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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.
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...
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...
A Comparison of the Performance of Horses from the International WBFSH Rankings in Dressage, Jumping and Eventing Based on Their Sex, Age, Proportion of Thoroughbred Genes and Affiliation to the Studbook. The aim of the research was to assess how the selected factors could influence the performance of the best horses in dressage, jumping and eventing competitions. The research was based on the Studbook Rankings published by the World Breeding Federation for Sport Horses from 2019 to 2024. Our analysis shows a statistically significant effect of each of the observed factors in at least one discipline. The leading factor in all disciplines was studbook affiliation. The Belgian warmblood, German Sport Horse, Hanoverian, Royal Dutch Sport Horse, Oldenburg and Westphalian studbooks are represented a...
Horse genetics, archaeology, and the beginning of riding. Recent papers argued that the domestication of horses can be equated with the appearance of favorable genetic mutations that are first evident in individuals in the DOM2 clade dated about ∼2200-2100 BCE. We challenge the idea that this genetic shift alone defines domestication. Evidence from archaeology, ancient DNA, osteology, and other disciplines shows that horses from multiple genetic backgrounds (DOM1, DOM2, and, as we suggest here, DOM3) were managed, milked, and ridden long before 2200 BCE. Yamnaya groups (∼3200-2600 BCE) rode DOM2 horses-the direct ancestors of modern domestic stoc...
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...
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...
The impact of barefoot racing in young Swedish trotters on career length. In several European countries, racing without shoes, i.e., barefoot, is a common strategy in trotting races to improve the speed of the horse. Why some trotters can race barefoot without damage to the hoof from excessive wear and others cannot, has been shown to partly be explained by differences in hoof composition. In particular, durable hind hooves are believed to be important to sustain racing without shoes. Also, variation in the proportion of the races the horse races with barefoot hind hooves, has been shown to be affected by genetic differences in Swedish Standardbred trotters (SB) and...
Genetic diversity of Toxoplasma gondii isolates from members of the families camelidae and equidae worldwide: a systematic review. Toxoplasma gondii is an apicomplexan parasite with a global distribution and significant public health and veterinary treatment implications. The present systematic review collates worldwide information on the genotypic diversity of T. gondii isolates infecting Camelidae (camels, alpacas, llamas, etc.) and Equidae (horses, donkeys, zebras, mules, etc.) and highlights their potential role as sentinels of environmental contamination and zoonotic spread. An exhaustive literature search of six electronic databases (PubMed, Web of Science, Scopus, ProQuest, Science Direct, and Google Scholar) from ...
Telomere-to-telomere Genome Assembly of Equus kiang (Tibetan wild donkey). The Tibetan wild donkey (Equus kiang) is an endemic equid species inhabiting the Qinghai-Tibet Plateau, exhibiting remarkable chromosomal diversity within the Equus genus. Here we present a chromosome-level, telomere-to-telomere genome assembly for E. kiang generated using Illumina short reads, PacBio HiFi long reads, and Hi-C sequencing data. The final assembly spans 4.02 Gb and comprises 27 pseudochromosomes. Specifically, 8 chromosomes are gapless, 8 chromosomes have one gap, 7 chromosomes have 2-4 gaps, and the remaining 4 chromosomes have five or more gaps. Benchmarking Universal Single...
Retrospective assessment of equine herpesvirus type 1 (EHV-1) genotype-associated clinical disease in Ontario. Equine herpesvirus type 1 (EHV-1) is an important viral pathogen in horses, associated with diverse clinical manifestations including fever, upper and lower respiratory disease, neurological signs, ocular disease, and abortion. Currently, EHV-1 variants (genotypes) are classified based on a single nucleotide polymorphism mutation of the open reading frame 30 (ORF30). Unassigned: The aim of this retrospective study was to evaluate the EHV-1 genotypes present in horses with various clinical presentations, including respiratory disease, abortion, and neurological disease, at a referral center in ...
miRNA Sequencing and Differential Analysis of Testis in 1-Year-Old and 2-Year-Old Kazakh Horses. The represents a significant genetic resource within China's population, characterized by notable resilience and an ability to thrive on coarse forage. Nevertheless, a decline in its numbers has been observed recently, making the improvement of its reproductive performance crucial for the preservation of this breed and the advancement of the related industry. In this study, testicular tissues from 1-year-old (pre-pubertal) and 2-year-old (post-pubertal) were analyzed. miRNA sequencing was conducted on tissues from these age groups, followed by bioinformatics analyses to elucidate the functi...
Machine Learning-Based Genome-Wide Association Study Reveals Genetic Loci Associated with Body Measurement Traits in Yili Horses. Body measurement traits are key indicators for evaluating growth performance, production potential, and breeding value in Yili horses. However, studies investigating the association between body measurement traits and mutation loci in Yili horses remain limited. In this study, 255 adult Yili mares were used as the study population, including 152 speed-type and 103 meat-type individuals. Whole-genome resequencing was performed, and four phenotypic traits and body weight were measured. A mixed linear model (MLM)-based genome-wide association study (GWAS) was conducted using GEMMA (v 0.98.5), inc...
