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Topic:Principal Component Analysis
Principal Component Analysis (PCA) is a statistical technique used to simplify complex datasets by reducing their dimensionality while preserving as much variance as possible. In equine research, PCA can be applied to various types of data, including genetic, physiological, and performance metrics, to identify patterns and relationships that may not be immediately apparent. By transforming original variables into a new set of uncorrelated variables called principal components, researchers can effectively analyze and interpret large datasets. PCA facilitates the identification of key factors influencing traits or conditions in horses, aiding in areas such as genetic studies, disease susceptibility, and performance optimization. This page compiles peer-reviewed research studies and scholarly articles that explore the application, methodology, and findings of Principal Component Analysis in equine science.
Body Condition, Metabolic Parameters and Semen Traits in Purebred Spanish Horses. The growing relevance of the Purebred Spanish horse has driven the extensive use of assisted reproductive technologies to preserve elite stallion genetics. Optimal reproductive performance is intrinsically linked to systemic health and high semen quality. This study aimed to evaluate the impact of body condition on the stallion's metabolic and endocrine profiles and their seminal parameters. Semen and blood samples were collected from 26 stallions (February-May in 2024-2025) whose body condition score (BCS) was assessed using the Henneke scale. They were classified into two groups, low BCS wit...
Comparative hematological and serum biochemical profiling of grassland Xichun and Xilingol horses. The Grassland Xichun horse is an emerging crossbred population developed from Xilingol mares and Thoroughbred stallions in Inner Mongolia, China, yet its blood physiological profile has not been systematically characterized. In this study, we compared 32 hematological and serum biochemical parameters between 177 Grassland Xichun horses and 35 Xilingol horses maintained under the same extensive grazing conditions. Following Benjamini-Hochberg FDR correction, 17 of 32 parameters differed significantly between breeds. Grassland Xichun horses showed markedly higher RBC count (9.145 vs 7.905 × 10...
Skull morphometry and sexual dimorphism in the Kyrgyz horse: A multivariate size-corrected analysis. This study aimed to evaluate sexual dimorphism in Kyrgyz horse skulls by separating size and shape components using Mosimann log-shape ratios, based on 18 linear cranial measurements recorded from 39 specimens. Raw linear data were analyzed alongside size-corrected Mosimann log-shape ratios to distinguish overall size from size-independent shape. Males showed larger raw means than females for all 18 variables, and 14 measurements remained significant after false-discovery-rate correction. The strongest raw differences involved skull length to nasale, total skull length, nasal length, breadth b...
From Concept to Perception: Equestrian Definitions of Harmony and Visual Attention in Horse-Rider Evaluation. In equestrian circles, horse-rider harmony is understood intuitively, yet clear criteria are lacking. This study examined how different equestrians conceptualized and visually assessed harmony and how this influenced scoring. Qualitative interviews were combined with eye tracking technology. Thirty equestrians assessed five videos of horse-rider combinations performing in dressage, showjumping, eventing, working equitation and Icelandic riding, with eye movements being recorded using a mounted eye tracker. Verbal definitions were analyzed using thematic analysis, revealing three overarching th...
Allogeneic Platelet-Rich Gel Supernatant Reprograms the Cytokine and Growth Factor Microenvironment in an Equine In Vitro Inflammatory Tendon System. Tendinopathy involves a dysregulated inflammatory microenvironment in which cytokines, growth factors (GF) and extracellular matrix components interact dynamically. Platelet-rich plasma (PRP) is widely used as a regenerative therapy, but its mechanisms of action in inflamed tendon remain unclear. This study evaluated whether platelet-rich gel supernatant (PRGS) reprograms the inflammatory-anabolic mediator network in an equine in vitro tendon explant system stimulated with lipopolysaccharide (LPS). Tendon explants were cultured under six experimental conditions, including non-stimulated contro...
Genetic Characterization of the Arabian Horse Population in Tunisia Using Microsatellites. The genetic diversity and population structure of Tunisian Arabian horses were assessed using highly polymorphic microsatellite markers, which are critical for conservation and breeding programs. Despite the cultural and economic importance of Arabian horses in Tunisia, molecular data supporting their management remain limited. In this study, DNA from 130 horses was genotyped with 17 ISAG-FAO-recommended microsatellites to evaluate diversity within Eastern and Western Arabian lineages and their relationship to Thoroughbreds. Eastern Arabians showed an average of 5.176 alleles per locus, observ...
Dynamic DIA proteomics of mare’s milk reveals distinct colostrum signatures and stage-specific lactation profiles. This study used data-independent acquisition (DIA) proteomics to analyze the changing protein content of mare's milk (n = 3) throughout the entire lactation period (days 1-120), with samples taken at seven different times. Principal component analysis (PCA) revealed that the protein composition of colostrum on day 1 differed markedly from that of later lactation stages. Colostrum-specific proteins such as IgG, IgM, IgE, AGPAT1, NPVF and CAMK2G were associated with rapid energy supply, neurodevelopment and immune defense. In contrast, mature milk was enriched in proteins involved in sustained...
Morphometric characteristics of quarter horses in barrel racing events: impacts on performance and competitive success. This study investigated the influence of morphometric characteristics on performance in Quarter Horses competing in barrel racing. Methods: A total of 125 horses were assessed using 28 linear and angular body measurements derived from standardized left-side photographs captured via smartphone and analyzed with open-source software. Results: Measurements were subjected to exploratory factor analysis, extracting six principal components (forequarters, hindquarters, midsection, posterior angles, scapular traits, age and weight), which together explained 83.0 % of the morphological variance. Foreq...
Variation in Four Horse Gait Categories Illustrated by Quantitative Analysis With ANALOC-E. Horse gaits are a trait highly selected and prized in diverse breeds. Meanwhile, gait classification relies mostly on subjective visual observations by evaluators. Noninvasive equipment able to track locomotion in horses and output quantitative gait parameters is not only helpful in evaluating locomotion but also in designating gait types and its variations. Equine locomotion pattern designation based solely on observer evaluation can be subjective; therefore, utilizing tools that provide quantitative results and track individual limb movements, especially during intermediate-speed gaits, can ...
Phenotypic Associations Between Linearly Scored Traits and Sport Horse Auction Sales Price in Ireland. This study examines the associations between linearly scored phenotypic traits and auction sales prices of young event horses in Ireland, aiming to identify key traits influencing market value. Data from 307 horses sold at public auctions (2022-2023) were analysed using regression analysis, binary optimisation, and Principal Component Analysis (PCA). Regression identified Head-neck Connection, Quality of Legs, Walk length of Stride, and Scope as highly significant predictors of sales price ( < 0.001), with Length of Croup, Trot Elasticity, Trot Balance, and Take-off Direction also significa...
Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic Traits. The core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. However, research on the genetic characteristics within this breed and the genes associated with athletic performance remains relatively limited. We conducted whole-genome resequencing of Grassland-Thoroughbred F1, F2, F3, and the crossbred population (CY) and obtained a total of 4056.23 Gb of high-qual...
Influences of Double Versus Snaffle Bridles on Equine Behaviour at Dressage Competitions and Factors That Interact with Their Effect. Despite welfare concerns, conflict behaviours (indicative of momentary states of acute stress) are common in horses during dressage competitions. Identifying factors that affect conflict behaviours during competition therefore has the potential to improve equine welfare. The aim of this exploratory study was to assess the effect of bridle type (double versus snaffle) in relation to other potential affecting factors (e.g., average head angle, competition level and type, tack variation) on conflict behaviours during dressage competition. An ethogram was created to analyse the conflict behaviour ...
Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing. Speed and endurance are the primary goals in racehorse breeding. The Grassland-Thoroughbred is a newly developed breed in northern China that combines speed, endurance, and environmental adaptability. However, current research on the genetic background of this breed and the genes associated with athletic performance remains limited. We conducted whole-genome resequencing on Mongolian (MG), Thoroughbred (TB), Xilingol (XL), and Grassland-Thoroughbred (CY) horses, generating 3813.74 Gb of clean data after quality control. The number of transitions was significantly higher than that of transversi...
Differences between facilities in horse welfare profiles: slight differences in management/working conditions may be enough. Many studies focus on animal welfare in terms of specific, either behavioural or physiological, indicators or on the impact of a particular management factor. However, an animal's welfare state results from the individual's perception of its general environment, which has consequences at both behavioural and physiological levels. Previous research on horses has shown that different riding schools could be characterised by different emotional/cognitive profiles of horses, in relation sometimes with one single management factor. In the present study, we aimed at determining if such facility-spec...
Multivariate analysis of morphometric traits of Malkangiri pony – a heritage germplasm of Odisha. The present study aimed to identify significant morphometric traits in Malkangiri ponies of Odisha through principal component analysis. The data were collected randomly from 200 ponies aged more than five years and 13 morphometric traits alongwith three indices were recorded. The mean height at wither, height at croup, body length, chest girth, punch girth, height at forearm, height at hock, fetlock to coronet, chest width, neck circumference, poll to wither, wither to croup and croup to head of the tail were 126.7 ± 0.39, 122.6 ± 0.29, 107.9 ± 0.2, 122 ± 0.31, 118.6 ±...
Einthoven’s triangle adapted for horses: Proposal for the Delta configuration. Reliable ECGs are crucial for diagnosing arrhythmias, yet a lack of standardization impedes arrhythmia diagnosis and treatment in horses. Objective: To objectively determine an optimal position of Einthoven's triangle for ECG recordings in horses at rest, which can form the basis for standardized ECG recording and improve diagnosis and treatment of arrhythmias. Methods: The study involved 72 healthy, warmblood horses aged between 3 and 20 years. Methods: In view of future 12-lead studies and vectorcardiography, requiring an orthogonal system, Einthoven's triangle was positioned around the he...
Feeding behaviour related to different feeding devices. Slow feeding devices (SFDs) are useful tools in order to improve the horse well-being and to reduce wastage, but their use may result in unnatural posture during feeding and frustration behaviours. Moreover, it may be important to evaluate the laterality during feeding. The aim of the study was to investigate ponies' feeding behaviour (i.e., lateralisation, frustration, postural eating style) with different hay feeding methods: on the ground (G), a fully filled hay net (HF), a partially filled hay net (HL), and a slow feeder hay box (HB). Nine ponies of two different breed types (Shetland and ...
Pony feeding management: the role of morphology and hay feeding methods on intake rate, ingestive behaviors and mouth shaping. In the last decade, haynets and slow feeders have been promoted as sustainable tools to improve the feeding management of horses and reduce forage waste, but little is known about their effects on ponies. Therefore, the aim of this study was to analyze the effects of different hay feeding methods on the ingestive behaviors, intake rate and mouth shaping of ponies belonging to two breed types, which are characterized by different head morphologies. Shetland type (SH, n = 5) and Welsh/Cob type (WC, n = 4) ponies were fed hay using four feeding methods: on the ground (G), a fully filled h...
Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses. Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the population structure and to compare the effective population size (Ne), LD decay, genetic diversity, and genomic inbreeding in Iranian native Caspian (n = 38), Turkmen (n = 24) and Kurdish (n = 29) breeds and some other exotic horses consisting of Arabian (n = 24), Fell pony (n = 21) and Akhal-Teke (n = 20). A variety of statistical population analysis techniques, such as principal component analysis (PCA), discriminant analysis of...
A cross-sectional study on performance evaluation in Italian standardbred horses’ real-time PCR-positive for Theileria equi. Inflammatory myopathy and perivasculitis have been recently described in horses with chronic equine piroplasmosis (EP). These alterations may be linked to poor performances. The aims of this study were to evaluate the prevalence for EP in clinically healthy Italian Standardbred (IS) racehorses and to compare laboratory parameters and performance metrics between positive and negative horses. Real-time PCR was applied for the detection of T. equi and B. caballi positivity. Haematology parameters, blood chemistry results, subjective muscle mass scores, and performance metrics were compared betwee...
Reported Agonistic Behaviours in Domestic Horses Cluster According to Context. Agonistic behaviours are often directed at other animals for self-defence or to increase distance from valued resources, such as food. Examples include aggression and counter-predator behaviours. Contemporary diets may boost the value of food as a resource and create unanticipated associations with the humans who deliver it. At the same time the domestic horse is asked to carry the weight of riders and perform manoeuvres that, ethologically, are out-of-context and may be associated with instances of pain, confusion, or fear. Agonistic responses can endanger personnel and conspecifics. They are...
The Postural and Body Surface Temperature Response of Leisure Horses to Lunging with Selected Lunging Aids. Incorporating lunging into a horse's daily routine aims to enhance fitness, physical condition, and specific skills or exercises when using lunging aids (LAs). To assess the effectiveness of lunging, non-contact technologies like geometric morphometrics and infrared thermography can be employed. This study seeks to evaluate lunging efficiency based on the horse's posture and surface temperature when lunging with different head and neck positions. The study aims to determine if changes in a horse's posture correspond to increased metabolic activity, as indicated by body surface temperature. Thi...
Genome-wide search reveals the uniqueness of DNA regions associated with coat color and innate immunity in Hokkaido Native Horse. Hokkaido Native Horse (HKD) is a horse breed native to Hokkaido in Japan known for the traits such as coat color with no white spots and adaptability to the local cold climate. To examine whether those traits of HKD are conferred at the DNA level, we attempted to identify fixed DNA regions in HKD individuals, that is, the selection signatures of HKD. A comparison of genome-wide single nucleotide polymorphism genotypes in 58 HKD individuals by principal component analysis, and cluster analysis between breeds, including HKD, and within the HKD individuals indicated the genetic independence of HK...
Development of a fixed list of descriptors for the qualitative behavioral assessment of thoroughbred horses in the racing environment. Horse racing is a major sport practiced worldwide. The environment to which horses are exposed during race meetings can influence their behavior. However, to the best of our knowledge, a method for assessing a horse's response to its surroundings during the pre- and post-race periods has not yet been reported. This study aimed to create a standard list of descriptors for use in a qualitative behavioral assessment (QBA) focused on assessing the emotional expressivity of horses before and after racing events. Unassigned: Seventy pre- or post-race 30-second videos of horses were randomly selected...
Fecal Microbiota and Diet Composition of Buryatian Horses Grazing Warm- and Cold-Season Grass Pastures. The Buryatian horse is an ancient breed and, as an indigenous breed, they have unique adaptive abilities to use scarce pastures, graze in winter, and survive in harsh conditions with minimal human care. In this study, fecal microbiota of Buryatian horses grazing in the warm and cold seasons were investigated using NGS technology on the Illumina MiSeq platform. We hypothesized that the composition of microbial communities in the feces of horses maintained on pasture would change in the different seasons, depending on the grass availability and different plant diets. We conducted microhistologic...
Detecting SNP markers discriminating horse breeds by deep learning. The assignment of an individual to the true population of origin using a low-panel of discriminant SNP markers is one of the most important applications of genomic data for practical use. The aim of this study was to evaluate the potential of different Artificial Neural Networks (ANNs) approaches consisting Deep Neural Networks (DNN), Garson and Olden methods for feature selection of informative SNP markers from high-throughput genotyping data, that would be able to trace the true breed of unknown samples. The total of 795 animals from 37 breeds, genotyped by using the Illumina SNP 50k Bead ch...
Anatomical variations of the equine femur and tibia using statistical shape modeling. The objective of this study was to provide an overarching description of the inter-subject variability of the equine femur and tibia morphology using statistical shape modeling. Fifteen femora and fourteen tibiae were used for building the femur and tibia statistical shape models, respectively. Geometric variations in each mode were explained by biometrics measured on ±3 standard deviation instances generated by the shape models. Approximately 95% of shape variations within the population were described by 6 and 3 modes in the femur and tibia shape models, respectively. In the femur shape mod...
Genetic Diversity and Maternal Phylogenetic Relationships among Populations and Strains of Arabian Show Horses. Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin cultur...
Cerebellar axonopathy in Shivers horses identified by spatial transcriptomic and proteomic analyses. Shivers in horses is characterized by abnormal hindlimb movement when walking backward and is proposed to be caused by a Purkinje cell (PC) axonopathy based on histopathology. Objective: Define region-specific differences in gene expression within the lateral cerebellar hemisphere and compare cerebellar protein expression between Shivers horses and controls. Methods: Case-control study of 5 Shivers and 4 control geldings ≥16.2 hands in height. Methods: Using spatial transcriptomics, gene expression was compared between Shivers and control horses in PC soma and lateral cerebellar hemisphere w...
Genomic association using principal components of morphometric traits in horses: identification of genes related to bone growth. The measurement of morphometric traits in horses is important for determining breed qualification and is one of the main selection criteria for the species. The development of an index (HPC) that consists of principal components weighted by additive genetic values allows to explore the most relevant relationships using a reduced number of variables that explain the greatest amount of variation in the data. Genome-wide association studies (GWAS) using HPC are a relatively new approach that permits to identify regions related to a set of traits. The aim of this study was to perform GWAS using HP...
