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.
Scott EY, Woolard KD, Finno CJ, Penedo MCT, Murray JD.Cerebellar Abiotrophy (CA) is a neurodegenerative disease in Arabian horses affecting the cerebellum, more specifically the Purkinje neurons. Although CA occurs in several domestic species, CA in Arabian horses is unique in that a single nucleotide polymorphism (SNP) has been associated with the disease. Total RNA sequencing (RNA-seq) was performed on CA-affected horses to address the molecular mechanism underlying the disease. This research expands upon the RNA-seq work by measuring the impact of the CA-associated SNP on the candidate gene MutY homolog (MUTYH) and its regulation, isoform-spec...
Lu G, Fu C, Huang J, Xu H, Wu P, Ping X, Li S.Equine pegivirus (EPgV) is a newly discovered equine virus, which is taxonomically classified in the Pegivirus genus of the Flaviviridae family. Until now, only the complete genome sequence of the first reported EPgV strain, from the USA (strain name: C0035) is available on online databases. Considering this, horse serum samples were collected from horses in China and screened for EPgV RNA by RT-PCR. One EPgV strain, LW/2016, was obtained and its near-complete genome sequence was acquired by standard PCR. Further analysis of its nucleotide sequence indicates LW/2016 is genetically divergent fr...
Gim JA, Kim HS.Endogenous retroviruses (ERVs) have been integrated into vertebrate genomes and have momentously affected host organisms. Horses () have been domesticated and selected for elite racing ability over centuries. ERVs played an important role in the evolutionary diversification of the horse genome. In the present study, we identified six equine ERV families (EqERVs-E1, I1, M2, P1, S1, and Y4), their full-length viral open reading frames (ORFs), and elucidated their phylogenetic relationships. The divergence time of EqERV families assuming an evolutionary rate of 0.2%/Myr indicated that EqERV-S3 (7...
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...
Davies MR.Despite tight biosecurity measures, an outbreak of respiratory disease rapidly spread across the Icelandic equine population in 2010. Horse transportation was brought to a halt in order to contain the spread of the infectious agent. In a recent article, Björnsdóttir and colleagues (S. Björnsdóttir et al., mBio 8:e00826-17, 2017, https://doi.org/10.1128/mBio.00826-17) employ the power and resolution of "genomic epidemiology," the combination of whole genomic sequencing and epidemiological approaches, to examine the source and spread of the outbreak. Intriguingly, the outbreak was not viral ...
Dong J, Zhu W, Yamashita N, Chambers JK, Uchida K, Kuwano A, Haga T.Although many studies have been conducted worldwide for Equus caballus papillomavirus (EcPV), limited information is available on the virus in Japan. We recently collected one classical viral papillomatosis sample (E150904) from a racing horse in Japan. Papillomavirus infection was confirmed by histopathology, immunohistochemistry and PCR assays, and the sample was diagnosed as epithelial papilloma. Full-length genome of the virus was cloned and sequenced. It was 7,613 bp in length and had the same genome organization with reported EcPV-1. Moreover, phylogenetic analysis based on L1 gene revea...
Cabezas J, Rojas D, Navarrete F, Ortiz R, Rivera G, Saravia F, Rodriguez-Alvarez L, Castro FO.Adult stromal mesenchymal stem cells (MSCs) have been postulated as responsible for cell renewal in highly and continuously regenerative tissues such as the endometrium. MSCs have been identified in the endometrium of many species including humans, rodents, pets and some farm animals, but not in horses. The objective of this work was to isolate such cells from the endometrium of mares and to compare their main biological attributes with horse adipose-derived MSCs. Here we successfully isolated and characterized endometrial MSCs (eMSCs) from mares. Said cells showed fibroblast-like morphology, ...
Braga MDSCO, Costa FN, Gomes DRM, Xavier DR, André MR, Gonçalves LR, Freschi CR, Machado RZ.Equine piroplasmosisis, a tick-borne disease caused by the intra-erythrocytic protozoans Babesia caballi and Theileria equi, has economic importance due to the international trade and the increased movement of horses all over the world. The goal of this study was to evaluate the occurrence of phylogenetic diversity of T. equi and B. caballi genotypes among infected equids from São Luís Island, state of Maranhão, northeastern Brazil. Between December of 2011 and June of 2012, EDTA-blood and serum samples were collected from 139 equids (90 donkeys, 39 horses and 10 mules). From 139 serum samp...
Li B, He X, Zhao Y, Bai D, Shiraigo W, Zhao Q, Manglai D.Studies on the molecular genetics of horse skin pigmentation have typically focused on very few genes and proteins. In this study, we used Illumina sequencing to determine the global gene expression profiles in horses with white-colored coats and those with black-colored coats, with the goal of identifying novel genes that could regulate horse coat color. Results: Genes encoding ribosomal-associated proteins were highly expressed in horse skin. We found a total of 231 unigenes that were differentially expressed between horses with white coats and horses with black coats; 119 were down-regulate...
Hall SE, Upton RMO, McLaughlin EA, Sutherland JM.The mare ovary is unique in its anatomical structure; however, the signalling pathways responsible for physiological processes, such as follicular activation, remain uncharacterised. This provided us with the impetus to explore whether signalling molecules from important folliculogenesis pathways, phosphoinositide 3-kinase/protein kinase B (PI3K/AKT) and Janus kinase/signal transducer and activator of transcription (JAK/STAT), are conserved in the mare ovary. Messenger RNA expression of six genes important in follicle development was measured using quantitative polymerase chain reaction and pr...
Kim HA, Kim MC, Kim NY, Ryu DY, Lee HS, Kim Y.Exercise capacity is a valuable trait in horses, and it has been used as a horse selection criterion. Although exercise affects molecular homeostasis and adaptation in horses, the mechanisms underlying these effects are not fully described. This study was carried out to identify changes in the blood profiles of microRNAs (miRNAs) and mRNAs induced by exercise in horse leukocytes. Total RNAs isolated from the peripheral blood leukocytes of four Warmblood horses before and after exercise were subjected to next-generation sequencing (NGS) and microarray analyses to determine the miRNA and mRNA ex...
Douet C, Parodi O, Martino NA, Lacalandra GM, Nicassio M, Reigner F, Deleuze S, Dell'Aquila ME, Goudet G.Most wild equids and many domestic horse breeds are at risk of extinction, so there is an urgent need for genome resource banking. Embryos cryopreservation allows the preservation of genetics from male and female and is the fastest method to restore a breed. In the equine, embryo production in vitro would allow the production of several embryos per cycle. Intracytoplasmic sperm injection (ICSI) is used to generate horse embryos, but it requires expensive equipment and expertise in micromanipulation, and blastocyst development rates remain low. No conventional in vitro fertilization (IVF) techn...
Han H, Chen N, Jordana J, Li C, Sun T, Xia X, Zhao X, Ji C, Shen S, Yu J, Ainhoa F, Chen H, Lei C, Dang R.Numerous studies have been conducted to investigate genetic diversity, origins and domestication of donkey using autosomal microsatellites and the mitochondrial genome, whereas the male-specific region of the Y chromosome of modern donkeys is largely uncharacterized. In the current study, 14 published equine Y chromosome-specific microsatellites (Y-STR) were investigated in 395 male donkey samples from China, Egypt, Spain and Peru using fluorescent labeled microsatellite markers. The results showed that seven Y-STRs-EcaYP9, EcaYM2, EcaYE2, EcaYE3, EcaYNO1, EcaYNO2 and EcaYNO4-were male specif...
Desantis S, Accogli G, Crovace A, Francioso EG, Crovace AM.The use of bone marrow-derived mesenchymal stem cells (MSCs) for clinical and experimental studies is increasing, but full characterization of MSCs in veterinary species is hindered by the variability in species-specific cell surface marker expression and antibody cross reactivity. Recent studies demonstrated that the glycans in the glycocalyx of MSCs are promising candidates as cell biomarkers. In the present study, we analyzed the glycocalyx of canine MSCs (cMSCs), ovine MSCs (oMSCs), and equine MSCs (eMSCs) using a cell microarray procedure in which MSCs were spotted on microarray slides an...
Holl HM, Vanhnasy J, Everts RE, Hoefs-Martin K, Cook D, Brooks SA, Carpenter ML, Bustamante CD, Lafayette C.Genetic markers are important resources for individual identification and parentage assessment. Although short tandem repeats (STRs) have been the traditional DNA marker, technological advances have led to single nucleotide polymorphisms (SNPs) becoming an attractive alternative. SNPs can be highly multiplexed and automatically scored, which allows for easier standardization and sharing among laboratories. Equine parentage is currently assessed using STRs. We obtained a publicly available SNP dataset of 729 horses representing 32 diverse breeds. A proposed set of 101 SNPs was analyzed for DNA ...
Liu Q, Wang XF, Du C, Lin YZ, Ma J, Wang YH, Zhou JH, Wang X.Integration is an important feature of retroviruses and retrovirus-based therapeutic transfection vectors. The non-primate lentivirus equine infectious anaemia virus (EIAV) primarily targets macrophages/monocytes . Investigation of the integration features of EIAV strains, which are adapted to donkey monocyte-derived macrophages (MDMs), is of great interest. In this study, we analysed the integration features of EIAV in equine MDMs during infection. Our previously published integration sites (IS) for EIAV in fetal equine dermal (FED) cells were also analysed in parallel as references. Sequenc...
Tessier L, Côté O, Clark ME, Viel L, Diaz-Méndez A, Anders S, Bienzle D.Severe equine asthma is a naturally occurring lung inflammatory disease of mature animals characterized by neutrophilic inflammation, bronchoconstriction, mucus hypersecretion and airway remodeling. Exacerbations are triggered by inhalation of dust and microbial components. Affected animals eventually are unable of aerobic performance. In this study transcriptomic differences between asthmatic and non-asthmatic animals in the response of the bronchial epithelium to an inhaled challenge were determined. Results: Paired endobronchial biopsies were obtained pre- and post-challenge from asthmatic ...
Jones CJP, Allen WRT, Wilsher S.In this study, we compare glycosylation at the fetomaternal interface in 3 equine species: horse, donkey and zebra, all of which can interbreed to produce hybrids, to assess their glycan similarities and differences. Methods: Sections cut from 3 specimens of horse (Equus caballus) placenta (50, 200 and 280 days gestation), one donkey (Equus asinus) placenta (65 cm crown-rump length) and 5 specimens of zebra (Equus quagga) placentae (81-239 days gestation) were stained with a panel of 24 biotinylated lectins using an avidin-peroxidase revealing system. Results: There were only slight quantitat...
Balmer P, Bauer A, Pujar S, McGarvey KM, Welle M, Galichet A, Müller EJ, Pruitt KD, Leeb T, Jagannathan V.Keratins represent a large protein family with essential structural and functional roles in epithelial cells of skin, hair follicles, and other organs. During evolution the genes encoding keratins have undergone multiple rounds of duplication and humans have two clusters with a total of 55 functional keratin genes in their genomes. Due to the high similarity between different keratin paralogs and species-specific differences in gene content, the currently available keratin gene annotation in species with draft genome assemblies such as dog and horse is still imperfect. We compared the National...
Bera BC, Virmani N, Kumar N, Anand T, Pavulraj S, Rash A, Elton D, Rash N, Bhatia S, Sood R, Singh RK, Tripathi BN.Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective. Results: The group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades. The consistent amino acid changes...
Barrón-Ortiz CI, Rodrigues AT, Theodor JM, Kooyman BP, Yang DY, Speller CF.Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to t...
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...
Bryan K, McGivney BA, Farries G, McGettigan PA, McGivney CL, Gough KF, MacHugh DE, Katz LM, Hill EW.A single bout of exercise induces changes in gene expression in skeletal muscle. Regular exercise results in an adaptive response involving changes in muscle architecture and biochemistry, and is an effective way to manage and prevent common human diseases such as obesity, cardiovascular disorders and type II diabetes. However, the biomolecular mechanisms underlying such responses still need to be fully elucidated. Here we performed a transcriptome-wide analysis of skeletal muscle tissue in a large cohort of untrained Thoroughbred horses (n = 51) before and after a bout of high-intensity exe...
Mack M, Kowalski E, Grahn R, Bras D, Penedo MCT, Bellone R.A unique eye color, called tiger-eye, segregates in the Puerto Rican Paso Fino (PRPF) horse breed and is characterized by a bright yellow, amber, or orange iris. Pedigree analysis identified a simple autosomal recessive mode of inheritance for this trait. A genome-wide association study (GWAS) with 24 individuals identified a locus on ECA 1 reaching genome-wide significance ( = 1.32 × 10). This ECA1 locus harbors the candidate gene, (), (), with known roles in pigmentation in humans, mice, and zebrafish. Humans with compound heterozygous mutations in have oculocutaneous albinism (OCA) type...
Cowled C, Foo CH, Deffrasnes C, Rootes CL, Williams DT, Middleton D, Wang LF, Bean AGD, Stewart CR.Hendra virus (HeV) is an emerging zoonotic pathogen harbored by Australian mainland flying foxes. HeV infection can cause lethal disease in humans and horses, and to date all cases of human HeV disease have resulted from contact with infected horses. Currently, diagnosis of acute HeV infections in horses relies on the productive phase of infection when virus shedding may occur. An assay that identifies infected horses during the preclinical phase of infection would reduce the risk of zoonotic viral transmission during management of HeV outbreaks. Having previously shown that the host microRNA ...
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...
Nemoto M, Bannai H, Ochi A, Niwa H, Murakami S, Tsujimura K, Yamanaka T, Kokado H, Kondo T.Getah virus is mosquito-borne and causes disease in horses and pigs. We sequenced and analyzed the complete genomes of three strains isolated from horses in Ibaraki Prefecture, eastern Japan, in 2016. They were almost identical to the genomes of strains recently isolated from horses, pigs, and mosquitoes in Japan.
Gao Y, Zhang Y, Yang X, Qiu JH, Duan H, Xu WW, Chang QC, Wang CR.Equine strongyles, the significant nematode pathogens of horses, are characterized by high quantities and species abundance, but classification of this group of parasitic nematodes is debated. Mitochondrial (mt) genome DNA data are often used to address classification controversies. Thus, the objectives of this study were to determine the complete mt genomes of three Cyathostominae nematode species (, and ) of horses and reconstruct the phylogenetic relationship of Strongylidae with other nematodes in Strongyloidea to test the hypothesis that spp. belong to Cyathostominae using the mt genomes...
Björnsdóttir S, Harris SR, Svansson V, Gunnarsson E, Sigurðardóttir ÓG, Gammeljord K, Steward KF, Newton JR, Robinson C, Charbonneau ARL....Iceland is free of the major infectious diseases of horses. However, in 2010 an epidemic of respiratory disease of unknown cause spread through the country's native horse population of 77,000. Microbiological investigations ruled out known viral agents but identified the opportunistic pathogen subsp. () in diseased animals. We sequenced the genomes of 257 isolates of to differentiate epidemic from endemic strains. We found that although multiple endemic clones of were present, one particular clone, sequence type 209 (ST209), was likely to have been responsible for the epidemic. Concurrent ...
Mandal S, Denham MM, Spencer SJ, Denham J.Ageing causes a gradual deterioration of bodily functions and telomere degradation. Excessive telomere shortening leads to cellular senescence and decreases tissue vitality. Six proteins, called shelterin, protect telomere integrity and control telomere length through telomerase-dependent mechanisms. Exercise training appears to maintain telomeres in certain somatic cells, although the underlying molecular mechanisms are incompletely understood. Here, we examined the influence of a single bout of vigorous exercise training on leukocyte telomerase reverse transcriptase (TERT) and shelterin gene...
Asadollahpour Nanaei H, Ayatollahi Mehrgardi A, Esmailizadeh A.The primary objective of most horse breeding operations was to maximize reproductive efficiency and minimize the cost of producing live foals. Here, we compared individual horses from the Thoroughbred population (n = 17), known as a horse breed with poor reproductive performance, with other six horse populations (n = 28), to detect genomic signatures of positive selection underlying of reproductive traits. A number of protein-coding genes with significant (p-value <.01) higher F values (616 genes) and a lower value for nucleotide diversity (π) (310 genes) were identified. The results of o...
Venturini C, Bowring B, Partridge SR, Ben Zakour NL, Fajardo-Lubian A, Lopez Ayala A, Qin J, Totsika M, van Galen G, Norris J, Iredell J.The global epidemiology of multidrug resistant Klebsiella pneumoniae, a serious threat to both animal and human health, is dominated by the spread of pathogenic clones, each separately evolving via acquisition of transferable antibiotic resistance or niche-specific virulence determinants. In horses, K. pneumoniae infection can lead to severe respiratory illness. Here, we characterized multiple isolates recovered from bronchial aspirates of a mare with pneumonia refractory to antibiotics. First, we used a combination of standard microbiology, bacteriophage cross-susceptibility and antibiotic re...
Kachroo P, Ivanov I, Seabury AG, Liu M, Chowdhary BP, Cohen ND.Rhodococcus equi is an intracellular bacterium primarily known as an equine pathogen that infects young foals causing a pyogranulomatuous pneumonia. The molecular mechanisms mediating the immune response of foals to R. equi are not fully elucidated. Hence, global genomic high-throughput tools like gene expression microarrays might identify age-related gene expression signatures and molecular pathways that contribute to the immune mechanisms underlying the inherent susceptibility of foals to disease caused by R. equi. The objectives of this study were 2-fold: 1) to compare the expression profil...
Saito S, Yokoyama K, Tamagawa T, Ishiwata I.We succeeded in the derivation and maintenance of pluripotent embryonic stem (ES) cells from equine and bovine blastocysts. These cells expressed markers that are characteristics of mouse ES cells, namely, alkaline phosphatase, stage-specific embryonic antigen 1, STAT 3 and Oct 4. We confirmed the pluripotential ability of these cells, which were able to undergo somatic differentiation in vitro to neural progenitors and to endothelial or hematopoietic lineages. We were able to use bovine ES cells as a source of nuclei for nuclear transfer and we generated cloned cattle with a higher frequency ...
Fisher M, Nebroski M, Davies J, Janzen E, Sullivan D, Lung O.The complete genome of a novel torque teno virus species (Torque teno equus virus 2 (TTEqV2) isolate Alberta/2018) was obtained by high-throughput sequencing (HTS) of nucleic acid extracted from the lung and liver tissue of a Quarter Horse gelding that died of nonsuppurative encephalitis in Alberta, Canada. The 2805 nucleotide circular genome is the first complete genome from the Mutorquevirus genus and has been approved as a new species by the International Committee on Taxonomy of Viruses. The genome contains several characteristic features of torque teno virus (TTV) genomes, including an OR...
BMC research notesJuly 19, 2016
Volume 9 353 doi: 10.1186/s13104-016-2161-9
Tarlinton RE, Alder L, Moreton J, Maboni G, Emes RD, Tötemeyer S.Toll like receptors are one of the major innate immune system pathogen recognition systems. There is little data on the expression of the TLR10 member of this family in the horse. Results: This paper describes the genetic structure of the Equine TLR10 gene and its RNA expression in a range of horse tissues. It describes the phylogenetic analysis of the Equine TLR1,6,10,2 annotations in the horse genome, firmly identifying them in their corresponding gene clades compared to other species and firmly placing the horse gene with other TLR10 genes from odd-toed ungulates. Additional 3' transcript e...
Raudsepp T, Otte K, Rozell B, Chowdhary BP.Three genomic subclones derived from a phage clone containing the equine IGF2 gene were used to FISH map the gene on horse (ECA) and donkey (EAS) metaphase chromosomes. The gene mapped on ECA 12q13 band and is the first locus mapped to this horse chromosome. In donkey the gene mapped very terminal on the long arm of one small submetacentric chromosome that shows almost identical DAPI-banding pattern with ECA12. This is the first locus mapped in donkey genome. Cross species chromosome painting of equine metaphase chromosomes with human Chromosome (Chr) 11-specific probe showed homoeology of thi...
Bordbari MH, Penedo MCT, Aleman M, Valberg SJ, Mickelson J, Finno CJ.In the horse, the term occipitoatlantoaxial malformation (OAAM) is used to describe a developmental defect in which the first cervical vertebra (atlas) resembles the base of the skull (occiput) and the second cervical vertebra (axis) resembles the atlas. Affected individuals demonstrate an abnormal posture and varying degrees of ataxia. The homeobox (HOX) gene cluster is involved in the development of both the axial and appendicular skeleton. Hoxd3-null mice demonstrate a strikingly similar phenotype to Arabian foals with OAAM. Whole-genome sequencing was performed in an OAAM-affected horse (O...
Kulikov EE, Golomidova AK, Efimov AD, Belalov IS, Letarova MA, Zdorovenko EL, Knirel YA, Dmitrenok AS, Letarov AV.Tailed bacteriophages constitute the bulk of the intestinal viromes of vertebrate animals. However, the relationships between lytic and lysogenic lifestyles of phages in these ecosystems are not always clear and may vary between the species or even between the individuals. The human intestinal (fecal) viromes are dominated mostly by temperate phages, while in horse feces virulent phages are more prevalent. To our knowledge, all the previously reported isolates of horse fecal coliphages are virulent. Temperate coliphage Hf4s was isolated from horse feces, from the indigenous equine Escherichia ...
Vosgerau S, Krattenmacher N, Falker-Gieske C, Seidel A, Tetens J, Stock KF, Nolte W, Wobbe M, Blaj I, Reents R, Kühn C, von Depka Prondzinski M....Reliability of genomic predictions is influenced by the size and genetic composition of the reference population. For German Warmblood horses, compilation of a reference population has been enabled through the cooperation of five German breeding associations. In this study, preliminary data from this joint reference population were used to genetically and genomically characterize withers height and to apply single-step methodology for estimating genomic breeding values for withers height. Using data on 2113 mares and their genomic information considering about 62,000 single nucleotide polymorp...
Rühl-Teichner J, Jacobmeyer L, Leidner U, Semmler T, Ewers C. is an opportunistic pathogen that causes severe infections in humans and animals, including horses. The occurrence of dominant international clones (ICs), frequent multidrug resistance, and the capability to form biofilms are considered major factors in the successful spread of in human and veterinary clinical environments. Since little is known about isolates from horses, we studied 78 equine isolates obtained from clinical samples between 2008 and 2020 for their antimicrobial resistance (AMR), clonal distribution, biofilm-associated genes (BAGs), and biofilm-forming capability. Based on ...
Ropka-Molik K, Stefaniuk-Szmukier M, Musiał AD, Piórkowska K, Szmatoła T.The ACTN3 gene codes for α-actinin-3, a protein localized in the Z-line in the skeletal muscle. Actinin-3 is critical in anchoring the myofibrillar actin filaments and plays a key role in muscle contraction. ACTN3 (α-actinin-3) cross-links glycogen phosphorylase (GP), which is the key enzyme catalysing glycogen metabolism. The aim of present study was to establish the expression level of the ACTN3 gene (for both isoforms separately and together in the gene expression analysis) in the gluteus medius muscle in order to verify if the α-actinin-3 gene can be related to training intensity in Ara...
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 ...
Quinlivan M, Cook F, Kenna R, Callinan JJ, Cullinane A.Equine infectious anemia virus (EIAV), the causative agent of equine infectious anaemia (EIA), possesses the least-complex genomic organization of any known extant lentivirus. Despite this relative genetic simplicity, all of the complete genomic sequences published to date are derived from just two viruses, namely the North American EIAV(WYOMING) (EIAV(WY)) and Chinese EIAV(LIAONING) (EIAV(LIA)) strains. In 2006, an outbreak of EIA occurred in Ireland, apparently as a result of the importation of contaminated horse plasma from Italy and subsequent iatrogenic transmission to foals. This EIA out...
Borkent D, Reardon RJM, McLACHLAN G, Glendinning L, Dixon PM.Although, peripheral caries (PC) affects almost half of UK horses, no comprehensive microbiological study has been performed on this disorder. As a high proportion of oral bacteria cannot be conventionally cultured, molecular microbiological techniques such as Next Generation Sequencing are required to examine the complex oral bacteria community. Objective: To identify the microbiota involved in equine PC, including comparing microbiota at the more commonly and severely affected three caudal cheek teeth with the less commonly affected three rostral cheek teeth. Methods: Equine dental plaque sa...
Zylicz-Stachula A, Zolnierkiewicz O, Jasiecki J, Skowron PM.Genomics and metagenomics are currently leading research areas, with DNA sequences accumulating at an exponential rate. Although enormous advances in DNA sequencing technologies are taking place, progress is frequently limited by factors such as genomic contig assembly and generation of representative libraries. A number of DNA fragmentation methods, such as hydrodynamic sharing, sonication or DNase I fragmentation, have various drawbacks, including DNA damage, poor fragmentation control, irreproducibility and non-overlapping DNA segment representation. Improvements in these limited DNA scissi...
Horín P, Matiasovic J.More than two nucleotide sequences of the second exon of the ELA-DQB region retrieved from a single animal and two different sequences isolated from horses homozygous in the major histocompatibility complex (MHC) region by descent indicated the existence of at least two ELA-DQB loci at the genomic level. New alleles detected by polymerase chain reaction single strand conformation polymorphism (SSCP) and defined by nucleotide sequencing of the second exon of the DQB gene(s) were described. Based on the level of nucleotide sharing, at least two groups of alleles were shown to exist. The newly de...
Frontiers in geneticsJanuary 23, 2023
Volume 14 1099896 doi: 10.3389/fgene.2023.1099896
Capomaccio S, Ablondi M, Colombi D, Sartori C, Giontella A, Cappelli K, Mancin E, Asti V, Mantovani R, Sabbioni A, Silvestrelli M. The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent "colonization". In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool. The Italian dataset comprised 1,3...
Tozaki T, Mashima S, Hirota K, Miura N, Choi-Miura NH, Tomita M.We performed efficient cloning and genotyping methods for isolation of a large number of polymorphic microsatellites. The methods contain the time-efficient cloning method of constructing microsatellite-enriched libraries and the economic genotyping method of fluorescent labeling of PCR products. Eighty novel equine microsatellites cloned were efficiently isolated from the enrichment library and analyzed for genotype polymorphism. Of these, 72 microsatellites were analyzed with a good resolution. The average heterozygosity of all loci was 0.52, and the number of alleles ranged from one to 9 wi...
Cirilli O, Pandolfi L, Rook L, Bernor RL.Evolution of the genus Equus has been a matter of long debate with a multitude of hypotheses. Currently, there is no consensus on either the taxonomic content nor phylogeny of Equus. Some hypotheses segregate Equus species into three genera, Plesippus, Allohippus and Equus. Also, the evolutionary role of European Pleistocene Equus stenonis in the origin of the zebra-ass clade has been debated. Studies based on skull, mandible and dental morphology suggest an evolutionary relationship between North American Pliocene E. simplicidens and European and African Pleistocene Equus. In this contributio...
Loux SC, Dini P, El-Sheikh Ali H, Kalbfleisch T, Ball BA.The placenta is a dynamic organ which undergoes extensive remodeling throughout pregnancy to support, protect and nourish the developing fetus. Despite the importance of the placenta, very little is known about its gene expression beyond very early pregnancy and post-partum. Therefore, we utilized RNA-sequencing to characterize the transcriptome from the fetal (chorioallantois) and maternal (endometrium) components of the placenta from mares throughout gestation (4, 6, 10, 11 m). Within the endometrium, 47% of genes changed throughout pregnancy, while in the chorioallantois, 29% of genes under...
Tozaki T, Hirota K, Hasegawa T, Tomita M, Kurosawa M.Linkage disequilibrium (LD) mapping is often used in searches for genes governing economically significant traits and diseases. The D' coefficient is a commonly used measure of the extent of LD between all possible pairs of alleles at two markers. This study aimed to test the utility of the D' coefficient for LD mapping of a trait in a thoroughbred population. Microsatellite genotype data and grey coat colour as a trait model in a thoroughbred population were used to assess the extent of LD. We demonstrated that LD mapping was a reasonable approach for initial genome-wide scans in a thoroughbr...
Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Kusano K, Nagata SI.Processed pseudogenes, also known as retrocopy genes, are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome. In this study, we identified 62 processed pseudogene candidates as intron-less genes from whole-genome sequencing (WGS) data of Thoroughbred horses using delly structural variation software. The 62 processed pseudogene candidates were confirmed by PCR amplification of intron-less products. A total of 11 processed pseudogenes were confirmed in the genome of all 23 analysed horses, whereas three processed pseudogenes with structures of ATP11...
Xing J, Xie L, Qi X, Liu G, Akhtar MF, Li X, Bou G, Bai D, Zhao Y, Dugarjaviin M, Zhang X.The proliferation and differentiation of skeletal muscle satellite cells (SCs) are necessary for the development of mature skeletal muscle. Leucine (Leu) is both an essential amino acid (EAA) and a branched-chain amino acid (BCAA), which has attracted worldwide attention due to its ability to repair and become new fibers. We separated the equine SCs into the control group (CON) and the Leu-supplemented group (LEU), which the cells were cultured in Leu-deprived and Leu-supplemented media respectively. We combined the transcriptome (RNA-Seq) and quantitative proteome (TMT) profiling analyses on ...
Zilch TJ, Lee JJ, Saleem MZ, Zhang H, Cortese V, Voris N, McDonough SP, Divers TJ, Chang YF.Little information is available about experimental inoculation of leptospirosis in horses and the pathogenicity of Leptospira interrogans serovar Bratislava in this host. Objective: To determine the serological, clinical, pathological and haematological responses of horses to L. interrogans serovar Bratislava strain PigK151. Methods: Randomised controlled in vivo experiment. Methods: Ten seronegative female foals were divided into 2 groups, control (n = 4) and challenged (n = 6). The challenged group received 1 × 109 leptospires divided equally between topical ocular and intraperitoneal...
Gahan J, Garvey M, Asmah Abd Samad R, Cullinane A.In August 2015, Malaysia experienced an outbreak of acute respiratory disease in racehorses. Clinical signs observed were consistent with equine influenza (EI) infection. The index cases were horses recently imported from New Zealand. Rapid control measures, including temporary cancellation of racing, were implemented to minimize the impact of the outbreak. By November, the disease outbreak was resolved, and movement restrictions were lifted. The aim of this study was to confirm the clinical diagnosis and characterize the causal virus. A pan-reactive influenza type A real-time RT-PCR was used ...
Gahan J, Garvey M, Gildea S, Gür E, Kagankaya A, Cullinane A.In 2013, there was an outbreak of acute respiratory disease in racehorses in Turkey. The clinical signs were consistent with equine influenza (EI). The aim was to confirm the cause of the outbreak and characterise the causal virus. A pan-reactive influenza type A real-time RT-PCR and a rapid antigen detection kit were used for confirmatory diagnosis of equine influenza virus (EIV). Immunological susceptibility to EIV was examined using single radial haemolysis and ELISA. Antigenic characterisation was completed by haemagglutinin inhibition using a panel of specific ferret antisera. Genetic cha...
Dorey-Robinson DLW, Locker N, Steinbach F, Choudhury B.Equine infectious anaemia virus (EIAV) is a retrovirus with worldwide distribution which is notifiable to the OIE. Despite its importance to the equine industry, most information regarding its biology have been obtained using only two strains (EIAV and EIAV ) from the USA and China, respectively. Recently full genome sequences from Ireland, Italy and Japan have been published; however, this is still not representative of the number of EIAV outbreaks experienced globally each year. The limited availability of published sequences makes design of a universal EIAV PCR difficult, hence diagnosis is...
sub. (SEZ) is described as a commensal bacterium of several animal species, including humans. Growing evidence supports the potential role of SEZ in the onset and progression of severe clinical manifestations of diseases in horses and other animals. In the present communication, we describe the diagnostic procedure applied to characterize the streptococcal infections caused by a novel SEZ sequence type (ST525) in donkeys raised on a farm in Abruzzo, Italy. The diagnostic process began with anamnesis and anatomopathological analysis, which revealed a severe bacterial suppurative bronchopneumo...
