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.
Tessier L, Côté O, Bienzle D.Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants of potential relevance to the pathogenesis of asthma. Methods: RNA-Seq data were generated from endobronchial biopsies collected from six asthmatic and seven non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequenc...
Tozaki T, Gamo S, Takasu M, Kikuchi M, Kakoi H, Hirota KI, Kusano K, Nagata SI.Doping control is an important and indispensable aspect of fair horse racing; genetic doping has been recently included to this. In this study, we aimed to develop a detection method of gene doping. A plasmid cloned with human erythropoietin gene (p.hEPO, 250 μg/head) was intramuscularly injected into a microminipig. Subsequently, p.hEPO was extracted from 1 mL of plasma and detected by droplet digital polymerase chain reaction. Results: The results confirmed that the maximum amount of plasmid was detected at 15 min after administration and the majority of the plasmid was degraded in the b...
Chassier M, Barrey E, Robert C, Duluard A, Danvy S, Ricard A.Genotype imputation is now a key component of genomic analyses as it increases the density of available genotypes within a population. However, many factors can influence imputation accuracy. The aim of this study was to assess and compare the accuracy of imputation of high-density genotypes (Affymetrix Axiom Equine genotyping array, 670,806 SNPs) from two moderate-density genotypes (Illumina Equine SNP50 BeadChip, 54,602 SNPs and Illumina Equine SNP70 BeadChip, 65,157 SNPs), using single-breed or multiple-breed reference sets. Genotypes were available from five groups of horse breeds: Arab (A...
Leiberich M, Marais HJ, Naidoo V.The plight of the white rhinoceros () and the increasing need of treatment options for injured poaching victims led to the necessity to expand the knowledge on applicable drugs in this endangered species. With very little information available on drug pharmacokinetics in rhino, veterinarians have to rely on information generated from other species. The horse being a closely related species, has served as the model for dose extrapolations. However, from recent research on enrofloxacin and carprofen, the white rhino showed considerable differences in the pharmacokinetic properties of these drugs...
Valberg SJ, Perumbakkam S, McKenzie EC, Finno CJ.Equine myofibrillar myopathy (MFM) causes exertional muscle pain and is characterized by myofibrillar disarray and ectopic desmin aggregates of unknown origin. To investigate the pathophysiology of MFM, we compared resting and 3 h postexercise transcriptomes of gluteal muscle and the resting skeletal muscle proteome of MFM and control Arabian horses with RNA sequencing and isobaric tags for relative and absolute quantitation analyses. Three hours after exercise, 191 genes were identified as differentially expressed (DE) in MFM vs. control muscle with >1 log fold change (FC) in genes involve...
Brooks SA, Stick J, Braman A, Palermo K, Robinson NE, Ainsworth DM.Equine recurrent laryngeal neuropathy (RLN) is a bilateral mononeuropathy with an unknown etiology. In Thoroughbreds (TB), we previously demonstrated that the haplotype association for height (LCORL/NCAPG locus on ECA3, which affects body size) and RLN was coincident. In the present study, we performed a genome-wide association scan (GWAS) for RLN in 458 American Belgian Draft Horses, a breed fixed for the LCORL/NCAPG risk alelle. In this breed, RLN risk is associated with sexually dimorphic differences in height, and we identified a novel locus contributing to height in a sex-specific manner:...
Melzer F, Raßbach A, Köenig-Mozes A, Elschner MC, Tomaso H, Busch A.Here, we report the draft genome sequence of Taylorella equigenitalis strain 210217RC10635, a Gram-negative bacterium belonging to the genus Taylorella and the order Burkholderiales. Taylorella equigenitalis is the causative agent of contagious equine metritis (CEM). The strain reported here was isolated in 2017 from a German stallion.
Scaravaggi I, Borel N, Romer R, Imboden I, Ulbrich SE, Zeng S, Bollwein H, Bauersachs S.Previous endometrial gene expression studies during the time of conceptus migration did not provide final conclusions on the mechanisms of maternal recognition of pregnancy (MRP) in the mare. This called for a cell type-specific endometrial gene expression analysis in response to embryo signals to improve the understanding of gene expression regulation in the context of MRP. Laser capture microdissection was used to collect luminal epithelium (LE), glandular epithelium and stroma from endometrial biopsies from Day 12 of pregnancy and Day 12 of the oestrous cycle. RNA sequencing (RNA-Seq) showe...
Kalinowski M, Grądzki Z, Jarosz Ł, Adaszek Ł.Rhodococcus equi (R. hoagii) is an opportunistic pathogen commonly found in foals up to 6 months old and animal environment. The R. equi genome contains genetically stable chromosomal DNA and an 80-90 kb plasmid containing vapA gene, responsible for virulence. Most reports from around the world focus on the determination of R. equi plasmid profiles. Few studies have attempted to determine differences in nucleotide sequences between virulent strains of R. equi isolated from foals and breeding environment. The aim of the study was to perform a molecular analysis of a fragment of the chromosomal ...
Bernet A, Bastien A, Soulet D, Jerczynski O, Roy C, Bianchi Rodrigues Alves M, Lecours C, Tremblay MÈ, Bailey JL, Robert C, Belleannée C.Where are primary cilia (PC) organelles located during postnatal epididymal development? Our findings unveil the existence of PC sensory organelles in different epididymal cell types according to postnatal development stage. Primary cilia are sensory organelles that orchestrate major signaling pathways during organ development and homeostasis. Epididymal PC have been detected in the horses, donkey and mules but their cell-lineage specificity has never been investigated in this organ. A longitudinal study was performed by examining tissue from n = 3 to n = 10 transgenic mice at different times ...
Stewart HL, Southwood LL, Indugu N, Vecchiarelli B, Engiles JB, Pitta D.The faecal microbiota is emerging as potentially important in intestinal disease. More research is needed to characterise the faecal microbiota from horses with colic. Objective: To compare the relative abundance of bacterial populations comprising the faecal microbiota in horses presenting for colic compared with an elective surgical procedure. Methods: Prospective observational clinical study. Methods: Admission faecal samples were collected from horses presenting for colic and elective surgical procedures. Faecal samples were extracted for genomic DNA, PCR- amplified, sequenced and analysed...
Lange-Consiglio A, Lazzari B, Pizzi F, Stella A, Girani A, Quintè A, Cremonesi F, Capra E.Conditioned medium (CM) and microvesicles (MVs) are produced using different protocols: CM is collected following 12-96 h of cell culture without renewal of tissue culture medium, while MVs are collected after overnight cell culture. For future comparative studies in regenerative medicine looking at the efficacy of CM and MVs, it is important to understand how the quality of cell secretions is affected by culture. The aim of this study was to evaluate whether the duration of culturing influences the micro-RNAs (miRNAs) cargo of equine amniotic mesenchymal cells (AMCs) and their MVs. The anal...
Yoon SH, Lee W, Ahn H, Caetano-Anolles K, Park KD, Kim H.The Thoroughbred horse breed was developed primarily for racing, and has a significant contribution to the qualitative improvement of many other horse breeds. Despite the importance of Thoroughbred racehorses in historical, cultural, and economical viewpoints, there was no temporal and spatial dynamics of them using the mitogenome sequences. To explore this topic, the complete mitochondrial genome sequences of 14 Thoroughbreds and two Przewalski's horses were determined. These sequences were analyzed together along with 151 previously published horse mitochondrial genomes from a range of breed...
Amilon KR, Cortes-Araya Y, Moore B, Lee S, Lillico S, Breton A, Esteves CL, Donadeu FX.Induced pluripotent stem cells (iPSCs) have revolutionized human biomedicine through their use in disease modeling and therapy. In comparison, little progress has been made toward the application of iPSCs in veterinary species. In that regard, skeletal myocytes from iPSCs would have great potential for understanding muscle function and disease in the equine athlete. In this study, we generated skeletal myotubes by transducing equine iPSC-derived mesenchymal derivatives with an inducible lentiviral vector coding for the human sequence of the myogenic factor, MyoD. Myosin heavy chain-positive my...
Skujina I, Winton CL, Hegarty MJ, McMahon R, Nash DM, Davies Morel MCG, McEwan NR.Height is an important characteristic in the equine industry although little is known about its genetic control in native British breeds of ponies. This study aimed to map QTL data with the withers height in four pony breeds native to the British Isles, including two different sections within Welsh Cobs. In this study, a genome-wide analysis approach using the Illumina EquineSNP50 Infinium BeadChip was applied to 105 ponies and cobs. Analysis identified 222 highly significant height-associated SNPs (P ≤ 10), among which three SNPs on ECA9 have also been previously reported elsewhere. The hig...
Mucha V, Hollý J, Varečková E, Kostolanský F.Avian influenza A viruses (IAVs) are able to overcome the interspecies barrier and adapt to the new non-avian host. The process of adaptation requires the adaptive changes of IAV genome resulting in amino acid substitutions. The aim of this work was the description of amino acid substitutions in avian influenza A viruses (IAVs) occurring during their adaptation to equine host. Today, viruses of the equine influenza H3N8 subtype, first isolated in 1963, represent a single genetic lineage of IAV causing a respiratory disease in horses. We compared the amino acid sequences of the conserve...
Velie BD, Fegraeus KJ, Solé M, Rosengren MK, Røed KH, Ihler CF, Strand E, Lindgren G.Although harness racing is of high economic importance to the global equine industry, significant genomic resources have yet to be applied to mapping harness racing success. To identify genomic regions associated with harness racing success, the current study performs genome-wide association analyses with three racing performance traits in the Norwegian-Swedish Coldblooded Trotter using the 670 K Axiom Equine Genotyping Array. Following quality control, 613 horses and 359,635 SNPs were retained for further analysis. After strict Bonferroni correction, nine genome-wide significant SNPs were id...
Murru F, Fliegerova K, Mura E, Mrázek J, Kopečný J, Moniello G.The diversity of the methanogenic archaea associated with the six segments of the horse and donkey hindgut (caecum, right ventral colon, left ventral colon, left dorsal colon, right dorsal colon, and rectum) was analyzed using 16S rDNA gene clone library. A total of 641 positive clones, 321 from the horse and 320 from the donkey hindgut, were examined by the RFLP, revealing 9 different ribotypes, 8 in the horse and 5 in the donkey hindgut. In both the animals Methanobacteriales (Methanobrevibacter-like sequences) and Methanomicrobiales (Methanocorpusculum-like sequences) were detected as the d...
Ablondi M, Vasini M, Beretti V, Superchi P, Sabbioni A.Genetic diversity is a key factor for both adaptation and response to selection. The loss of genetic diversity causes a decrease in individual fitness, and it has a dramatically negative effect on population lifespan in the long term. This study aimed at exploring the genetic diversity at pedigree level of the Bardigiano horse breed, which is a native breed from Italy shaped for living in rural areas. In 1977, the Bardigiano studbook was founded to preserve the breed and for improving its use for riding and draft purposes. Pedigree data contained 9,469 horses, of which 3,416 were alive. Demog...
Zhang B, Huang H, Wang H, Zhang D, Chu H, Ma X, Ge Y, Ente M, Li K.Gasterophilus species are widely distributed around the world. The larvae of these flies parasitize the digestive tract of equids and cause damage, hindering horse breeding and protection of endangered species. However, study of the genetic structure of geographically distinct Gasterophilus populations is lacking. Here, we analyzed the genetic diversity of Gasterophilus pecorum, G. intestinalis, G. nasalis and G. nigricornis from three typical grasslands (meadow, desert and alpine steppes) in China as compared to published sequences from Italy, Poland and China (Daqing and Yili), based on the ...
Soghigian J, Andreadis TG, Molaei G.Eastern Equine Encephalitis (EEE) (Togaviridae, Alphavirus) is a highly pathogenic mosquito-borne arbovirus that circulates in an enzootic cycle involving Culiseta melanura mosquitoes and wild Passeriformes birds in freshwater swamp habitats. Recently, the northeastern United States has experienced an intensification of virus activity with increased human involvement and northward expansion into new regions. In addition to its principal role in enzootic transmission of EEE virus among avian hosts, recent studies on the blood-feeding behavior of Cs. melanura throughout its geographic range sugg...
Amano T, Onogi A, Yamada F, Kawai M, Shirai K, Ueda J.Previously, a single nucleotide polymorphism (SNP) related to gait type was identified at position 22 999 655 of chromosome 23 in the coding region of DMRT3 (DMRT3:Ser301Ter) by showing that a cytosine (C) to adenine (A) mutation of this SNP induced pace in the Icelandic horse. We investigated the effect of DMRT3:Ser301Ter on the gait of Hokkaido Native Horses, a Japanese native breed, and examined genetic factors other than DMRT3 by exploring genome-wide SNPs related to gait determination. All animals exhibiting pace were AA for DMRT3:Ser301Ter, confirming the association of DMRT3:Ser301Ter...
Kim NY, Seong HS, Kim DC, Park NG, Yang BC, Son JK, Shin SM, Woo JH, Shin MC, Yoo JH, Choi JW.The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju × Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas r values were lowest in Jeju horse. Expected heterozygos...
Mason VC, Schaefer RJ, McCue ME, Leeb T, Gerber V.Severe equine asthma, also known as recurrent airway obstruction (RAO), is a debilitating, performance limiting, obstructive respiratory condition in horses that is phenotypically similar to human asthma. Past genome wide association studies (GWAS) have not discovered coding variants associated with RAO, leading to the hypothesis that causative variant(s) underlying the signals are likely non-coding, regulatory variant(s). Regions of the genome containing variants that influence the number of expressed RNA molecules are expression quantitative trait loci (eQTLs). Variation associated with RAO ...
Stewart HL, Pitta D, Indugu N, Vecchiarelli B, Engiles JB, Southwood LL.OBJECTIVE To characterize the fecal microbiota of horses and to investigate alterations in that microbiota on the basis of sample collection site (rectum vs stall floor), sample location within the fecal ball (center vs surface), and duration of environmental exposure (collection time). ANIMALS 6 healthy adult mixed-breed mares. PROCEDURES From each horse, feces were collected from the rectum and placed on a straw-bedded stall floor. A fecal ball was selected for analysis immediately after removal from the rectum and at 0 (immediately), 2, 6, 12, and 24 hours after placement on the stall floor...
Schurink A, da Silva VH, Velie BD, Dibbits BW, Crooijmans RPMA, Franҫois L, Janssens S, Stinckens A, Blott S, Buys N, Lindgren G, Ducro BJ.Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated w...
Eberth JE, Graves KT, MacLeod JN, Bailey E.Chondrodysplastic dwarfism in Miniature horses appeared to be a recessive genetic trait based on the occurrence of affected offspring by normal parents. Dwarf phenotypes vary and range from abnormal abortuses to viable offspring with evidence of skeletal dysplasia. A genome-wide association study implicated a region of ECA1 with dwarfism in Miniature horses. Aggrecan (ACAN) was a candidate gene in that region, and exons were sequenced to compare DNA sequences for dwarf and non-dwarf horses. Sequencing led to the discovery of variants in exons 2, 6, 7 and 15 associated with dwarfism. The four v...
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...
Solé M, Valera M, Fernández J.The Pura Raza Español (PRE) is an autochthonous Spanish horse population distributed in 65 countries and managed by a single association. Since 1960s, breeding animals have been steadily exported to other countries to establish local subpopulations. We analysed the genetic structure of a PRE horse meta-population (MP) of 215,500 animals from countries with at least 80 active animals (27 countries comprising 77% of the total animals in the complete pedigree). Genotypes from active animals (59% of the total animals in the complete pedigree) were also studied. Genetic analysis of the MP was perf...
Johnson GP, Lloyd AT, O'Farrelly C, Meade KG, Fair S.?-defensins are small cationic proteins with potent immunoregulatory and antimicrobial activity. The number of genes encoding these peptides varies significantly between and within species but they have not been extensively characterised in the horse. Here, we describe a systematic search of the Equus caballus genome that identified a cluster of novel ?-defensin genes on Chromosome 22, which is homologous to a cluster on bovine Chromosome 13. Close genomic matches were found for orthologs of 13 of the bovine genes, which were named equine ?-defensins (eBD) 115, eBD116, eBD117, eBD119, eBD120, ...
Tozaki T, Miyake T, Kakoi H, Gawahara H, Hirota K, Nakano Y, Kurosawa M.This study evaluated the differences between linear and non-linear modelled heritability estimates of racing performance based on lifetime earnings (LE) and lifetime ranking (LR) in Japanese Thoroughbred racehorses. The heritability estimate (h(2) = 0.25) obtained from a non-linear model based on formal Japan Racing Association ranking was much higher than that obtained from a linear model based on the original trait phenotype (h(2) = 0.11). The linear models showed slightly higher heritability estimates under the trait categorizations than under the original phenotypes, while the non-linear c...
Artiushin S, Tong Y, Timoney J, Lemieux B, Schlegel A, Kong H.A simple and portable assay for detection of Streptococcus equi subspecies equi has been developed based on amplification of S. equi-specific sequence using a thermophilic helicase-dependent reaction followed by visual detection of the amplicon in a disposable lateral flow cassette. An experimental kit (IsoAmp™ SE) was evaluated. Analytical sensitivity was 50 copies of S. equi genomic DNA per reaction. The IsoAmp SE assay had 100% specificity when applied to nasal swabs and washes. The assay was more sensitive than culture but less sensitive than nested polymerase chain reaction (PCR). The t...
Leeb T, Müller EJ, Roosje P, Welle M.Molecular genetics has made significant advances in the analysis of hereditary dermatoses during the last several years. Objective: To provide an update on currently available genetic tests for skin diseases of dogs, cats and horses, and to aid the veterinary clinician in the appropriate selection and applications of genetic tests. Methods: The scientific literature on the topic was critically reviewed. The list of known causative variants for genodermatoses and hair morphology traits was compiled by searching the Online Mendelian Inheritance in Animals (OMIA) database. Results: Genetic testin...
Dierks C, Löhring K, Lampe V, Wittwer C, Drögemüller C, Distl O.A genome-wide scan was performed to detect quantitative trait loci (QTLs) for osteochondrosis (OC) and osteochondrosis dissecans (OCD) in horses. The marker set comprised 260 microsatellites. We collected data from 211 Hanoverian warmblood horses consisting of 14 paternal half-sib families. Traits used were OC (fetlock and/or hock joints affected), OCD (fetlock and/or hock joints affected), fetlock OC, fetlock OCD, hock OC, and hock OCD. The first genome scan included 172 microsatellite markers. In a second step 88 additional markers were chosen to refine putative QTLs found in the first scan....
Dahlgren AR, Scott EY, Mansour T, Hales EN, Ross PJ, Kalbfleisch TS, MacLeod JN, Petersen JL, Bellone RR, Finno CJ.Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A selection. In the past 10 years, methods to perform ribosomal RNA (rRNA) depletion of total RNA have been developed as an alternative, aiming for better coverage of whole transcriptomic RNA, both polyadenylated and non-polyadenylated transcripts. The purpose of this study was to determine which librar...
Pozharskiy A, Abdrakhmanova A, Beishova I, Shamshidin A, Nametov A, Ulyanova T, Bekova G, Kikebayev N, Kovalchuk A, Ulyanov V, Turabayev A....Horses are traditionally used in Kazakhstan as a source of food and as working and saddle animals as well. Here, for the first time, microarray-based medium-density single nucleotide polymorphism (SNP) genotyping of six traditionally defined types and breeds of indigenous Kazakh horses was conducted to reveal their genetic structure and find markers associated with animal size and weight. The results showed that the predefined separation between breeds and sampled populations was not supported by the molecular data. The lack of genetic variation between breeds and populations was revealed by t...
Jäderkvist Fegraeus K, Hirschberg I, Árnason T, Andersson L, Velie BD, Andersson LS, Lindgren G.The Icelandic horse is a breed known mainly for its ability to perform the ambling four-beat gait 'tölt' and the lateral two-beat gait pace. The natural ability of the breed to perform these alternative gaits is highly desired by breeders. Therefore, the discovery that a nonsense mutation (C>A) in the DMRT3 gene was the main genetic factor for horses' ability to perform gaits in addition to walk, trot and canter was of great interest. Although several studies have demonstrated that homozygosity for the DMRT3 mutation is important for the ability to pace, only about 70% of the homozygous mutan...
Fritz KL, McCue ME, Valberg SJ, Rendahl AK, Mickelson JR.Recurrent exertional rhabdomyolysis is a heritable disorder that results in painful skeletal muscle cramping with exercise in up to 10% of all Thoroughbred racehorses. Here, we report a genome-wide association study with 48 282 SNPs analyzed among 48 case and 37 control Thoroughbreds. The most significant SNPs spanned approximately 13 Mb on ECA16, and the P-value of the most significant SNP after correcting for population structure was 8.0 × 10(-6) . This region on ECA16 was further evaluated by genotyping 247 SNPs in both the initial population and a second population of 34 case and 98 contr...
Nikitkina EV, Dementieva NV, Shcherbakov YS, Atroshchenko MM, Kudinov AA, Samoylov OI, Pozovnikova MV, Dysin AP, Krutikova AA, Musidray AA....The semen quality of stallions including sperm motility is an important target of selection as it has a high level of individual variability. However, effects of the molecular architecture of the genome on the mechanisms of sperm formation and their preservation after thawing have been poorly investigated. Here, we conducted a genome-wide association study (GWAS) for the sperm motility of cryopreserved semen in stallions of various breeds. Methods: Semen samples were collected from the stallions of 23 horse breeds. The following semen characteristics were examined: progressive motility (PM), p...
Battista JM, Tallmadge RL, Stokol T, Felippe MJ.We investigated how the equine fetus prepares its pre-immune humoral repertoire for an imminent exposure to pathogens in the neonatal period, particularly how the primary hematopoietic organs are equipped to support B cell hematopoiesis and immunoglobulin (Ig) diversity. We demonstrated that the liver and the bone marrow at approximately 100 days of gestation (DG) are active sites of hematopoiesis based on the expression of signature messenger RNA (mRNA) (c-KIT, CD34, IL7R, CXCL12, IRF8, PU.1, PAX5, NOTCH1, GATA1, CEBPA) and protein markers (CD34, CD19, IgM, CD3, CD4, CD5, CD8, CD11b, CD172A)...
Maharana BR, Potliya S, Ganguly A, Bisla RS, Mishra C, Ganguly I.Equine ocular setariasis arising mainly from ectopic infestation of Setaria digitata is a common vision impairing ophthalmic disease in India, and the identification of this filarial nematode is based solely on morphology. However, morphological characters alone are inadequate to detect and differentiate S. digitata from its congeners. The present communication reports the first phylogenetic characterization of equine S. digitata from India based on sequences derived from the mitochondrial cytochrome c oxidase subunit 1 (COI), the mitochondrial small subunit ribosomal DNA (12S rDNA), and the n...
Brown JJ, Thomson W, Clegg P, Eyre S, Kennedy LJ, Matthews J, Carter S, Ollier WE.The full extent of the polymorphism of ELA-DRA in Equidae is not yet known. Given the apparent differences in DRA polymorphisms between Equidae and other species, the aims of this study were to more fully characterize ELA-DRA, determine the extent of gene polymorphism and establish the allele-frequency distribution. An allele reference panel for the second exon of ELA-DRA was established by sequence-based typing of 69 equine DNA samples consisting of various breeds of domestic horse (Equus caballus), together with donkeys (Equus asinus), Grant's zebras (Equus boehmi) and one onager (Equus hemi...
Ahrens E, Stranzinger G.Previous research revealed that the karyotypes of Equus przewalskii (2n = 66) and Equus caballus (2n = 64) differ by one pair of metacentric chromosomes, present in ECA but not in EPR, and two pairs of acrocentric chromosomes found only in the EPR karyotype. The formation of a trivalent during meiosis in a male F1 hybrid and the homologies in G-banding patterns suggest that ECA 5 corresponds to two acrocentric EPR chromosomes resulting from a Robertsonian fusion or fission event. Chromosomal investigations of a female interspecies F1 hybrid including banded karyograms and fluorescence in situ ...
Nelis H, D'Herde K, Goossens K, Vandenberghe L, Leemans B, Forier K, Smits K, Braeckmans K, Peelman L, Van Soom A.Equine embryos remain for 6 days in the oviduct and thus there is a need for an in vitro model to study embryo-oviductal interactions in the horse, since this subtle way of communication is very difficult to analyse in vivo. Until now, no equine oviduct explant culture model has been characterised both morphologically and functionally. Therefore, we established a culture system for equine oviduct explants that maintained epithelial morphology during 6 days of culture, as revealed by light microscopy and transmission electron microscopy. We demonstrated the presence of highly differentiated, ta...
Lee W, Park KD, Taye M, Lee C, Kim H, Lee HK, Shin D.This study was intended to identify genes positively selected in Thoroughbred horses (THBs) that potentially contribute to their running performances. Methods: The genomes of THB and Jeju horses (JH, Korean native horse) were compared to identify genes positively selected in THB. We performed cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio test (XP-CLR) statistical methods for our analysis using whole genome resequencing data of 14 THB and 6 JH. Results: We identified 98 (XP-EHH) and 200 (XP-CLR) genes that are under positive selection ...
Dam Van P, Desmecht D, Garigliany MM, Bui Tran Anh D, Van Laere AS.Type I/III interferons provide powerful and universal innate intracellular defense mechanisms against viruses. Among the antiviral effectors induced, Mx proteins of some species appear as key components of defense against influenza A viruses. It is expected that such an antiviral protein must display a platform dedicated to the recognition of said viruses. In an attempt to identify such platform in human MxA, an evolution-guided approach capitalizing on the antagonistic arms race between MxA and its viral targets and the genomic signature it left on primate genomes revealed that the surface-ex...
Bidaud P, Hébert L, Barbey C, Appourchaux AC, Torelli R, Sanguinetti M, Laugier C, Petry S.Rhodococcus equi is one of the most widespread causes of disease in foals aged from 1 to 6 months. R. equi possesses antioxidant defense mechanisms to protect it from reactive oxygen metabolites such as hydrogen peroxide (H(2)O(2)) generated during the respiratory burst of phagocytic cells. These defense mechanisms include enzymes such as catalase, which detoxify hydrogen peroxide. Recently, an analysis of the R. equi 103 genome sequence revealed the presence of four potential catalase genes. We first constructed ΔkatA-, ΔkatB-, ΔkatC-and ΔkatD-deficient mutants to study the ability of R. ...
Zamansky GB, Arundel C, Nagasawa H, Little JB.The growth of two human diploid skin fibroblast cell lines, originally grown in medium supplemented with foetal bovine serum and later adapted to medium supplemented with newborn bovine, bovine calf or horse serum, has been studied. Prolonged generation times increased cell volumes and decreased plating efficiencies were observed in cultures grown in newborn bovine, bovine calf or horse serum. In general, the deleterious effects were most severe as a result of growth in bovine calf or horse serum. In the light of the present findings, we believe investigators should exert great caution in swit...
Pacholewska A, Marti E, Leeb T, Jagannathan V, Gerber V.Lipopolysaccharide (endotoxin, LPS) is a strong inducer of the innate immune response. It is widespread in our environment, e.g. in house dust and contributes to asthma. Compared to humans, horses are even more sensitive to LPS. However, data on LPS effects on the equine transcriptome are very limited. Using RNA-seq we analysed LPS-induced differences in the gene expression in equine peripheral blood mononuclear cells at the gene and gene-network level in two half-sib families and one group of unrelated horses. 24 h-LPS challenge of equine immune cells resulted in substantial changes in the t...
Tanaka J, Leeb T, Rushton J, Famula TR, Mack M, Jagannathan V, Flury C, Bachmann I, Eberth J, McDonnell SM, Penedo MCT, Bellone RR.Mushroom is a unique coat color phenotype in Shetland Ponies characterized by the dilution of the chestnut coat color to a sepia tone and is hypothesized to be a recessive trait. A genome wide association study (GWAS), utilizing the Affymetrix 670K array (MNEc670k) and a single locus mixed linear model analysis (EMMAX), identified a locus on ECA7 for further investigation ( = 2.08 × 10). This locus contained a 3 Mb run of homozygosity in the 12 mushroom ponies tested. Analysis of high throughput Illumina sequencing data from one mushroom Shetland pony compared to 87 genomes from horses of var...
Paterson YZ, Cribbs A, Espenel M, Smith EJ, Henson FMD, Guest DJ.Tendon injuries occur frequently in human and equine athletes. Treatment options are limited, and the prognosis is often poor with functionally deficient scar tissue resulting. Fetal tendon injuries in contrast are capable of healing without forming scar tissue. Embryonic stem cells (ESCs) may provide a potential cellular therapeutic to improve adult tendon regeneration; however, whether they can mimic the properties of fetal tenocytes is unknown. To this end, understanding the unique expression profile of normal adult and fetal tenocytes is crucial to allow validation of ESC-derived tenocytes...
Shrestha M, Eriksson S, Schurink A, Andersson LS, Sundquist M, Frey R, Broström H, Bergström T, Ducro B, Lindgren G.Insect bite hypersensitivity (IBH) is the most common allergic skin disease in horses and is caused by biting midges, mainly of the genus Culicoides. The disease predominantly comprises a type I hypersensitivity reaction, causing severe itching and discomfort that reduce the welfare and commercial value of the horse. It is a multifactorial disorder influenced by both genetic and environmental factors, with heritability ranging from 0.16 to 0.27 in various horse breeds. The worldwide prevalence in different horse breeds ranges from 3% to 60%; it is more than 50% in Icelandic horses exported to ...
Gao JF, Liu GH, Duan H, Gao Y, Zhang Y, Chang QC, Fang M, Wang CR.Triodontophorus serratus and Triodontophorus nipponicus are two of the most common nematodes inhabiting in the large intestine of horse. In the present study, the complete mitochondrial (mt) genome sequences of T. serratus and T. nipponicus have been determined. The mt genomes of T. serratus and T. nipponicus are circular molecules with 13,794 bp and 13,701 bp in size, respectively. These circular mt genomes encode 36 genes, including 12 protein-coding genes, two rRNA genes and 22 tRNA genes. All of these genes are transcribed in the same direction and gene arrangements are consistent with...
Tang Z, Li X, Wang X, Zhang C, Zou L, Ren H, Liu W. () is one of the foremost pathogens responsible for diarrhea in foals. As antibiotic resistance increases, phages that specifically lyse bacteria are of great interest to us with regard to . In this study, a novel phage DCp1 was isolated from the sewage of a donkey farm. Phage DCp1 had a non-contractile short tail (40 nm in length) and a regular icosahedral head (46 nm in diameter). Whole-genome sequencing indicated that phage DCp1 had a linear double-stranded DNA genome with a total length of 18,555 bp and a G + C content of 28.2%. A total of 25 ORFs were identified in the genome, 6 of whic...
Plummer G, Bowling CP, Goodheart CR.Four equine herpesviruses (equine abortion virus, equine herpesvirus types 2 and 3, and equine cytomegalovirus) were compared. The equine abortion virus did not cross-neutralize with any of the other viruses, but the other three did show varying degrees of cross-neutralization among themselves. Equine abortion virus grew more quickly in tissue cultures than did the others, and attained higher titers of infectivity in the culture fluid; it also formed plaques in a wider range of tissue culture species, although the other three were not specific for one tissue culture system only, in that they w...
Potgieter AC, Cloete M, Pretorius PJ, van Dijk AA.The outer capsid protein VP2 of African horsesickness virus (AHSV) is a major protective antigen. We have cloned full-length VP2 genes from the reference strains of each of the nine AHSV serotypes. Baculovirus recombinants expressing the cloned VP2 genes of serotypes 1, 2, 4, 6, 7 and 8 were constructed, confirming that they all have full open reading frames. This work completes the cloning and expression of the first full set of AHSV VP2 genes. The clones of VP2 genes of serotypes 1, 2, 5, 7 and 8 were sequenced and their amino acid sequences were deduced. Our sequencing data, together with t...
Han H, Chen Q, Gao Y, Li J, Li W, Dang R, Lei C.In the biological process of testicular spermatogenesis, the expression and interaction of many genes are regulated by microRNAs (miRNAs). However, comparisons of miRNA expression between descended testes (DTs) and undescended testes (UDTs) are rarely done in horses. In this study, we selected two UDTs (CKY2b and GU4b) from Chakouyi (CKY) and Guanzhong (GU) horses and eight DTs (GU1-3, CKY1, CKY3, CKY2a, GU4a, and GU5). Three groups were compared to evaluate expression patterns of testicular miRNA in stallion testes. Group 1 compared normal CKY horses and GU horses (CKY1 and CKY3 vs. GU1-3). G...
Roy Chowdhury P, DeMaere M, Chapman T, Worden P, Charles IG, Darling AE, Djordjevic SP.Clostridium difficile infections (CDI) are a significant health problem to humans and food animals. Clostridial toxins ToxA and ToxB encoded by genes tcdA and tcdB are located on a pathogenicity locus known as the PaLoc and are the major virulence factors of C. difficile. While toxin-negative strains of C. difficile are often isolated from faeces of animals and patients suffering from CDI, they are not considered to play a role in disease. Toxin-negative strains of C. difficile have been used successfully to treat recurring CDI but their propensity to acquire the PaLoc via lateral gene transfe...
Bleumink-Pluym NM, van Dijk L, van Vliet AH, van der Giessen JW, van der Zeijst BA.The 16S ribosomal DNA sequence of Taylorella equigenitalis (formerly Haemophilus equigenitalis), the causative organism of contagious equine metritis, was determined. A phylogenetic analysis of this sequence revealed a phylogenetic position of T. equigenitalis in the beta subclass of the class Proteobacteria apart from the position of Haemophilus influenzae, which belongs to the gamma subclass of Proteobacteria. A close phylogenetic relationship among T. equigenitalis, Alcaligenes xylosoxidans, and Bordetella bronchiseptica was detected; Spirillum volutans and Chromobacterium fluviatile (Iodob...
