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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.
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 ...
Equine Sarcoid: From BPV-Driven Oncogenesis to Host-Sustained Tumor Persistence. Equine sarcoid is the most common cutaneous neoplasm of equids and represents a distinctive model of virus-associated tumor persistence. Although bovine papillomaviruses, particularly BPV-1 and BPV-2, are recognized as the main etiological agents, viral infection alone does not fully explain the clinical heterogeneity, frequent recurrence, and limited spontaneous regression of these lesions. This review summarizes current evidence on the molecular and cellular mechanisms underlying equine sarcoid pathogenesis, with emphasis on the interaction between BPV infection, host signaling pathways, tum...
Effects of the Freezing Diluent Tonicity and Prefreezing Cooling Rates on Post-Thaw Sperm Quality Markers in the Pure-Bred Arabian Stallion. Stallion semen cryopreservation remains limited by inconsistent post-thaw sperm quality and fertility. This study evaluated the effects of freezing extender effective tonicity and prefreezing cooling rate on post-thaw sperm characteristics in pure-bred Arabian stallions. In a two-phase design, ejaculates ( = 40) from 10 stallions were processed using extenders with different osmotic conditions (330, 390, and 450 mOsm/kg) and subjected to cooling durations of 45 min, 1.5 h, or 3 h. Sperm quality was assessed using CASA, functional assays, flow cytometry, transcriptomic analysis, and...
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...
Molecular Detection of Anaplasma spp. in Horses From Golestan Province, Northern Iran. Anaplasmosis is a bacterial zoonotic disease that affects both humans and many animals. In horses, anaplasmosis manifests as a seasonal, infectious, and febrile disease caused by bacteria of the genus Anaplasma. Since the transmission of this disease is primarily mediated by arthropods such as ticks, it holds significant public health importance. Objective: The present study aims to investigate the prevalence of anaplasmosis in horses in northern Iran (Golestan Province). Methods: A total of 350 blood samples were randomly collected from asymptomatic horses between December 2023 and April 2024...
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...
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...
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...
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 ...
Sequencing and Differential Analysis of miRNA in the Ovaries of Kazakh Horses During Estrus and Anestrus States. To reveal the regulatory role of miRNA in the estrous cycle transition of Kazakh horse ovaries and improve their reproductive efficiency, this study took the ovaries of Kazakh horses in the estrus period (DY group) and the quiescent period (DB group) as research objects. Small RNA sequencing and bioinformatics analysis were used to systematically analyze the expression characteristics and functional pathways of miRNA under the two physiological states. A total of 161 million high-quality miRNA tags were obtained through sequencing. Principal component analysis showed that the intra-group repea...
Isolation of high-quality stallion spermatozoa: a comparison of methods and their effects on sperm quality and yield, DNA damage, and functional competence by ICSI. Intracytoplasmic sperm injection (ICSI) is the primary method for equine in vitro embryo production, yet outcomes may be influenced by sperm selection techniques. Objective: This study compared four isolation methods: EquiPure™, Vetmotl™, Felix™, and Samson™, to assess effects on sperm quality and embryo development. Methods: Semen was collected from four fertile stallions, processed and evaluated for sperm motility, viability, DNA integrity, and yield of high-quality cells relative to input. Isolated samples were compared to non-isolated (centrifuged) samples. Spermatozoa were used fo...
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 ...
Mitochondrial DNA reveals high maternal diversity within a weak breed structure in native Kazakhstani horses. Understanding the genetic diversity and evolutionary history of domestic horses () is essential for reconstructing their population dynamics and origins. In this study, we analyzed mitochondrial DNA variation (COI and cytb) in six Kazakhstani horse populations representing four native breeds (Kazakh, Kostanay, Adai, and Mugalzhar) to assess genetic diversity, population structure, and evolutionary relationships within a broader phylogenetic framework. High haplotype diversity combined with low nucleotide diversity revealed population expansion and admixture. Population structure analyses revea...
Rapid bacterial community profiling of equine faecal, skin, milk and saliva samples using Oxford Nanopore long-read 16S rRNA amplicon sequencing. The composition of the equine gut microbiome is associated with many aspects of gastrointestinal, respiratory and musculoskeletal health that have been reported in the horse. Scientific studies exploring the microbiome non-intestinal ecological niches in or on horses are lacking. The clinical use of bacterial community profiling in horses is currently limited by cost and by slow analytical workflows. Most equine microbiome studies have relied on 16S rRNA amplicon sequencing of bacterial DNA, using high-throughput short-read sequencing technologies. This is often provided by an external servic...
Tick-borne bacterial and protozoal pathogens in horses in Austria – A cross-sectional study on current and past infections and potential risk factors. Tick-borne bacterial and protozoal pathogens are a major threat to equine health worldwide. In Austria, studies on pathogens such as piroplasms, Anaplasma phagocytophilum and Borrelia spp. in horses are scarce and do not cover the countrywide horse population. To address this, blood samples from horses without prior record of infection with tick-borne pathogens (n = 588) were tested for the presence of Theileria equi, Babesia caballi or A. phagocytophilum DNA by PCR and for specific antibodies against these pathogens and Borrelia burgdorferi with commercially available assays. While no DNA of ...
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...
