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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.
Selective oncolytic activity of newcastle disease virus in equine sarcoid primary cells: a preclinical investigation. Equine sarcoids are the most common skin tumors in horses and are characterized by local invasiveness, high recurrence rates, and inconsistent responses to current therapies. Oncolytic virotherapy represents a promising alternative approach that exploits defects in antiviral signaling pathways in tumor cells. Newcastle disease virus (NDV), an avian paramyxovirus that is nonpathogenic in mammals, has demonstrated tumor-selective activity in several species; however, its effects on equine sarcoids have not been previously investigated. In this study, primary cell cultures derived from equine sar...
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...
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...
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 ...
Complete genome of Bacillus anthracis strain ter21 from an infected zoo pony in Ternopil, Ukraine, 2021. Using rapid nanopore whole-genome sequencing, we assembled the genome of strain ter21 (5,229,480 bp), a Tsiankovskii-I group isolate cultured from a fatal case in 2021 of a pony from a zoo in Ternopil, Ukraine, identifying virulence plasmid pXO1 that encodes anthrax toxin, and pXO2.
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...
