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Topic:Phenotype
Phenotype in horses refers to the observable physical and behavioral traits of an individual horse, which result from the interaction of its genetic makeup and environmental influences. These traits include characteristics such as coat color, height, conformation, and temperament. Phenotypic expression is a focal point in equine breeding and management, as it influences performance, health, and suitability for specific disciplines. Research in this area examines the genetic basis of phenotypic traits, the impact of environmental factors, and the interaction between genetics and environment. This page aggregates peer-reviewed research studies and scholarly articles that explore the genetic determinants, environmental effects, and practical implications of phenotypic traits in horses.
Inter- and intra-rater reliability of linear scoring in warmblood breeding. Reliable phenotypes are essential for successful animal breeding programmes. Subjective phenotypic assessment may lead to under- or overestimation of heritability estimates and thereby affect the power of genome-based analyses. In Warmblood horses, conformation traits are commonly assessed using linear scoring, but its reliability has not been sufficiently quantified. Objective: In this study, we investigated inter- and intra-rater reliability of linear scoring of conformation traits in German warmblood horses. Methods: Professional equine breeding experts (e.g. breeding judges) completed an o...
Implications of dominance deviations for reproductive and morphological traits in the genetic management of the Pura Raza Española horse. Dominance is a non-additive genetic effect involving allele interaction at the same locus. In animal breeding, it has often been ignored due to its complexity and the low accuracy of pedigree-based estimates. This study analysed dominance variance components for reproductive traits [age at first foaling (AFF), reproductive efficiency (RE), interval between first and second foaling (I12)] and morphological traits [scapulo-ischial length (SIL), dorsal sternal diameter (DSD), knee circumference (KC)] in Pura Raza Española (PRE) mares. The aim was to assess the magnitude of dominance effects acro...
A Global Structural Variation Map Reveals Novel Variants for Body Conformation and Racing Ability in Horses. The selection of horses has been instrumental in shaping long-range mobility, advancing warfare strategies, and diversifying equine phenotypes. However, the structural variants (SVs) favored by this process remain largely unexplored. Utilizing high-fidelity Pacific Biosciences sequencing, we assembled three high-quality horse genomes, incorporating 237 Mb (9.48%) of novel sequences relative to the existing reference genome. These assemblies achieved an average Benchmarking Universal Single-Copy Orthologs completeness of 95.1%. By employing a graph-based approach, we genotyped 23,163 high-con...
Phenotypic Definition Influences Genetic Inference and Predictive Ability for Reining Performance in Quarter Horses Using Random Regression Models. Reining performance is influenced by subjectivity and competition structure, challenging genetic evaluation. This study estimated genetic parameters for reining performance in Brazilian Quarter Horses using random regression models (RRM) and evaluated how alternative phenotypic definitions affect genetic inference and predictive ability. A dataset comprising 21,165 longitudinal records from 1603 horses was analyzed, comparing within-group rank (RANK) and Blom-transformed rank (BLOM). Model comparison indicated that cubic RRM provided the best fit for both phenotypes. Heritability estimates wer...
Effects of IGF1 Knockdown and Overexpression on the Phenotype and Function of Equine Primary Skeletal Muscle Cells. Skeletal muscle serves as the direct executor of movement, and the proliferation and migration capacities of its constituent cells represent the key physiological foundation determining equine endurance and speed. Previous whole-transcriptome analysis has shown that Insulin-like Growth Factor 1 () is significantly upregulated in following racing and is involved in the PI3K-Akt signaling pathway; however, its specific regulatory mechanism in equine skeletal muscle cells remains unclear. This study utilized primary equine skeletal muscle cells as a model. By constructing an overexpression plas...
Phenotypic and genetic factors that affect the likelihood of Standardbred foals achieving a race start. This study was conducted to quantify the probability of a Standardbred foal attaining early career milestones and to estimate some environmental and genetic factors that influence achievement of those milestones. Data for all Standardbred foals registered at birth in New Zealand from 1995 to 2018 were used to estimate variance components and fixed effects influencing attainment of three early-career traits; registered with trainer (REG), starting in a trial (TRIAL) and starting in a race (RACE). The study population comprised 65,256 foals. Of these, 65.5% attained REG, 55.4% progressed to TRIA...
When genes meet money: Genotype-by-prize interaction in Quarter Horses. Barrel racing performance reflects a complex interplay among genetic merit, rider ability, training strategies, and competition-specific conditions. In practice, events differ substantially in their economic scale, and prize money can serve as a proxy for management intensity, rider expertise, and selection pressure. Objective: This study investigated whether economic stratification, represented by total prize money per event, is associated with changes in (co)variance components for barrel racing time in Brazilian Quarter Horses. Methods: A reaction-norm model was implemented using 349,262 ra...
Genetic Indicators of Performance Resilience in Barrel Racing Quarter Horses. Resilience, defined as the capacity to maintain consistent performance under variable conditions, has emerged as a relevant breeding objective in livestock systems, yet remains largely unexplored in equine populations. The objectives of this study were to (1) derive indicators of resilience from longitudinal barrel racing time (BRT) records in Brazilian Quarter Horses, (2) estimate genetic parameters for these indicators, and (3) quantify their genetic relationships with BRT and accumulated career earnings (ACE). The dataset comprised BRT records from barrel racing events held between 2010 and...
Phenotypic characterization through identification of gait and coat color phenotype of the Mountain Pleasure Horse. Phenotypic characterization of traits like gait and coat color is useful for minor breed identification and conservation. The Mountain Pleasure Horse (MPH) is a minor American breed as it is listed as threatened by the Livestock Conservancy. Objective: The study objective was to utilize phenotypic characterization for identifying gait and coat color phenotype of the MPH. Methods: Gait was characterized utilizing frame-by-frame analysis to identify spatiotemporal variables of purebred horses (n = 6) performing the flat walk and saddle rack. Coat color was characterized using coat color assi...
The “gait keeper” mutation does not influence gait scores in Pêga donkeys: a preliminary result. The DMRT3 "gait keeper" mutation is a major determinant of locomotor patterns in horses, but its role in donkeys remains unclear. This study evaluated the association between this polymorphism and gait performance in Pêga donkeys, a breed selected for gaited locomotion. A total of 260 animals were phenotyped for gait scores and genotyped by PCR-sequencing targeting exon 2 of DMRT3. All individuals were homozygous for the wild-type allele (CC), and the mutant A allele was not detected. The monomorphism precludes any association with gait scores, possibly indicating that this DMRT3 mutation has...
Machine learning-based gait classification and genome-wide association identify a QTL for gait type in Colombian paso horses. Coordinated mammalian locomotion relies on spinal circuits where regulates strides and alternative gaits. However, does not explain differences between the Colombian paso horse breed's specialized gaits, Colombian trocha and Colombian trot. We used inertial sensors and machine learning to develop accurate phenotyping ( = 225 horses), before performing genome-wide association analysis ( = 85 horses, 670K array). We identified a 2.43 Mb quantitative trait locus (QTL) on ECA16, where haplotypes featuring lead variants (rs1147402472, = 1.95 × 10; rs1136628503, = 8.52 × 10) explained 48.6% of...
Cytogenetic, genomic, and reproductive characterization of four pura Raza Española mares carrying a 64, X, del(X),t(X; Y) complex karyotype. Chromosomal abnormalities involving the sex chromosomes constitute critical genetic factors influencing fertility in horses. Nevertheless, a substantial proportion of individuals carrying sex chromosomal abnormalities exhibit normal reproductive phenotypes, which complicates their identification until adulthood. Here, we present four mares carrying a complex deletion/translocation rearrangement with the karyotype formula 64, X, del(X)(p∼25),t(X; Y)(p∼25; q∼15). The cases analyzed belong to three unrelated families of Pura Raza Española (PRE), all presenting the same chromosomal abnormal...
Is the walk and trot efficiency a hereditary trait in primitive Konik Polski horses? Performance testing is a critical tool for achieving genetic progress, yet its long-term effectiveness in primitive breeds under conservation programs is poorly documented. The Konik Polski horse breeding program aims to improve utility while preserving primitive characteristics. Unassigned: This retrospective study analyzed a 25-year longitudinal dataset ( = 1,608) from the official Field Performance Test to quantify genetic trends in gait efficiency, using nonparametric methods to assess the effects of test type, year, and age on stride length and speed at the walk and trot. To estimate he...
Genome-Wide Association Study Reveals Genetic Loci Associated with Body Measurement Traits in Yanqi Horses. Body measurement traits are a direct production indicator reflecting growth status and guiding genetic selection. Identifying molecular markers associated with body measurement traits could accelerate animal breeding programs. The Yanqi horse, an important indigenous breed in Xinjiang, is primarily distributed in the Bayingolin Mongol Autonomous Prefecture. However, molecular markers linked to body measurement traits in Yanqi horses remain uncharacterized. In the present study, whole-genome resequencing was performed on 183 Yanqi horses, yielding 13,366,672 single-nucleotide polymorphisms (SNP...
Unraveling the genomic architecture of hock conformation defects in Pura Raza Española horses. Conformational traits define a horse's shape and morphology, heavily influencing its functionality, sport performance, health, and appearance, making conformation a critical selection criterion in horse breeding. However, the genomic basis of conformational defects, specifically those affecting the hock, remains largely unexplored. This research aimed to identify the genomic regions associated with hock defects using a large cohort of Pura Raza Española (PRE) horses. A total of 58,930 horses were evaluated for hock angle, with 4,122 genotyped on high or medium density arrays. For this purpose...
Additional Evidence Fails to Associate Variation in KCNE4 With Equine Anhidrosis. A prior genome-wide association (GWA; N = 200) including Thoroughbreds and stock horses implicated chromosome 6 (NC_009149.3) in owner-reported equine anhidrosis. A missense variant in KCNE4 (NC_009149.3:g.11813731A>G) was proposed as a risk allele, although its association with anhidrosis was not reported. Variant annotation and protein modelling in the original study suggested the G allele conferred risk. We reported no association of the G allele with anhidrosis in 50 horses phenotyped by an intradermal terbutaline sweat test (ITST); all horses produced sweat regardless of genotype. ...
Evidence of occipitoatlantoaxial malformations independent of the HOXD3 mutation in an Arabian horse. Occipitoatlantoaxial malformations (OAAM) are developmental disorders occurring at the occiput, atlas and axis. OAAM type 1 is a familial disorder affecting Arabian horses. Currently, a single genetic mutation in the HOXD3 gene region can be tested to confirm the diagnosis. This case describes a 3-year-old Arabian gelding affected with OAAM. Clinical examination revealed a proximal cervical deformation on the right side and severe stiffness of the neck in the sagittal plane without associated pain. Neurological examination demonstrated a generalized proprioceptive ataxia. Radiographs revealed ...
Haplotype GWAS in swedish warmblood horses for conformation and jumping traits. The aim of this study was to better understand the genomic architecture behind performance-related traits in sport horses. In this study, we conducted a haplotype-based genome-wide association study (GWAS) for 36 conformation and free jumping phenotypes recorded during routinely conducted young horse evaluation tests involving 380 Swedish Warmblood (SWB) horses. The horses were evaluated by expert judges using both traditional and linear evaluation systems. All samples were genotyped using the 670K Affymetrix® Axiom® Equine Genotyping Array, haplotypes were first phased, and haplotype blocks...
Prevotella mikamonis sp. nov., isolated from equine clinical specimens. In this study, five strains of anaerobic, Gram-negative, rod-shaped bacteria were characterized phenotypically, biochemically and genotypically. These strains were clinically isolated from horse specimens in Japan. Phylogenetic trees constructed based on 16S rRNA gene sequence comparisons showed distinct clustering of the five strains with the type strains of closely related species. The genomic DNA G+C content was 46.7 mol%. The major cellular fatty acids identified were C, 3-OH-C and 3-OH-iso-C. Whole-genome comparisons based on average nucleotide identity using blast (ANIb) and digital DNA...
Serum-free medium modulates the immunomodulatory and anabolic function of equine bone marrow-derived mesenchymal stromal cells. Adult bone marrow-derived mesenchymal stromal cells (BM-MSCs) hold significant therapeutic potential in human and veterinary medicine. Traditionally, BM-MSC cultures use fetal bovine serum (FBS) to promote growth, but this practice introduces batch variability and xenogeneic contamination that complicate clinical translation. While serum-free medium (SFM) alternatives have been optimized for human MSCs, limited options have been explored for alternative or veterinary species. Here, we compared a chemically defined, customizable SFM formulation with conventional serum-containing medium (SCM) fo...
Genetic background and phenotypic features of the endangered Miyako horse. The Miyako horse is one of the eight Japanese native horse breeds and is scarce in terms of population size. Japanese native horses are believed to be descended from Mongolian horses and represent a precious lineage that has preserved its traits for over a thousand years in Japan. Genetic analysis of the endangered Miyako horse is useful for preserving its original phenotypic traits. This study analysed the genetic variation in trait-related genes for coat colour (), body composition (), gait (), and temperament () in 46 extant Miyako horses. In addition, because numerous Miyako horses have ve...
Heritability Estimates of Traits Assessed in Field Performance Tests of Polish Warmblood Mares. : Knowledge of the genetic background of evaluated traits has been the basis for genetic progress in every horse-breeding population and is essential for precise breeding and up-to-date decision-making. The study aimed to estimate the heritability coefficients for field performance traits in mares. : The research was based on 1408 evaluations of mares conducted during the years 2002-2021 in 51 training centers in Poland. The preliminary analyses of the effects, significant for the investigated traits, were obtained using analysis of variance, and these additional data are also presented (SAS p...
Genetic and phenotypic insights into thermal load and racing performance of Quarter Horses. Thermal load is a major welfare and performance concern for athletic horses, as physical exertion increases internal heat production. Although several phenotypic strategies have been developed to mitigate its effects, the genetic basis of thermal tolerance in horses remains largely unexplored. This study aimed to (1) evaluate the influence of thermal indices on the racing performance of Brazilian Quarter Horses, and (2) investigate the genetic basis of thermal tolerance through the estimation of genetic parameters across temperature gradients. We analyzed 21,857 racing-time (RT) records from 5...
Is There a Genetic Link Between Resting Infrared Thermography in Young Horses and Longevity in Jumping Competition? The objective was to evaluate the genetic relationship between the surface temperature of regions of interest, measured using infrared images of young horses and functional longevity in jumping. This relationship was assessed by comparing the temperatures measured in the offspring of two groups of sires, one favourable and one unfavourable, to longevity. The study used a specific data collection protocol on a sample of 921 young progeny, before they began competing, of 141 extreme stallions, comprising 61 favourable and 80 unfavourable sires. These stallions had been selected based on estimate...
A SLC45A2 mutation is strongly associated with the cream dilution in Baroque donkeys. Domestic Baroque donkeys are popular animals in many European parks and zoos. Although their cream coat color is very charismatic, the underlying genetics is still undiscovered. Addressing this question, a candidate approach was used to search for the causative mutation.Considering the knowledge from domestic horses, the () was identified as the most promising candidate. Samples from 77 domesticated donkeys, 11 wild equids, 1 mule and 2 domestic horses were included in comparison. All exons and the flanking intron sequences of the were sequenced (2774bp).Sequence comparison revealed that a m...
Genetic parameter estimates of performance traits in Iranian Thoroughbred race horses using a Bayesian approach. Race performance in Thoroughbred horses is influenced by both genetic and environmental factors. Understanding their genetic architecture is essential for designing effective breeding programs. Objective: This study aimed to estimate genetic parameters and trends for key performance traits in Iranian Thoroughbred racehorses. Methods: Performance data, including race completion time (RCT), rank at the end of the competition (REC), and average speed (AS), were obtained from the Iranian Equestrian Federation (2002-2021). Pedigree data from 14,391 individuals were analyzed using CFC software. Gene...
The Role of Genetic and Environmental Factors in White Leg Markings: Prevalence and Heritability Analysis in Pura Raza Española Horses. White leg markings in horses are phenotypic traits influenced by genetic and environmental factors. This study analyzed their prevalence, symmetry, and genetic parameters in 38,825 Pura Raza Española (PRE) horses registered in the official studbook. White markings were scored using a binary (affected/unaffected) and a four-level ordinal scale. Most horses (38,341 out of 38,825; 98.8%) had at least one limb without white markings. The prevalence of white markings was higher in the hindlegs (17.9% LH; 14.5% RH) than in the forelegs (5.3% LF; 4.6% RF). Markings were most frequent above the fetlo...
Genetic inbreeding depression load for conformation defects and dressage traits in the Pura Raza Española horse. Investigate the genetic inbreeding depression load (IDL) on two dressage traits and two conformational defects in horses. Unassigned: The dataset included performance records for Walk and Points per Reprise (PPR) (N:43,838) and conformation data for Closed and Convergent hocks (N:57,949). Pedigree information spanned over 400,000 individuals. Inbreeding coefficients (F, F6, Fk) and partial inbreeding coefficient (Fij) were computed to quantify the IDL using Bayesian approach. Linear and ordinal logistic regressions were used to assess the relationship between inbreeding and phenotypic values. ...
Early allergen introduction overrides allergy predisposition in offspring of horses with Culicoides hypersensitivity. The origins of allergy are both genetic and environmental. We performed a full-sibling study to determine the role of early-in-life or delayed allergen introduction on hypersensitivity development in a cohort with history of an allergic phenotype and Culicoides hypersensitivity. IgE-mediated allergies naturally develop in many mammalian species, and we used a horse model of allergy called hypersensitivity. hypersensitivity is a seasonal, recurrent, IgE-mediated allergy caused by the salivary proteins of biting midges. Unassigned: The study included four cohorts that lived together in the s...
