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Topic:DNA
DNA in horses refers to the genetic material that carries the hereditary information necessary for the growth, development, functioning, and reproduction of equine species. It consists of sequences of nucleotides that encode the genetic instructions used in the development and functioning of horses. DNA analysis in horses can provide insights into genetic diversity, lineage, and breed characteristics. It is also utilized in identifying genetic disorders, understanding hereditary traits, and assisting in selective breeding programs. This page compiles peer-reviewed research studies and scholarly articles that explore the structure, function, and applications of DNA analysis in equine genetics and breeding.
Exploring the role of epigenetics in the processes related to the development of endometrosis in the mare. Endometrosis is a chronic degenerative condition of the mare endometrium characterized by progressive fibrosis and glandular alterations that impair uterine function and fertility. Its pathogenesis involves persistent inflammation, the activation of myofibroblasts, and the accumulation of extracellular matrix (ECM), leading to disrupted glandular secretion and compromised maintenance of pregnancy. While histopathological studies of endometrosis are well described, the underlying molecular mechanisms remain incompletely understood. Emerging evidence highlights the crucial role of epigenetic reg...
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...
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 ...
An unusual presentation of a sarcoid in Australia. Sarcoids are a common skin tumour affecting all equids. To date, only one case of a sarcoid in the oral cavity of the horse has been reported. In the present case, an oral sarcoid was identified using histology and polymerase chain reaction to detect bovine papillomavirus type 2 DNA. The lesion was known to be incompletely surgically excised and did not recur over a 15-month period. This case report describes the first oral sarcoid identified in Australia.
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.
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...
First molecular detection of Theileria haneyi infection in horses in Southern Spain. Equine piroplasmosis (EP) is a tick-borne disease of equids caused by the hemoparasites , and . , a close relative of that causes mild clinical signs under experimental conditions, has been reported in several countries, adding complexity to EP ecology, diagnosis, and treatment. However, its presence in Spain remains unknown, which is concerning given the country's importance in equine genetics and international trade. Hereby, we investigated the presence of in blood samples from equids in Spain. Unassigned: Blood samples from 222 equids (218 horses, two donkeys, two mules) suspected of EP a...
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...
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...
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...
Macroscale and microscale mechanical and biochemical properties of the equine superficial digital flexor tendon are regionally dependent. To examine regional mechanical and biochemical differences across the length of the equine superficial digital flexor tendon (SDFT). Unassigned: Equine SDFTs were collected postmortem from 9 donors and divided into proximal, middle, and distal regions based on the location of the musculotendinous and osteotendinous junctions. Tensile testing was performed on samples to obtain macroscale mechanical properties, and atomic force microscopy was done to obtain microscale mechanical properties. Biochemical assays and histological staining were done to assess glycosaminoglycan (GAG), collagen, and DN...
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...
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...
Molecular prevalence of equine parvovirus hepatitis in healthy horses from the Northern region of the state of Rio Grande do Sul, Brazil. The equine parvovirus hepatitis (EqPV-H) was initially linked to fatal cases of equine serum hepatitis but, more recently, it has also been detected in sick or asymptomatic horses around the world, including in a limited number of horses in southeastern Brazil. In this study we aimed to assess the prevalence of EqPV-H DNA in the serum of healthy horses in the northern region of Rio Grande do Sul state, Brazil. For this purpose, we used 1000 serum samples collected from horses from 40 municipalities and organized them into 200 pools of five samples each, based on origin and age. Using a nested ...
Detection of papillomavirus DNA in uterine flushing samples from healthy mares reveals diverse genotypes with differing host ranges. A molecular study to assess the presence of some papillomaviruses was performed on 105 uterine flushing samples of healthy mares using real time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR). Bovine, equine, and ovine papillomavirus DNA was detected in 27 uterine flushing samples through dPCR (~ 25.71%); qPCR was able to detect 18 positive samples (~ 17.14%). Differences between the two molecular protocols were significant as shown by McNemar's test (p˂ 0.005). EcPV DNA was detected in 10 samples by dPCR (~ 9.52%) of uterine flushing samples. qPCR detected EcPV DN...
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...
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...
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...
Klossiella equi, an underreported parasite of equids in the Americas. Klossiella equi Baumann, 1946 (Apicomplexa: Coccidia) is a globally distributed adeleorinid parasite that infects the kidneys of equid hosts. Considered an uncommon parasite, when K. equi is detected, it is typically an incidental finding during histologic examination of the kidneys as part of routine necropsy. In the present study, kidney was collected opportunistically from 3 different equine populations: 1) routine necropsies at the Ontario Veterinary College (OVC; n = 48); 2) natural mortalities from the Sable Island wild horse herd (n = 25); and 3) routine necropsies of animals fr...
Genetic diversity in the Criollo Argentino horse from SNP array data. The Criollo Argentino horse is a national symbol and a heritage breed that represents both cultural identity and a key component of traditional production systems in Argentina. This study aimed to assess the genetic differentiation of the Criollo Argentino relative to other horse breeds and to infer potential factors shaping its diversity through the genomic analysis of 24 representative animals. Samples were genotyped using a medium-density SNP array containing 65,157 markers, and genetic diversity analyses were conducted across autosomal SNP sets filtered under different criteria. Contempora...
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 ...
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...
United States stakeholder insights on genetic testing for equine health and breeding. The S1094 United States Department of Agriculture Multistate Research Project is a collaborative effort utilizing equine genetics and genomics to improve horse health and well-being. It also provides educational resources and genetic testing tools to equine industry stakeholders. Objective: A survey assessed the knowledge, priorities, and information sources of U.S. horse owners and enthusiasts regarding equine genetic testing to inform future outreach and research efforts. Methods: An online survey was distributed from March to October 2024, targeting horse owners and enthusiasts across the U...
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 ...
Unveiling genetic diversity in Egyptian Arabian horses (Equus caballus) through cytogenetic and ISSR marker analysis. This study combined classical cytogenetics and ISSR molecular markers to characterize genetic diversity in 24 Egyptian Arabian horses. Karyotyping revealed the standard equine chromosome number (2n = 64) with no numerical or structural abnormalities. Chromosome measurements were consistent with ISCN Equine standards: autosomal relative lengths (RL%) followed the expected size hierarchy, biarmed chromosomes displayed metacentric to submetacentric morphology (CI = 37-50%), and recalculated centromeric indices confirmed the presence of measurable p-arms on all acrocentric chromosomes. ISSR an...
An increased number of heterozygous calls in the AxiomTM Equine Genotyping Array. Single nucleotide polymorphism (SNP) arrays are commonly used in livestock genetics to investigate complex traits including genome-wide associations and fine mapping, genomic prediction and genetic diversity analyses. In a European equine diversity study, we analysed the AxiomTM Equine 670K SNP genotype data from 2,768 equids representing 20 horse breeds and one donkey breed. Using a strict detection setting to identify genome-wide runs of homozygosity (ROH), 169 purebred horses displayed fewer ROH segments than F1 crosses. Under medium and relaxed settings, ROH counts increased, while some ho...
