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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.
Studying the Shape Variations of the Back, the Neck, and the Mandibular Angle of Horses Depending on Specific Feeding Postures Using Geometric Morphometrics. The effects of specific feeding positions upon the horse's shape variations of the back and neck postures as well as the variations of the mandibular angle have never been objectively studied. For this reason, geometric morphometrics was applied. Six horses, aged 14 ± 8 years (mean ± standard deviation, SD), were video-recorded while using three different feeding positions: on the ground-control position (CP); neck held 15 ± 3° below withers height with low hay net position (LP); neck held 15 ± 3° above withers height with high hay net position (HP). Data were analyzed using principal co...
The pelvic flexure separates distinct microbial communities in the equine hindgut. As hindgut fermenters, horses are especially dependent on the microbiota residing in their cecum and large intestines. Interactions between these microbial populations and the horse are critical for maintaining gut homeostasis, which supports proper digestion. The current project was motivated to determine if any features of the fecal microbiota are informative of the microbial communities from the cecum, ventral colon, or dorsal colon. Digesta from the cecum, ventral colon, dorsal colon and feces were collected from 6 yearling miniature horses. Microbial DNA was isolated and the microbiota fr...
Genomic comparisons of Persian Kurdish, Persian Arabian and American Thoroughbred horse populations. The present research aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred horses were genotyped across 670,796 markers. After quality control and pruning to eliminate linkage disequilibrium between loci which resulted in 13,554 SNPs in 52 Kurdish, 24 Persian Arabian and 58 Thoroughbred horses, the Kurdish horses were generally distinguished from the Persian Arabian samples by Principal Component Analyses, cluster analyses and calcul...
Development, Validation, and Reliability of a Sedation Scale in Horses (EquiSed). The lack of standardization of sedation scales in horses limits the reproducibility between different studies. This prospective, randomized, blinded, horizontal and controlled trial aimed to validate a scale for sedation in horses (EquiSed). Seven horses were treated with intravenous detomidine in low/high doses alone (DL 2.5 μg/kg + 6.25 μg/kg/h; DH 5 μg/kg +12.5 μg/kg/h) or associated with methadone (DLM and DHM, 0.2 mg/kg + 0.05 mg/kg/h) and with low (ACPL 0.02 mg/kg) or high (ACPH 0.09 mg/kg) doses of acepromazine alone. Horses were filmed at (i) baseline (ii) peak, (iii) intermediate,...
Comparative Analysis of Serum Mineral and Biochemical Parameter Profiles Between Late Pregnant and Early Lactating Jennies. The purpose of this study was to investigate the profile change of serum trace and major elements, and biochemical and hematological parameters in jennies during late pregnancy and early lactation. Twenty-five healthy Chinese Liaoxi jennies were used in late pregnancy and early lactation. Results showed that the levels of Fe, total protein (TP), and aspartate aminotransferase (AST) were highly variable interindividual among the jennies. Early lactating jennies showed significantly lower serum levels of K, Se, AST, total cholesterol (TC), and triglyceride than late pregnant jennies (P < .05)...
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 acceler...
Genetic consistency between gait analysis by accelerometry and evaluation scores at breeding shows for the selection of jumping competition horses. The aim was to assess the efficiency of gaits characteristics in improving jumping performance of sport horses and confront accelerometers and judge scores for this purpose. A sample of 1,477 young jumping horses were measured using accelerometers for walk, trot, and canter. Of these, 702 were genotyped with 541,175 SNPs after quality control. Dataset of 26,914 horses scored by judges in breeding shows for gaits and dataset of 142,682 horses that performed in jumping competitions were used. Analysis of accelerometric data defined three principal components from 64% to 89% of variability explai...
The Composition and Predictive Function of the Fecal Microbiota Differ Between Young and Adult Donkeys. The community of microorganisms inhabiting the gastrointestinal tract of monogastric herbivores played critical roles in the absorption of nutrients and keeping the host healthy. However, its establishment at different age groups has not been quantitatively and functionally examined. The knowledge of microbial colonization and its function in the intestinal tract of different-age donkeys is still limited. By applying the V3-V4 region of the bacterial 16S rRNA gene and functional prediction on fecal samples from different-age donkeys, we characterized the gut microbiota during the different age...
Principal components for morphometric traits in Campolina horses. Principal component analysis (PCA) was applied to evaluate the genetic variability and relationship between 15 morphometric traits in 91,483 Campolina horses, as well as to propose an index based on an aggregate genotype that promotes a particular selection objective. PCA was applied to the genetic (co)variance matrix among variables. After calculation of the principal components, the breeding values were estimated to obtain an index related to the component that explained most of the variation. The first principal component (PC1) accounted for 97.8% of the total additive genetic variance of t...
The Development of a Novel Questionnaire Approach to the Investigation of Horse Training, Management, and Behaviour. The Equine Behaviour Assessment and Research Questionnaire (E-BARQ) is a questionnaire instrument developed to obtain quantitative data on the domestic equine triad of training, management, and behaviour of horses. The E-BARQ was developed to identify how changes in training and management impact behaviour over time, to define normal behaviour in horses, and to discover how to improve rider safety and horse welfare, leading to ethical equitation. During the development of the E-BARQ, we also investigated how best to motivate stakeholders to engage with this citizen science project. The pilot v...
No-contact microchip measurements of body temperature and behavioural changes prior to foaling. Gestational length is highly variable in horses ranging from 320 to 360 days. Thus, determining parturition time is an important challenge for the horse industry. Body temperature can be used in cows and ewes as an indicator of parturition. Thus, the aim of this study is to determine if temperature can also be used as indicator of foaling. Thirty-nine mares were monitored over two foaling seasons (2018 and 2019). They were housed in 16 m stalls with access to pasture in group three times a week from 10:00 to 16:00. Night watch as well as video monitoring was ensured during foaling periods. Bo...
Muscle modes of the equestrian rider at walk, rising trot and canter. Equestrian sports have been a source of numerous studies throughout the past two decades, however, few scientists have focused on the biomechanical effects, including muscle activation, that the horse has on the rider. Because equitation is a sport of two (the horse-human dyad), we believe there is a need to fill in the knowledge gap in human biomechanics during riding. To investigate the differences between novice and advanced riders at a neuromuscular level we characterized the motor output of a set of riders' key muscles during horse riding. Six recreational riders (24 ± 7 years) and nine ...
The use of the geometric morphometric method to illustrate shape difference in the skulls of different-aged horses. The geometric morphometrics method (GMM) is a technique to study scale and shape relationships of structures using Cartesian geometric coordinates rather than linear, areal (of area), or volumetric variables. GMM has been of great value in many biological studies, but does not appear to have been used to examine equine skulls.In this exploratory study, twenty-nine normal equine heads of three different age groups: 16 years old (N = 10) were examined.Computed tomography (CT) bone window DICOM images were reconstructed into isosurfaces (3-dimensional contoured surfaces), onto which landm...
Horse Behavior, Physiology and Emotions during Habituation to a Treadmill. A treadmill is an important tool in the equine analysis of gait, lameness, and hoof balance, as well as for the evaluation of horse rehabilitation or poor performance including dynamic endoscopy. Before all of these uses, horses have to be habituated to a treadmill locomotion. We used principal component analysis to evaluate the relationship between aspects of the horse's temperament and emotional response, and progress in the behavioral habituation to a treadmill. Fourteen horses were tested, by the same familiar handler, using the novel object test, the handling test, and both positive and n...
Prematurity and Dysmaturity Are Associated With Reduced Height and Shorter Distal Limb Length in Horses. The long-term effects of gestational immaturity in the premature (defined as height at the withers), from those that are more square (body length = height at the withers). Varimax rotation of PC1 and analysis of different gestational groups showed a significant effect of gestational immaturity (P = .001), with the premature group being more affected than the dysmature group (P = .009, P = .012). Mean values for the four dominant indices showed that these groups have significantly lower distal limb to body length relationships than controls. The observed differences suggest that gestationa...
Lineal Discrimination of Horses and Mules. A Sympatric Case from Arauca, Colombia. This is the first morphological comparative study between local horses and mules from Arauca, Colombia. It was realized to compare morphological traits between both species by analysing 15 adult mules (7 males and 8 females) and 150 adult horses (137 males and 13 females), with an age interval from 2 to 22 years. Data consisted of 24 different body quantitative traits which can explain the body conformation: thoracic circumference, body length (BL), thoracic depth and width, withers height (WH), sternum height, shoulders width, chest width, forelimb cannon perimeter and length, head length and...
Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites. STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of structure-based studies could not be reproduced (, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the his...
Effect of work on body language of ranch horses in Brazil. The horses' responses to exercise are commonly monitored using physiological variables, nonetheless physical and mental states can also be expressed through body language. The aims of this study were: (i) to identify how facial expressions and other behavioural variables change in ranch horses after a routine workday, and (ii) to investigate if these changes can be used as indicators of physical tiredness by relating them to known variables of physical fitness and workload. Fourteen crossbred ranch horses were assessed pre- and post-workday on two farms, recording the body language, physiologi...
A Comparison of Traditional and Geometric Morphometric Techniques for the Study of Basicranial Morphology in Horses: A Case Study of the Araucanian Horse from Colombia. Skull size and shape have been widely used to study domestic animal populations and breeds. Although several techniques have been proposed to quantify cranial form, few attempts have been made to compare the results obtained by different techniques. While linear morphometrics has traditionally been used in breed characterization, recent advances in geometric morphometrics have created new techniques for specifically quantifying shape and size. The objective of this study was to compare two morphometric methods for their ability to describe external morphology. For this purpose, 20 skull specim...
Metabolomic analysis of synovial fluid from Thoroughbred racehorses diagnosed with palmar osteochondral disease using magnetic resonance imaging. Palmar osteochondral disease (POD) is a common cause of lameness in competition horses. Magnetic resonance imaging (MRI) is the most sensitive diagnostic modality currently available, however it may not be financially or logistically practical for routine screening of POD. There is increasing interest in the use of metabolomics for diagnosis prior to progression to irreversible damage. Objective: To determine metabolite levels in synovial fluid (SF) of horses with a clinical diagnosis of POD based on diagnostic analgesia and MRI, with the hypothesis that metabolomic profiles differ between dis...
Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines. The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low breeding values (EBVs) for show jumping. We analyzed high density genotype information from 380 SWB horses born in the period 2010-2011, and used Principal Coordinates Analysis and Discriminant...
Local origin or external input: modern horse origin in East Asia. Despite decades of research, the horse domestication scenario in East Asia remains poorly understood. The study identified 16 haplogroups with fine-scale phylogenetic resolution using mitochondrial genomes of 317 horse samples. The time to the most recent common ancestor of the 16 haplogroups ranges from [0.8-3.1] thousand years ago (KYA) to [7.9-27.1] KYA. With combined analyses of the mitochondrial control region for 35 extant Przewalski's horses, 3544 modern and 203 ancient horses across the world, researchers provide evidence for that East Asian prevalent haplogroups Q and R were indigenou...
Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations. The Mongolian horse is one of the oldest extant horse populations and although domesticated, most animals are free-ranging and experience minimal human intervention. As an ancient population originating in one of the key domestication centers, the Mongolian horse may play a key role in understanding the origins and recent evolutionary history of horses. Here we describe an analysis of high-density genome-wide single-nucleotide polymorphism (SNP) data in 40 globally dispersed horse populations (n = 895). In particular, we have focused on new results from Chinese Mongolian horses (n = 100) that ...
Identification of metabolomic changes in horse plasma after racing by liquid chromatography-high resolution mass spectrometry as a strategy for doping testing. Recently, the illegal use of novel technologies, such as gene and cell therapies, has become a great concern for the horseracing industry. As a potential way to control this, metabolomics approaches that comprehensively analyze metabolites in biological samples have been gaining attention. However, it may be difficult to identify metabolic biomarkers for doping because physiological conditions generally differ between resting and exercise states in horses. To understand the metabolic differences in horse plasma between the resting state at training centres and the sample collection stage after...
Exploring the genetics underpinning dynamic laryngeal collapse associated with poll flexion in Norwegian-Swedish Coldblooded Trotter racehorses. Dynamic laryngeal collapse (DLC) associated with poll flexion is the most common disorder of the upper respiratory tract (URT) in the Norwegian-Swedish Coldblooded Trotter (NSCT). The disorder, which has also been diagnosed in other breeds of trotters and gaited horses, appears to be related to anatomic phenotypes and only occurs during poll flexion when the horse is exercised 'on the bit'. Objective: Identify genomic regions associated with DLC in the NSCT by combining a rigorous phenotyping protocol with genomic data from a high-density equine genotyping array. Methods: Prospective case/cont...
Analysis of genetic variation contributing to measured speed in Thoroughbreds identifies genomic regions involved in the transcriptional response to exercise. Despite strong selection for athletic traits in Thoroughbred horses, there is marked variation in speed and aptitude for racing performance within the breed. Using global positioning system monitoring during exercise training, we measured speed variables and temporal changes in speed with age to derive phenotypes for GWAS. The aim of the study was to test the hypothesis that genetic variation contributes to variation in end-point physiological traits, in this case galloping speed measured during field exercise tests. Standardisation of field-measured phenotypes was attempted by assessing horse...
Determinants of Undesirable Behaviors in American Quarter Horses Housed in Box Stalls. The objective of this study was to investigate the management practices that affect undesirable behaviors in American Quarter Horses (AQH) confined to box stalls. A total of 105 adult AQH, comprising 29 females, 22 intact males, and 54 castrated males, housed in box stalls for at least 30 days, were included in the study. Behavioral activities were recorded through visual inspection at 5-min intervals over a 24-h period by two observers who took turns in shifts of 4 hours. Parameters related to animal characteristics, stall conditions, handling, training, nutrients supplied, and feeding beha...
Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy to diagnose osteoarthritis in equine serum. Reliable and validated biomarkers for osteoarthritis (OA) are currently lacking. Objective: To develop an accurate and minimally invasive method to assess OA-affected horses and provide potential spectral markers indicative of disease. Methods: Observational, cross-sectional study. Methods: Our cohort consisted of 15 horses with OA and 48 without clinical signs of the disease, which were used as controls. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy was used to investigate serum samples (50 μL) collected from these horses. Spectral processing and multivariat...
The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data. The Jinjiang horse is a unique Chinese indigenous horse breed distributed in the southern coastal areas, but the ancestry of Jinjiang horses is not well understood. Here, we used Equine SNP70 Bead Array technology to genotype 301 horses representing 10 Chinese indigenous horse breeds, and we integrated the published genotyped data of 352 individuals from 14 foreign horse breeds to study the relationships between Jinjiang horses and horse breeds from around the world. Principal component analysis (PCA), linkage disequilibrium (LD), runs of homozygosity (ROH) analysis, and ancestry estimating m...
Effect of oral supplementation of probiotic strains of Lactobacillus rhamnosus and Enterococcus faecium on the composition of the faecal microbiota of foals. Effects of probiotics on the intestinal microbiota of foals are yet insufficiently studied. The aim of this study was to investigate whether supplementation of Lactobacillus rhamnosus (DSM 7133) and Enterococcus faecium (DSM 7134) influences the bacterial composition of the faecal microbiota of foals. A total of 34 newborn foals were randomly assigned to the placebo group (PG, n = 16) and the treatment group (TG, n = 18). From day 1 to day 14 of life, foals orally received 3 ml of either a probiotic preparation (1.05 × 10 CFU E. faecium and 4.50 × 10 CFU L. rhamnosus) or placebo (...
