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Topic:Alleles
Alleles in horses refer to the different versions of a gene that exist within the equine genome, contributing to the diversity of traits observed in horse populations. These genetic variations can influence a wide range of characteristics, including coat color, height, temperament, and susceptibility to certain diseases. Understanding alleles is crucial for breeding programs, as they help predict the inheritance of desirable traits and manage genetic disorders. Common examples include the alleles responsible for coat color variations, such as the Extension (E) and Agouti (A) loci. This page compiles peer-reviewed research studies and scholarly articles that explore the identification, function, and impact of alleles on equine genetics, offering insights into their role in shaping the phenotypic and health-related traits of horses.
Allele frequencies of 7 inherited disorders in performance and random cohorts of American Quarter Horses (2020-2024). To estimate allele frequencies for genetic diseases in the American Quarter Horse (QH), including hyperkalemic periodic paralysis (HYPP), type 1 polysaccharide storage myopathy (PSSM1), malignant hyperthermia (MH), myosin-heavy chain myopathy (MYHM), glycogen branching enzyme deficiency (GBED), hereditary equine regional dermal asthenia (HERDA), and equine juvenile spinocerebellar ataxia (EJSCA), and to compare these frequencies over time among elite performance subgroups and a random cohort of registered horses. Unassigned: In this prospective genetic survey, DNA was extracted from 300 elite ...
Characterization of Lipizzan Horse Population From Lipica Stud Using Molecular and Pedigree Data. In this study, we analysed genetic diversity, population structure and inbreeding in the Lipica Stud Farm population by integrating pedigree records, microsatellite (STR) and genome-wide SNP data generated using the GGP Equine 70K BeadChip. The dataset comprised 233 horses from the Lipica Stud Farm, which served as the reference population for comparisons of diversity estimates based on pedigree-, STR- and SNP data. The STR data were originally generated for routine parentage verification and were included here to compare inbreeding estimates based on pedigree, STR and genome-wide SNP data. Pe...
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...
Identification of a Novel Slow-Gray STX17 Lineage in Japanese Thoroughbreds via a Multi-tiered Copy Number Analysis Workflow. Gray is a dominant coat color phenotype in horses caused by a ~ 4.6 kb tandem triplication within intron 6 of syntaxin 17 (STX17). The copy number variation (CNV) of the duplicated segment influences the graying rate. The rare G2 allele (CNV = 2) is associated with a slower graying rate compared to the common G3 allele (CNV = 3) and is also relevant to melanoma risk. Current assays are limited because long and accurate PCR (LA-PCR) detects only the presence or absence of duplications, while droplet digital PCR (ddPCR) cannot reliably distinguish certain genotypes such as G3/g and ...
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...
Genetic variability and associations of Trakehner and other horse populations in Lithuania. To obtain genetic parameters relevant for the management of animal genetic resources, this study provides a comparative characterization of the Trakehner (TRAK) horse population in relation to four other horse populations maintained in Lithuania - Arabian (ARAB), Baltic Warmblood (BW), Lithuanian Warmblood (LW), and Zemaitukai (ZEM). These populations represent diverse histories, selection goals, and breeding practices. Pedigree data ( 22 666) and parentage verification genetic data based on blood group markers ( 1293) were used to evaluate genetic diversity, population structure, and inter-...
Genetic Diversity and Population Structure in Seven Lipizzan Populations Based on Microsatellite Genotyping. Lipizzan horses, bred for over four centuries, represent a unique genetic, cultural and historic resource. This study assessed genetic diversity and population structure across seven European Lipizzan populations, with emphasis on the Bosnia and Herzegovina population. A total of 547 Lipizzan horses were genotyped using 12 microsatellite markers. The parameters of genetic variability, admixture level and migration rate were calculated. The mean number of alleles, effective number of alleles and Shannon's information index were 5.78, 3.24 and 1.31, respectively. The average fixation indices wer...
CXCL16-associated genetic susceptibility to equine viral arteritis in export-bound horses from Spain. Equine viral arteritis (EVA) remains a relevant health and economic concern due to the ability of some infected stallions to establish long-term persistent infection with equine arteritis virus (EAV). Allelic variation in the CXCL16 gene has been identified as a determinant of susceptibility or resistance to the carrier state, positioning genotyping as a useful tool for risk-based reproductive and health management. Objective: To characterise the distribution of CXCL16 genotypes in export-bound horses from Spain and to assess the utility of CXCL16 genotyping for EVA prevention and control. Met...
High frequency and high genetic diversity of Pneumocystis sp. in foals. Twenty-two foals, aged one to seven months, which died from interstitial pneumonia (15 foals) or unrelated illnesses and injuries (7 foals), were enrolled in this study. Sampling of the lungs was performed post-mortem for a total of 52 specimens. Pneumocystis was detected in 21/22 foals (48/52 specimens) using a PCR assay targeting the gene encoding the small subunit of the mitochondrial rRNA (mtSSUrRNA) of the horse-related Pneumocystis (Pneumocystis sp. 'Equus ferus caballus'). The sequencing of the PCR products was successful in 34/48 specimens. The sequences were identical to the horse-rel...
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. ...
Genomic diversity and structure in arabian horses revealed by whole-genome sequencing: establishment of an allele frequency database of common genetic variation. BACKGROUND: The Arabian horse is a culturally and historically influential breed that has contributed to the development of many modern horse populations. However, genomic resources for this breed remain limited, particularly population-level allele frequency datasets that support studies of genetic diversity, selection, and disease. The aim of this study was to generate a comprehensive allele frequency database for Arabian horses using representative sampling and high-coverage whole-genome sequencing. RESULTS: We generated the first publicly available allele frequency database for the Arabian...
HERDA-associated variant in bull-catching (vaquejada) Brazilian Northeastern bull-catching Quarter Horses. Bull-catching (vaquejada) accounting for approximately 13% of sport horses in Brazil. Genetic screening has enabled strategies to reduce the spread of inherited disorders, including Hereditary Equine Regional Dermal Asthenia (HERDA), a major skin disease included in the Six Panel required for registration by the Brazilian Quarter Horse Breeders Association. Although the HERDA-associated variant has been extensively studied in other disciplines, it had not been evaluated in Bull-catching Quarter Horses (QH). Objective: The present study aimed to determine the allele frequency of the pathogenic ...
DMRT3 Gene Variations in Horse Breeds Selected for Gaited Movement – Established Research and Novel Findings. The DMRT3 gene, often referred to as the "gait keeper," plays a key role in controlling alternative gaits in horses, such as tölt and pace. This study aimed to determine the frequency of known and to screen for potential novel polymorphisms within the second exon of the DMRT3 gene. Methods: A total of 244 blood or hair samples were collected from representative individuals of the six horse breeds: gaited (Icelandic Horse, French Trotter), non-gaited (Arabian Horse, Malopolski Horse), and pony breeds (Welsh Pony, Shetland Pony). Methods: The second exon of the DMRT3 gene analyzed using Sanger ...
Pedigree-Based Assessment of Genetic Structure and Disease-Associated Variants in Friesian Horses in Brazil. Background: Friesian horses are recognized for severe genetic restriction due to intensive selection. Still, the genetic diversity, founder representation, and prevalence of inherited disorders in the Brazilian Friesian population, which is comprised of fewer than 500 individuals, have not been previously investigated AIMS/OBJECTIVES: characterize the genetic diversity, inbreeding, founder representation using pedigree-based tools, and frequency of known pathogenic, behavioral, and white spotting alleles in Friesian horses registered in Brazil METHODS: Pedigree data from 411 Friesian horses (2...
Evidence That GYPA (Glycophorin A) Encodes the K Blood Group System in Horses. Although serological and genetic studies of equine blood group systems have been conducted for many years, the molecular basis of erythrocyte antigens' variability has remained largely unexplored. In this study, we aimed to elucidate the genetic basis of serological variation within equine blood group K. Using mRNA extracted from peripheral blood samples (n = 100) collected from horses with known serological blood types (Ka or K-), we performed a transcriptome-wide association study (TWAS), which revealed a significantly associated region on equine chromosome 2 (ECA2). A detailed analysis ...
Deficiency in homozygous haplotypes reveals recessive lethal variants affecting fertility and viability in the Friesian horse. BACKGROUND: Recessive lethal alleles causing pre- or postnatal death in homozygous mutant animals, could lead to reduced fertility success. The Friesian horse breed has signs of reduced fertility and has faced high inbreeding rates in the past (∆F > 1%). Consequently, by genetic drift lethal alleles may have reached moderate to high frequencies in the population. Our aim was to identify lethal recessive alleles that — when homozygous — may cause pre- or postnatal death in the Friesian horse. RESULTS: We analyzed genotypes (70 K SNP) of over 8,000 Friesian horses, looking for hapl...
Pedigree tracing to determine the origin of the golden coat phenotype within the golden American saddlebred horse. Due to the incorporation of the Golden American Saddlebred Horse Association (GASHA) into the American Saddlebred Horse and Breeders Association (ASHBA), breeding for coat color has become more challenging for horse breeders. However, with this merger, pedigree tracing can be of value in pinpointing foundation bloodlines within the GASHA that influence production of the golden coat phenotype. Objective: The study objective was to document the historical origins of the GASHA through pedigree tracing to determine the influence of dilution alleles that produce the golden coat phenotype. Methods: ...
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...
Temporal and intra-horse consistency of circulating myostatin concentrations in Thoroughbred racehorses. In Thoroughbred horses, a highly prevalent short interspersed nuclear element (SINE) mutation in the myostatin gene (MSTN) promoter influences circulating myostatin concentration and is associated with muscle morphology, fracture risk and optimal race distance. Our prior data reveal that within horses there is substantial variation in serum myostatin concentration, particularly in MSTN heterozygotes and wild type horses but it was unclear whether such variation relates to within-horse differences or to environmental or temporal effects. Here we report the intra-horse consistency of circulating...
Characterization of the lambda light chain repertoire and non-coding regions of equine immunoglobulins using the EquCab3 genome. Horse immunoglobulins have been utilized for over a century in serotherapy to treat venomous animal bites and various other conditions. However, molecular-level information about these immunoglobulins remains limited, particularly regarding immunoglobulin lambda light chains (Igλ), which constitute over 90 % of circulating antibodies. Despite the sequencing of the equine genome, the International ImMunoGeneTics information system (IMGT) has not yet annotated Igλ in its database, restricting the analysis of the horse antibody repertoire. In this study, we analyzed the equine Igλ repertoire...
A de novo FBN1 variant likely causes congenital bilateral ectopia lentis in a crossbred horse. Although several inherited ocular disorders have been extensively studied in horses, few reports of equine ectopia lentis exist and no genetic investigations have been reported. Ectopia lentis in humans and other species is reported to be caused by trauma, genetic variants, and systemic diseases. The most commonly reported genetic causes are dominant alleles in FBN1. Here we examined a 3-day old Oldenburg x Thoroughbred colt due to concerns over bilateral ocular anomalies and hypothesized that either a recessively inherited allele or a dominant de novo allele was the genetic cause. Examination...
Genome-wide association study reveals candidate loci on ECA1 and ECA9 for withers height in Friesian horses. In Friesian horses, withers height is an important trait as a minimum has been set to be eligible to the studbook. Several loci for withers height have been identified in horses. However, withers height has not been studied in the Friesian horse. Therefore, our aim was to identify loci associated with withers height in the Friesian horse population. We performed a genome-wide association study using 70 K SNP data of 2192 Friesian horses. We found ECA1 and ECA9 to be significantly associated with withers height, explaining 19.6% and 3.5% of the phenotypic variance, respectively. In other hors...
Connections Between Gene Polymorphism and Fetlock and Hock Measurements in Polish Sport Horses. Finding the causative mutations for musculoskeletal system development and health status is of a higher priority for all sport horse breeders' associations. Of the regulating proteins involved in animal ossification, 15 gene polymorphisms were chosen to be identified as connected with the nine fetlock and 14 hock bone structures measurements of 198 horses. All measurements were taken using X-rays of the limbs, which were available at the beginning and end of the horse training. The analysis of variance (GLM, SAS program) was performed taking into account identified training and horse-connected...
Insights into Genomic Patterns of Homozygosity in the Endangered Dülmen Wild Horse Population. Dülmen wild horses are kept in a fenced wooden and marsh area around Dülmen in Westphalia, Germany, since 1856. Previous analyses supported early genetic divergence from other domesticated horse populations and the Przewalski horse. Therefore, the objective of this study was to evaluate genetic diversity using high-density genomic data. Methods: We collected 337 one-year-old male Dülmen wild horses, captured at 12 annual auctions, for genotyping on the Illumina GGP Equine Plus Beadchip. All analyses were performed for 63,123 autosomal SNPs. Results: On average, each horse had 27.96 ROH with...
The rise of rideable horses. Early horse riders selected a rare mutation in a single gene to enhance rideability.
Selection at the GSDMC locus in horses and its implications for human mobility. Horsepower revolutionized human history through enhanced mobility, transport, and warfare. However, the suite of biological traits that reshaped horses during domestication remains unclear. We scanned an extensive horse genome time series for selection signatures at 266 markers associated with key traits. We detected a signature of positive selection at -known to be a modulator of behavior in mice-occurring ~5000 years ago (ya), suggesting that taming was one of the earliest steps toward domestication of horses. Intensive selection at began ~4750 ya with the domestication bottleneck, leading ...
Comparative Study of Reprogramming Efficiency and Regulatory Mechanisms of Placental- and Fibroblast-Derived Induced Pluripotent Stem Cells (iPSCs) in Mules. As an interspecies hybrid inheriting genetic material from horse and donkey lineages, mules provide a unique model for studying allele-specific regulatory dynamics. Here, we isolated adult fibroblasts (AFs) and placental fibroblasts (PFs) from mule tissues and reprogrammed them into induced pluripotent stem cells (iPSCs). Intriguingly, placental fibroblast-derived iPSCs (mpiPSCs) exhibited reduced reprogramming efficiency compared to adult fibroblast-derived iPSCs (maiPSCs). Through allele-specific expression (ASE) analysis, we systematically dissected transcriptional biases in parental cell t...
Identification of a Novel Haplotype Associated with Roan Coat Color in American Quarter Horses. Roan coat color is described as the dispersion of white hairs within an otherwise solid background-color coat. This phenotype is primarily expressed on the body of the horse, with the head and legs exhibiting few or no white hairs. Previous studies mapped the locus for roan to the region and observed linked variants in a small number of breeds. Recently, we reported evidence for two independent haplotypes, and , in the region, which account for approximately 38% and 36% of roan horses, respectively. In the current report, using whole genome sequencing for unknown roan samples. We present a ...
DNA Methylation of Igf2r Promoter CpG Island 2 Governs Cis-Acting Inheritance and Gene Dosage in Equine Hybrids. Genomic imprinting is critical for mammalian development, but its regulation varies across species. The insulin-like growth factor 2 receptor (IGF2R), which is a maternally expressed imprinted gene critical for cell proliferation and differentiation, as well as embryonic and placental development, is classically regulated by differentially methylated regions (DMRs) and lncRNA- in mice. However, studies on this in equus are scarce, especially in terms of mechanistic studies. In the present study, heart, liver, spleen, lung, kidney, brain, and muscle samples were obtained from horses, donkeys, a...
