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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.
Interobserver Reliability of the Animal Welfare Indicators Welfare Assessment Protocol for Horses. Objective tools for the assessment of animal welfare are needed. The present study analyzed the interobserver reliability of the Animal Welfare Indicators (AWIN) welfare assessment protocol for horses to further enhance knowledge concerning reliability. Therefore, two trained observers conducted 18 assessments on farm at the same time and on the same animals. The results were compared at individual level by calculation of Cohen's kappa (κ), weighted kappa (κ), and prevalence-adjusted, bias-adjusted kappa (PABAK). Spearman rank correlation coefficient (RS), intraclass correlation coefficient ...
The lipidome of Thoroughbred racehorses before and after supramaximal exercise. A comprehensive study of the effect of supramaximal exercise in lipid homeostasis of Thoroughbreds provides the basis for future research on the role of lipids on energy metabolism in racehorses. Objective: To compare the plasma lipidome of Thoroughbreds before and after supramaximal exercise using an untargeted lipidomics approach. Methods: Pilot experimental study. Methods: Four Thoroughbred horses were used. The maximal oxygen consumption (VO ) was calculated for each horse. Horses then underwent treadmill exercise at the speed for which the oxygen requirements had been calculated to be 11...
Genetic Diversity of Persian Arabian Horses and Their Relationship to Other Native Iranian Horse Breeds. The principal aims of this study were to explore genetic diversity and genome-wide selection signatures in Persian Arabian horses and to determine genetic relationship of Persian Arabians with other Iranian horse breeds. We evaluated 71 horses from 8 matrilineal strains tracing to 47 mares from the mid to late 19th century, using the equine 670k single nucleotide polymorphism (SNP) BeadChip. Mean observed and expected heterozygosity were (0.43) and (0.45), respectively, average inbreeding measures (inbreeding estimates based on runs of homozygosity and pedigree information) were low, indicatin...
Equine Personality: Association With Breed, Use, and Husbandry Factors. Temperament can be defined as innate properties of the nervous system, whereas personality includes the complex behavioral traits acquired through life. Association between personality and behavior is important for breeding, selection, and training of horses. For the first time, we evaluated if equine personality components previously identified in Japan and Europe were consistent when applied to American horses. We examined the association of personality with breed, age, sex, management, training, stereotypies, and misbehaviors. The owner directed personality survey consisted of 25 questions....
Genetic variability of Akhal-Teke horses bred in Italy. The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods: Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on oth...
Repeatability, reproducibility and consistency of horse shape data and its association with linearly described conformation traits in Franches-Montagnes stallions. Linear description (LD) of conformation traits was introduced in horse breeding to minimise subjectivity in scoring. However, recent studies have shown that LD traits show essentially the same problems as traditionally scored traits, such as data converging around the mean value with very small standard deviations. To improve the assessment of conformation traits of horses, we investigated the application of the recently described horse shape space model based upon 403 digitised photographs of 243 Franches-Montagnes (FM) stallions and extracted joint angles based on specific landmark triplets....
Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array. The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju × Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas r values were lowest in Jeju horse. Expected heterozygos...
Characterization of trotter horses urine metabolome by means of proton nuclear magnetic resonance spectroscopy. Metabolomics has been recognized as a powerful approach for disease screening. In order to highlight potential health issues in subjects, a key factor is the possibility to compare quantitatively the metabolome of their biofluids with reference values from healthy individuals. Such efforts towards the systematic characterization of the metabolome of biofluids in perfect health conditions, far from concluded for humans, have barely begun on horses. The present work attempts, for the first time, to give reference quantitative values for the molecules mostly represented in the urine metabolome of...
Use of principle component analysis to quantitatively score the equine metabolic syndrome phenotype in an Arabian horse population. Equine metabolic syndrome (EMS), like human metabolic syndrome, comprises a collection of clinical signs related to obesity, insulin dysregulation and susceptibility to secondary inflammatory disease. Although the secondary conditions resulting from EMS can be life-threatening, diagnosis is not straightforward and often complicated by the presence of other concurrent conditions like pituitary pars intermedia dysfunction (PPID). In order to better characterize EMS, we sought to describe the variation within, and correlations between, typical physical and endocrine parameters for EMS. Utilizing ...
Progressive habituation to separation alleviates the negative effects of weaning in the mother and foal. Early and definitive separation between offspring and their mothers has negative consequences on behavioral and physiological responses. This study compared sudden and definitive weaning (Sudd group, N = 16) and weaning involving progressive habituation to separation using a fence line during the month preceding definitive separation (Prog group, N = 18). The impact of these two methods was assessed in both foals and their mothers through behavioral and biological parameters, including salivary cortisol, telomere length and blood transcriptomes. On the day of definitive separation, Pro...
Statistical modeling of the equine third metacarpal bone incorporating morphology and bone mineral density. The objective of this study was to describe the three-dimensional shape and subchondral bone mineral density (BMD) variation of the equine distal third metacarpal bone (MC3) using a statistical shape model. The association between form and function builds upon previous two-dimensional observations of MC3 epiphyseal structure. It was expected that the main source of variation would be an increase in overall MC3 bone size, correlated to an increase in subchondral BMD. Geometry and bone mineral density was obtained from CT image data of 40 healthy Thoroughbred horses. This was used to create a st...
Subchondral bone morphology in the metacarpus of racehorses in training changes with distance from the articular surface but not with age. The repetitive large loads generated during high-speed training and racing commonly cause subchondral bone injuries in the metacarpal condyles of racehorses. Adaptive bone modelling leads to focal sclerosis at the site of highest loading in the palmar aspect of the metacarpal condyles. Information on whether and how adaptive modelling of subchondral bone changes during the career of a racehorse is sparse. The aim of this cross-sectional study was to describe the changes in subchondral bone micromorphology in the area of highest loading in the palmar aspect of the metacarpal condyle in thorough...
Using partial least squares regression as a predictive tool in describing equine third metacarpal bone shape. Population variance in bone shape is an important consideration when applying the results of subject-specific computational models to a population. In this letter, we demonstrate the ability of partial least squares regression to provide an improved shape prediction of the equine third metacarpal epiphysis, using two easily obtained measurements.
Hydrochemical and multivariate analysis of groundwater quality in the northwest of Sinai, Egypt. The northwestern coast of Sinai is home to many economic activities and development programs, thus evaluation of the potentiality and vulnerability of water resources is important. The present work has been conducted on the groundwater resources of this area for describing the major features of groundwater quality and the principal factors that control salinity evolution. The major ionic content of 39 groundwater samples collected from the Quaternary aquifer shows high coefficients of variation reflecting asymmetry of aquifer recharge. The groundwater samples have been classified into four clu...
Genetic diversity of Syrian Arabian horses. Although Arabian horses have been bred in strains for centuries and pedigrees have been recorded in studbooks, to date, little is known about the genetic diversity within and between these strains. In this study, we tested if the three main strains of Syrian Arabian horses descend from three founders as suggested by the studbook. We examined 48 horses representing Saglawi (n = 18), Kahlawi (n = 16) and Hamdani (n = 14) strains using the Equine SNP70K BeadChip. For comparison, an additional 24 Arabian horses from the USA and three Przewalski's horses as an out group were added. Observed h...
Phenotypic and Genetic Analysis of the Leopard Complex Spotting in Noriker Horses. Genetic analyses of coat colors are frequently restricted to subjectively categorized phenotype information. The aim of this study was to develop a method to numerically quantify the variability of leopard complex (LP) spotting phenotypes introducing tools from image analysis. Generalized Procrustes analysis eliminates systematic errors due to imaging process. The binarization of normalized images and the application of principal component analysis (PCA) on the derived pixel matrices, transform pixel information into numerical data space. We applied these methods on 90 images to ascertain the ...
Application of Genomic Estimation Methods of Inbreeding and Population Structure in an Arabian Horse Herd. Horse breeders rely heavily on pedigrees for identification of ancestry in breeding stock. Inaccurate pedigrees may erroneously assign individuals to false lineages or breed memberships resulting in wrong estimates of inbreeding and coancestry. Moreover, discrepancies in pedigree records can lead breeders seeking to limit inbreeding into making misguided breeding decisions. Genome-wide SNPs provide a quantitative tool to aid in the resolution of lineage assignments and the calculation of genomic measures of relatedness. The aim of this project was to pilot a comparison between pedigree and gen...
Prediction of the fertility of stallion frozen-thawed semen using a combination of computer-assisted motility analysis, microscopical observation and flow cytometry. Spermatozoa from some stallions do not maintain an acceptable fertility after freezing and thawing. The selection of frozen ejaculates that would be suitable for insemination is mainly based on post-thaw motility, but the prediction of fertility remains limited. A recent study in our laboratory has enabled the determination of a new protocol for the evaluation of fresh stallion semen, combining microscopical observation, computer-assisted motility analysis and flow cytometry, and providing a high level of fertility prediction. The purpose of the present experiment was to perform similar invest...
Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies. The Plio-Pleistocene evolution of and the subsequent domestication of horses and donkeys remains poorly understood, due to the lack of phenotypic markers capable of tracing this evolutionary process in the palaeontological/archaeological record. Using images from 345 specimens, encompassing 15 extant taxa of equids, we quantified the occlusal enamel folding pattern in four mandibular cheek teeth with a single geometric morphometric protocol. We initially investigated the protocol accuracy by assigning each tooth to its correct anatomical position and taxonomic group. We then contrasted the ph...
An epidemiological analysis of equine welfare data from regulatory inspections by the official competent authorities. Determining welfare status in a population is the first step in efforts to improve welfare. The primary objective of this study was to explore a new epidemiological approach for analysis of data from official competent authorities that pertain to compliance with animal welfare legislation. We reviewed data already routinely collected as part of Swedish official animal welfare inspections for 2010-13, using a checklist containing 45 checkpoints (CPs). These covered animal-, resource- and management-based measures of equine welfare. The animal-based CPs were measures that directly related to the...
Neural modulators of temperament: A multivariate approach to personality trait identification in the horse. A relationship between dopamine and temperament has previously been described in human cases of dopaminergic dysfunction. Adjustment in temperament prior to disease manifestation can enable the early identification of individuals at risk of such conditions, and scope exists to extend this application of temperament alterations to cases of dopaminergic dysfunction in horses. A multivariate and mixed-methods approach utilising a questionnaire along with two inferred measurements of dopamine activity (Spontaneous Blink Rate [SBR] and behavioral initiation rate [BIR]) were recorded from direct obs...
Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material. There are many choices for methods of extracting bacterial DNA for Next Generation Sequencing (NGS) from fecal samples. Here, we compare our modifications of a phenol/chloroform extraction method plus an inhibitor removal solution (C3) (ph/Chl+C3) to the PowerFecal® DNA Isolation Kit (MoBio-K). DNA quality and quantity coupled to NGS results were used to assess differences in relative abundance, Shannon diversity index, unique species, and principle coordinate analysis (PCoA) between biological replicates. Six replicate samples, taken from a single ball of horse feces manually collected from ...
Characterization and differentiation of equine experimental local and early systemic inflammation by expression responses of inflammation-related genes in peripheral blood leukocytes. Local inflammation may progress into systemic inflammation. To increase our understanding of the basic immunological processes during transition of equine local inflammation into a systemic state, investigation into the equine systemic immune response to local inflammation is warranted. Therefore, the aim of this study was to investigate the innate peripheral blood leukocyte (PBL) immune response to local inflammation in horses, and to compare this response with the PBL immune response during the early phase of acute systemic inflammation. Expression of 22 selected inflammation-related genes w...
Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region. Conformation has long been a driving force in horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait vari...
The MC1R and ASIP Coat Color Loci May Impact Behavior in the Horse. Shared signaling pathways utilized by melanocytes and neurons result in pleiotropic traits of coat color and behavior in many mammalian species. For example, in humans polymorphisms at MC1R cause red hair, increased heat sensitivity, and lower pain tolerance. In deer mice, rats, and foxes, ASIP polymorphisms causing black coat color lead to more docile demeanors and reduced activity. Horse (Equus caballus) base coat color is primarily determined by polymorphisms at the Melanocortin-1 Receptor (MC1R) and Agouti Signaling Protein (ASIP) loci, creating a black, bay, or chestnut coat. Our goal was...
Targeted Metabolomics Approach To Detect the Misuse of Steroidal Aromatase Inhibitors in Equine Sports by Biomarker Profiling. The use of anabolic androgenic steroids (AAS) is prohibited in both human and equine sports. The conventional approach in doping control testing for AAS (as well as other prohibited substances) is accomplished by the direct detection of target AAS or their characteristic metabolites in biological samples using hyphenated techniques such as gas chromatography or liquid chromatography coupled with mass spectrometry. Such an approach, however, falls short when dealing with unknown designer steroids where reference materials and their pharmacokinetics are not available. In addition, AASs with fast...
Comparing the effect of modeled climatic variables on the distribution of African horse sickness in South Africa and Namibia. Africa horse sickness (AHS) is a lethal disease of horses with a seasonal occurrence that is influenced by environmental conditions that favor the development of Culicoides midges (Diptera: Ceratopogonidae). This study compared and evaluated the relationship of various modeled climatic variables with the distribution and abundance of AHS in South Africa and Namibia. A comprehensive literature review of the historical AHS reported data collected from the Windhoek archives as well as annual reports from the Directorate of Veterinary services in Namibia were conducted. South African AHS reported ...
Evidence for the effect of serotonin receptor 1A gene (HTR1A) polymorphism on tractability in Thoroughbred horses. Tractability, or how easily animals can be trained and controlled, is an important behavioural trait for the management and training of domestic animals, but its genetic basis remains unclear. Polymorphisms in the serotonin receptor 1A gene (HTR1A) have been associated with individual variability in anxiety-related traits in several species. In this study, we examined the association between HTR1A polymorphisms and tractability in Thoroughbred horses. We assessed the tractability of 167 one-year-old horses reared at a training centre for racehorses using a questionnaire consisting of 17 items....
Modeling equine race surface vertical mechanical behaviors in a musculoskeletal modeling environment. Race surfaces have been associated with the incidence of racehorse musculoskeletal injury, the leading cause of racehorse attrition. Optimal race surface mechanical behaviors that minimize injury risk are unknown. Computational models are an economical method to determine optimal mechanical behaviors. Previously developed equine musculoskeletal models utilized ground reaction floor models designed to simulate a stiff, smooth floor appropriate for a human gait laboratory. Our objective was to develop a computational race surface model (two force-displacement functions, one linear and one nonlin...
Impact of race training on volumetric bone mineral density and its spatial distribution in the distal epiphysis of the third metatarsal bone of 2-year-old horses. The aim of the study was to use spatial and multiple correspondence analysis (MCA) to describe and compare the regional proportion and spatial pattern of volumetric bone mineral density (BMDv) values within loaded regions of the plantar metatarsal epiphysis of young horses in race training. A single 2 mm transverse peripheral quantitative computed tomography 'slice', 10 mm proximal from the distal limit of the sagittal ridge of the distal metatarsal epiphysis was obtained from 14 2-year-old Thoroughbred fillies (7 exercised and 7 controls). Six regions of interest were generated and examin...
