1210 horses from seven breeds demonstrated, that the G/G genotype of the DPF3 associated SNP exhibits putative melanoma suppression effects. As a conclusion DPF3 represents a candidate gene, which might play an essential role for gray horses coping with high genetic melanoma related tumor load.

Genomic Correlations Between the Gaits of Young Horses Measured by Accelerometry and Functional Longevity in Jumping Competition.

Functional longevity is essential for the well-being of horses and the satisfaction of riders. Conventional selection using longevity breeding values calculated from competition results is not efficient because it takes too long to obtain reliable information. Therefore, the objective was to identify early criteria for selection. We assessed two types of early criteria: gait traits of young horses and QTLs. Thus, our aim was to estimate the genetic correlation between gait traits and longevity and to perform a genome-wide association study (GWAS) for longevity. Measurements of gaits by accelerometry were recorded on 1,477 show jumping horses that were 4 to 5 years old. Gait analysis provided 9 principal components describing trot, canter, and walk. Longevity estimated breeding values (EBVs) for stallions were calculated using a survival analysis of more than 900,000 years of performances by 179,448 show jumping horses born from 1981 onwards. Longevity was measured as the number of years spent in competition. Model included region and month of birth, age at first competition, year, and performance level. Longevity EBVs were deregressed to obtain weighted pseudo-performances for 1,968 stallions. Genomic data were available for 3,658 jumping horses. Seventy-eight percent of the horses measured for gaits and twenty-five percent of those measured for longevity were genotyped. A GWAS of longevity revealed no significant QTLs. Genetic parameters between each of the 9 principal components of the gait variables and longevity were evaluated with a bi-trait animal linear mixed model using single-step GBLUP analysis with the relationship matrix constructed from genomic data and genealogy (24,448 ancestors over four generations). The heritability of the gait traits varied from 0.11 to 0.44. The third principal component for trot (high lateral activity) and the first principal component for canter (high dorsoventral activity and low stride frequency) were moderately genetically correlated with higher longevity: rg = 0.38 (0.15) and 0.28 (0.13), respectively. Our study revealed that functional longevity is a polygenic trait with no major genes. We found new correlations between longevity and gait traits. Before using gait characteristics in a selection plan, these correlations need to be understood better at the biomechanical level.

Validation of models for analysis of ranks in horse breeding evaluation.

BACKGROUND: Ranks have been used as phenotypes in the genetic evaluation of horses for a long time through the use of earnings, normal score or raw ranks. A model, ("underlying model" of an unobservable underlying variable responsible for ranks) exists. Recently, a full Bayesian analysis using this model was developed. In addition, in reality, competitions are structured into categories according to the technical level of difficulty linked to the technical ability of horses (horses considered to be the "best" meet their peers). The aim of this article was to validate the underlying model through simulations and to propose a more appropriate model with a mixture distribution of horses in the case of a structured competition. The simulations involved 1000 horses with 10 to 50 performances per horse and 4 to 20 horses per event with unstructured and structured competitions. RESULTS: The underlying model responsible for ranks performed well with unstructured competitions by drawing liabilities in the Gibbs sampler according to the following rule: the liability of each horse must be drawn in the interval formed by the liabilities of horses ranked before and after the particular horse. The estimated repeatability was the simulated one (0.25) and regression between estimated competing ability of horses and true ability was close to 1. Underestimations of repeatability (0.07 to 0.22) were obtained with other traditional criteria (normal score or raw ranks), but in the case of a structured competition, repeatability was underestimated (0.18 to 0.22). Our results show that the effect of an event, or category of event, is irrelevant in such a situation because ranks are independent of such an effect. The proposed mixture model pools horses according to their participation in different categories of competition during the period observed. This last model gave better results (repeatability 0.25), in particular, it provided an improved estimation of average values of competing ability of the horses in the different categories of events. CONCLUSIONS: The underlying model was validated. A correct drawing of liabilities for the Gibbs sampler was provided. For a structured competition, the mixture model with a group effect assigned to horses gave the best results.

On two equations about brain volume, cranial capacity and age.

AIM: We decided to study the relationship between brain volume and cranial capacity and the relationship between brain volume and age on a series of CT from healthy adults. METHODS: Fifty-eight healthy volunteers (27 women, 31 men, age range 18-95 years) were examined using our imaging protocols. The volunteers had no present or past neuropsychiatric illness and no abuse of alcohol or illicit drugs. RESULTS: Mean intracranial volume was 1,384.6 cm(3) (standard deviation = 135.27, range 1,106-1,656) and mean brain volume was 1,201.0 cm(3) (standard deviation = 142.52, range 791-1,500). Linear regression between brain volume and cranial capacity yielded this formula: brain volume = 182.3 + 0.7 × cranial capacity. Multivariate analysis yielded a relationship between cranial capacity, brain volume and age as follows: brain volume = 396.5-3.5 × age + 0.7 × cranial capacity. CONCLUSION: This study could be supplemented by the collection of data such as, the size of the individuals in order to study the relationship between size of the brain and stature because this relation remains unclear.

Accelerometers Provide Early Genetic Selection Criteria for Jumping Horses.

The aim of this study was to evaluate the genetic component of the locomotor jumping ability, via a wearable accelerometer sensor, and to estimate the genetic correlation with performance in competition, to introduce such criteria in selection schema. A sample of 1,056 young 3-year-old horses were equipped with a 3-dimensional accelerometer during a free jumping test, in regular breeding shows from 2015 to 2017. Seven variables were extracted from the dorso-ventral acceleration curve for the last three jumps over a double bar obstacle of 1.15 m for the front pole and 1.20 m for the back pole with a 1.20 m spread. Variables were the peaks of forelimbs, hindlimbs, and landing acceleration, the duration between peaks at take-off, the peak of forelimb acceleration and start of jump, jump duration and duration between the beginning of the impact of forelimbs and the peak at landing. During breeding shows, judges scored balance, strength, style, and reactivity for free jumping and jumping tests under saddle. Jumping competition results were recorded by logarithm of the sum of points earned in each competition. All horses in official competitions were included, i.e., 160,257 horses born in 1997 with a total of 649,491 annual performances. An animal mixed model with complete pedigree over four generations (353,236 horses) were used with fixed effects of jumping test location and date, morning/afternoon, gender, month of birth, rank of jump for accelerometric data, effect of year of competition, combined with age and gender for competition results. As a result, jump duration was the most heritable and repeatable for jump variables: h 2 = 0.16 (0.06), r = 0.52 (0.02), while accelerations were moderately heritable (h 2 = 0.05-0.09, r = 0.39-0.51). Judgement scores were heritable: 0.21 (0.07)-0.33 (0.09) and were highly correlated. Scores during free jumping were genetically correlated to jump duration: 0.71 (0.15)-0.88 (0.16). Both jump duration and judgement scores were genetically correlated to competition performance: 0.59 (0.13) for jump duration, from 0.60 (0.11) to 0.77 (0.12) for scores. Jump duration and judgement scores can be used as early selection criteria. The advantage of the accelerometric measurement is its objectivity and the ease of recording.