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Topic:Molecular biology
Molecular biology in horses involves the study of molecular processes and genetic mechanisms that underpin equine physiology and health. This field encompasses the analysis of DNA, RNA, proteins, and other biomolecules to understand gene expression, genetic variation, and cellular functions in horses. Techniques such as genomic sequencing, gene expression profiling, and molecular diagnostics are employed to explore topics like hereditary diseases, performance traits, and immune responses in equines. This page assembles peer-reviewed research studies and scholarly articles that investigate the molecular biology of horses, focusing on genetic research, molecular techniques, and their applications in equine science.
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 ...
Surveillance on African Horse Sickness Virus in China’s Southern Border Regions. African horse sickness (AHS) is a vector-borne and noncontagious disease caused by African horse sickness virus (AHSV) that poses a severe threat to the global equine industry. As a country historically free from AHS, China faces elevated risks due to recent outbreaks in Southeast Asia in 2020 and its ecological suitability of its border regions for AHSV vectors. Therefore, we conducted consecutive molecular and serological surveillance for AHSV in high-risk border regions from 2020 to 2024. A total of 3203 equine serum samples, 2909 whole-blood samples, and 1037 collections of blood-sucking...
Genes Associated With Fracture Risk in Thoroughbred Horses Have Novel Roles in Osteogenesis. Bone fractures in Thoroughbred racehorses are a major welfare problem. Genetic factors contribute to fracture risk. Cell models have previously identified 112 differentially expressed genes in bone-forming osteoblasts derived from horses at high and low genetic risk of fracture. However, 42 of these genes have no published role in bone. In this study, we identified novel roles for a subset of these genes in bone formation. Twenty-six of the 42 genes were expressed in Saos2 cells during basal culture and/or after 21 days of osteogenic culture. Five of these genes (ADSSL1, CABP1, ENO2, SPARCL1...
Endometritis and endometrial fibrosis are associated with alterations in mare endometrial proteome. Equine persistent post-breeding endometritis may lead to endometrosis, characterized by excessive fibrosis, which is a major cause of subfertility/infertility. Endometrial proteomic changes induced by endometritis, when associated with fibrosis, were investigated to identify the biological processes (BP) involved. Cyclic mares´ endometrial biopsies were histologically classified (Kenney and Doig's) as: category IIA (n = 5), category IIA with endometritis (IIA-E; n = 4), category IIB (n = 5), or category IIB with endometritis (IIB-E; n = 5). Proteome was assessed by LC-MS/MS. I...
Genomic diversity and historical legacy of Baroque horses: a living cultural heritage. Baroque horses represent a distinctive group of breeds that emerged mainly between the 16th and 18th centuries, shaped by the demands of European royalty and their courts. Although recognised as separate breeds, they share common ancestry, breeding goals, and historical gene flow. This study aimed to evaluate their genomic diversity, population structure, and admixture patterns. We analysed 1 160 individuals from eight breeds - Lipizzan, Old Kladruby Horse, Pura Raza Española, Lusitano, Friesian, Criollo, Peruvian Paso, and Puerto Rican Paso Fino - using 34 026 single-nucleotide polymorphis...
Detection of ionisable lipids in equine plasma by supported liquid extraction and liquid chromatography-high-resolution tandem mass spectrometry for doping control of mRNA agents. Messenger ribonucleic acid (mRNA) has emerged as a new class of therapeutic agent with unprecedented potential. In particular, the lipid nanoparticle (LNP)-mRNA formulations enabled safe and effective delivery of mRNA in vivo, leading to the success of mRNA vaccines during the COVID-19 pandemic. To control the potential misuse of LNP-mRNA agents in equine sports, a simple and sensitive method has been developed for the detection of ionisable lipids in equine plasma using supported liquid extraction (SLE) followed by liquid chromatography-high-resolution tandem mass spectrometry. To overcome th...
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...
Systematic establishment of approaches to the detection of equine macrophage polarization and their application in pathogenic infection. Macrophage phenotypic adaptation critically regulates inflammatory balance during infection; however, progress in equine immunology has been limited by a lack of specific tools for standardized identification. To address this gap, we established a reliable, antibody-based detection method for characterizing equine macrophage M1-like and M2-like marker profiles. After initially validating canonical marker genes via qPCR, we developed specific monoclonal antibodies targeting the differentially expressed surface proteins CD80 (M1-like) and CD163 (M2-like). These novel antibodies enabled the creat...
Identification of candidate genes and metabolites associated with lactation performance in Kazakh mares using blood multi-omics and machine learning. The Kazakh mare, an indigenous breed of Xinjiang, exhibits strong adaptability to arid and cold conditions while maintaining relatively stable milk production under low-input extensive farming systems. However, its genetic improvement has been constrained by traditional management practices. Results: In this study, we monitored milk yield and milk composition over a 105-day lactation period and recorded 15 phenotypic traits. Milk yield was significantly correlated with body length, teat diameter, and teat length. The high-yield (HY) versus low-yield (LY) and high-fat (HF) versus low-fat (LF) c...
Circulating microRNAs as potential predictive biomarkers of equine metabolic syndrome. Equine Metabolic Syndrome (EMS) is a complex endocrine disorder characterized by insulin dysregulation (ID), and an increased risk of developing laminitis, often accompanied by generalized or regional adiposity. Despite growing awareness of EMS, early and accurate diagnosis remains challenging. In this pilot study, we investigated changes in the levels of circulating microRNAs (miRNAs) in plasma samples from horses diagnosed with EMS (n=13), compared to overweight/obese (OW/OB) non-ID horses (n=16) and healthy controls (n=16). Using a targeted OpenArray, followed by a Kruskal-Wallis and Dunn's...
Cryo-EM structure of African horse sickness virus VP2 receptor-binding protein enables nanoparticle vaccine design. African horse sickness virus (AHSV) is a lethal equine pathogen with no licensed vaccine other than vaccines containing attenuated virus, which pose safety risks. Endemic to sub-Saharan Africa, AHSV has caused epizootics in Spain and Portugal, Cyprus, Morocco, the Middle East, India and Pakistan and, most recently, Thailand. Here, we resolve the 3.11 Å cryo-EM structure of full-length VP2 from AHSV serotype 4, adopting its native triskelion architecture and shedding light on an α-helical domain anchoring the triskelion core, which is absent in other structurally characterized orbiviruses. ...
Conserved skeletal muscle transcriptomic responses to pacing strategies in Thoroughbred horses. This study investigated whether different pacing patterns during high-intensity exercise elicit distinct transcriptional responses in equine skeletal muscle. Eight Thoroughbred horses completed two treadmill exercise sessions in a randomized crossover design. In the positive-pacing condition, horses exercised at 110% maximal O₂ uptake (V˙O₂max) for 1 min followed by 90% V˙O₂max for 1 min, whereas in the negative-pacing condition, the order was reversed. At 4 h after exercise, the positive-pacing protocol resulted in upregulation of 1,989 genes and downregulation of 840 genes, whereas t...
Interleukin 12 on extracellular matrix-related factors and functional characteristics of equine endometrial fibroblasts. Tissue fibrosis is described as the excessive accumulation of extracellular matrix (ECM) components. This process is associated with inflammation, and the interaction between fibroblasts and immune cells plays a key role, driving the progression of fibrosis. Results of recent study suggest that interleukin (IL)-12 may play a role in the processes associated with the development of fibrosis. This proinflammatory cytokine is synthesized and released by macrophages, dendritic cells, and B cells. Objective: The objective of this study was to determine: (i) the expression of IL-12 and its receptor ...
Genome-Wide Characterization of the TGF-β Gene Family in Donkey (Equus asinus) Reveals Lineage-Specific Gene Duplications and Deleterious Mutations. The transforming growth factor-beta (TGF-β) superfamily regulates diverse biological processes, including proliferation, differentiation, apoptosis, tissue remodeling, and reproductive signaling across metazoans. Here, we performed a genome-wide characterization of the TGF-β gene family in donkey (, ASM1607732v2) using comparative genomics and bioinformatics analyses, with horse (, EquCab3.0) as a reference to investigate evolutionary conservation and functional divergence. Genome assemblies and proteomes were retrieved from NCBI, and TGF-β genes were identified using BLASTp and HMMER searc...
Prevalence of Clostridioides difficile in hospitalized neonatal mare-foal pairs from Alberta and direct comparison of fecal culture with toxin gene detection. is an important pathogen in the feces of adult horses and foals. It can be clinically diagnosed using several testing methods, including culture isolation and, more commonly, direct toxin gene detection from feces using molecular methods. The importance of monitoring shedding in foals or dams during hospitalization remains unclear. The objectives of this study were to determine the prevalence of fecal shedding in mare-foal pairs and to compare detection using isolation and a commercial real-time polymerase chain reaction (qPCR) for toxin A and B genes in feces. Foals and their mares admitte...
Diagnosis of bacteraemia in neonatal foals using 16S rRNA high-throughput sequencing. Sepsis is an important cause of morbidity and mortality in foals. Early diagnosis can improve outcome but is complicated by non-specific clinical signs and delayed confirmation of infection via blood culture. Molecular assays represent a rapid and more sensitive alternative. Objective: To evaluate and compare bacterial load and composition in blood and blood culture media (BCM) of sick and healthy foals using molecular assays and to compare results with traditional bacterial culture. Methods: Cross-sectional observational clinical study. Methods: Thirteen septic foals, 10 sick non-septic and 8...
Genetic Diversity in Domestic Horses: Temporal Patterns, the Influence of Assisted Reproductive Technologies, and Implications for the American Quarter Horse. Genetic diversity is the heritable variation within and among populations and is essential for the long-term health and selection potential of domestic horses. Previous studies show diversity across breeds is shaped by effective population size, founder events, artificial selection, and levels of inbreeding. While some closed-studbook breeds retain moderate genetic diversity, others have experienced rapid losses due to popular-sire effects and recent and extensive inbreeding. Even so, mare lines continue to help maintain genetic diversity within these populations. Assisted Reproductive Technol...
Identification of Genomic Differences Resulting from Selection in Iranian Kurdish and Turkmen Horse Breeds Using Single Nucleotide Polymorphisms. Breakthroughs in genomic technologies have enabled the formulation of methods to identify genomic variation in domestic animal species. Detection of the variation is necessary because it is associated with breed characteristics and economic importance in domestic animal genetics. Unassigned: This study aimed to identify the genomic regions in Turkmen and Kurdish horse breeds that have been the target of different selections over many years. It also sought to locate the genes and Quantitative trait loci (QTL) in these regions that contributed to the differentiation of these two breeds or the di...
Cell-Type Deconvolution of Equine BALF RNA-Seq: A Critical Comparison with Matched Single-Cell Data. Bulk RNA sequencing (RNA-seq) averages signals across heterogeneous cell populations. Computational deconvolution methods aim to infer cell type composition and cell type-specific gene expression from bulk data, but their performance in equine samples has not been evaluated. In this study, we assessed the ability of computational deconvolution to recover cellular composition and differential expression signals in bronchoalveolar lavage fluid (BALF) from horses with severe equine asthma (SEA) and controls (CTL). Cryopreserved BALF samples from six SEA and five CTL horses previously analyzed b...
Inhaled Corticosteroids Influence Pulmonary Microbiota in Severe Equine Asthma. The use of inhaled corticosteroids (ICs) could influence the respiratory microbiota. In animals with asthma it is, however, difficult to separate the immunomodulatory effects of ICs from their indirect effects via improvement of ventilation. Our objective was to determine if ICs alter the pulmonary microbiota independently from their effects on lung function, using a blinded, controlled trial in an experimental model of asthma exacerbation in horses. We treated horses with severe asthma with either bronchodilators alone, or in combination with ICs. Twelve horses in exacerbation received long-a...
Dendritic-cell diversity in equine blood revealed by single-cell transcriptomics. Detailed classification of equine dendritic cells (DC) is necessary to address various research questions, such as the role of DC subsets in immune-mediated diseases of horses. Unassigned: We applied single-cell RNA sequencing (scRNA-seq) on DC enriched from the blood of two horses. Unassigned: All main DC subsets were detected by key gene expression, including conventional DC type 1 (cDC1; ) and type 2 (cDC2; , ), as well as plasmacytoid DC (pDC; ). In addition, we detected a small cluster of hematopoietic progenitors, as well as transitional DC (tDC; , ) and putative DC type 3 (DC3; , ). Our...
Screening Equine Skin and Mucous Membranes for Carriage of Coagulase-Positive Staphylococci. Commensal populations of coagulase-positive Staphylococcus spp. (CoPS) in healthy horses are not well-defined. Objective: To determine the point prevalence, anatomical distribution, antimicrobial susceptibility and genomic characteristics of CoPS in healthy horses. Methods: One-hundred and fifty privately owned, systemically healthy horses from seven facilities were enrolled in this study. Methods: Horses were sampled from the nares, buccal mucosa and three skin sites. Isolates were identified using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry, and antimicrobial...
Integrated transcriptomic profiling reveals oncogenic pathways and chimeric transcripts in equine sarcoid lesions with predominant BPV1 detection. Sarcoids are the most common cutaneous tumors in horses, representing up to 90% (35%-90%) of skin neoplasms. Mostly caused by Bovine Papillomavirus (BPVs) infections, sarcoids are highly resistant to therapy and prone to recurring, posing a significant threat to equine health. The aim of this study is to explore molecular pathogenetic mechanisms underlying the development of equine sarcoids, by applying transcriptomic approach. After testing samples for viral DNA, both mRNA and small RNA expression was analyzed via high-throughput Illumina sequencing comparing 12 sarcoids and 12 healthy skin s...
First serological evidence of circulation of equine rhinitis A virus and molecular detection of equine rhinitis B virus in horses in North Africa. Equine rhinitis A virus (ERAV) and equine rhinitis B virus (ERBV) are major respiratory pathogens of horses with a global distribution. The aim of this study was to evaluate, for the first time in Algeria, the seroprevalence of ERAV antibodies, and to investigate a wide range of equine viruses (EIV, EHV-1, EHV-4, ERAV and ERBV). A total of 298 serum samples were collected between May 2022 and October 2023, from 11 provinces. Serological analysis for the presence of ERAV was performed using the complement fixation test (CFT). Our results revealed that 16.8% (50/298) samples tested positive for ...
Matched embryo-endometrium RNA-seq reveals coordinated but asymmetric transcriptomic reprogramming at the onset of early equine pregnancy. Maternal recognition of pregnancy (MRP) in the mare requires coordinated adaptations of both the conceptus and the endometrium during the peri-recognition interval; however, integrated transcriptomic analyses of both compartments within the same biological window remain limited. Here, we analyzed conceptus RNA-seq data across embryonic age (Days 8 and 12 post ovulation) and endometrial RNA-seq data across pregnancy status (pregnant versus non-pregnant mares sampled between Days 8 and 12 post ovulation). In pregnant mares, conceptus recovery and endometrial biopsy collection were performed with...
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...
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...
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...
