Genetic sequencing in horses involves the analysis of equine DNA to identify the order of nucleotides within the genome. This process provides insights into genetic variations, hereditary traits, and potential predispositions to diseases. By mapping the equine genome, researchers can explore genetic markers associated with specific breeds, performance traits, and health conditions. Genetic sequencing can also aid in understanding evolutionary relationships among horse breeds and contribute to conservation efforts. This page compiles peer-reviewed research studies and scholarly articles that investigate the methodologies, applications, and implications of genetic sequencing in equine science.
Unger L, Fouché N, Leeb T, Gerber V, Pacholewska A.Circulating miRNAs in body fluids, particularly serum, are promising candidates for future routine biomarker profiling in various pathologic conditions in human and veterinary medicine. However, reliable standardized methods for miRNA extraction from equine serum and fresh or archived whole blood are sorely lacking. We systematically compared various miRNA extraction methods from serum and whole blood after short and long-term storage without addition of RNA stabilizing additives prior to freezing. Time of storage at room temperature prior to freezing did not affect miRNA quality in serum. Fur...
Ghosh M, Cho HW, Park JW, Choi JY, Chung YH, Sharma N, Singh AK, Kim NE, Mongre RK, Huynh D, Jiao ZJ, Do KT, Lee HK, Song KD, Cho BW, Jeong D.The athletic abilities of the horse serve as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. We analyzed differentially expressed genes in triceps brachii muscle tissues collected from Eonjena Taeyang and Jigusang Seryeok Thoroughbred horses and their co-expression networks in a large-scale RNA-sequence dataset comparing expression before and after exercise. High-quality horse transcriptome data were generated, with over 22 million 90-bp pair-end reads. By comparing the annotations, we found that MYH3, MPZ, and PDE8B genes in Eonjena Ta...
Livengood JL, Lanka S, Maddox C, Tewari D.Streptococcus equi subspecies equi (S. equi), the causative agent of strangles, is an important equine pathogen. Strangles is a highly contagious disease and a commercial modified live vaccine (MLV) is used for protection, which although effective, may also result in clinical signs of the disease. A rapid means to differentiate between the MLV and wild-type infection is crucial for quarantine release and limiting the disease spread. This study describes the use of a pyrosequencing assay targeting a single nucleotide deletion upstream of the SzPSe gene to distinguish between the wild-type and v...
Woo PC, Lau SK, Choi GK, Huang Y, Wernery R, Joseph S, Wong EY, Elizabeth SK, Patteril NA, Li T, Wernery U, Yuen KY.Among all known picornaviruses, only two species, equine rhinitis A virus and equine rhinitis B virus (ERBV) are known to infect horses, causing respiratory infections. No reports have described the detection of ERBV in fecal samples of horses and no complete genome sequences of ERBV3 are available. Methods: We performed a molecular epidemiology study to detect ERBVs in horses from Dubai and Hong Kong. Complete genome sequencing of the ERBVs as well as viral loads and genome, phylogenetic and evolutionary analysis were performed on the positive samples. Results: ERBV was detected in four (13.8...
Franke A, Kershaw O, Jenckel M, König L, Beer M, Hoffmann B, Hoffmann D.The article describes the isolation of a cowpox virus (CPXV) isolate originating from a horse. The skin of a foal, aborted in the third trimester, displayed numerous cutaneous papules. The histological examination showed A-type inclusion bodies within the lesion, typical for CPXV infections. This suspicion was confirmed by real-time PCR where various organs were analyzed. From skin samples, virus isolation was successfully performed. Afterwards, the whole genome of this new isolate "CPXV Amadeus" was sequenced by next-generation technology. Phylogenetic analysis clearly showed that "CPXV Amade...
Vandewege MW, Platt RN, Ray DA, Hoffmann FG.PIWI proteins and PIWI-interacting RNAs (piRNAs) are part of a cellular pathway that has evolved to protect genomes against the proliferation of transposable elements (TEs). PIWIs and piRNAs assemble into complexes that are involved in epigenetic and post-transcriptional repression of TEs. Most of our understanding of the mechanisms of piRNA-mediated TE silencing comes from fruit fly and mouse models. However, even in these well-studied animals it is unclear how piRNA responses relate to variable TE expression and whether the strength of the piRNA response affects TE content over time. Here, w...
Brinkmann J, Jagannathan V, Drögemüller C, Rieder S, Leeb T, Thaller G, Tetens J.The casein genes are known to be highly variable in typical dairy species, such as cattle and goat, but the knowledge about equine casein genes is limited. Nevertheless, mare milk production and consumption is gaining importance because of its high nutritive value, use in naturopathy, and hypoallergenic properties with respect to cow milk protein allergies. In the current study, the open reading frames of the 4 casein genes CSN1S1 (αS1-casein), CSN2 (β-casein), CSN1S2 (αS2-casein), and CSN3 (κ-casein) were resequenced in 253 horses of 14 breeds. The analysis revealed 21 nonsynonymous nucle...
Kennedy R, Lappin DF, Dixon PM, Buijs MJ, Zaura E, Crielaard W, O'Donnell L, Bennett D, Brandt BW, Riggio MP.Equine periodontal disease is a common and painful condition and its severe form, periodontitis, can lead to tooth loss. Its aetiopathogenesis remains poorly understood despite recent increased awareness of this disorder amongst the veterinary profession. Bacteria have been found to be causative agents of the disease in other species, but current understanding of their role in equine periodontitis is extremely limited. The aim of this study was to use high-throughput sequencing to identify the microbiome associated with equine periodontitis and oral health. Subgingival plaque samples from 24 h...
Schrimpf R, Gottschalk M, Metzger J, Martinsson G, Sieme H, Distl O.Stallion fertility is an economically important trait due to the increase of artificial insemination in horses. The availability of whole genome sequence data facilitates identification of rare high-impact variants contributing to stallion fertility. The aim of our study was to genotype rare high-impact variants retrieved from next-generation sequencing (NGS)-data of 11 horses in order to unravel harmful genetic variants in large samples of stallions. Methods: Gene ontology (GO) terms and search results from public databases were used to obtain a comprehensive list of human und mice genes pred...
Yang Y, Zhu Q, Liu S, Zhao C, Wu C.The origin of domestic horses in China was a controversial issue and several hypotheses including autochthonous domestication, introduction from other areas, and multiple-origins from both introduction and local wild horse introgression have been proposed, but none of them have been fully supported by DNA data. In the present study, mitochondrial DNA (mtDNA) sequences of 714 Chinese indigenous horses were analyzed. The results showed that Chinese domestic horses harbor some novel mtDNA haplogroups and suggested that local domestication events may have occurred, but they are not the dominant ha...
Klein C."Maternal recognition of pregnancy" (MRP) is commonly used to describe the ongoing embryo-maternal communication during early pregnancy that culminates in prevention of luteolysis and ensures ongoing progestin support. The conceptus-derived pregnancy recognition signal has not yet been identified in the mare. Although equine conceptuses produce substantial amounts of estrogens, there is a lack of evidence that estrogens are the pregnancy recognition signal in mares. Conceptus mobility is integral to MRP and is driven by conceptus-derived prostaglandin production. Cessation of conceptus mobilit...
Kováts N, Horváth E, Jancsek-Turóczi B, Hoffer A, Gelencsér A, Urbán P, Kiss ÍE, Bihari Z, Fekete C.Air quality in the stables is characterized by elevated level of dust and aeroallergens which are supposed to directly cause or exacerbate several respiratory disorders. The most often recognized problem is recurrent airway obstruction (RAO), previously known as chronic obstructive pulmonary disease (COPD). There is some indication that aeroallergens (among them endotoxins) may also cause inflammation in human airways and may exceed safe levels in stables. Monitoring studies have covered mainly the determination of the concentration of respirable particles and of culturable fungi and their tox...
Mach N, Plancade S, Pacholewska A, Lecardonnel J, Rivière J, Moroldo M, Vaiman A, Morgenthaler C, Beinat M, Nevot A, Robert C, Barrey E.The adaptive response to extreme endurance exercise might involve transcriptional and translational regulation by microRNAs (miRNAs). Therefore, the objective of the present study was to perform an integrated analysis of the blood transcriptome and miRNome (using microarrays) in the horse before and after a 160 km endurance competition. A total of 2,453 differentially expressed genes and 167 differentially expressed microRNAs were identified when comparing pre- and post-ride samples. We used a hypergeometric test and its generalization to gain a better understanding of the biological functio...
Raudsepp T, Chowdhary BP.The association between chromosomal abnormalities and reduced fertility in domestic animals is well recorded and has been studied for decades. Chromosome aberrations directly affect meiosis, gametogenesis, and the viability of zygotes and embryos. In some instances, balanced structural rearrangements can be transmitted, causing fertility problems in subsequent generations. Here, we aim to give a comprehensive overview of the current status and future prospects of clinical cytogenetics of animal reproduction by focusing on the advances in molecular cytogenetics during the genomics era. We descr...
Dong HJ, Ho H, Hwang H, Kim Y, Han J, Lee I, Cho S.Equine gastric ulcer syndrome is one of the most frequently reported diseases in thoroughbred racehorses. Although several risk factors for the development of gastric ulcers have been widely studied, investigation of microbiological factors has been limited. In this study, the presence of Helicobacter spp. and the gastric microbial communities of thoroughbred racehorses having mild to severe gastric ulcers were investigated. Although Helicobacter spp. were not detected using culture and PCR techniques from 52 gastric biopsies and 52 fecal samples, the genomic sequences of H. pylori and H. ganm...
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...
Smits K, De Coninck DI, Van Nieuwerburgh F, Govaere J, Van Poucke M, Peelman L, Deforce D, Van Soom A.Although the equine oviduct clearly affects early embryo development and the selective transport of equine embryos through the oviduct indicates a reciprocal interaction, the influence of the embryo on gene expression in the oviduct remains to be determined in the horse. The aim of this study was to examine this by means of RNA sequencing. Four days after ovulation, epithelial cells ipsilateral and contralateral to the ovulation side from five cyclic and five pregnant mares were collected from the oviduct. RNA was extracted, samples were sequenced, and data analysis was performed to determine ...
Vaz PK, Horsington J, Hartley CA, Browning GF, Ficorilli NP, Studdert MJ, Gilkerson JR, Devlin JM.Recombination in alphaherpesviruses allows evolution to occur in viruses that have an otherwise stable DNA genome with a low rate of nucleotide substitution. High-throughput sequencing of complete viral genomes has recently allowed natural (field) recombination to be studied in a number of different alphaherpesviruses, however, such studies have not been applied to equine herpesvirus 1 (EHV-1) or equine herpesvirus 4 (EHV-4). These two equine alphaherpesviruses are genetically similar, but differ in their pathogenesis and epidemiology. Both cause economically significant disease in horse popul...
Costa MC, Stämpfli HR, Allen-Vercoe E, Weese JS.The intestinal microbiota is a complex polymicrobial ecosystem that exerts extremely important roles in the development and maintenance of health. Recently, as new sequencing technologies have become more available, there has been a revolution in the understanding of the equine intestinal microbiota. However, studies characterising the pioneer intestinal bacteria colonising foals and its development over time are still limited. Objective: The objectives of this study were to characterise the intestinal bacterial colonisation of newborn foals and to follow individual animals over time until age...
Zhao Y, Li B, Bai D, Huang J, Shiraigo W, Yang L, Zhao Q, Ren X, Wu J, Bao W, Dugarjaviin M.The hindgut of horses is an anaerobic fermentative chamber for a complex and dynamic microbial population, which plays a critical role in health and energy requirements. Research on the gut microbiota of Mongolian horses has not been reported until now as far as we know. Mongolian horse is a major local breed in China. We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions from gut fecal material to characterize the gut microbiota of Mongolian horses and compare them to the microbiota in Thoroughbred horses. Fourteen Mongolian and 19 Thoroughbred horses were use...
Schoster A, Guardabassi L, Staempfli HR, Abrahams M, Jalali M, Weese JS.The microbiota plays a key role in health and disease. Probiotics are a potential way to therapeutically modify the intestinal microbiota and prevent disease. Objective: The aim of this study was to investigate the effects of probiotics on the bacterial microbiota of foals during and after administration. Methods: Randomised placebo controlled field trial. Methods: Thirty-eight healthy neonatal foals enrolled in a previous study were selected. The foals had received a multi-strain probiotic (four Lactobacillus spp. 3-4 × 10 colony-forming units (cfu)/g each, Bifidobacterium animalis spp. lact...
Guthrie AJ, Coetzee P, Martin DP, Lourens CW, Venter EH, Weyer CT, Joone C, le Grange M, Harper CK, Howell PG, MacLachlan NJ.This is a report of the complete genome sequences of plaque-selected isolates of each of the four virus strains included in a South African commercial tetravalent African horse sickness attenuated live virus vaccine.
Holl HM, Brooks SA, Archer S, Brown K, Malvick J, Penedo MC, Bellone RR.Leopard complex spotting (LP), the result of an incompletely dominant mutation in TRPM1, produces a collection of unique depigmentation patterns in the horse. Although the LP mutation allows for expression of the various patterns, other loci are responsible for modification of the extent of white. Pedigree analysis of families segregating for high levels of patterning indicated a single dominant gene, named Pattern-1 (PATN1), as a major modifier of LP. Linkage analysis in two half-sibling families segregating for PATN1 identified a 15-Mb region on ECA3p that warranted further investigation. Wh...
Gao W, Chan Y, You M, Lacap-Bugler DC, Leung WK, Watt RM.This study explored the range of bacterial taxa present within healthy subgingival (below the gum-line) niches in the horse oral cavity using 16S rRNA gene amplicon pyrosequencing. Pooled subgingival plaque samples were collected from approximately 200 sulcus sites from two horses (EQ1, EQ2) for analysis. A total of 14,260 quality-filtered pyrosequencing reads were obtained, which were assigned to 3875 operational taxonomic units (OTUs; 99% identity cut-off); 1907 OTUs for EQ1 and 2156 OTUs for EQ2. Diverse taxa from 12 phyla were identified, including Actinobacteria (3.17%), Bacteroidetes (25...
Back H, Ullman K, Leijon M, Söderlund R, Penell J, Ståhl K, Pringle J, Valarcher JF.Equid herpesvirus 5 (EHV-5) is related to the human Epstein-Barr virus (human herpesvirus 4) and has frequently been observed in equine populations worldwide. EHV-5 was previously assumed to be low to non-pathogenic; however, studies have also related the virus to the severe lung disease equine multinodular pulmonary fibrosis (EMPF). Genetic information of EHV-5 is scanty: the whole genome was recently described and only limited nucleotide sequences are available. In this study, samples were taken twice 1 year apart from eight healthy horses at the same professional training yard and samples f...
Figueiredo AS, Lampe E, do Espírito-Santo MP, Mello FC, de Almeida FQ, de Lemos ER, Godoi TL, Dimache LA, Dos Santos DR, Villar LM.Non-primate hepacivirus (NPHV), as described in horses, is the virus most genetically related to hepatitis C virus (HCV). Although detected worldwide, limited data on genomic variability and distribution of NPHV are available in Latin America. The aim of this study was to investigate the genetic diversity and prevalence of equine NPHV in Brazil. Thirteen percent of 202 equines from three Brazilian states were positive for NPHV genome by reverse transcriptase PCR. Nucleotide sequences of the partial NS5B genome presented the greatest diversity described to date (25.6%), which is comparable to t...
Frischknecht M, Jagannathan V, Plattet P, Neuditschko M, Signer-Hasler H, Bachmann I, Pacholewska A, Drögemüller C, Dietschi E, Flury C, Rieder S....The identification of quantitative trait loci (QTL) such as height and their underlying causative variants is still challenging and often requires large sample sizes. In humans hundreds of loci with small effects control the heritable portion of height variability. In domestic animals, typically only a few loci with comparatively large effects explain a major fraction of the heritability. We investigated height at withers in Shetland ponies and mapped a QTL to ECA 6 by genome-wide association (GWAS) using a small cohort of only 48 animals and the Illumina equine SNP70 BeadChip. Fine-mapping re...
Metzger J, Karwath M, Tonda R, Beltran S, Águeda L, Gut M, Gut IG, Distl O.Modern horses represent heterogeneous populations specifically selected for appearance and performance. Genomic regions under high selective pressure show characteristic runs of homozygosity (ROH) which represent a low genetic diversity. This study aims at detecting the number and functional distribution of ROHs in different horse populations using next generation sequencing data. Methods: Next generation sequencing was performed for two Sorraia, one Dülmen Horse, one Arabian, one Saxon-Thuringian Heavy Warmblood, one Thoroughbred and four Hanoverian. After quality control reads were mapped t...
Stefaniuk M, Ropka-Molik K.RNA sequencing (RNA-seq) by next-generation technology is a powerful tool which creates new possibilities in whole-transcriptome analysis. In recent years, with the use of the RNA-seq method, several studies expanded transcriptional gene profiles to understand interactions between genotype and phenotype, supremely contributing to the field of equine biology. To date, in horses, massive parallel sequencing of cDNA has been successfully used to identify and quantify mRNA levels in several normal tissues, as well as to annotate genes. Moreover, the RNA-seq method has been applied to identify the ...
Holl HM, Gao S, Fei Z, Andrews C, Brooks SA.Laminitis, the structural failure of interdigitated tissue that suspends the distal skeleton within the hoof capsule, is a devastating disease that is the second leading cause of both lameness and euthanasia in the horse. Current transcriptomic research focuses on the expression of known genes. However, as this tissue is quite unique and equine gene annotation is largely derived from computational predictions, there are likely yet uncharacterized transcripts that may be involved in the etiology of laminitis. In order to create a novel annotation resource, we performed whole transcriptome seque...
Sato T, Itou T, Sato G, Kobayashi Y, Endo H, Sakai T.In order to investigate the utilization of glucose in equine skeletal muscle, we determined the coding and proximal promoter sequences of the hexokinase type II (HKII) gene in thoroughbred horse, Grevy's zebra and Hartmann's mountain zebra. The deduced amino acid sequence of thoroughbred horse HKII showed 100, 100, 94.4, 92.7 and 92.6% identities with Grevy's zebra, Hartmann's mountain zebra, human, mouse and rat HKIIs, respectively. In equine HKIIs, specific amino acid substitutions, Ile 159 and Arg 610, were found in the potential binding site for glucose. In addition, the nucleotide sequenc...
Broad TE, Forrest JW, Lewis PE, Pearce PD, Phua SH, Pugh PA, Stewart-Scott IA.A DNA repeat element, revealed initially by digestion of horse DNA with TaqI, was cloned and characterized by Southern and in situ hybridization studies and nucleotide sequencing. The clone, e4/1, consisted of 32 tandem reiteration of a unit repeat of 21-22 bp, and produced multilocus DNA fingerprinting profiles that were useful for parentage analysis in horses. The tandem repeat element was shown by in situ hybridization to be localized in the centromeres of the acrocentric but not metacentric classes of horse chromosomes.
Ropka-Molik K, Stefaniuk-Szmukier M, Musiał AD, Velie BD.Arabian horses are commonly believed to be one of the oldest and most influential horse breeds in the world. The high financial benefits obtained from races tend to search for genetic markers strongly correlated with the results achieved. To date, the modern approaches such as transcriptome, miRNAome, and metabolome analyses have been used to investigate the genetic background of racing performance as well as endurance capacity in Arabians. The analysis of polymorphisms at the genome level has also been applied to the detection of genetic variants associated with exercise phenotype in the Arab...
Zhu C, Li Q, Guo W, Lu G, Yin X, Qi T, Xiang W, Ran D, Qu J.We report the complete genomic sequence of A/equine/Heilongjiang/1/2010, a strain of Florida sublineage clade 2 of H3N8 subtype equine influenza virus (EIV) isolated in northern China. This is the first announcement of a complete genomic sequence of EIV of such a clade in China.
Morice P, Allano M, Provost C, Fairbrother JH, Gagnon CA, Sauvé F.Genomic characterization was conducted on 2 methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from 2 horses hospitalized during an overlapping period of time and 2 methicillin-sensitive S. aureus (MSSA) strains isolated from 2 distinct horses. Phylogenetic proximity was traced and the genotypic and phenotypic characteristics of the antimicrobial resistance of the strains were compared. Whole genome sequencing of MRSA strains for this report was similar but differed from whole genome sequencing of MSSA strains. The MRSA strains were closely related, belonging to sequence type ...
Maniego J, Giles O, Hincks P, Stewart G, Proudman C, Ryder E.We present here the use of targeted, long-read sequencing of the myostatin (MSTN) gene as a model to detect potential gene editing events in Thoroughbred horses. MSTN is a negative regulator of muscle development, making the gene a prime candidate target for gene doping. By sequencing the complete gene in one PCR product, we can catalogue all mutations without the need to produce short-fragment libraries. A panel of reference material fragments with defined mutations was constructed and successfully sequenced by both Oxford Nanopore and Illumina-based methods, showing that gene doping editing ...
Díaz S, Echeverría MG, It V, Posik DM, Rogberg-Muñoz A, Pena NL, Peral-García P, Vega-Pla JL, Giovambattista G.The polymorphism of equine lymphocyte antigen (ELA) class II DRA gene had been detected by polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) and reference strand-mediated conformation analysis. These methodologies allowed to identify 11 ELA-DRA exon 2 sequences, three of which are widely distributed among domestic horse breeds. Herein, we describe the development of a pyrosequencing-based method applicable to ELA-DRA typing, by screening samples from eight different horse breeds previously typed by PCR-SSCP. This sequence-based method would be useful in high-throug...
Zhu Y, Wang X, Liu B, Yi Z, Zhao Y, Deng L, Holyoak R, Li J.Silage is fed to horses in China and other areas in the world, however, knowledge about the impact of feeding silage on horse health is still limited. In the current study, 12 horses were assigned into two groups and fed ryegrass silage and ryegrass hay, respectively, for 8 weeks. High-throughput sequencing was applied to analyze fecal microbiota, while liquid chromatography-tandem mass spectrometry (LC-MS/MS) based metabolomics technique was used for blood metabolite profile to investigate the influence of feeding ryegrass silage (group S) compared to feeding ryegrass hay (group H) on equine ...
Hisey EA, Martins BC, Donnelly CG, Cassano JM, Katzman SA, Murphy CJ, Thomasy SM, Leonard BC.This study aimed to define the antimicrobial peptide (AMP) expression pattern of the equine ocular surface and amniotic membrane using a targeted qPCR approach and 3'Tag-sequencing. It will serve as a reference for future studies of ocular surface innate immunity and amniotic membrane therapies. Methods: A targeted qPCR approach was used to investigate the presence of orthologs for three of the most highly expressed beta-defensins (DEFB1, DEFB4B, and DEFB103A) of the human ocular surface and amniotic membrane in equine corneal epithelium, conjunctiva, and amniotic membrane. 3'Tag-sequencing wa...
Morris ERA, Boyle AG, Riihimäki M, Aspán A, Anis E, Hillhouse AE, Ivanov I, Bordin AI, Pringle J, Cohen ND.Streptococcus equi subsp. equi (SEE) is a host-restricted bacterium that causes the common infectious upper respiratory disease known as strangles in horses. Perpetuation of SEE infection appears attributable to inapparent carrier horses because it neither persists long-term in the environment nor infects other host mammals or vectors, and infection results in short-lived immunity. Whether pathogen factors enable SEE to remain in horses without causing clinical signs remains poorly understood. Thus, our objective was to use next-generation sequencing technologies to characterize the genome, me...
Weber KS, Wagener K, Blanco M, Bauersachs S, Bollwein H.Subfertility is a major problem in modern horse breeding. Especially, mares without clinical signs of reproductive diseases, without known uterine pathogens and no evidence of inflammation but not becoming pregnant after several breeding attempts are challenging for veterinarians. To obtain new insights into the cause of these fertility problems and aiming at improving diagnosis of subfertile mares, a comparative analysis of the intrauterine transcriptome in subfertile and fertile mares was performed. Uterine cytobrush samples were collected during estrus from 57 mares without clinical signs o...
Maniego J, Pesko B, Habershon-Butcher J, Hincks P, Taylor P, Tozaki T, Ohnuma A, Stewart G, Proudman C, Ryder E.Gene editing and subsequent cloning techniques offer great potential not only in genetic disease correction in domestic animals but also in livestock production by enhancement of desirable traits. The existence of the technology, however, leaves it open to potential misuse in performance-led sports such as horseracing and other equestrian events. Recent advances in equine gene editing, regarding the generation of gene-edited embryos using CRISPR/Cas9 technology and somatic cell nuclear transfer, have highlighted the need to develop tools to detect potential prohibited use of the technology. On...
Broad TE, Ede AJ, Forrest JW, Lewis PE, Phua SH, Pugh PA.DNA repeats, revealed initially by digestion of horse DNA with restriction enzymes, were cloned and characterized by cross-hybridization studies and nucleotide sequencing. The Sau-like family of tandem repeats contained two classes of repetitive elements with unit repeats of about 80 bp that shared no sequence similarity. Both unit repeats were present, frequently in tandem, in cloned segments of horse DNA of less than 600 bp. Evidence is presented, based on their ladderlike patterns of hybridization to horse DNA and their high level of similarity to published sequences of satellites from equi...
Derisoud E, Jouneau L, Dubois C, Archilla C, Jaszczyszyn Y, Legendre R, Daniel N, Peynot N, Dahirel M, Auclair-Ronzaud J, Wimel L, Duranthon V....Breeding a mare until she is not fertile or even until her death is common in equine industry but the fertility decreases as the mare age increases. Embryo loss due to reduced embryo quality is partly accountable for this observation. Here, the effect of mare's age on blastocysts' gene expression was explored. Day 8 post-ovulation embryos were collected from multiparous young (YM, 6-year-old, N = 5) and older (OM, > 10-year-old, N = 6) non-nursing Saddlebred mares, inseminated with the semen of one stallion. Pure or inner cell mass (ICM) enriched trophoblast, obtained by embryo bise...
Livengood JL, Lanka S, Maddox C, Tewari D.Streptococcus equi subspecies equi (S. equi), the causative agent of strangles, is an important equine pathogen. Strangles is a highly contagious disease and a commercial modified live vaccine (MLV) is used for protection, which although effective, may also result in clinical signs of the disease. A rapid means to differentiate between the MLV and wild-type infection is crucial for quarantine release and limiting the disease spread. This study describes the use of a pyrosequencing assay targeting a single nucleotide deletion upstream of the SzPSe gene to distinguish between the wild-type and v...
Cook SJ, Li G, Zheng Y, Willand ZA, Issel CJ, Cook RF.Although the equine lentivirus (equine infectious anemia virus [EIAV]) poses a major threat to equid populations throughout most regions of the world, detailed knowledge concerning its molecular epidemiology is still in its infancy. Such information is important because the few studies conducted to date suggest there is extensive genetic variation between viral isolates that if confirmed has significant implications for future vaccine design and development of newer diagnostic procedures. Here, we avoid potential assembly artifacts inherent in composite sequencing techniques by using long-rang...
Xie T, Zhang S, Shen W, Zhang G, Guo R, Zhang W, Cao Y, Pan Q, Liu F, Sun Y, Liu S.Twinning trait in donkeys is an important manifestation of high fecundity, but few reports are available elucidating its genetic mechanism. To explore the genetic mechanism underlying the twin colt trait in Dezhou donkeys, DNA from 21 female Dezhou donkeys that had birthed single or twin colts were collected for whole-genome resequencing. FST, θπ and Tajima’s D were used to detect the selective sweeps between single and twin colt fecundity in the Dezhou donkey groups. Another set of 20 female Dezhou donkeys with single or multiple follicles during estrus were selected to compare concentrat...
Tallmadge RL, Miller SC, Parry SA, Felippe MJB.The value of prophylactic neonatal vaccination is challenged by the interference of passively transferred maternal antibodies and immune competence at birth. Taken our previous studies on equine B cell ontogeny, we hypothesized that the equine neonate generates a diverse immunoglobulin repertoire in response to vaccination, independently of circulating maternal antibodies. In this study, equine neonates were vaccinated with 3 doses of keyhole limpet hemocyanin (KLH) or equine influenza vaccine, and humoral immune responses were assessed using antigen-specific serum antibodies and B cell Ig var...
Tachibana Y, Sakurai T, Bai H, Shiota K, Nambo Y, Nagaoka K, Imakawa K.Extensive studies have been conducted to characterize the unique phenomena of equine pregnancy. Most studies have focused on embryo transmigration when the embryo is covered with a mucin-like glycoprotein capsule and on the characterization of the chorionic girdle and chorionic gonadotropin (CG) secretion. However, the events preceding and following capsule disappearance have not been well studied. In this study, the mRNA expression in conceptus membranes at days 19, 21, and 25 (day 0 = day of ovulation) was analyzed by RNA-seq (SOLiD3), and transcript levels on these three days and day 13...
Tozaki T, Inoue S, Mashima S, Ohta M, Miura N, Tomita M.Microsatellites are useful tools for the construction of a linkage map and parentage testing of equines, but only a limited number of equine microsatellites have been elucidated. Thus, we constructed the equine genomic library enriched for DNA fragments containing (CAG)n repeats. The enriched method includes hybridization-capture of repeat regions using biotin-conjugated oligonucleotides, nucleotide substrate-biased polymerase reaction with the oligonucleotides and subsequent PCR amplification, because these procedures are useful for the cloning of less abundant trinucleotide microsatellites. ...
Liu C, Lei H, Ran X, Wang J.The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including , , and and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. had the lowest / ratio (0.560) compared with the other three loci, indicating that was conserved and could be conserved after undergoing selective processes. Nine , five , nine and seven codons were under significant positive selection at the antigen b...
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...
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.
Liu X, Zhang Y, Pu Y, Ma Y, Jiang L.Transposable elements (TEs) are diverse, abundant, and complicated in genomes. They not only can drive the genome evolution process but can also act as special resources for adaptation. However, little is known about the evolutionary processes that shaped horses. In this work, 126 horse assemblages involved in most horse breeds in China were used to investigate the patterns of TE variation for the first time. By using RepeatMasker and melt software, we found that the horse-specific short interspersed repetitive elements family, equine repetitive elements (ERE1), exhibited polymorphisms in hors...
Shnaiderman-Torban A, Navon-Venezia S, Paitan Y, Archer H, Abu Ahmad W, Bonder D, Hanael E, Nissan I, Zizelski Valenci G, Weese SJ, Steinman A.We aimed to investigate the prevalence, molecular epidemiology and prevalence factors for Extended Spectrum β-Lactamase-producing Enterobacteriaceae (ESBL-E) shedding by race horses. A cross-sectional study was performed involving fecal samples collected from 169 Thoroughbred horses that were housed at a large racing facility in Ontario, Canada. Samples were enriched, plated on selective plates, sub-cultured to obtain pure cultures and ESBL production was confirmed. Bacterial species were identified and antibiotic susceptibility profiles were assessed. E. coli sequence types (ST) and ESBL gen...
Mienaltowski MJ, Belt A, Henderson JD, Boyd TN, Marter N, Maga EA, DePeters EJ.Prophylactic supplementation of psyllium husk is recommended to enhance passage of ingested sand from the gastrointestinal tracts of horses. We hypothesized that psyllium supplementation would increase fecal sand passage and favorably alter bacterial populations in the hindgut. Six yearlings and six mature mares were fed a psyllium supplement in the diet daily for seven days. Voluntarily-voided feces were collected over the course of 29 days, prior, during, and after treatment. Feces were analyzed for acid detergent fiber (ADF) and acid detergent insoluble ash analyses. Microbial DNA was also...
Bao W, Yu J, He Y, Liu M, Yang X.The intestinal flora has a variety of physiological functions involved in the regulation of host metabolism, immunity and endocrinology, and plays an important role in maintaining the health of the host. In this study, we used high-throughput sequencing technology to analyze the intestinal bacterial diversity and their gene functions in three equine species of the genus Shetland Pony (SP), Mongolian Wild Ass (MA), and Plain Zebra (PZ) in captivity in two wildlife parks in Inner Mongolia Autonomous Region, China. The results showed that only the SP intestinal bacterial abundance index (Chao1) w...
Premont A, Saadeh K, Edling C, Lewis R, Marr CM, Jeevaratnam K.Understanding cardiomyocyte ion channel expression is crucial to understanding normal cardiac electrophysiology and underlying mechanisms of cardiac pathologies particularly arrhythmias. Hitherto, equine cardiac ion channel expression has rarely been investigated. Therefore, we aim to predict equine cardiac ion channel gene expression. Raw RNAseq data from normal horses from 9 datasets was retrieved from ArrayExpress and European Nucleotide Archive and reanalysed. The normalised (FPKM) read counts for a gene in a mix of tissue were hypothesised to be the average of the expected expression in e...
Leng J, McNally S, Walton G, Swann J, Proudman C, Argo C, Emery S, La Ragione R, Eustace R.Gut microbial communities are increasingly being linked to diseases in animals and humans. Obesity and its associated diseases are a concern for horse owners and veterinarians, and there is a growing interest in the link among diet, the intestinal microbiota and metabolic disease. Objective: Assess the influence of long-term hay or haylage feeding on the microbiota and metabolomes of 20 Welsh mountain ponies. Methods: Longitudinal study. Methods: Urine, faeces and blood were collected from 20 ponies on a monthly basis over a 13-month period. Urine and faeces were analysed using proton magnetic...
