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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.
Transcriptomic and Meat Quality Differences in Longissimus Dorsi Muscle of Surgically Castrated Three-Year-Old Kazakh Horses. Although the Kazakh horse is a dual-purpose breed renowned for both milk and meat production, the extent to which surgical castration alters gene expression in its muscles has not yet been fully elucidated. In this study, left longissimus dorsi muscle (LDM) samples were obtained from six Kazakh stallions (W group) and six Kazakh geldings (S group) to comparatively evaluate meat quality parameters, examine histological characteristics in tissue sections, and apply transcriptomic profiling to comprehensively explore the principal regulatory pathways and candidate genes through which surgical cas...
A Comprehensive Analysis of the Agreement and Performance of Variant Annotation Programs in Equine Genomes. Advances in whole-genome sequencing (WGS) technology have led to the widespread adoption of WGS for investigating genetic diseases and traits in domestic animals. This has created a need for improved methods for prioritizing candidate causal variants. One way variants are prioritized is using variant annotators that predict variant effects based on their proximity to genomic features and effect on amino acid sequence. However, validation of variant annotators for domestic animal genomes is lacking. In this study, we calculated the agreement of three popular variant annotators, Ensembl Varian...
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...
Integrative Advances in Equine Genomics From Reference Assemblies to Evolutionary History and Key Traits. Horses are major domestic animals and cultural symbols that have accompanied humans for millennia. They underpin transport, agriculture, warfare and sport, and also provide a model for studying domestication, complex traits and adaptive evolution. Recent work in equine genomics has now generated a much richer picture of how these roles are grounded in the genome. This review brings together advances in several connected areas: the construction and refinement of reference assemblies; genomic reconstructions of origin, domestication and dispersal; global and regional patterns of genetic diversit...
Chromosomal chaos: understanding aneuploidy associated with assisted reproductive technologies. Pregnancy loss remains a significant challenge for the equine breeding industry, with substantial economic and management consequences. Chromosomal abnormalities have emerged as a central driver of pregnancy loss, particularly during early gestation, highlighting the need to better understand the etiology of this inherent genetic instability. Concurrently, the rapid expansion of assisted reproductive technologies (ART) offers promise for improving equine reproductive efficiency alongside the traditional practice of natural cover. However, the increasing use of in vitro embryo production (IVP) ...
Prevalence and Genetic Characterization of Giardia duodenalis and Blastocystis sp. in Horses in Shanxi Province, North China. (synonyms and ) and sp. are prevalent zoonotic intestinal protozoans with significant public health and economic importance. Both parasites infect various hosts, including humans and most livestock. can cause infections ranging from asymptomatic carriage to clinical manifestations such as acute diarrheal disease, growth stunting and malabsorption, whereas sp. infection is often asymptomatic and its pathogenicity remains debated. Following the rapid expansion of modern equine industries (horse racing, equestrian sports, production, and tourism), concern about the spread of parasitic diseas...
Prevalence, molecular characterization and zoonotic potential of Cryptosporidium spp. in horses from diverse husbandry systems across four provinces of northern and eastern China. Cryptosporidium is an obligate intracellular zoonotic protozoan causing diarrheal disease in humans and animals globally. Horses have more frequent close contact with humans through equestrian sports, breeding, and cross-regional trade. However, comprehensive molecular epidemiological data on diverse equine husbandry systems in China are limited. We tested 412 fecal samples from horses across four Chinese provinces via small subunit ribosomal RNA (SSU rRNA) nested polymerase chain reaction (PCR). C. parvum and C. equi were subtyped using the 60 kDa glycoprotein (gp60) gene, and C. andersoni ...
Sport predispositions in warmblood horses: insights from Grand Prix competitions. The aim of this study was to pilot the assessment of sport predispositions in warmblood horse breeds, both domestic and foreign, and to evaluate factors influencing their performance. Data from 293 horses (725 starts) competing in national Grand Prix events with obstacle heights of 140-145 cm were analysed using general mixed models. The origins of Polish Halfbred Horses were examined, and correlations between results in the Young Horse Championships and later Grand Prix performance were assessed. Results showed that performance is significantly influenced by genetic factors, such as breed and...
A Breed-Specific SNP Panel With Higher Theoretical Exclusion Power and Practical Equivalence to International Standards for Parentage Testing in Pura Raza Española Horses. Accurate parentage assignment is essential for managing livestock breeding and genetic improvement. This study evaluated a breed-specific SNP panel (375 SNPs) for the Pura Raza Española (PRE) horse, comparing its performance against the traditional STR reference panel (18 microsatellite) and the international ISAG SNP core panel (378 SNPs) across population scenarios differing in levels of inbreeding and kinship. The PRE-specific SNPs were selected from the Axiom EQUIGENE array based on high genotyping reliability (call-rate > 99%), Mendelian error minimization, Hardy-Weinberg equilibr...
Towards a Comprehensive Screening Approach for Detecting Gene Doping in Racehorses and Sport Horses by Targeting Common and Intrinsic Plasmid Sequences. The evolution of biotechnology and gene therapy has unfortunately facilitated the emergence of gene doping. Those misused applications are prohibited in equestrian sports (International Equestrian Federation (FEI)) and in horseracing (International Federation of Horseracing Authorities [IFHA]), reflecting major concerns regarding horse welfare and the integrity of competitions. Among the biotechnological tools that could be misused, eukaryotic expression plasmids represent a particular threat due to their ease of production, customisable design and ability to carry a wide range of performance ...
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...
Prevalence, genomic diversity and emerging antimicrobial resistance of Taylorella asinigenitalis in Grand Noir du Berry breeding donkeys. Taylorella asinigenitalis is a fastidious Gram-negative bacterium of the equine genital tract, found more commonly in donkeys than horses. Although considered non-pathogenic, it is closely related to Taylorella equigenitalis, the agent of contagious equine metritis, and has been linked to experimental and natural cases of endometritis. The SAFRAN project (French acronym for "Sauvegarde de la fertilité de l'âne", meaning "Preservation of donkey fertility"), launched in 2024 by the French National Research Institute for Agriculture, Food and Environment (INRAE) with support from the Centre-Val...
Genetic diversity of horses of the Sargarinsko-Alexeevskaya and Irmen cultures of the Ob-Irtysh region of Western Siberia and their genetic proximity to modern horses of indigenous breeds. Genetic diversity of horses of the Sargarinsko-Alexeevskaya and Irmen cultures of the Ob-Irtysh region of Western Siberia and their genetic proximity to modern horses of indigenous breeds. Генетическое разнообразие лошадей саргаринско-алексеевской и ирменской культур Западной Сибири и их генетическое родство с современными лошадьми аборигенных пород.
Thermal Thresholds and Genetic Sensitivity in Barrel Racing Performance of Quarter Horses Across Temperature-Humidity Indices. Heat stress is an increasingly important challenge for the performance and welfare of equine athletes, particularly in competitions conducted across diverse climatic conditions. Understanding the genetic basis of performance responses to increasing thermal load is therefore essential to support robust genetic evaluation and sustainable selection strategies. The objective of this study was to evaluate barrel racing performance of Brazilian Quarter Horses across thermal environments defined by two widely used indicators, the temperature-humidity index (THI) and the wet bulb globe temperature (WB...
Comparative metagenomic analysis of gut microbiomes in Yunnan ponies and Dutch warmblood horses. The Yunnan pony is an officially protected pony breed in China. However, its gut microbiome characteristics remain largely unexplored. This study aimed to compare the gut microbiome and antibiotic resistance genes (ARGs) profiles between Yunnan ponies and Dutch warmblood horses. Unassigned: A total of 14 fresh fecal samples were collected from Yunnan ponies and Dutch warmblood horses. Metagenomic sequencing was employed to comprehensively analyze and compare the gut microbial composition, function, and ARGs profiles between the two breeds. Unassigned: The results showed no significant differen...
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-...
Research Trends and Emerging Frontiers in Racehorse Genetics: A Bibliometric Analysis. The global horse racing industry relies heavily on elite breeding. Therefore, a molecular understanding of athletic traits is crucial for the industry's advancement. This study utilized Bibliometrix, VOSviewer, and CiteSpace to conduct a comprehensive bibliometric analysis of 869 publications in the Web of Science Core Collection (2011-2025), decoding the academic landscape and evolutionary trajectory of equine genetics. The results indicate a significant upward trend in academic output since 2019, with the United States, South Korea, and the United Kingdom emerging as the primary contributors...
Whole Genome Data Uncover the Complex Origins of Polish Konik Horses. Polish Konik is a native horse breed from Poland often regarded as living descendants of the extinct Tarpan, which has been crucial to the breed's conservation status and cultural importance. To evaluate Polish Konik origins, we sequenced 12 whole genomes and compared them with 148 horse genomes, including those of modern breeds, ancient Polish horses, Przewalski horses, and the Tarpan. The ADMIXTURE results showed that Polish Konik is dominated by a single ancestral component, which is also common among ancient Polish samples and several primitive breeds. The PCA places Polish Konik in a comp...
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...
Extinct Dalian horse as a genetic bridge between Late Pleistocene North American and Eurasian equids. Pleistocene caballine horses exhibited considerable genetic diversity and maintained broad population connectivity across their range. The extinct Dalian horse (Equus dalianensis) from northeastern China likely contributed to this network. Here, we sequenced 20 complete mitochondrial and two nuclear genomes, establishing the Dalian horse as a distinct genetic clade within Northeast Eurasian caballines and extending its known geographic distribution. Ancestry component analyses revealed a distinctive component of Eastern Beringian (E-EBer), i.e. American ancestry in Dalian horses, absent from o...
Integrative and conjugative elements carrying high-level gentamicin resistance genes in Streptococcus dysgalactiae subsp. equisimilis from horses. In streptococci, the acquisition of high-level gentamicin resistance (HLGR) abolishes the synergy with beta-lactams, constituting a medical concern for humans and animals. This synergy between gentamicin and beta-lactams is useful to treat severe infections like endocarditis, among others. HLGR has been characterized mostly in roup B Streptococci mediated by the bi-functional gene (6)-(2).HLGR- subsp. () (=27) were isolated from the uterus of mares during a routine screening before fecundation. One HLGR- was isolated from a lymph node of a mare. The mares resided in six different studs locat...
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...
Theileria equi sensu lato genetic diversity and phylogeny: new insights from mitochondrion, apicoplast and nucleus multilocus gene analysis. Equine piroplasmosis is a significant tick-borne disease with a global distribution. Among the two causative agents, Theileria equi has undergone numerous taxonomic reclassifications over time, reflecting advances in our understanding of its biology, molecular characteristics, and phylogenetic relationships. Formerly named Babesia equi, now classified in the Equus group apart from Babesia and Theileria species, its genus name will again certainly change. The genetic diversity also within T. equi lead to the renaming of one lineage as Theileria haneyi. Theileria equi should better now be consid...
A Genetic Algorithm-Based Approach for Quantitative Prediction of Drug-Drug Interactions Caused by Cytochrome P450 3A Inhibition or Induction in Horses. A genetic algorithm (GA)-based approach was designed to predict drug-drug interactions (DDIs) triggered by cytochrome P450 3A (CYP3A) inhibition or induction in horses. Area under the concentration-time curve ratios (AUCRs), obtained from published in vivo DDI studies in horses, were used to compute the following parameters: (1) the contribution ratio (CR), i.e., the fraction of the substrate dose metabolized via the CYP3A pathway, and (2) the interacting drug's inhibitory potency or inducing efficacy (IR or IC, respectively). AUCRs for 9 substrates, 12 inhibitors, and 1 inducer of equine C...
Genomics in Equine MEED: Whole-Genome Sequencing and Target Mutation Identification. Multisystemic eosinophilic epitheliotropic disease (MEED) is a rare and severe equine disorder characterized by chronic eosinophilic inflammation, epithelial disruption, and multi-organ involvement, with an undefined genetic basis. We performed the high-depth (~40×) whole-genome sequencing of an affected horse and compared it to 40 control genomes. Over 6.3 million variants were identified, with moderate- and high-impact variants enriched in low-frequency categories, including rare and private variants absent from the controls. The affected horse was dominated by missense mutations, with rela...
An intronic variant in Ferredoxin Reductase (FDXR) creates a cryptic exon in Quarter Horses with Equine Juvenile Spinocerebellar Ataxia. Equine Juvenile Spinocerebellar Ataxia (EJSCA) is a novel autosomal recessive neurologic disease in Quarter Horses. Affected foals display a progressive proprioceptive ataxia by 1-5 weeks of age, leading to recumbency and necessitating euthanasia. Whole genome sequencing was performed on 7 EJSCA cases and unaffected horses that included 4 obligate carriers, 4 unaffected half or full-siblings, and 28 unrelated, unaffected control Quarter Horses. An 82 kb region of association was identified (EquCab3.0, chr11: 6963986-7045999), containing 9 candidate SNPs across four genes (FADS6, FDXR, GRIN2C a...
Identification of gene conversion events in horse IGHV suggests preferential hotspots for diversification. The humoral immune response relies on a diverse antibody repertoire, which is expanded through processes such as somatic hypermutation, class-switch recombination and gene conversion. These processes are primarily mediated by activation-induced cytidine deaminase (AID). Gene conversion generates diversity in immunoglobulin heavy and light chains (IGHVs) in species such as chickens and rabbits, though it has not been widely studied. Since 80% of the equine IGHV repertoire originates from only three functional gene segments, we examined gene conversion events in horses to assess their role in an...
Genetic diversity of Dermacentor nitens (Acari: Ixodidae) collected on horses from western Cuba. The tropical horse tick, Dermacentor nitens Neumann, 1897, has a wide distribution throughout the Neotropics, and is a vector of protozoan haemoparasites that cause equine piroplasmosis. Despite this, little is known about the genetic diversity of this tick species, particularly in Cuba, where horses are important domestic animals used in agriculture and for transportation. The objective of this study was to assess the magnitude of genetic variation in 115 D. nitens adults (57 females and 58 males) collected from horses in the Cuban province of Mayabeque using sequence data of two mitochondria...
