Genomics in horses involves the study and analysis of the horse genome to understand genetic variations and their implications for equine health, performance, and breeding. This field encompasses the identification and mapping of genes associated with specific traits, diseases, and conditions in horses. Techniques such as whole-genome sequencing and genome-wide association studies (GWAS) are employed to explore genetic diversity and inheritance patterns among different horse breeds. Genomics provides insights into hereditary disorders, informs selective breeding practices, and aids in the development of personalized veterinary care. This page compiles peer-reviewed research studies and scholarly articles that explore the applications, methodologies, and findings of genomic research in equine science.
Frontiers in geneticsAugust 29, 2025
Volume 16 1651628 doi: 10.3389/fgene.2025.1651628
Su Y, Ren W, Ma S, Meng J, Yao X, Zeng Y, Li Z, Li L, Wang R, Wang J.This study employed Yili horses participating in a 5000-meter race as a model to investigate exercise-induced gene expression alterations in peripheral blood using whole transcriptome sequencing. Jugular vein blood samples from the three leading horses were collected pre- and immediately post-race, yielding 2,171 differentially expressed mRNAs (2,080 upregulated, 91 downregulated), 4,375 differentially expressed LncRNAs (4,354 upregulated), and 68 differentially expressed circRNAs (64 upregulated). GO/KEGG analyses demonstrated significant enrichment of differential mRNAs in transmembrane tran...
Science (New York, N.Y.)August 28, 2025
Volume 389, Issue 6763 925-930 doi: 10.1126/science.adp4581
Liu X, Jia Y, Pan J, Zhang Y, Gong Y, Wang X, Ma Y, Alvarez N, Jiang L, Orlando L.Horsepower revolutionized human history through enhanced mobility, transport, and warfare. However, the suite of biological traits that reshaped horses during domestication remains unclear. We scanned an extensive horse genome time series for selection signatures at 266 markers associated with key traits. We detected a signature of positive selection at -known to be a modulator of behavior in mice-occurring ~5000 years ago (ya), suggesting that taming was one of the earliest steps toward domestication of horses. Intensive selection at began ~4750 ya with the domestication bottleneck, leading ...
Marchio SP, El-Sheikh Ali H, Scott MA, Barbosa Fernandes C, Scoggin KE, Troedsson M, Boakari Y.Despite its critical role in protecting the fetus, the amniotic membrane remains poorly understood in the context of disease response. The equine amniotic membrane is an important physical barrier to the amniotic compartment, and there is evidence that it may contribute to surfactant synthesis. Surfactants are essential for normal fetal lung development, and disruptions in its availability may be linked to future neonatal complications. Therefore, understanding the molecular changes that occur in fetal-maternal tissues during placentitis would clarify how this condition leads to abortion, pret...
Sahoo DK, Wong D, Paital B, Ruby RE, Patel A.The progression of inflammation during sepsis represents a multifaceted biological cascade that requires effective therapeutic interventions to improve survival. In septic neonatal foals, oxidative stress (OS) arises due to a compromised antioxidant defense system. Oxidative stress may disrupt the functionality of redox-sensitive organelles, such as the endoplasmic reticulum (ER). Endoplasmic reticulum stress disorder affects multiple cellular signaling pathways, including redox balance, inflammation, and apoptosis, and contributes to the pathogenesis of sepsis. The study aimed to elucidate wh...
Toda J, Miyasaka J, Osako H, Murata K, Yunus M, Amalia R, Soe BK, Sato H.Food poisoning caused by consuming raw horsemeat contaminated with Sarcocystis is a significant public health concern. Two morphotypes of sarcocysts in horsemeat, characterized by upright and folded villar protrusions, are typically identified as Sarcocystis fayeri and S. bertrami, respectively. However, recent molecular studies focusing on the ribosomal RNA gene (rDNA) and mitochondrial cytochrome c oxidase subunit I gene (cox1) have indicated a conspecific relationship between these two morphotypes using a limited number of specimens. To explore further genetic diversity in equid sarcocysts,...
Liu F, Zhang J, Kong L, Wu R, Jiang Q, Lu Y, Li X.As an interspecies hybrid inheriting genetic material from horse and donkey lineages, mules provide a unique model for studying allele-specific regulatory dynamics. Here, we isolated adult fibroblasts (AFs) and placental fibroblasts (PFs) from mule tissues and reprogrammed them into induced pluripotent stem cells (iPSCs). Intriguingly, placental fibroblast-derived iPSCs (mpiPSCs) exhibited reduced reprogramming efficiency compared to adult fibroblast-derived iPSCs (maiPSCs). Through allele-specific expression (ASE) analysis, we systematically dissected transcriptional biases in parental cell t...
Schwochow D, Alameddine A, Spörndly-Nees E, Montigny M, Naboulsi R, Jansson A, Niazi A, Lindgren G.Racing without protective shoes is common in the Swedish harness racing industry, as it can enhance horses' performance on the track. Trainers typically decide whether a horse will race barefoot based on practical experience rather than objective measures. However, this practice can sometimes lead to excessive hoof wear, posing potential welfare concerns for racing horses. Gene expression differences may help reveal the underlying genetic mechanisms associated with different phenotypic traits. To explore an objective measure for assessing which horses are best suited for barefoot racing, we co...
Van Buren SL, Petersen JL, Brown CT, Finno CJ.With advancing genomic technologies, single-nucleotide polymorphism (SNP) arrays and whole genome sequencing (WGS) have become essential tools in equine genetic research. In this study, we assessed the concordance in SNP calls and trait-mapping efficacy by comparing data of 21 horses both genotyped on the Equine 670 K SNP array and sequenced at either ~12× or ~30× depth. Our analysis revealed that higher sequencing depths were significantly associated with fewer discordant calls between platforms. Additionally, we investigated the most frequent no-call and discordant positions and identifi...
Everts RE, Caron R, Foster G, McLoone K, Simiele L, Martin K, Brooks SA, Lafayette C.Roan coat color is described as the dispersion of white hairs within an otherwise solid background-color coat. This phenotype is primarily expressed on the body of the horse, with the head and legs exhibiting few or no white hairs. Previous studies mapped the locus for roan to the region and observed linked variants in a small number of breeds. Recently, we reported evidence for two independent haplotypes, and , in the region, which account for approximately 38% and 36% of roan horses, respectively. In the current report, using whole genome sequencing for unknown roan samples. We present a ...
Sharif MB, Mohaseb AF, Orlando L, Saliari K, Kunst GK, Czeika S, Mashkour M, Cucchi T, Peters J, Trixl S, Mohandesan E.The Roman conquest of the northern Alpine foreland in 15 BCE introduced larger-sized horses and hybrid mules to the region. To investigate their genetic profiles and influence on local breeding, we analyzed our previously generated shallow shotgun DNA data from 402 Late Iron Age and Roman equids, supplemented with mitochondrial and nuclear capture data from 40 to 31 equids from the same regions and periods. Late Iron Age and Roman horses exhibit high matrilineal diversity, with unique haplogroups in the latter indicating exogenous animals. The preferred use of male mounts in army service menti...
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D.Speed is not only the primary objective of racehorse breeding but also a crucial indicator for evaluating racehorse performance. This study investigates a newly developed racehorse breed in China. Through whole-genome resequencing, we selected 60 offspring obtained from the crossbreeding of Thoroughbred horses and Xilingol horses for this study. This breed is tentatively named "Grassland-Thoroughbred", and the samples were divided into two groups based on racing ability: 30 racehorses and 30 non-racehorses. Based on whole-genome sequencing data, the study achieved an average sequencing depth o...
Drögemüller M, Fouché N, Wyler M, Gurtner C, Meister SL, Neuditschko M, Jagannathan V, Gerber V, Leeb T.Hypertriglyceridemia (HTG) may be inherited and caused by variants in genes encoding enzymes of lipid metabolism. This study was prompted by the observation of eight Franches-Montagnes (FM) foals showing elevated plasma triglyceride levels and episodes of fatal acute pancreatitis. We termed this phenotype hypertriglyceridemia-induced pancreatitis (HIP). The affected foals were distantly related and inbred to a prominent stallion suggesting autosomal recessive inheritance. Whole genome sequencing of an affected foal identified a homozygous loss of function variant in LMF1 encoding lipase matura...
Sawicki S, Bugno-Poniewierska M, Żurowski J, Szmatoła T, Semik-Gurgul E, Bochenek M, Karnas E, Gurgul A. Mesenchymal stem cells (MSCs) are a promising tool in regenerative medicine due to their ability to secrete paracrine factors that modulate tissue repair. Extracellular vesicles (EVs) released by MSCs contain bioactive molecules (e.g., mRNAs, miRNAs, proteins) and play a key role in intercellular communication. This study compared the transcriptomic profiles (mRNA and miRNA) of equine MSCs derived from adipose tissue (AT-MSCs), bone marrow (BM-MSCs), and ovarian fibroblasts (as a differentiated control). Additionally, miRNAs present in EVs secreted by these cells were characterized using nex...
Horses have inhabited Iberia (present-day Spain and Portugal) since the Middle Pleistocene, shaping a complex history in the region. Iberia has been proposed as a potential domestication centre and is renowned for producing world-class bloodlines. Here, we generate genome-wide sequence data from 87 ancient horse specimens (median coverage = 0.97X) from Iberia and the broader Mediterranean to reconstruct their genetic history over the last ~26,000 years. Here, we report that wild horses of the divergent IBE lineage inhabited Iberia from the Late Pleistocene, while domesticated DOM2 horses, nati...
Ren M, Michaelson LP, Mungunsukh O, Bedocs P, Friel L, Cofer K, Dartt CE, Sambuughin N, O'Connor FG.Exertional rhabdomyolysis (ER) is primarily driven by mechanical stress on muscles during strenuous or unaccustomed exercise, often exacerbated by environmental factors like heat and dehydration. While the general cellular pathway involving energy depletion and calcium overload is understood in horse ER models, the underlying mechanisms specific to the ER are not universally known within humans. This study aimed to evaluate whether patients with ER exhibited transcriptional signatures that were significantly different from those of healthy individuals. Methods: This study utilized RNA sequenci...
Zhao Y, Liu Y, Tao J, Cao J, Lin Y, He Q, Fang X, Yun S, Du M, Su S, Bao T, Bai D, Zhang X, Dugarjaviin M.Reproductive health in mares is pivotal for the sustainability of the equine industry, yet vaginal microbiota dysbiosis remains an underrecognized contributor to infections such as endometritis and bacterial vaginosis. While spp. dominate healthy vaginal ecosystems in humans and livestock, their role in equine reproductive health, particularly in resilient breeds like Mongolian mares, is poorly understood. This study aimed to isolate and characterize a novel strain from the vaginal microbiota of healthy Mongolian mares and evaluate its probiotic potential for mitigating equine reproductive d...
Belhout C, Wang F, Rossano A, Collaud A, Fernandez JE, Marchionatti E, Keller JE, Overesch G, Kaessmeyer S, Schwendener S, Perreten V.Nine Gram-positive, non-motile, facultatively anaerobic cocci, designated EM39Eᵀ, JEK85, 18KM676, 21M1142, 18KM445, 18KM444, 18KM245, 18KM583 and 21KM1573, were isolated from diverse animal material, including horse and pig skin, bovine mastitis milk and feline urine from a urinary tract infection. Phylogenomic analysis based on amino-acid alignment obtained from translated whole-genome sequences; digital DNA-DNA hybridization (dDDH); 16S rRNA, , , and gene comparison; and MALDI-TOF MS spectral profiles placed the strains within the clade. They were closely related to CCM 7100ᵀ, CCM 7...
Bazvand B, Rashidi A, Zandi MB, Moradi MH, Rostamzadeh J, Mahmoudi P.Iran is home to genetically distinct horse breeds shaped by geography and history. Breeds like the Kurdish, Caspian pony, and Turkmen reflect deep-rooted diversity and unique adaptive traits. Objective: This study aimed to identify genomic regions exhibiting signatures of selection and to detect candidate genes and biological pathways related to body size that may influence performance in various Iranian and exotic horse breeds. Methods: Samples were collected from three Iranian native breeds (Caspian pony, Turkmen, and Kurdish) and three exotic breeds (Fell pony, Arabian, and Akhal-Teke) orig...
Tasnim Y, Rahman MK, Awosile B.We aimed to determine the genetic relatedness among β-lactamase-producing Escherichia coli isolated from soil, lake water, and feces of geese, pigs, dogs, cattle, coyotes, wild hogs, and horses at one health interface in West Texas. Results: Previously isolated 56 β-lactamase-producing E. coli isolates from the feces of geese, pigs, horses, coyotes, dogs, cattle, and wild hogs, and soil and lake water from different locations in West Texas were analyzed for genetic relatedness using whole-genome sequencing, core genome multilocus sequence typing, and phylogenetic single-nucleotide polymorphi...
Wubulikasimu M, Liu J, Yao X, Meng J, Wang J, Zeng Y, Li L, Ren W.Kazakh horses, a distinguished breed in China known for their dual-purpose use in milk and meat production, exhibit early maturation, tolerance to coarse feeding, and strong resistance to environmental stress. However, the gene expression differences across various muscle tissues of Kazakh horses have yet to be elucidated. In this study, transcriptomic sequencing was performed on muscle tissues from three anatomical regions of Kazakh horses, including the longissimus dorsi (Gb), external oblique (Gf), and diaphragm (Gg) muscles. In the Gb and Gf groups, 426 differentially expressed genes (DEGs...
Lu Z, Wen M, Yao X, Meng J, Wang J, Zeng Y, Li L, Ren W.The reproductive performance of horses is closely associated with testicular development, which involves a complex network of gene regulation. The molecular mechanisms underlying the reproductive traits of Kazakh horses are yet to be fully understood. In this study, transcriptomic analysis was performed on testicular tissues from Kazakh horses at different developmental stages using whole-transcriptome sequencing, aiming to investigate differential gene expression and regulatory mechanisms during testicular development. The results revealed significant differential expression of 7678 mRNAs, in...
Ghielmetti G, Stevens MJA, Schmitt S, Kittl S, Cernela N, Biggel M, Schulthess B, Keller PM, Schrenzel J, Stephan R.Rhodococcus equi is an intracellular bacterial pathogen that can cause infections in various hosts, including humans and animals. Host-associated virulence plasmids have been identified as key contributors to the pathogenicity of R. equi and potentially play a role in determining the host tropism of the bacteria. The investigation of additional clinical and environmental isolates is likely to provide novel insights into the population structure, infection pathways, and drug resistance of this important pathogen. We combined whole-genome sequencing and antimicrobial-susceptibility testing of 37...
McGlennon AA, Verheyen KL, Newton JR, van Tonder A, Wilson H, Parkhill J, de Brauwere N, Frosth S, Waller AS.Strangles (Streptococcus equi infection) remains endemic in the UK, with ~300 laboratory diagnoses annually. Sub-clinically infected long-term carriers are considered a key driver of endemicity. Analysing genomes of circulating strains could provide valuable transmission insights of this pathogen. Objective: To determine the population structure and diversity of UK S. equi isolates and to model transmission using epidemiological and whole genome sequencing data. Methods: Retrospective cross-sectional epidemiological and genomic surveillance. Methods: A dated phylogenetic tree derived from 511...
Frontiers in geneticsJuly 18, 2025
Volume 16 1630614 doi: 10.3389/fgene.2025.1630614
Gong W, Ding W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D.Ferulic acid (FA), a natural antioxidant, has attracted considerable attention for its regulatory potential in skeletal muscle development, energy metabolism, and muscle fiber type transformation. Unassigned: This study established a research system based on Mongolian horse skeletal muscle satellite cells to elucidate the molecular basis by which ferulic acid regulates muscle fiber type transformation through a non-coding RNA interaction network. Unassigned: A total of 18 differentially expressed miRNAs (DEMIRs) and 128 differentially expressed lncRNAs (DELs) were identified through transcript...
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D.The core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. However, research on the genetic characteristics within this breed and the genes associated with athletic performance remains relatively limited. We conducted whole-genome resequencing of Grassland-Thoroughbred F1, F2, F3, and the crossbred population (CY) and obtained a total of 4056.23 Gb of high-qual...
Jia H, Tang L, Fu Y, Xiong Y, Yan L, Shao C, Li K, Zhang D, Hu D.Petrovinema skrjabini (Nematoda: Strongylidae, Cyathostominae) is a parasitic nematode colonizing the cecum and colon of equids. Like other cyathostomins, its larvae (L3) invade the intestinal mucosa, forming encysted nodules that may remain dormant for years. Mass larval emergence triggers larval cyathostominosis-a severe syndrome characterized by hemorrhagic typhlocolitis and diarrhea, with mortality rates exceeding 50%. However, owing to the morphological indistinguishability of cyathostomin and frequent mixed infections in natural settings, species-specific contributions to pathogenesis re...
Zhang Z, Lu Z, Yao X, Li L, Meng J, Wang J, Zeng Y, Ren W.Kazakh mares have drawn significant attention for their outstanding lactation traits. Lactation, a complex physiological activity, is modulated by multiple factors. This study utilized high-throughput sequencing to conduct whole-transcriptome sequencing analysis on the mammary gland tissue of eight Kazakh mares, of which four were pregnant and four were non-pregnant, to systematically reveal the molecular regulatory mechanisms. The results showed differential expression in 2136 mRNAs, 180 lncRNAs, 104 miRNAs, and 1162 circRNAs. Gene ontology functional annotation indicates that these different...
Martin G, Tyson GH, Guag J, Strain E, Ceric O.Klebsiella spp. is an important human and animal pathogen, and it is commonly found with resistance to clinically important antimicrobials worldwide. The main goals of this study were to determine the prevalence of antimicrobial resistance genes in our study population and to assess the relatedness between Klebsiella spp. isolated from humans and animals. Isolates were collected in 2019 and 2020 from various animal hosts that presented to veterinary hospitals in the U.S. that participate in the FDA's Center for Veterinary Medicine Veterinary Laboratory Investigation and Response Network's anti...
Brodesser DM, Schlangen K, Rodríguez-Rojas A, Kuropka B, Doulidis PG, Brandt S, Pratscher B.Malignant melanoma (MM) affects not only humans but also animals, with gray horses being particularly predisposed to acquiring the disease. Multiomics have greatly advanced the understanding of human MM. In contrasty little is known regarding the pathogenesis of gray-horse melanoma and the unique phenomenon of melanoma "dormancy" in some animals. To help close this gap in knowledge, melanoma tissue and intact skin collected from gray horses were subjected to transcriptome analysis using RNAseq. In the next step, cultured primary tumor cells and normal skin fibroblasts were established from gra...
Peffers M, Liu X, Clegg P.Age is an important factor in the development of osteoarthritis. Microarray studies provide insight into cartilage aging but do not reveal the full transcriptomic phenotype of chondrocytes such as small noncoding RNAs, pseudogenes, and microRNAs. RNA-Seq is a powerful technique for the interrogation of large numbers of transcripts including nonprotein coding RNAs. The aim of the study was to characterise molecular mechanisms associated with age-related changes in gene signatures. Methods: RNA for gene expression analysis using RNA-Seq and real-time PCR analysis was isolated from macroscopicall...
The Journal of hereditySeptember 1, 1991
Volume 82, Issue 5 369-377 doi: 10.1093/oxfordjournals.jhered.a111106
Wichman HA, Payne CT, Ryder OA, Hamilton MJ, Maltbie M, Baker RJ.We describe a molecular model for rapid chromosomal evolution that proposes tandemly repeated DNA sequences as a driving force. A prediction of this model is that when extensive rearrangements of euchromatin have been facilitated by heterochromatin, genomes will be characterized by tandemly repeated sequences that have actively changed chromosomal fields by intragenomic movement. Alternatively, it is proposed that in conservative chromosomal lineage each class of tandemly repeated sequences will be restricted to a specific chromosomal field. To provide baseline data to test this model we exami...
Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G.The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most wi...
Park KD, Park J, Ko J, Kim BC, Kim HS, Ahn K, Do KT, Choi H, Kim HM, Song S, Lee S, Jho S, Kong HS, Yang YM, Jhun BH, Kim C, Kim TH, Hwang S, Bhak J....Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes. Results: We present a large-scale analysis of whole transcriptome data. We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current genome annotations, we identified 32,361 unigene cluster...
Ezashi T, Yuan Y, Roberts RM.This review deals with the latest advances in the study of embryonic stem cells (ESC) and induced pluripotent stem cells (iPSC) from domesticated species, with a focus on pigs, cattle, sheep, goats, horses, cats, and dogs. Whereas the derivation of fully pluripotent ESC from these species has proved slow, reprogramming of somatic cells to iPSC has been more straightforward. However, most of these iPSC depend on the continued expression of the introduced transgenes, a major drawback to their utility. The persistent failure in generating ESC and the dependency of iPSC on ectopic genes probably s...
Forrester NL, Wertheim JO, Dugan VG, Auguste AJ, Lin D, Adams AP, Chen R, Gorchakov R, Leal G, Estrada-Franco JG, Pandya J, Halpin RA, Hari K, Jain R....Venezuelan equine encephalitis (VEE) complex alphaviruses are important re-emerging arboviruses that cause life-threatening disease in equids during epizootics as well as spillover human infections. We conducted a comprehensive analysis of VEE complex alphaviruses by sequencing the genomes of 94 strains and performing phylogenetic analyses of 130 isolates using complete open reading frames for the nonstructural and structural polyproteins. Our analyses confirmed purifying selection as a major mechanism influencing the evolution of these viruses as well as a confounding factor in molecular cloc...
Iacono E, Brunori L, Pirrone A, Pagliaro PP, Ricci F, Tazzari PL, Merlo B.Mesenchymal stem cells (MSCs) have been derived from multiple sources of the horse including umbilical cord blood (UCB) and amnion. This work aimed to identify and characterize stem cells from equine amniotic fluid (AF), CB and Wharton's Jelly (WJ). Samples were obtained from 13 mares at labour. AF and CB cells were isolated by centrifugation, while WJ was prepared by incubating with an enzymatic solution for 2 h. All cell lines were cultured in DMEM/TCM199 plus fetal bovine serum. Fibroblast-like cells were observed in 7/10 (70%) AF, 6/8 (75%) CB and 8/12 (66.7%) WJ samples. Statistically ...
McCue ME, Valberg SJ, Miller MB, Wade C, DiMauro S, Akman HO, Mickelson JR.Polysaccharide storage myopathy (PSSM) is a novel glycogenosis in horses characterized by abnormal glycogen accumulation in skeletal muscle and muscle damage with exertion. It is unlike glycogen storage diseases resulting from known defects in glycogenolysis, glycolysis, and glycogen synthesis that have been described in humans and domestic animals. A genome-wide association identified GYS1, encoding skeletal muscle glycogen synthase (GS), as a candidate gene for PSSM. DNA sequence analysis revealed a mutation resulting in an arginine-to-histidine substitution in a highly conserved region of G...
de Jonge N, Carlsen B, Christensen MH, Pertoldi C, Nielsen JL.The gut microbiome plays a critical role in many aspects of host life, and the microbial community composition is heavily influenced by the prevailing conditions in the gut environment. Community composition has been suggested to have large implications for conservation efforts, and gut health has become of interest for optimizing animal care in captivity. In this study, we explore the gut microbiome of a wide range of animals in the context of conservation biology. The composition of the gut microbial community of 54 mammalian animal species was investigated using 16S rRNA gene amplicon seque...
Janečka JE, Davis BW, Ghosh S, Paria N, Das PJ, Orlando L, Schubert M, Nielsen MK, Stout TAE, Brashear W, Li G, Johnson CD, Metz RP, Zadjali AMA....Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X-Y gametologs recorded in eutherians, in addition to novel Y-born and transp...
Endimiani A, Hujer KM, Hujer AM, Bertschy I, Rossano A, Koch C, Gerber V, Francey T, Bonomo RA, Perreten V.We investigated whether Acinetobacter baumannii isolates of veterinary origin shared common molecular characteristics with those described in humans. Methods: Nineteen A. baumannii isolates collected in pets and horses were analysed. Clonality was studied using repetitive extragenic palindromic PCR (rep-PCR) and multilocus sequence typing (MLST). PCR and DNA sequencing for various β-lactamase, aminoglycoside-modifying enzyme, gyrA and parC, ISAba1 and IS1133, adeR and adeS of the AdeABC efflux pump, carO porin and class 1/2/3 integron genes were performed. Results: Two main clones [A (n =...
Doan R, Cohen N, Harrington J, Veazey K, Juras R, Cothran G, McCue ME, Skow L, Dindot SV.Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a whole-exome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein- and...
Druart X, Rickard JP, Mactier S, Kohnke PL, Kershaw-Young CM, Bathgate R, Gibb Z, Crossett B, Tsikis G, Labas V, Harichaux G, Grupen CG, de Graaf SP.Seminal plasma contains a large protein component which has been implicated in the function, transit and survival of spermatozoa within the female reproductive tract. However, the identity of the majority of these proteins remains unknown and a direct comparison between the major domestic mammalian species has yet to be made. As such, the present study characterized and compared the seminal plasma proteomes of cattle, horse, sheep, pig, goat, camel and alpaca. GeLC-MS/MS and shotgun proteomic analysis by 2D-LC-MS/MS identified a total of 302 proteins in the seminal plasma of the chosen mammali...
Brooks SA, Gabreski N, Miller D, Brisbin A, Brown HE, Streeter C, Mezey J, Cook D, Antczak DF.Lavender Foal Syndrome (LFS) is a lethal inherited disease of horses with a suspected autosomal recessive mode of inheritance. LFS has been primarily diagnosed in a subgroup of the Arabian breed, the Egyptian Arabian horse. The condition is characterized by multiple neurological abnormalities and a dilute coat color. Candidate genes based on comparative phenotypes in mice and humans include the ras-associated protein RAB27a (RAB27A) and myosin Va (MYO5A). Here we report mapping of the locus responsible for LFS using a small set of 36 horses segregating for LFS. These horses were genotyped usin...
da Silveira JC, Carnevale EM, Winger QA, Bouma GJ.Ovarian follicle growth and maturation requires extensive communication between follicular somatic cells and oocytes. Recently, intercellular cell communication was described involving cell-secreted vesicles called exosomes (50-150 nm), which contain miRNAs and protein, and have been identified in ovarian follicular fluid. The goal of this study was to identify a possible role of exosomes in follicle maturation. Methods: Follicle contents were collected from mares at mid-estrous (~35 mm, before induction of follicular maturation) and pre-ovulatory follicles (30-34 h after induction of folli...
Gurgul A, Jasielczuk I, Semik-Gurgul E, Pawlina-Tyszko K, Stefaniuk-Szmukier M, Szmatoła T, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M.The genetic differentiation of the current horse population was evolutionarily created by natural or artificial selection which shaped the genomes of individual breeds in several unique ways. The availability of high throughput genotyping methods created the opportunity to study this genetic variation on a genome-wide level allowing detection of genome regions divergently selected between separate breeds as well as among different horse types sharing similar phenotypic features. In this study, we used the population differentiation index (FST) that is generally used for measuring locus-specifi...
Benachour N, Sipahutar H, Moslemi S, Gasnier C, Travert C, Séralini GE.Roundup is the major herbicide used worldwide, in particular on genetically modified plants that have been designed to tolerate it. We have tested the toxicity and endocrine disruption potential of Roundup (Bioforce on human embryonic 293 and placental-derived JEG3 cells, but also on normal human placenta and equine testis. The cell lines have proven to be suitable to estimate hormonal activity and toxicity of pollutants. The median lethal dose (LD(50)) of Roundup with embryonic cells is 0.3% within 1 h in serum-free medium, and it decreases to reach 0.06% (containing among other compounds 1.2...
Biddle AS, Black SJ, Blanchard JL.Laminitis is a chronic, crippling disease triggered by the sudden influx of dietary starch. Starch reaches the hindgut resulting in enrichment of lactic acid bacteria, lactate accumulation, and acidification of the gut contents. Bacterial products enter the bloodstream and precipitate systemic inflammation. Hindgut lactate levels are normally low because specific bacterial groups convert lactate to short chain fatty acids. Why this mechanism fails when lactate levels rapidly rise, and why some hindgut communities can recover is unknown. Fecal samples from three adult horses eating identical di...
Steinrücken M, Bhaskar A, Song YS.The increased availability of time series genetic variation data from experimental evolution studies and ancient DNA samples has created new opportunities to identify genomic regions under selective pressure and to estimate their associated fitness parameters. However, it is a challenging problem to compute the likelihood of non-neutral models for the population allele frequency dynamics, given the observed temporal DNA data. Here, we develop a novel spectral algorithm to analytically and efficiently integrate over all possible frequency trajectories between consecutive time points. This advan...
Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, Elton D, Newton JR, Kellam P, Wood JL, Holmes EC, Murcia PR.The ability of influenza A viruses (IAVs) to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales - from the individual to the population - are essential for devising effective measures to predict, prevent or contain influenza emergence. Understanding how IAVs spread and evolve during outbreaks is critical for the management of epidemics. Reconstructing the transmission network during a single outbreak by sampling viral genetic data in time and space can generate insights about these processes. Here, we ob...
Whalley JM, Robertson GR, Davison AJ.The genome of an Australian isolate of equine herpesvirus type 1 (equine abortion virus) has been analysed using the restriction endonucleases EcoRI, BglII and BamHI, and a physical map constructed. Terminal fragments were identified by exonuclease treatments, and linkage of fragments was deduced by a combination of single- and double-digest experiments and cross-blot hybridizations. The genome has a mol. wt. of 100 x 10(6) and is comprised of a short unique region bounded by repetitive sequences, which is present in both orientations in approximately equal amounts in the DNA population, and a...
Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G....The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern Euro...
Liu G, Cao W, Salawudeen A, Zhu W, Emeterio K, Safronetz D, Banadyga L.Vesicular stomatitis virus (VSV), which belongs to the Vesiculovirus genus of the family Rhabdoviridae, is a well studied livestock pathogen and prototypic non-segmented, negative-sense RNA virus. Although VSV is responsible for causing economically significant outbreaks of vesicular stomatitis in cattle, horses, and swine, the virus also represents a valuable research tool for molecular biologists and virologists. Indeed, the establishment of a reverse genetics system for the recovery of infectious VSV from cDNA transformed the utility of this virus and paved the way for its use as a vaccine ...
Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Cooper A, Weinstock J, Willerslev E, Shapiro B, Hofreiter M.Modern domestic horses display abundant genetic diversity within female-inherited mitochondrial DNA, but practically no sequence diversity on the male-inherited Y chromosome. Several hypotheses have been proposed to explain this discrepancy, but can only be tested through knowledge of the diversity in both the ancestral (pre-domestication) maternal and paternal lineages. As wild horses are practically extinct, ancient DNA studies offer the only means to assess this ancestral diversity. Here we show considerable ancestral diversity in ancient male horses by sequencing 4 kb of Y chromosomal DNA ...
Attoui H, Mendez-Lopez MR, Rao S, Hurtado-Alendes A, Lizaraso-Caparo F, Mohd Jaafar F, Samuel AR, Belhouchet M, Pritchard LI, Melville L, Weir RP....During 1997, two new viruses were isolated from outbreaks of disease that occurred in horses, donkeys, cattle and sheep in Peru. Genome characterization showed that the virus isolated from horses (with neurological disorders, 78% fatality) belongs to a new species the Peruvian horse sickness virus (PHSV), within the genus Orbivirus, family Reoviridae. This represents the first isolation of PHSV, which was subsequently also isolated during 1999, from diseased horses in the Northern Territory of Australia (Elsey virus, ELSV). Serological and molecular studies showed that PHSV and ELSV are very s...
Bujacz A, Zielinski K, Sekula B.Serum albumin, a protein naturally abundant in blood plasma, shows remarkable ligand binding properties of numerous endogenous and exogenous compounds. Most of serum albumin binding sites are able to interact with more than one class of ligands. Determining the protein-ligand interactions among mammalian serum albumins is essential for understanding the complexity of this transporter. We present three crystal structures of serum albumins in complexes with naproxen (NPS): bovine (BSA-NPS), equine (ESA-NPS), and leporine (LSA-NPS) determined to 2.58 Å (C2), 2.42 Å (P61), and 2.73 Å (P2₁2₁...
van der Weyden L, Brenn T, Patton EE, Wood GA, Adams DJ.In contrast to other cancer types, melanoma incidence has been increasing over the last 50 years, and while it still represents less than 5% of all cutaneous malignancies, melanoma accounts for the majority of skin cancer deaths, due to its propensity to metastasise. Whilst melanoma most commonly affects the skin, it can also arise in mucosal surfaces, the eye, and the brain. For new therapies to be developed, a better understanding of the genetic landscape, signalling pathways, and tumour-microenvironmental interactions is needed. This is where animal models are of critical importance. The ...
Golomidova A, Kulikov E, Isaeva A, Manykin A, Letarov A.The diversity of coliphages and indigenous coliform strains (ICSs) simultaneously present in horse feces was investigated by culture-based and molecular methods. The richness of coliforms (as estimated by the Chao1 method) is about 1,000 individual ICSs distinguishable by genomic fingerprinting present in a single sample of feces. This unexpectedly high value indicates that some factor limits the competition of coliform bacteria in the horse gut microbial system. In contrast, the diversity of phages active against any selected ICS is generally limited to one to three viral genotypes present in...
Imsland F, McGowan K, Rubin CJ, Henegar C, Sundström E, Berglund J, Schwochow D, Gustafson U, Imsland P, Lindblad-Toh K, Lindgren G, Mikko S....Dun is a wild-type coat color in horses characterized by pigment dilution with a striking pattern of dark areas termed primitive markings. Here we show that pigment dilution in Dun horses is due to radially asymmetric deposition of pigment in the growing hair caused by localized expression of the T-box 3 (TBX3) transcription factor in hair follicles, which in turn determines the distribution of hair follicle melanocytes. Most domestic horses are non-dun, a more intensely pigmented phenotype caused by regulatory mutations impairing TBX3 expression in the hair follicle, resulting in a more circu...
Baer A, Lundberg L, Swales D, Waybright N, Pinkham C, Dinman JD, Jacobs JL, Kehn-Hall K.Venezuelan equine encephalitis virus (VEEV) is a previously weaponized arthropod-borne virus responsible for causing acute and fatal encephalitis in animal and human hosts. The increased circulation and spread in the Americas of VEEV and other encephalitic arboviruses, such as eastern equine encephalitis virus and West Nile virus, underscore the need for research aimed at characterizing the pathogenesis of viral encephalomyelitis for the development of novel medical countermeasures. The host-pathogen dynamics of VEEV Trinidad donkey-infected human astrocytoma U87MG cells were determined by car...
