Explore the vast range of titles available.

Background The Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of the study was to ascertain fine-scale population structures of the FM breed, including estimation of individual admixture levels and genomic inbreeding (F ROH ) by means of Runs of Homozygosity. Results To assess fine-scale population structures within the FM breed, we applied a three-step approach, which combined admixture, genetic contribution, and F ROH of individuals into a high-resolution network visualization. Based on this approach, we were able to demonstrate that population substructures, as detected by model-based clustering, can be either associated with a different genetic origin or with the progeny of most influential sires. Within the FM breed, admixed horses explained most of the genetic variance of the current breeding population, while OF horses only accounted for a small proportion of the variance. Furthermore, we illustrated that FM horses showed high TB admixture levels and we identified inconsistencies in the origin of FM horses descending from the Arabian stallion Doktryner. With the exception of WB, FM horses were less inbred compared to the other breeds. However, the relatively few but long ROH segments suggested diversity loss in both FM subpopulations. Genes located in FM- and OF-specific ROH islands had known functions involved in conformation and behaviour, two traits that are highly valued by breeders. Conclusions The FM remains the last native Swiss breed, clearly distinguishable from other historically introgressed breeds, but it suffered bottlenecks due to intensive selection of stallions, restrictive mating choices based on arbitrary definitions of pure breeding, and selection of rare coat colours. To preserve the genetic diversity of FM horses, future conservation managements strategies should involve a well-balanced selection of stallions (e.g., by integrating OF stallions in the FM breeding population) and avoid selection for rare coat colours.

he aim was to assess the efficiency of gaits characteristics in improving jumping performance of sport horses and confront accelerometers and judge scores for this purpose. A sample of 1,477 young jumping horses were measured using accelerometers for walk, trot, and canter. Of these, 702 were genotyped with 541,175 SNPs after quality control. Dataset of 26,914 horses scored by judges in breeding shows for gaits and dataset of 142,682 horses that performed in jumping competitions were used. Analysis of accelerometric data defined three principal components from 64% to 89% of variability explained for each gait. Animal mixed models were used to estimate genetic parameters with the inclusion to up 308,105 ancestors for the relationship matrix. Fixed effects for the accelerometric variables included velocity, gender, age, and event. A GWAS was performed on residuals with the fixed effect of each SNP. The GWAS did not reveal other QTLs for gait traits than the one related to the height at withers. The accelerometric principal components were highly heritable for the one linked to stride frequency and dorsoventral displacement at trot (0.53) and canter (0.41) and moderately for the one linked to longitudinal activities (0.33 for trot, 0.19 for canter). Low heritabilities were found for the walk traits. The genetic correlations of the accelerometric principal components with the jumping competition were essentially nil, except for a negative correlation with longitudinal activity at canter (-0.19). The genetic correlation between the judges' scores and the jumping competition reached 0.45 for canter (0.31 for trot and 0.17 for walk). But these correlations turned negative when the scores were corrected for the known parental breeding value for competition at the time of the judging. In conclusion, gait traits were not helpful to select for jumping performances. Different gaits may be suitable for a good jumping horse.

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.

This paper reports a quantitative genetics and genomic analysis of undesirable coat color patterns in goats. Two undesirable coat colors have routinely been recorded for the past 15 years in French Saanen goats. One fifth of Saanen females have been phenotyped \"pink\" (8.0%) or \"pink neck\" (11.5%) and consequently have not been included in the breeding program as elite animals. Heritability of the binary \"pink\" and \"pink neck\" phenotype, estimated from 103,443 females was 0.26 for \"pink\" and 0.21 for \"pink neck\". Genome wide association studies (using haplotypes or single SNPs) were implemented using a daughter design of 810 Saanen goats sired by 9 Artificial Insemination bucks genotyped with the goatSNP50 chip. A highly significant signal (-log10pvalue = 10.2) was associated with the \"pink neck\" phenotype on chromosome 11, suggesting the presence of a major gene. Highly significant signals for the \"pink\" phenotype were found on chromosomes 5 and 13 (-log10p values of 7.2 and, 7.7 respectively). The most significant SNP on chromosome 13 was in the ASIP gene region, well known for its association with coat color phenotypes. Nine significant signals were also found for both traits. The highest signal for each trait was detected by both single SNP and haplotype approaches, whereas the smaller signals were not consistently detected by the two methods. Altogether these results demonstrated a strong genetic control of the \"pink\" and \"pink neck\" phenotypes in French Saanen goats suggesting that SNP information could be used to identify and remove undesired colored animals from the breeding program.

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 (r g = − 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.

The following information is missing from the Funding section: PMM received a doctoral research grant from “Région Midi-Pyrénées”, Animal Genetics Department from INRA and GENOMCAP research program including INRA, APIS-GENE, ALLICE (formerly UNCEIA), CAPGENES and FCEL. 1. Martin PM, Palhière I, Ricard A, Tosser-Klopp G, Rupp R (2016) Genome Wide Association Study Identifies New Loci Associated with Undesired Coat Color Phenotypes in Saanen Goats.

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.

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.

Genomic evaluations often use as pseudo-phenotypes corrected means of progeny performances, like daughter yield deviations (DYD) in dairy species. In horse breeding, own performances are also available and performances from other relatives (as half sibs) may play an important part in the EBV because the number of progeny remains low, even for stallions. The first step for genomic selection in horses is therefore to generate pseudo-phenotypes for genomic analysis when parental or own information is considered. This work presents an easy method to compute deregressed EBV from regular pedigree-based genetic evaluations (EBV, reliabilities) to be used in genomic evaluations. The proposed methodology builds deregressed proofs so that they combine own performances (from genotyped individuals) and performances of relatives (outside of the genotyped sample). An application to show jumping horse data is presented. A sample of 908 stallions specialized in show jumping [71% Selle Français (SF), 17% foreign sport horses (FH), 13% Anglo Arab (AA)] were genotyped. Genotyping was performed using the Illumina Equine SNP50 BeadChip, and after quality tests, 44,444 SNP were retained. Two methods were used for genomic evaluation: GBLUP and BayesCπ, and 6 validation data sets were compared, chosen according to breeds SF + FH + AA or SF + FH, family structure (more than 3 half sibs), reliability of sires (>0.97) or sons (>0.72). In spite of a favorable genetic structure [linkage disequilibrium equal to 0.24 at 50 kb pairs], results showed low advantage of genomic evaluation. On the validation sample SF + FH + AA, the correlation between deregressed proofs and GBLUP or BayesCπ predictions was 0.39, 0.37, 0.51 according to the different validation data sets, compared with 0.36, 0.33, 0.53 obtained with BLUP predictions. Correlations were much lower on the SF + FH sample. Research is pursued to understand this low advantage of genomic selection and to improve the methodology for genomic evaluation in this context, which is less favorable than dairy cattle breeding.

The longevity of sport horses is an economic and ethical issue. The aim of this study was to analyze the duration of the competitive life of jumping horses in France to assess the potential for genetic evaluation and to propose rules of management for sport horses. Data included lifetimes spent in jumping competitions for the 209,296 horses born from 1968 onward with performances between 1972 and 2008; the data set contained 22% right-censored records. Longevity was measured in years. Discrete survival analysis included fixed effects of region of birth, month of birth, year of recording, age at first competition, interaction between sex and level of jumping performance as measured by the logarithm of earnings adjusted for sex, age, year, and random sire and maternal grand-sire effects. There were 16,668 sires and maternal grand-sires. All fixed effects were highly significant (P < 0.001). Management of the sports career had an important effect on longevity: against common belief, the younger the horse started competing, the longer it stayed in competition. For horses that started competing at an age of 6 yr, the risk of culling was 1.33-fold that of horses having started at 4 yr of age. The less success in competition, the greater was the chance for leaving competition, especially for horses without earnings. For a gelding without earnings, the risk of culling was 1.40-fold that of an average-performance gelding and 2.57-fold that of a top-rated gelding (performance at least 2 SD above the mean). Mares always had greater relative risk than geldings or stallions because they may be culled from competition to be used for breeding. The risk of culling for females was 1.45-fold that of a gelding with the same performance. The heritability of the length of competitive life was 0.10. Breeding values were predicted for sires, and 3,303 sires showed an accuracy greater than 0.60. Among these sires, 262 were used for breeding in 2008.