Relationship between morphology and performance: Signature of mass-selection in Pura Raza Español horse

Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes

BACKGROUND

Body conformation, including withers height, is a major selection criterion in horse breeding and is associated with other important traits, such as health and performance. However, little is known about the genomic background of equine conformation. Therefore, the aim of this study was to use imputed sequence-level genotypes from up to 4891 German Warmblood horses to identify genomic regions associated with withers height and linear conformation traits. Furthermore, the traits were genetically characterised and putative causal variants for withers height were detected.

RESULTS

A genome-wide association study (GWAS) for withers height confirmed the presence of a previously known quantitative trait locus (QTL) on Equus caballus (ECA) chromosome 3 close to the LCORL/NCAPG locus, which explained 16% of the phenotypic variance for withers height. An additional significant association signal was detected on ECA1. Further investigations of the region on ECA3 identified a few promising candidate causal variants for withers height, including a nonsense mutation in the coding sequence of the LCORL gene. The estimated heritability for withers height was 0.53 and ranged from 0 to 0.34 for the conformation traits. GWAS identified significantly associated variants for more than half of the investigated conformation traits, among which 13 showed a peak on ECA3 in the same region as withers height. Genetic parameter estimation revealed high genetic correlations between these traits and withers height for the QTL on ECA3.

CONCLUSIONS

The use of imputed sequence-level genotypes from a large study cohort led to the discovery of novel QTL associated with conformation traits in German Warmblood horses. The results indicate the high relevance of the QTL on ECA3 for various conformation traits, including withers height, and contribute to deciphering causal mutations for body size in horses.

Designing an early selection morphological traits index for reproductive efficiency in Pura Raza Española mares

The low rate of reproductive efficiency in horses may be linked to the equine industry's practice of maintaining breeding stock that stands out for its athletic or morphological performance but exhibits poor reproductive efficiency. In this study, the age at first foaling, age at last foaling, interval between first and second foaling, average interval between foaling, foaling number and reproductive efficiency, and their relationship with the morphological records in 19,758 Pura Raza Española (PRE) mares were analyzed. After a partial least squares analysis height at withers, lateral hock angle, dorsal-sternal diameter, perimeter of anterior cannon bone, angle of shoulder, thoracic perimeter, hip-stifle distance, and angle of croup were the most important traits related with reproductive traits in PRE mares. A multivariate animal model with both morphological and reproductive traits was applied, including age, geographical area, coat color, and average stud size in the decade of the mare's first foaling. The results indicate that reproductive selection is feasible, and is enhanced by the use of morphological traits, given the moderate to high magnitudes of heritability values in both types of traits, which oscillated between 0.1 (interval between first and second foaling) and 0.95 (height at withers). The resulting genetic parameters were used to develop a series of selection indexes based on morphological or morphological and reproductive combination traits to improve reproductive efficiency traits in PRE mares and thus compute the expected genetic response (EGR) for the different strategies. The increase in EGR, when comparing EGR using only reproductive traits as selection criteria vs. using a combined index of both morphological and reproductive traits, oscillated between 4.0% for the age at first foaling to 46.8% for the interval between first and second foaling. In addition, two precocity indexes showed positive EGR when the age at last foaling and the interval between first and second foaling, both with and without morphological traits, were used as selection criteria. Therefore, this analysis reveals that the preselection of reproductive traits based on morphological traits is possible in PRE mares. Ultimately, this knowledge will help breeders achieve genetic progress in reproductive traits, leading to healthier and more successful breeding outcomes in horses.

Quantitative analysis of parent-of-origin effect in reproductive and morphological selection criteria in the Pura Raza Española horse

It is generally assumed that parents make a genetically equal contribution to their offspring, but this assumption might not always hold. This is because the expression of a gene can be blocked by methylation during gametogenesis, and the degree of methylation can depend on the origin of the parental gene (imprinting) or by preferential management associated with genetic merit. The first consequences of this for quantitative genetics is that the mean phenotypes of reciprocal heterozygotes need no longer be the same, as would be expected according to Mendelian heritage. We analysed three mare reproductive traits (reproductive efficiency, age at first foaling and foaling number) and three morphological traits (height at withers, thoracic circumference, and scapula-ischial length) in the Pura Raza Española (PRE) horse population, which possesses a deep and reliable pedigree, making it a perfect breed for analysing the quantitative effect of parent-of-origin. The number of animals analysed ranged from 44,038 to 144,191, all of them with both parents known. The model comparison between a model without parent-of-origin effects and three different models with parent-of-origin effects revealed that both maternal and paternal gametic effects influence all the analysed traits. The maternal gametic effect had a higher influence on most traits, accounting for between 3% and 11% of the total phenotypic variance, while the paternal gametic effect accounted for a higher proportion of variance in one trait, age at first foaling (4%). As expected, the Pearson's correlations between additive breeding values of models that consider parent-of-origin and that do not consider parent-of-origin were very high; however, the percentage of coincident animals slightly decreases when comparing animals with the highest estimated breeding values. Ultimately, this work demonstrates that parent-of-origin effects exist in horse gene transmission from a quantitative point of view. Additionally, including an estimate of the parent-of-origin effect within the PRE horse breeding program could be a great tool for a better parent's selection and that could be of interest for breeders, as this value will determine whether the animals acquire genetic categories and are much more highly valued.

Phenotypic and Genetic Study of the Presence of Hair Whorls in Pura Raza Español Horses

Hair whorls are a hereditary feature in horses that may be associated with temperament and coat color. Hair whorls are described as changes in the hair pattern and may take various forms, such as circular and linear whorls. We first carried out a frequency analysis of hair whorls (circular and linear). Next, a Generalized Non-Linear Model was computed to assess the significance of some potential influencing factors, and a genetic parameter estimation was performed. ENDOG software v4.8 was used to estimate the inbreeding coefficient of all the animals analyzed. It was more common to find horses with circular hair whorls than with linear whorls. The heritability ranges obtained were, in general, medium-high for both circular whorls (0.20 to 0.90) and linear whorls (0.44 to 0.84). High positive correlations were found on the between left and right positions, indicating a tendency to symmetry in certain locations. The laterality of hair whorls was also evidenced, with the biggest concentration on the left-hand side, particularly in gray horses, showing circular whorls below the central line of eyes, which has been associated in a previous paper with a calmer and more docile temperament.

Comparison of American Quarter Horses Competing in Western Pleasure, Hunter under Saddle, and Reining Using Linear Traits

Simple Summary

This study analyzed differences between successful American Quarter Horses competing in different disciplines by using linear traits. The goal was to detect whether American Quarter Horses successful in specific disciplines significantly differed in exterior traits. Traits were measured analogically and photometrically. Differences in lengths, angles, ratios, and circumferences were detected. Further studies are needed to better examine the specialized traits and the effect of genomic variance.

Abstract

To investigate differences in American Quarter Horses conformation suggesting specialization and subpopulations within the breed, a total of 45 horses were studied. These horses were classified according to their specific sport discipline: Western Pleasure (WPL, n = 15), Hunter under Saddle (HUS, n = 15), and Reining (RN, n = 15). Fifteen linear traits (comprising lengths, angles, and circumferences) were measured analogically and photometrically. Afterwards, 9 ratios and differences were calculated, so that a total of 24 traits were examined. The results showed significant differences between horses depending on their sport discipline. HUS horses were significant taller and were characterized by higher values in (nearly) all length traits; they were followed by WPL and RN horses. RN horses displayed the lowest values in length traits but the largest difference between height at withers and height at croup. Nine parameters were analyzed through correlations to the height at withers; all differences were significant, with high to moderate correlation coefficients. The detected differences between the groups support recent studies on the conformation and genotype of subpopulations within a breed and reveal new findings in relation to the selected disciplines. Image analysis worked well and provided reliable data; therefore, this method can be used to examine horses in a time-efficient manner, reducing the stress caused to the animal. Further studies are required to gain more information and to associate the features of AQH anatomic structures with successful performance.

A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses

BACKGROUND

The back plays a vital role in horse locomotion, where the spine functions as a spring during the stride cycle. A complex interaction between the spine and the muscles of the back contribute to locomotion soundness, gait ability, and performance of riding and racehorses. Conformation is commonly used to select horses for breeding and performance in multiple horse breeds, where the back and croup conformation plays a significant role. The conformation of back and croup plays an important role on riding ability in Icelandic horses. However, the genes behind this trait are still unknown. Therefore, the aim of this study was to identify genomic regions associated with conformation of back and croup in Icelandic horses and to investigate their effects on riding ability. One hundred seventy-seven assessed Icelandic horses were included in the study. A genome-wide association analysis was performed using the 670 K+ Axiom Equine Genotyping Array, and the effects of different haplotypes in the top associated region were estimated for riding ability and additional conformation traits assessed during breeding field tests.

RESULTS

A suggestive quantitative trait loci (QTL) for the score of back and croup was detected on Equus caballus (ECA) 22 (p-value = 2.67 × 10- 7). Haplotype analysis revealed two opposite haplotypes, which resulted in higher and lower scores of the back and croup, respectively (p-value < 0.001). Horses with the favorable haplotype were more inclined to have a well-balanced backline with an uphill conformation and had, on average, higher scores for the lateral gaits tölt (p-value = 0.02) and pace (p-value = 0.004). This genomic region harbors three genes: C20orf85, ANKRD60 and LOC100056167. ANKRD60 is associated with body height in humans. C20orf85 and ANKRD60 are potentially linked to adolescent idiopathic scoliosis in humans.

CONCLUSIONS

Our results show that the detected QTL for conformation of back and croup is of importance for quality of lateral gaits in Icelandic horses. These findings could result in a genetic test to aid in the selection of breeding horses, thus they are of major interest for horse breeders. The results may also offer a gateway to comparative functional genomics by potentially linking both motor laterality and back inclination in horses with scoliosis in humans.

Genetic parameters for canalization analysis of morphological traits in the Pura Raza Español horse

Measurements from 13 different morphological traits of importance in the Pura Raza Español (PRE) horse were used to estimate genetic and environmental parameters following a heteroscedastic model in which data were assigned to stallions. Data sets used ranged from 20,610 (height at withers) to 48,486 measurements (length of shoulder), and the number of animals analysed in the pedigrees varied from 17,662 (height at withers) to 23,962 (dorsal-sternal diameter). Results of heritabilities of the traits varied from 0.09 (width of chest and upper neck line) to 0.30 (muscular development). Further, genetic correlations between traits and their environmental variability were estimated, obtaining values from -0.56 (muscular development) to 0.69 (height at withers). Also, predicted breeding values for the mean and for the environmental variability were obtained for all horses in the pedigrees, providing individual information about not only the expected phenotypic value of their offspring but also the expected heterogeneity among them. Results proved the possibility of improving morphological traits and reducing the heterogeneity of offspring at a time by the selection of animals and levels of systematic effects.

Genetic inbreeding depression load for morphological traits and defects in the Pura Raza Española horse

Background

Inbreeding is caused by mating between related individuals and is associated with reduced fitness and performance (inbreeding depression). Several studies have detected heterogeneity in inbreeding depression among founder individuals. Recently, a procedure was developed to predict hidden inbreeding depression load that is associated with founders using the Mendelian sampling of non-founders. The objectives of this study were to: (1) analyse the population structure and general inbreeding, and (2) test this recent approach for predicting hidden inbreeding depression load for four morphological traits and two morphology defects in the Pura Raza Española (PRE) horse breed.

Results

The regression coefficients that were calculated between trait performances and inbreeding coefficients demonstrated the existence of inbreeding depression. In total, 58,772,533 partial inbreeding coefficients (F_ij) were estimated for the whole PRE population (328,706 horses). We selected the descendants of horses with a F_ij ≥ 6.25% that contributed to at least four offspring and for which morphological traits were measured for the subsequent analysis of inbreeding depression load (639 horses). A pedigree was generated with the last five generations (5026 animals) used as the reference population (average inbreeding coefficient of 8.39% and average relatedness coefficient of 10.76%). Heritability estimates ranged from 0.08 (cresty neck) to 0.80 (height at withers), whereas inbreeding depression load ratios ranged from 0.01 (knock knee) to 0.40 (length of shoulder), for an inbreeding coefficient of 10%. Most of the correlations between additive and inbreeding depression load genetic values and correlations between inbreeding depression load genetic values for the different traits were positive or near 0.

Conclusions

Although the average inbreeding depression loads presented negative values, a certain percentage of the animals showed neutral or even positive values. Thus, high levels of inbreeding do not always lead to a decrease in mean phenotypic value or an increase in morphological defects. Hence, individual inbreeding depression loads could be used as a tool to select the most appropriate breeding animals. The possibility of selecting horses that have a high genetic value and are more resistant to the deleterious effects of inbreeding should help improve selection outcomes.

Survey of Risk Factors and Genetic Characterization of Ewe Neck in a World Population of Pura Raza Español Horses

Simple Summary

Ewe Neck is a common morphological defect of the Pura Raza Español (PRE) population, which seriously affects the horse’s development. In this PRE population (35,267 PRE), a total of 9693 animals (27.12% of total) was Ewe Neck-affected. It has been demonstrated that genetic and risk factors (sex, age, geographical area, coat color, and stud size) are involved, being more prevalent in the males, 4–7 years old, chestnut coat, from small studs (less than 5 mares), and raised in North America. The morphological traits height at chest, length of back, head-neck junction, and bottom neck-body junction and the body indices, head index, and thoracic index were those most closely related with the appearance of this morphological defect. The additional genetic base of Ewe Neck in PRE, which presents low-moderate heritability (h2: 0.23–0.34), shows that the prevalence of this defect could be effectively reduced by genetic selection.

Abstract

Ewe Neck is a relatively common morphological defect in Pura Raza Español (PRE) horses and other Baroque type horse breeds, which adversely affects the breeding industry; (1) objectives: to establish the within-breed prevalence, possible associated factors, and heritability of Ewe Neck in PRE horses; (2) methods: the database included evaluations of 35,267 PRE horses. The Ewe Neck defect, 16 morphological traits, and 4 body indices were recorded. A Bayesian genetic animal model included the following systematic effects: sex, age, coat color, geographical area of the stud, and birth stud size were used; (3) results: in this PRE population, a total of 27.12% was affected. All the risk factors studied were significantly associated with the Ewe Neck score. The heritability coefficient for Ewe Neck score ranged from 0.23 to 0.34. Morphological traits (height at chest, length of back, head-neck junction, and bottom neck-body junction) and the indices (head and thoracic index) were those most closely related with the appearance of Ewe Neck; (4) conclusions: Ewe Neck is a relatively frequent defect in PRE horses, associated with risk factors and other morphological traits, with a moderate level of heritability. Breeding to select against this condition may therefore be beneficial in this breed.

Genetic Parameters and Inbreeding Effect of Morphological Traits in Sardinian Anglo Arab Horse

The purpose of this study was to estimate the heritability and genetic correlations of four biometric measurements and an overall score (OS) in the Sardinian Anglo-Arab horse (SAA); moreover, the effect of inbreeding on these traits was investigated. A dataset with 43,624 horses (27,052 females and 16,572 males) was provided by the Agricultural Research Agency of Sardinia (AGRIS). Cannon bone circumference (BC), chest girth (CG), shoulder length (SL), and withers height (WH) were measured on 6033 SAA horses born in Sardinia between 1967 and 2005; beside the measurements, an overall score (OS) was taken comparing the morphology of each horse to an "ideal type" that is scored out of 100. The mean value is 20.5 cm for BC, 185.9 cm for CG, 67.6 cm for SL, 160.8 cm for WH, and 73.2 for the OS. The heritability estimates ranged from 0.78 to 0.23. The results allow to foresee high genetic progress through the breeding programs. The most affected trait by the inbreeding rate seems to only be the withers height.

First steps to establishing an equestrian morphology: can Vitruvian ratios help?

Within equestrianism there is increasing focus on rider position and posture, not only in terms of aesthetics and the overall harmonious picture it may portray of the horse-rider combination, but more importantly on the rider’s physical ability to deliver clear, well-timed signals to the horse during training and competitive performance. Anthropometry has been successfully used in a wide range of non-equestrian sports to identify morphologies that are more likely to be successful than others in completing the tasks required by the particular sport or discipline. As physical data have become more readily accessible questions have arisen regarding the rider’s physical ability to achieve and maintain ‘ideal’ and symmetrical riding positions allowing them to transfer their weight and manage their limbs and consequently deliver distinguishable signals to the horse. Clearly identified ideal morphologies exist for a wide range of sports, but there is nothing for equestrianism. Da Vinci’s Vitruvian ‘man’ possesses ideal geometric proportions that depict perfect symmetry and proportion. Within equestrian it is common belief that riders (and horses) should be symmetrical. This study explored how the dimensions of a population of 51 female riders (24.8±8.29 years) aligned with Vitruvian ideals. Ten relative body proportions, selected as potentially the most relevant to horse riding, were obtained for each subject and ratios with total height derived. Only arm span, shoulder width and upper chest to the top of the head in relation to total height aligned with Vitruvian ratios (all P>0.05). Two primary principal components were identified – total height and arm span that could be of potential use for development of an equestrian morphology. Although horse riders’ physical dimensions failed to align well with Vitruvian measures, total height and arm length may have the potential to explain differences in riders’ ability to physically interact with horses and consequently impact their welfare.

Morphological and genetic diversity of Pura Raza Español horse with regard to the coat colour

Gene mutations influencing melanocytes also impact on physiological and behavioural functions. In this study, we investigated their association with four different coat colours in the Pura Raza Español (PRE) horse using morphological traits and molecular datasets. Four different subpopulations were identified according to individual coat colour: grey, bay, chestnut and black. Coat colour significantly associated with morphological measurements. Observed and expected heterozygosity values were low in grey compared with the other three subpopulations, suggesting the presence of unique ancestral alleles probably arisen by genetic drift and selection mechanism effects. Nei's distance demonstrated a clear division among subpopulations, the grey being the most divergent group. Gene flow estimates were similar, showing the lowest values in grey. Divergence times among subpopulations assessed with the average square distance suggested that grey was the original PRE population which diverged from bay, chestnut and black. Our results also demonstrated a clear morphological differentiation according to coat colour. The close genetic structure of bay and chestnut PRE subpopulations and the clear differences in most morphological traits of grey and chestnut PRE mares would suggest the pleiotropic effect of genomic regions determining coat colour in horses. However, further analysis including genomic information would be necessary to elucidate the mechanisms involved.

Detecting genetic regions associated with height in the native ponies of the British Isles by using high density SNP genotyping

Height is an important characteristic in the equine industry although little is known about its genetic control in native British breeds of ponies. This study aimed to map QTL data with the withers height in four pony breeds native to the British Isles, including two different sections within Welsh Cobs. In this study, a genome-wide analysis approach using the Illumina EquineSNP50 Infinium BeadChip was applied to 105 ponies and cobs. Analysis identified 222 highly significant height-associated SNPs (P ≤ 10^-5), among which three SNPs on ECA9 have also been previously reported elsewhere. The highest number of significant SNPs associated to height in the native British horses were located on ECA1, ECA8, and ECA16.

Population study of the Pura Raza Español Horse regarding its coat colour

Coat colour has always been a valuable trait for horse breeders. However, preferences for this feature have changed over the years. In this research, the Pura Raza Español horse (PRE) population was divided into four subpopulations (Grey, Bay, Black and Others), according to the most frequent coat colours and those of their ancestors. The purpose was to analyse genetic variability, reproductive parameters and distances among subpopulations during three key periods in the history of the breed: before 1960, from 1960 to 2000 and after 2000. The subpopulations composed of animals with ancestors with the same coat colour showed higher values of recent inbreeding (ranging from 7.13% to 10.44%) and a greater Nei’s minimum distance between them, as a result of more inbred matings than those carried out in families with members with different coat colours. Non-pure subpopulations also showed more similar recent inbreeding values (between 6.63% and 6.74%). Strikingly, the productive life of Pure bay, Pure black and other subpopulations with minority coat colours was considerably longer (10.79, 10.08 and 9.11 years, respectively) compared to the values of grey PRE horses (6.01 and 7.98 years), which is the subpopulation with the highest census. These results, together with shorter generation intervals of black stallion-offspring (5.51 years via father-son and 6.39 years via father-daughter) and the fact that this coat colour was not present in the breed until two decades ago, highlight the recent trend towards the breeding of black animals.

Designing an early selection morphological linear traits index for dressage in the Pura Raza Español horse

Making a morphological pre-selection of Pura Raza Español horses (PRE) for dressage is a challenging task within its current breeding program. The aim of our research was to design an early genetic selection morphological linear traits index to improve dressage performance, using 26 morphological linear traits and six dressage traits (walk, trot, canter, submission, general impression - partial scores - and total score) as selection criteria. The data set included morphological linear traits of 10 127 PRE (4159 males and 5968 females) collected between 2008 and 2013 (one record per horse) and 19 095 dressage traits of 1545 PRE (1476 males and 69 females; 12.4 records of average) collected between 2004 and 2014. A univariate animal model was applied to predict the breeding values (PBV). A partial least squares regression analysis was used to select the most predictive morphological linear traits PBV on the dressage traits PBV. According to the Wold Criterion, the 13 morphological linear traits (width of head, head-neck junction, upper neck line, neck-body junction, width of chest, angle of shoulder, lateral angle of knee, frontal angle of knee, cannon bone perimeter, length of croup, angle of croup, ischium-stifle distance and lateral hock angle) most closely related to total score PBV, partial scores PBV and gait scores PBV (walk, trot and canter) were selected. A multivariate genetic analysis was performed among the 13 morphological linear traits selected and the six dressage traits to estimate the genetic parameters. After it, the selection index theory was used to compute the expected genetic response using different strategies. The expected genetic response of total score PBV (0.76), partial scores PBV (0.04) and gait scores PBV (0.03) as selection objectives using morphological linear traits PBV as criteria selection were positive, but lower than that obtained using dressage traits PBV (1.80, 0.16 and 0.14 for total score PBV, partial scores PBV and gait scores PBV) or dressage traits PBV and morphological linear traits PBV (2.97, 0.16 and 0.15 for total score PBV, partial scores PBV and gait scores PBV), as selection criteria. This suggests that it is possible to preselect the PRE without dressage traits PBV using as selection criteria the morphological linear traits PBV, but the expected genetic response will be lower.