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Topic:Genetics
Genetics in horses encompasses the study of hereditary traits and the genetic makeup that influences various characteristics and health conditions in equine populations. This field involves the analysis of genes and their functions, inheritance patterns, and the impact of genetic variations on traits such as coat color, performance ability, and susceptibility to diseases. Research in equine genetics employs techniques such as genome mapping, sequencing, and genetic testing to identify specific genes and mutations associated with these traits. This page gathers peer-reviewed research studies and scholarly articles that explore the genetic basis of equine traits, the methodologies used in genetic research, and the implications for breeding, health management, and conservation of horse breeds.
Cyathostomin species richness and alpha diversity at egg reappearance following fecal egg count-based selective ivermectin treatment. Cyathostomin nematodes are ubiquitous in grazing horses. The overuse of anthelmintics has led to increasing problems with drug resistance to benzimidazoles and pyrantel. Although macrocyclic lactones (ML), such as ivermectin, generally retain the highest efficacy, reduced ML efficacy has increasingly been reported. A shortened egg reappearance period (ERP) is frequently used as an indicator of reduced susceptibility. However, the species-specific response dynamics after ivermectin treatment are inadequately characterized in cyathostomins. The objective of this study was to compare the cyathost...
Management practices and human-horse relationships are associated with horse personality traits. The human-horse relationship has evolved through centuries of domestication, shaping how horses are managed and interact with people. Horses show interindividual behavioural differences that constitute personality, with implications for welfare, management and human-horse interactions. Although equine personality has a genetic component, environmental and relational factors may influence its expression, yet effects of everyday management practices remain poorly understood. This study examined associations between owner-rated horse personality traits and human-controlled environmental and relat...
The Polish Konik Horse: A Multidisciplinary Review of Its Origin, Genetics, Ecology, Health, Behaviour and Reproductive Biology. The Polish Konik horse (PKH) is one of Europe's best-known native conservation breeds. Traditionally associated with the extinct Eurasian tarpan and conservation grazing, the breed has recently become the subject of multidisciplinary research encompassing genetics, ecology, health, behaviour and reproduction. This narrative review summarises current knowledge on the biological characteristics and contemporary scientific significance of the PKH. Literature published between 2005 and 2026 was identified through searches of PubMed, Scopus, Web of Science and Google Scholar and narratively synthes...
Ortholog-specific Spatial Expression of Vanins in the Respiratory Tract of Horses. Equine asthma (EA) is the most prevalent chronic respiratory disease in horses, but molecules thought to be relevant in its pathogenesis are not yet fully understood. Recently, increased Vanin-1 (VNN1) levels were found in bronchoalveolar lavage fluid from horses with severe EA. Human VNN1 is known as a pantetheinase, which is associated with respiratory diseases such as asthma, but the equine vanins (eVNNs) are uncharacterized. We identified the domain architecture of eVNN in silico and analyzed its tissue expression in healthy horses using RT-PCR (=5) and in situ hybridization (=3). Recombin...
Molecular Survey and Genetic Characterization of Tetratrichomonas buttreyi and Pentatrichomonas hominis in Horses in Shanxi Province, Northern China. Trichomonads include species of veterinary and zoonotic importance, yet infections with trichomonads in horses remain uncharacterized in Shanxi Province, Northern China. In the present study, we conducted a molecular survey of and using 631 horse fecal samples collected from Datong, Taiyuan, and Yuncheng cities in Shanxi Province between March and June 2023. Nested PCR assays targeting the small subunit ribosomal RNA (SSU rRNA) gene were used to detect the two trichomonad species. The overall molecular prevalences were 3.7% (23/631; 95% CI, 2.5-5.5%) for and 0.8% (5/631; 95% CI, 0.3-1.9%) f...
Comparative genomics of Standardbred horses reveals candidate regions under selection for harness racing performance. Harness racing performance in horses is a complex polygenic trait influenced by genetic background, breeding history, training, and environment. Understanding genomic patterns shaped by long-term artificial selection provides insights into performance-related traits and breed-specific genomic variation. Objective: This study aimed to characterize genomic differentiation, population structure, and candidate genomic regions potentially influenced by historical selection in Standardbred horses using comparative whole-genome sequencing involving diverse horse breeds. Methods: Whole-genome sequenci...
Equine herpesvirus myeloencephalopathy-associated mutations in equine herpesvirus 1 DNA polymerase confer the ability to replicate at elevated temperatures. Equine herpesvirus myeloencephalopathy (EHM), caused by equine herpesvirus type 1 (EHV-1), poses a major threat to the equine industry because of its devastating impact on animal welfare and athletic performance. A single-nucleotide polymorphism (SNP), G2254, in ORF30 (UL30), which encodes the viral DNA polymerase, has been used as a marker of neuropathogenic EHV-1 strains, although its contribution to EHM pathogenesis remains controversial. In addition, other ORF30 SNPs have been reported in association with EHM, but their functional significance is unclear. Clinical observations indicate tha...
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 ...
Comparative analysis of the karyotypes of Equus caballus and Equus asinus in the context of contemporary genomic data. Karyotypes of species within the genus Equus display considerable variation in chromosome number and are characterised by numerous structural rearrangements that have played a pivotal role in their evolutionary divergence and speciation. Equus caballus (horse), 2n = 64 and Equus asinus (donkey), 2n = 62, constitute particularly interesting models for comparative studies due to the diversified morphology of their chromosomes, including acrocentric and submetacentric pairs, documented Robertsonian translocations, and centric fusions. In recent decades, widely applied molecular cytogenetic techni...
Adaptive variation in butyrylcholinesterase-influenced lipid metabolism during horse domestication. Lipid metabolism influences horse athletic performance, yet its genetic basis remains unclear. Here, we investigate the genetic basis of lipid metabolic traits by quantifying key metabolic parameters and sequencing the genomes of 298 horses. We identify a missense mutation (ECA19:9,198,989, G>C) in the BCHE gene that is strongly associated with lipid metabolism, especially butyrylcholinesterase (BChE) activity. The "C" allele is associated with increased BChE activity and reduced intracellular triglyceride levels, hepatic adiposity, and overall fat mass, highlighting a central role for BCHE in...
Genetic variants of EcPV2 E6 and E7 in equine genital and oronasal squamous cell carcinoma. Since its discovery in 2008, equine papillomavirus type 2 (EcPV2) has been detected in up to 100% of equine genital and up to 40% of equine oronasal squamous cell carcinomas (SCCs). Preliminary sequence data point to the existence of EcPV2 E6 and E7 oncogene variants compared to the British reference sequence from 2008. Objective: To Identify E6 and E7 sequence variations in EcPV2-positive tumours of horses from Continental Europe and Iceland. Methods: Cross-sectional study. Methods: EcPV2 E6 and E7 were amplified from DNA of 60 EcPV2-positive SCCs/SCC precursor lesions. Amplicons were gel-pur...
Genetic parameter estimation of novel international show-jumping indicators in horses. Genetic improvement of show-jumping competition results has a clear breeding goal which is to produce horses that can repeatedly clear technically demanding courses at maximum height, resulting in placement results. However, how to achieve this, and thus how to accurately choose breeding candidates, is far from straightforward due to the heterogeneity of competition outcomes. In this study, we analyzed Fédération Équestre Internationale (FEI) competition records from 19,232 horses together with pedigree data to evaluate novel phenotypes suitable for international genetic evaluations. Tradit...
First-time description of MHC diversity in Straight Egyptian Arabian horses using immune-linked microsatellite markers. Understanding the immunogenetic structure of the major histocompatibility complex (MHC) in Arabian horses helps to clarify the population health structure-related phenotypes of this historically influential breed. Straight Egyptian (SE) Arabian horses, which fall under , are of global value but are limited in number, raising concerns about their distribution and the genetic diversity associated with immunity. In this study, we examined 57 Egyptian Arabian horses from two breeding programs: one in Germany (AR-DE) and the other in Qatar (AR-QA). Sixteen polymorphic intra-MHC microsatellite marke...
Questionnaire-Based Investigation into Stallion Management Practices in 28 Countries. Modern stud farm practices may limit stallion social contact, with potential welfare and safety implications. Objective: To describe housing, management and safety outcomes for stallions kept at horse breeding operations throughout the world and to assess regional differences. Methods: An online questionnaire was distributed via mailing lists and WhatsApp; 116 complete responses from breeding operations were collected and analysed. The focus was on management of the breeding facility, and stallion welfare indicated by management, handling and housing. Results: Respondents were from Europe (40....
Comparative genomic analysis of oxytocin and oxytocin receptor genes in the family Equidae. The oxytocin (OXT) - oxytocin receptor (OXTR) system regulates diverse biological processes including social behavior, stress responses, and processes related to domestication. While OXT is highly conserved, OXTR shows greater variability, which may contribute to species-specific adaptations. Methods: Comparative genomic analyses of OXT and OXTR coding sequences were performed across equid species using available genome assemblies and newly generated sequences obtained by next-generation sequencing. Phylogenetic relationships were inferred using maximum likelihood methods. Selection was assess...
Extreme male reproductive skew limits effective population size in American Standardbred horses. Standardbred horses are widely used for harness racing in North America, Europe, Australia, and New Zealand. In the U.S., two gaits (Pacers and Trotters) are genetically differentiated at a level typical for different horse breeds. We used the complete pedigree for all registered American Standardbred foals born 1970-2014 (>200 K Trotters and > 500 K Pacers) to calculate annual and lifetime reproductive skew and its consequences for the effective number of breeders per year (Nb) and effective size per generation (Ne). With rare exceptions, females can only produce 0 or 1 foal per year, w...
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...
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...
Whole-genome characterization and phylogenetic analysis of Equine Rotavirus A isolated from Jeju Island, Korea. Equine Rotavirus A (ERVA) is a major cause of acute diarrhea in neonatal foals, leading to significant economic losses. Genetic variation and global transmission complicate disease control efforts. Objective: To analyze the complete genome of an ERVA strain from Jeju Island, Korea, and assess its genetic and phylogenetic relationships with global ERVA strains. Methods: Twenty-five fecal and swab samples were collected from diarrheic horses in Jeju during spring and summer 2025. Samples were screened using antigen testing and RT-PCR. One PCR-positive, antigen-test-positive sample was selected f...
Phased T2T horse and donkey assemblies from a mule reveal peculiar equid centromere evolution. We present telomere-to-telomere genome assemblies of a Thoroughbred horse and a donkey derived from their mule offspring. Now adopted and annotated by NCBI as reference genomes, these assemblies resolve previously inaccessible regions, including satellite arrays, duplications, and telomeres. Equids are known to exhibit an uncoupling between satellite DNA and centromeric function. The completeness of these assemblies enabled annotation of both satellite-based and satellite-free centromeres, as well as non-centromeric satellite loci, revealing notable centromeric plasticity. They also allowed de...
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...
Approaches to Thoroughbred Horse Identification in Diverse Sample Types Using Multiplexed SNP-PCR Sequencing Panels. The ability to determine the identity of equine samples would be highly advantageous in cases of ambiguous sample source, as individual-specific controls for gene editing detection, or forensic examination of suspect biological materials in potential doping cases. To this end, a SNP-PCR sequencing-based panel comprising 93 markers in one reaction was designed and investigated for use in Thoroughbred horses. Marker amplification performance and discriminating power were calculated against a population survey of 264 Thoroughbred whole blood samples from routine doping testing. The sensitivity of...
Somatic cell nuclear transfer as a complementary tool for genetic conservation of the Peruvian Paso horse. The Peruvian Paso horse, a breed of national significance in Peru known for its unique gait, has been selectively bred for nearly 500 years and now faces potential risks due to reduced genetic diversity. To investigate the potential of somatic cell nuclear transfer to enhance genetic conservation strategies, a program was initiated to produce cloned Peruvian Paso foals. Skin biopsies from a highly awarded stallion with exceptional breed-defining traits were used as the source of donor somatic cells. Of the 15 cloned embryos reconstructed, seven blastocysts were produced, and five were transfer...
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...
Environmental and genetic effects on measured hock bone proportions in young Polish Warmblood horses undergoing performance test training for breeding horses. The hock bone proportions in young Polish Warmblood horses (69) were studied based on x-ray image measurements done during official breeding horse performance testing. Six measurements were used to identify 4 width and length proportion indices. The radiological examinations were done before and after horse training, which consists of work with or without the rider at walk, trot and canter (40-50min) with some light class (< 100cm) jumping (<12 jumps) 6 days a week. The training effect was investigated using analysis of variance (procedure MIXED, Statistical Analysis System). The statist...
Compartmentalization of DHCR7 links 7-DHC metabolism to B-ring unsaturated steroid synthesis in the equine fetal gonad. The endocrinology of equine pregnancy is unique, but many of its unusual phenomena closely resemble pregnancy in women. Placental estrone synthesis uses fetal adrenal androgen precursors in women, but from the fetal gonads in mares, peaking midway through the 11-month gestation. Unique to equine pregnancies, other estrogens like equilin, typified by an unsaturated B-ring sterol structure, are synthesized from 7-dehydrocholesterol (7-DHC), the immediate precursor to cholesterol, without cholesterol formation, peaking later in gestation. Currently, the spatial and temporal regulation underlying ...
Effects of equine sperm incubation under capacitation-supporting conditions on homologous and heterologous ICSI outcomes. Intracytoplasmic sperm injection (ICSI) in horses has become sufficiently efficient to be considered for clinical and commercial application; however, several factors influencing its efficiency remain poorly understood. This study evaluated whether incubating equine sperm under capacitating conditions induces capacitation-associated changes and affects embryo development following homologous equine ICSI, as well as oocyte activation, early cleavage, and 5-methylcytosine (5 mC) and 5-hydroxymethylcytosine (5hmC) levels following heterologous ICSI using bovine oocytes. Equine spermatozoa were ...
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...
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...
