Early life jumping traits: Are they good proxies for success in show jumping competitions in Belgian warmblood horses?

The main goal of the Belgian Warmblood horse studbook (BWP) is to breed successful competition horses, with emphasis on show jumping. However, competition results are only available later in life and competition traits are lowly heritable. Hence, the use of phenotypes that record performance-related traits at an early life stage could help increase genetic progress. In this study, we evaluated the potential of eleven linear scored early life jumping traits assessed during jumping in freedom (2-5 years old) or under the saddle (4-6 years old) as proxies for later success in show jumping competitions. To this end, we estimated their heritabilities and genetic correlations with the competition trait, adjusted fence height, by using 2170 free jumping records, 1588 jumping under saddle records, 674,527 show jumping competition records and almost 81,000 informative horses in the pedigree. As participation of young horses in these contests is on a voluntary basis, a pre-selection most probably exists. To verify this hypothesis, we investigated the association between participation to young horse contests and participation to show jumping competitions later on (called here start status phenotype). We also estimated heritabilities for "start status in free jumping contest", "start status in jumping under saddle contest" and "start status in free jumping or jumping under saddle contest" by fitting threshold models. Furthermore, we calculated genetic correlations between these traits and adjusted fence height and calculated the correlations between EBVs for start status in young horse contests and EBVs for success in competitions. Estimated heritabilities of early life jumping traits ranged between 0.05 and 0.30. Their genetic correlations with adjusted fence height were moderate to high (rg  = 0.37-0.63). Relatively more horses that participated in young horse contests competed later on compared to horses that did not participate in young horse contests (p-value < 0.001). They were also significantly more successful in show jumping competitions. Furthermore, start status in young horse contests was moderately heritable in BWP horses (h2  = 0.56-0.65) and moderately to highly correlated with later success in competitions (rg  = 0.30-0.77). Hence, we showed that ELJ traits are good proxies for later success in competitions and that a pre-selection of horses occurs in young horse contests. It is suggested to stimulate participation to young horse contests to achieve a more representative sample of the population. Early life jumping traits can therefore optimize the genetic progress for show jumping performance.

Improving Genomic Prediction with Machine Learning Incorporating TPE for Hyperparameters Optimization

Depending on excellent prediction ability, machine learning has been considered the most powerful implement to analyze high-throughput sequencing genome data. However, the sophisticated process of tuning hyperparameters tremendously impedes the wider application of machine learning in animal and plant breeding programs. Therefore, we integrated an automatic tuning hyperparameters algorithm, tree-structured Parzen estimator (TPE), with machine learning to simplify the process of using machine learning for genomic prediction. In this study, we applied TPE to optimize the hyperparameters of Kernel ridge regression (KRR) and support vector regression (SVR). To evaluate the performance of TPE, we compared the prediction accuracy of KRR-TPE and SVR-TPE with the genomic best linear unbiased prediction (GBLUP) and KRR-RS, KRR-Grid, SVR-RS, and SVR-Grid, which tuned the hyperparameters of KRR and SVR by using random search (RS) and grid search (Gird) in a simulation dataset and the real datasets. The results indicated that KRR-TPE achieved the most powerful prediction ability considering all populations and was the most convenient. Especially for the Chinese Simmental beef cattle and Loblolly pine populations, the prediction accuracy of KRR-TPE had an 8.73% and 6.08% average improvement compared with GBLUP, respectively. Our study will greatly promote the application of machine learning in GP and further accelerate breeding progress.

Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses

In horses, parentage control is currently performed based on an internationally standardized panel of 17 microsatellite (MS) markers comprising 12 mandatory and five optional markers. Unlike MS, single nucleotide polymorphism (SNP) profiles support a wider portfolio of genomic applications, including parentage control. A transition to SNP-based parentage control is favorable, but requires additional efforts for ensuring generation-overlapping availability of marker genotypes of the same type. To avoid double genotyping of either parents or offspring for changing to SNP technology and enable efficient transition, we tested whether MS genotypes used for parentage control could be reliably imputed from a medium-density SNP panel in German warmblood horses. Imputation accuracy was tested in a tenfold cross-validation with two approaches: within breed (option A) and across breeds (option B). Average imputation accuracies of 97.98% (A) and 96.17% (B) were achieved, respectively. Due to interbreed differences in genotyping rates, five MS markers of low genotyping rate (GTR; < 90%) could be imputed with higher accuracy within breed (98.18%) than across breeds (90.73%). MS markers with high GTR performed homogeneously well in option B (98.44%) and showed slightly lower accuracy in option A (97.90%). Among these markers, AHT5 proved to be problematic for imputation regardless of the approach, revealing accuracies of 86.40% (A) and 88.70% (B). Better results for MS markers with high GTR and savings in computational processing justified the choice of option B for routine implementation. To date, more than 9500 horses have undergone the new parentage control based on imputed MS genotypes.

An overview of international genetic evaluations of show jumping in sport horses

The breeding of sport horses to compete in the Olympic disciplines of show jumping, eventing, and dressage is fast becoming a global industry with the increased use of reproductive technologies, including artificial insemination and embryo transfer. Reproductive technologies have facilitated the dissemination of genetics from elite horses across multiple countries and breeds as breeders are no longer limited by location. Due to this increased level of crossbreeding, there is an increased need for estimated breeding values (EBVs) for sport horse performance that can be compared across breeds and countries. However, the implementation of across-breed or across-country genetic evaluations has been limited by the differences in each studbook’s individual breeding programs and genetic evaluations. Consequently, the aim of this review was to compare the genetic evaluations for show jumping of sport horse studbooks worldwide. The top sport horse studbooks in the world according to the World Breeding Federation for Sport Horses Studbook Rankings 2019 were contacted by email to request information on their current breeding programs and genetic evaluations. Twenty-six of the 51 studbooks contacted replied to this request but only 18 of these studbooks conducted their own genetic evaluations or were part of a larger genetic evaluation in their country of origin. The other eight studbooks were not involved in genetic evaluations at present but expressed an interest in the implementation of such in the future. Overall, many differences were identified among the genetic evaluations of each studbook or each country. The definition of show jumping performance differed within each evaluation and the methods and models utilized also differed. Despite some stallions and mares being registered in multiple studbooks or having progeny in multiple studbooks, these differences make comparison of EBVs across studbooks difficult. Further transparency and collaboration of sport horse studbooks with organizations such as Interstallion, will be essential to facilitate any future implementation of international genetic evaluations for show jumping performance.

Genetic and genomic characterization followed by single-step genomic evaluation of withers height in German Warmblood horses

Reliability of genomic predictions is influenced by the size and genetic composition of the reference population. For German Warmblood horses, compilation of a reference population has been enabled through the cooperation of five German breeding associations. In this study, preliminary data from this joint reference population were used to genetically and genomically characterize withers height and to apply single-step methodology for estimating genomic breeding values for withers height. Using data on 2113 mares and their genomic information considering about 62,000 single nucleotide polymorphisms (SNPs), analysis of the genomic relationship revealed substructures reflecting breed origin and different breeding goals of the contributing breeding associations. A genome-wide association study confirmed a known quantitative trait locus (QTL) for withers height on equine chromosome (ECA) 3 close to LCORL and identified a further significant peak on ECA 1. Using a single-step approach with a combined relationship matrix, the estimated heritability for withers height was 0.31 (SE = 0.08) and the corresponding genomic breeding values ranged from − 2.94 to 2.96 cm. A mean reliability of 0.38 was realized for these breeding values. The analyses of withers height showed that compiling a reference population across breeds is a suitable strategy for German Warmblood horses. The single-step method is an appealing approach for practical genomic prediction in horses, because not many genotypes are available yet and animals without genotypes can by this way directly contribute to the estimation system.

Role of genes related to performance and reproduction of Thoroughbreds in training and breeding - A review

Thoroughbreds have been selected for speed and stamina since the 1700s. This selection resulted in structural and functional system-wide adaptations that enhanced physiological characteristics for outstanding speed of 61-71 kph (38-44 mph) between 1,000 and 3,200 m (5 furlongs - 2 miles). At present, horseracing is still an economically important industrial sector, therefore intensive research is underway to explore genes that allow the utilisation of genetic abilities and are significant in breeding and training. This study aims to provide an overview of genetic research and its applicability related to Thoroughbreds.

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: r_g = 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.

Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes

Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport horse breeds. The major goal of this study was to shed light on genomic regions and biological pathways under selective pressures in sport horses. In this study, whole-genome sequences of 16 modern sport and 35 non-sport horses were used to investigate the genomic selective signals of sport performance, by employing fixation index, nucleotide diversity, and Tajima's D approaches. A total number of 49 shared genes were identified using these approaches. The functional enrichment analysis for candidate genes revealed novel significant biological processes related to musculoskeletal system development, such as limb development and morphogenesis, having been targeted by selection in sport breeds.

Genetic parameters estimation in an Italian horse native breed to support the conversion from agricultural uses to riding purposes

Horses are nowadays mainly used for sport and leisure purposes, and several local breeds, traditionally used in agriculture, are exposed to the risk of extinction. The long-term survival of local horse breeds depends on strategies to both monitor their genetic diversity and to find their sustainable role in the equine market. Thus, several local horse breeds need to adapt their breeding objective to allow a modernization process. The Bardigiano is an example of such horse breeds; we, therefore, studied the existing evaluation protocol from a genetic standpoint to assess the protocol's suitability to convert the Bardigiano from an agricultural to a riding horse. To this end, we estimated genetic parameters for four conformation measurements, ten grading traits and 23 linear traits. For conformation measurements, the heritabilities ranged from 0.31 for cannon bone circumference to 0.63 for height at withers. For conformation and attitude grading traits, the highest heritability (0.34) was estimated for development and the lowest (0.09) for gaits. The heritabilities for linear traits ranged from 0.05 for the leg straightness to 0.32 for the coat colour. Genetic correlations between linear traits and corresponding grading traits varied considerably, ranging from -0.42 to 0.98. This study showed that the current evaluation protocol in the Bardigiano horse is appropriate for genetic evaluation. Genetic parameters estimation can, in turn, be used to develop novel breeding values to help this conversion. Our study paves the way to optimize the Bardigiano horse breeding programme, and it may help several other local horse breeds experiencing similar issues.