Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse

Background: Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou’s ancestral, Kalinowski’s ancestral, Kalinowski’s new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability. Results: The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated. Conclusions: Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.Fil: Perdomo González, Davinia Isabel. Universidad de Sevilla; EspañaFil: Laseca, Nora. Universidad de Córdoba; EspañaFil: Demyda-peyrás, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias; ArgentinaFil: Valera, Mercedes. Universidad de Sevilla; EspañaFil: Cervantes, Isabel. Universidad Complutense de Madrid; EspañaFil: Molina, Antonio. Universidad de Córdoba; Españ

Testing eye temperature assessed with infrared thermography to evaluate stress in meat goats raised in a semi-intensive farming system: A pilot study

The Blanca Serrana goat is selected for meat production and usually raised in an extensive farm system. The meat goat industry is getting bigger in Spain, evolving to more intensive farming systems. The negative influence of stress produced by daily management on animal welfare is even bigger in these animals as they are not used to getting so close to humans. Eye temperature has recently appeared as an appropriate and noninvasive tool for welfare assessment in cattle, but no previous studies have been developed in goats. Thus, the main aim of this pilot study was to test eye temperature as a noninvasive tool to explore stress levels associated with a semi-intensive farming system for meat goats in comparison with the standard measurements of stress. For that, 24 Blanca Serrana goats were used. Heart rate (HR), respiratory rate (RR) and eye temperature (ET), assessed with infrared thermography samples, were collected just before and just after a stressful situation created to check how the routine management of semi-intensive farming systems affected this species. A factorial ANOVA, least square means and Scheffe post hoc comparison analyses found statistically significant differences due to the stress test moment for RR (p<0:05) and ET (p<0:001) with higher values shown after the stress test than before it. Differences due to age were found just for HR (p<0:05) and RR (p<0:01) stress parameters, with kids showing higher results than adults. Pearson correlations between HR, RR and ET parameters showed a medium-high positive correlation of 0.56 between RR and ET. Thus, ET appears as an appropriate and noninvasive tool to explore stress levels associated with a semiintensive farming system for meat goats.Fil: Bartolomé Medina, Ester. Universidad de Sevilla; EspañaFil: Azcona, Florencia. Universidad de Córdoba; España. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Cañete Aranda, María. Universidad de Córdoba; EspañaFil: Perdomo González, Davinia Isabel. Universidad de Córdoba; EspañaFil: Ribes Pons, Joana. Universidad de Córdoba; EspañaFil: Teran, Ester Mercedes. Universidad de Córdoba; España. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Orthopedic Diseases in the Pura Raza Española Horse: The Prevalence and Genetic Parameters of Angular Hoof Deviations

Abnormalities in hoof shape are usually connected with limb conformation defects. The role of angular hoof deviations is important for longevity in sports competitions and is increasingly recognized as a factor associated with lameness in performance horses. In this paper, we measured the prevalence of four defects related to the angulation of the hoof in the Pura Raza Española horse (PRE): splay-footed forelimb (SFF), pigeon-toed forelimb (PTF), splay-footed rear limb (SFR), and pigeon-toed rear limb (PTR). A total of 51,134 animals were studied, of which only 15.75% did not have any of the four angular hoof defects investigated, while 26.61%, 23.76%, 79.53%, and 3.86% presented SFF, PTF, SFR, and PTR, respectively. Angular defects were evaluated using two different models; model A was a linear scale composed of three categories, where 0 corresponded to the absence of defects, 1 to a minor presence of the defect and 2 to the highest degree of the defect. Model B was composed of two categories, where 0 corresponded to the absence of defects and 1 to the presence of defects, joining classes 1 and 2. We measured the factors influencing the appearance of these defects: age, inbreeding coefficient, sex, and birth stud size. The heritability of each defect was also estimated using a multivariate animal model, using the Gibbsf90+ software from the BLUPF90 family, resulting in heritability estimates of 0.18 (s.d. = 0.009), 0.20 (s.d. = 0.010), 0.11 (s.d. = 0.009), and 0.31 (s.d. = 0.010) for SFF, PTF, SFR, and PTR defects, respectively, for model A, and 0.17 (s.d. = 0.008), 0.19 (s.d. = 0.009), 0.11 (s.d. = 0.009), and 0.29 (s.d. = 0.009) for SFF, PTF, SFR, and PTR defects, respectively, for model B. Finally, the genetic correlation between the diameter of the superficial digital flexor tendon (SDFT) and the proportionality index (PI) in relation to the higher or lower prevalence of the defects was analyzed. We concluded that diameter of SDFT development is strongly correlated with inward toe conditions (PTF, PTR; P≠0 ≥ 0.95), while PI is associated with outward toe defects (SFF, SFR; P≠0 ≥ 0.95)

Evaluation of potential effects and genetic parameters in conformational limb defects in Pura Raza Española horses

Morphological limbs defects are the most frequent defects in horses. The aim of this study was to establish the prevalence, associated effects and genetic parameters of hock and knee defects in Pura Raza Española horses, using two different approaches. In Approach_1, the hock defects analysed were closed, open, convergent and divergent and the knee defects studied were buck, calf, bench and knock. Defects were classified into 3 levels: 0 no defect, 1 slight defect and 2 serious defects. Approach_2, which used a linear scale, in a pair of opposing defects, divided into 5 levels, from −2 to 2, where 0 corresponded to the absence of defects: Lateral view (closed/open) and rear view (convergent/divergent) hock defect, lateral view (buck/calf) and frontal view (bench/knock) knee defect. A total of 43,358 horses, with an average age of 5.07 years, were evaluated, with a prevalence of horses affected ranging from 3.31% (bench) to 74.12% (convergent). Genetic parameters were estimated using a Bayesian procedure with the BLUPF90 software. Heritability in Approach_1, ranged from 0.25 (bench) to 0.42 (divergent) and in Approach_2, from 0.18 (bench/knock) to 0.24 (convergent/divergent). The opposing defects may be related to different genes, and it is therefore better to study them as separate defects and not on the same linear scale. The highest positive genetic correlation was between calf vs knock (0.70). Our results imply that selection against limb defects is possible and would allow us to reduce the genetic risk of the horses’ offspring suffering from them.Highlights There high prevalence of hock and knee defects in PRE horses make the animals unsuitable for sport and cause a significant economic loss to the breeding herds. The evaluation of limb defects independently instead of the traditional linear scale, where the opposite defects are located at the extremes, has good results for its genetic evaluation. Using the hock and knee defects as a selection criteria in the PRE' s breeding program could contribute to the eradication of major conformation defects which make the animals unsuitable for sport

The Relevance of the Expected Value of the Proportion of Arabian Genes in Genetic Evaluations for Eventing Competitions

The Arabian horse is a generally reliable sport horse, and continues to be a remarkable endurance horse, so the relevance of the expected value of the proportion of Arabian genes (EV%AG) in horses participating in eventing could be a relevant factor. A total of 1089 horses participating in eventing (8866 records) were used. A GLM revealed that the EV%AG was significant in dressage, show jumping and cross-country. A BLUP genetic evaluation was computed with five genetic models (without the EV%AG (0) using as a covariate (A), as a fixed effect (B), with variance heterogeneity, and in genetic groups without (C) and with (D)). Dressage heritability ranged from 0.103 to 0.210, show jumping ranged from 0.117 to 0.203 and cross-country ranged from 0.070 to 0.099. The lowest DIC value was used as a criterion of fitness. The best fits (those which included variance heterogeneity) showed fewer than two points of difference in DIC values. The highest average estimated breeding value in dressage, show jumping and cross-country was found for horses with an expected value of the proportion of Arabian genes of 0%, ≥1% to <25%, and 100%, respectively. Therefore, the best way to model the EV%AG effect seems to be by considering the variance heterogeneity

Genetic Parameters of Effort and Recovery in Sport Horses Assessed with Infrared Thermography

The way a horse activates (effort phase-EP) and recovers (recovery phase-RP) during a sport event can affect its sport performance. The aim of this manuscript was to test horses’ adaptation to sport performance and its genetic basis, using eye temperature assessed with infrared thermography. EP and RP were measured in 495 Spanish Sport Horses, during a performance test, considering sex (2) and genetic lines (5) as fixed effects. The ranking position obtained on an official sport competition was also collected. Differences in variables due to genetic line and sex effects were found, showing that, regardless of the genetic line, stallions tended to recover better than mares after the sport test developed. High positive intra-class correlations (p < 0.001) were found between EP and RP for both fixed effects, so that the higher the EP, the higher the RP. However, for the ranking position, a low negative correlation (p < 0.01) was found, so that the higher the eye temperature increase, the better the position. Heritabilities showed medium–high values with a medium positive genetic correlation between them. Thus, breed origins and sex influence horses’ effort and recovery during sport performance, showing a genetic basis adequate for selection

A genome-wide association study of mare fertility in the Pura Raza Español horse

Despite the economic importance of fertility for the horse industry, few efforts have been made to achieve a better understanding of the genetic mechanisms underlying its control. This is probably due to the difficulty of obtaining reliable phenotypes and the complexity of modelling the environmental and management factors. This work is novel in that we propose to use reproductive efficiency (RE) as an indicator of mare fertility. To achieve this, we performed a genome-wide association study in the Pura Raza Español horse aimed at identifying genomic variants, regions, and candidate genes associated with fertility in mares. The dataset included 819 animals genotyped with the Affymetrix Axiom™ Equine 670 K single-nucleotide polymorphisms (SNPs) Genotyping Array and the deregressed breeding values for RE trait, obtained using a ssBLUP model, employed as pseudo-phenotypic data. Our results showed 28 SNPs potentially associated with RE, which explained 87.19% of the genetic variance and 6.61% of the phenotypic variance. Those results were further validated in BayesB, showing a correlation between observed and predicted RE of 0.57. In addition, 15 candidate genes (HTRA3, SPIRE1, APOE, ERCC1, FOXA3, NECTIN-2, KLC3, RSPH6A, PDPK1, MEIOB, PAQR4, NM3, PKD1, PRSS21, IFT140) previously related to fertility in mammals were associated with the markers and genomic regions significantly associated with RE. To our knowledge, this is the first genome-wide association study performed on mare fertility.Fil: Laseca, Nora. Universidad de Córdoba; EspañaFil: Demyda Peyrás, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Valera Córdoba, Mercedes. Universidad de Sevilla; EspañaFil: Ramón, Manuel. Centro Regional de Selección y Reproducción Animal; EspañaFil: Escribano, Begoña María. Universidad de Córdoba; EspañaFil: Perdomo González, Davinia Isabel. Universidad de Sevilla; EspañaFil: Molina, Antonio José. Universidad de Córdoba; Españ