Genetics of Thoroughbred Racehorse Performance

Effect of the intrinsic and extrinsic factors on the growth and development of young foals under subtropical conditions of Pakistan

This study was designed to explore the impact of intrinsic (breed of foal, age of dam, and age of foal at weaning) and extrinsic (season of birth and housing type) factors on the growth and survival of foals in the subtropical conditions of Pakistan. For the growth study, retrospective data analysis of foals (n = 150) born from purebred brood mares of Thoroughbred, Arabs, and Percheron breeds (n1, n2, and n3 = 50 each) was made. Six hundred and twenty-four (n = 624) foals born between 2020 to 2022 were observed for the study of foal survival rate. The survival of these foals till the age of one year was considered. To study the growth and development of foals, height, bone, and girth measurements were taken at multiple developmental stages (3, 6, 9, 12, 15, and 18 months of age). Statistical analysis revealed that late-weaned foals demonstrated superior growth metrics compared to early-weaned foals (P = 0.001) and sheltered housing conditions markedly enhanced growth parameters across all breeds and measurement intervals (P = 0.002). However, no significant effect of season (P > 0.05) on the growth measurements across breeds was found. Arab and Thoroughbred breeds demonstrated significant early growth advantages in foals from middle-aged dams, with marked differences in height, bone width, and girth; however, by 15 months, these differences were not statistically significant (P > 0.05). In contrast, Percheron foals showed consistent growth regardless of the dam's age, suggesting breed-specific developmental influences (P = 0.885). Regarding the effects of extrinsic and intrinsic factors on foal survival, environmental conditions, and maternal age significantly impacted survival rates. Extreme winter conditions were associated with a notably lower survival probability (P = 0.002), and middle-aged dams exhibited significantly enhanced survival odds (P = 0.03). However, the influences of housing conditions and weaning age on survival were not statistically significant (P > 0.05), indicating these factors do not substantially affect foal survival within the first year. These results underscore the critical roles of weaning age, housing conditions, and age of dams in influencing foal growth and survival, highlighting the importance of tailored management practices in optimizing outcomes for the growth and development of young equines under subtropics.

Unravelling the speed-going relationship: A proof of concept study from British turf flat and jump race meetings

The maximum galloping speeds of racehorses during a race are influenced by the functional performance of the ground ('going') amongst other factors. For turf racecourses in Britain, the ground is descriptively classified and numerically quantified on the morning of a race meeting by the clerk of the course and subsequently published to assist decision making. Importantly, this includes deciding whether a horse should or should not run. The going is also assessed and classified during the meeting by racing analysts using the normalized winning times from each race result. Differences between going assessments are regularly reported, therefore this study aimed to evaluate whether an alternative method of measuring going could better predict going measured from performances. Measurement and performance data from 25 flat and 25 jump meetings were compared using linear and nonlinear regression models. A continuous two-phase polynomial model for cushioning was found to be the best predictor of performance going for all 50 meetings (adjusted r2=0.819, P<0.001). As cushioning can provide a going related indicator of the forces that the horse will experience at gallop, this measurement may be useful when evaluating racecourse going. This initial model suggests that there is little performance advantage at maximal galloping speeds above a cushioning value of approximately10 kN, possibly due to changes in limb contact timings to manage limb forces limits as the ground becomes firmer. An expansion of objective measurements of going that relate to performance across a wider geographic region, if not internationally are needed to confirm this limit.

A genome-wide association study of the racing performance traits in Yili horses based on Blink and FarmCPU models

Racing performance traits are the main indicators for evaluating the performance and value of sport horses. The aim of this study was to identify the key genes for racing performance traits in Yili horses by performing a genome-wide association study (GWAS). Breeding values for racing performance traits were calculated for Yili horses (n = 827) using an animal model. Genome-wide association analysis of racing performance traits in horses (n = 236) was carried out using the Blink, and FarmCPU models in GAPIT software, and genes within the significant regions were functionally annotated. The results of GWAS showed that a total of 24 significant SNP markers (P < 6.05 × 10- 9) and 22 suggestive SNP markers (P < 1.21 × 10- 7) were identified. Among them, the Blink associated 16 significant SNP loci and FarmCPU associated 12 significant SNP loci. A total of 127 candidate genes (50 significant) were annotated. Among these, CNTN6 (motor coordination), NIPA1 (neuronal development), and DCC (dopamine pathway maturation) may be the main candidate genes affecting speed traits. SHANK2 (neuronal synaptic regulation), ISCA1 (mitochondrial protein assembly), and KCNIP4 (neuronal excitability) may be the main candidate genes affecting ranking score traits. A common locus (ECA1: 22698579) was significantly associated with racing performance traits, and the function of the genes at this locus needs to be studied in depth. These findings will provide new insights into the detection and selection of genetic variants for racing performance and will help to accelerate the genetic improvement of Yili horses.

Comparative analysis of breeding patterns and reproductive efficiency of mares in subtropical conditions of Pakistan

BACKGROUND AND AIM

The present study aimed to evaluate and compare the overall and breed-specific seasonal breeding patterns, fertility rates, cyclicity, and follicular dynamics of Arab, Thoroughbred, and Percheron mares under the subtropical conditions of Pakistan.

MATERIALS AND METHODS

A retrospective analysis of climatic data and breeding records of eleven breeding studs spanning four years (2020-2023) was made to find out the overall seasonality in the breeding pattern of mares. Fifty mares of each breed (n = 150 in total) were scanned by ultrasonography for a calendar year to find the cyclicity pattern and follicular dynamics (follicular growth rate, size of ovulatory follicle, and days from estrus till ovulation).

RESULTS AND DISCUSSION

The statistical analysis of breeding records demonstrated a clear pattern of seasonal breeding (p< 0.05). The highest monthly foalings were noted in March (247 ± 45.37), and overall breeding activities peaked in Spring season (p< 0.05). Breed-specific results of Arab, Thoroughbred, and Percheron mares revealed that Arab mares maintained stable breeding activity throughout the year, with the highest activity in spring and peak conception rate in winter (56.25% ± 32.78; p > 0.05). Thoroughbred mares experienced significant seasonal declines from spring to winter with a peak conception rate in winter (63.89% ± 27.37, p > 0.05). Percherons showed the most pronounced seasonal effects, especially with a high fall conception rate (73.04% ± 19.61) and a sharp decrease in winter breeding metrics (p< 0.05). Furthermore, Thoroughbred and Percheron mares displayed the most pronounced seasonal effects on the percentage of cyclic mares 77.3% and 56% in winters (p< 0.05). Moreover, the follicular dynamics of the three breeds also exhibited significant differences (p< 0.05).

CONCLUSION

The current study concludes that seasonal and breed-specific variability exists among the reproductive parameters of Arab, Thoroughbred, and Percheron mares in subtropics, necessitating breed-specific reproductive management measures to maximize mare breeding efficiency.

Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection

In different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.

The Genetic Diversity of Horse Native Breeds in Russia

Horses were domesticated later than other farm animals. Horse breeds have been selectively developed by humans to satisfy different needs and purposes. The factory and indigenous breeds are of particular interest, having been bred in purity for many centuries without the addition of foreign blood. Data from 31 stud farms, as well as ranches, located in fifteen regions of the Russian Federation were used in this work. DNA was sampled from 102 stallions of 11 breeds: Arabian, Akhal-Teke, Don, Orlov Trotter, Vladimir Heavy Draft, Russian Heavy Draft, Soviet Heavy Draft, Kabardin, Yakut, Tuva, and Vyatka. Data on the origin of each animal from which the material was collected were taken into account. DNA genotyping was carried out using GGP Equine 70 k ® array chips (Thermo Fisher Scientific, USA). Genetic diversity of horse breeds was estimated using Admixture 1.3. and PLINK 1.9 software. FROH inbreeding was computed via the R detectRUNS package. The minimum length for ROH was set at 1 Mb to reduce the occurrence of false positives. We conducted PCA analysis using PLINK 1.9, and used the ggplot2 library in R for visualizing the results. Indigenous equine breeds, such as Vyatka, Tuva, and Yakut, are very hardy, and well adapted to local environmental and climatic conditions. They are employed as draft power, as well as for milk and meat. Both the Akhal-Teke breed and the Arabian breed have retained a minimum effective population size over many generations. We note significant accumulations of homozygosity in these breeds. In equestrian sports, performance is a top priority. ADMIXTURE and PCA analyses showed similarities between Don equine breeds and Kabardin, as well as some Arabian breed animals. Earlier research indicated the presence of thoroughbred traits in Don stallions. The Orlov Trotter breed stands out as a separate cluster in the structural and PCA analyses. Considering the small population size of this breed, our study found high FROH in all tested animals. The general reduction in the diversity of the horse breed gene pool, due to numerous crosses for breed improvement with thoroughbreds, has lead to a decline in the differences between the top sporting breeds. Our study presents new opportunities for exploring the genetic factors that influence the formation of adaptive traits in indigenous breeds, and for finding ways to preserve genetic diversity for effective population reproduction.

Influence of horse demographics, country of training and race distance on the rating of Thoroughbreds

The aim of the research was to assess how age, sex, sire, country of foaling, country of training and race distance influenced the international racing and performance of Thoroughbreds. The research was based on performance ratings of 6216 horses assigned by the International Federation of Racing Authorities between 2004 and 2022. The most common sex was stallion (58.54 %) and more than half of the population consisted of 3- and 4-year-old horses (54.68 %). The majority of the horses had the USA as their country of foaling (25.92 %) and also as their country of training (24.87 %). The sire with the largest number of offspring in the International Federation of Horseracing Authorities (IFHA) databases was Galileo (IRE) (193 horses). Four of the 10 most frequently represented sires belonged to the Sadler's Wells (USA) paternal line. The analysis of the statistics in the database as a whole established a significant (p < 0.001 ) influence of all observed factors. Stallions achieved a significantly higher rating (117.85) compared to geldings (117.17) and mares (117.13). The horses originating in Ireland achieved a statistically higher rating (117.99) than horses from Argentina, Australia, Brazil, New Zealand, a group of other countries designated "Others" and South Africa. Statistically conclusive differences were found between horses trained in Ireland (118.80) and all other countries except Great Britain and France. Five of the 10 sires with the best offspring rating belong to the Mr. Prospector (USA) paternal line.

Genetic structure and genome-wide association study of the traditional Kazakh horses

Horses are traditionally used in Kazakhstan as a source of food and as working and saddle animals as well. Here, for the first time, microarray-based medium-density single nucleotide polymorphism (SNP) genotyping of six traditionally defined types and breeds of indigenous Kazakh horses was conducted to reveal their genetic structure and find markers associated with animal size and weight. The results showed that the predefined separation between breeds and sampled populations was not supported by the molecular data. The lack of genetic variation between breeds and populations was revealed by the principal component analysis, ADMIXTURE, and distance-based analyses, as well as the general population parameters expected and observed heterozygosity (He and Ho) and between-group fixation index (Fst). The analysis revealed that the studied types and breeds should be considered as a single breed, namely the 'Kazakh horse'. The comparison with previously published data on global horse breed diversity revealed the relatively high level of individual diversity of Kazakh horses in comparison with the well-known foreign breeds. The Mongolian and Tuva breeds were identified as the closest horse landraces, demonstrating similar patterns of internal variability. The genome-wide association analysis was performed for animal size and weight as the traits directly related with the meat productivity of horses. The analysis identified a set of 60 SNPs linked with horse genes involved in the regulation of processes of development of connective tissues and the bone system, neural system, immune system regulation, and other processes. The present study is novel and introduces Kazakh horses as a promising genetic source for horse breeding and selection both on the domestic and international levels.

Imputed genomes of historical horses provide insights into modern breeding

Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with higher genetic similarity to those in the past and unveiled increased inbreeding in recent times. We genotyped variants associated with appearance and behavior to uncover previously unknown characteristics of these important historical horses. Overall, we provide insights into the history of Thoroughbred and Clydesdale breeds and highlight genomic changes in the endangered Przewalski's horse following a century of captive breeding.

Exploring the Italian equine gene pool via high-throughput genotyping

Introduction: The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent "colonization". In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool. Materials and Methods: The Italian dataset comprised 1,308 individuals and 22 breeds genotyped at a 70 k density that was merged with publicly available data to facilitate comparison with the global equine diversity. After quality control and supervised subsampling to ensure consistency among breeds, the merged dataset with the global equine diversity contained data for 1,333 individuals from 54 populations. Multidimensional scaling, admixture, gene flow, and effective population size were analyzed. Results and Discussion: The results show that some of the native Italian breeds preserve distinct gene pools, potentially because of adaptation to the different geographical contexts of the peninsula. Nevertheless, the comparison with international breeds highlights the presence of strong gene flow from renowned breeds into several Italian breeds, probably due to historical introgression. Coldblood breeds with stronger genetic identity were indeed well differentiated from warmblood breeds, which are highly admixed. Other breeds showed further peculiarities due to their breeding history. Finally, we observed some breeds that exist more on cultural, traditional, and geographical point of view than due to actual genetic distinctiveness.

The Enrichment of Specific Hair Follicle-Associated Cell Populations in Plucked Hairs Offers an Opportunity to Study Gene Expression Underlying Hair Traits

Gene expression differences can assist in characterizing important underlying genetic mechanisms between different phenotypic traits. However, when population-dense tissues are studied, the signals from scarce populations are diluted. Therefore, appropriately choosing a sample collection method that enriches a particular type of effector cells might yield more specific results. To address this issue, we performed a polyA-selected RNA-seq experiment of domestic horse (Equus ferus caballus) plucked-hair samples and skin biopsies. Then, we layered the horse gene abundance results against cell type-specific marker genes generated from a scRNA-seq supported with spatial mapping of laboratory mouse (Mus musculus) skin to identify the captured populations. The hair-plucking and skin-biopsy sample-collection methods yielded comparable quality and quantity of RNA-seq results. Keratin-related genes, such as KRT84 and KRT75, were among the genes that showed higher abundance in plucked hairs, while genes involved in cellular processes and enzymatic activities, such as MGST1, had higher abundance in skin biopsies. We found an enrichment of hair-follicle keratinocytes in plucked hairs, but detected an enrichment of other populations, including epidermis keratinocytes, in skin biopsies. In mammalian models, biopsies are often the method of choice for a plethora of gene expression studies and to our knowledge, this is a novel study that compares the cell-type enrichment between the non-invasive hair-plucking and the invasive skin-biopsy sample-collection methods. Here, we show that the non-invasive and ethically uncontroversial plucked-hair method is recommended depending on the research question. In conclusion, our study will allow downstream -omics approaches to better understand integumentary conditions in both health and disease in horses as well as other mammals.