Testing and characterization of herding dogs' behaviors.

Breeding for phenotype in herding dogs (HDs) mainly relies on their performance in national field trial competitions, which has been shown to be inadequate for identifying HDs suited for real livestock farming conditions. In this study, a different field trial with a new scoring system consisting of 28 items to consider was designed to assess young HDs, the results of which culminated in a statement of adequate phenotype (AP) or non-adequate phenotype (NAP). An AP HD was defined as being able: to control the direction of a flock, to keep it grouped close to a handler when needed, to confront animals it is dealing with in a respectful manner, and able to create movement of the flock without excessive disturbance, threatening or attacking it through chasing, or uncontrolled biting. This innovative trial is composed of a pre-test (PT) and a test (T) phase. To evaluate its efficiency in detecting AP/NAP, 460 French Border Collies aged between 8 and 24 mo, underwent the trial. Its average duration (PT + T) was 3 min and 16 s (SD = 26 s). According to experts' assessments (Gold Standard), 16.5% of tested HD reached an AP score, and the Idele scoring system correctly identified 93.3% of them (sensitivity). Specificity and accuracy values were of 96.1% and 95.7%, respectively (P value < 0.0004). Recursive feature elimination identified 25 of the 118 features (categories of items) from the scoring system as significant predictors of AP/NAP. An AP HD was statistically defined as a dog who completed the PT and T phases, showed keenness, correct position in relation to the handler, and absence of prey drive. Four environmental effects significantly influenced AP/NAP: the field trial session, the owner's experience with HDs, the conditions of the HD's first contact with livestock, and the type of livestock with which the HD is accustomed to working (P-values <0.0005, <0.05, <0.05, and <0.007, respectively). Inter-evaluator agreement was substantial (0.70). The field trial proved to be a short, easily implemented, standardized, reproducible method for detecting AP/NAP. Hence, the field trial and its scoring system could provide a basis for a breeding program based on phenotype pending additional testing of HDs and genetic analyses.

Herding dogs are extremely useful in handling all types of livestock. They are selectively bred for success in herding dog competitions, but the abilities which that to success in these are not always the same as those needed on a farm. To produce efficient herding dogs, other abilities therefore needed to be tested, via new trials. So, a new field trial, with a specific scoring system, was set up and tried out using 460 young French Border Collies, with the aim of correctly assessing herding dogs that would be fully adapted to French farmers' needs. This corresponded to an "Adequate Phenotype". A herding dog with an adequate phenotype was defined as being able: to control the direction of a flock, to keep it grouped close to the handler when needed, to confront the animals it is dealing with in a respectful manner, and able to create movement of the flock without excessive disturbance, threatening or attacking through chasing or uncontrolled biting. The new protocol was found efficient in detecting such herding dogs. Moreover, it was easy to set up, short, standardized, and reproducible.

Genetic consistency between gait analysis by accelerometry and evaluation scores at breeding shows for the selection of jumping competition horses.

The 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.

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.