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.
Mehdizadeh Gohari I, Kropinski AM, Weese SJ, Whitehead AE, Parreira VR, Boerlin P, Prescott JF.Clostridium perfringens is an important cause of foal necrotizing enteritis and canine acute hemorrhagic diarrhea. A major virulence determinant of the strains associated with these diseases appears to be a beta-sheet pore-forming toxin, NetF, encoded within a pathogenicity locus (NetF locus) on a large tcp-conjugative plasmid. Strains producing NetF also produce the putative toxin NetE, encoded within the same pathogenicity locus, as well as CPE enterotoxin and CPB2 on a second plasmid, and sometimes the putative toxin NetG within a pathogenicity locus (NetG locus) on another separate large c...
Daneshvar Amoli A, Mohebali N, Farzaneh P, Shahzadeh Fazeli SA, Nikfarjam L, Ashouri Movasagh S, Moradmand Z, Ganjibakhsh M, Nasimian A, Izadpanah M....Caspian horse, a rare horse breed found in 1965 by Louise Firouz in northern Iran, is a small horse which is reported to be in danger of extinction in its original homeland. There seems to be a great need to prevent extinction of this valuable horse. In this study, 51 fibroblast cell lines from Caspian horse ear marginal tissue were successfully established by sampling 60 horses using primary explant technique. Cells were authenticated and growth curve was plotted. According to results obtained, population doubling time (PDT) was calculated 23 ± 0.5 h for all cell lines. Multiplex polymera...
Walter S, Rasche A, Moreira-Soto A, Pfaender S, Bletsa M, Corman VM, Aguilar-Setien A, García-Lacy F, Hans A, Todt D, Schuler G....The hepatitis C virus (HCV) is a major human pathogen. Genetically related viruses in animals suggest a zoonotic origin of HCV. The closest relative of HCV is found in horses (termed equine hepacivirus [EqHV]). However, low EqHV genetic diversity implies relatively recent acquisition of EqHV by horses, making a derivation of HCV from EqHV unlikely. To unravel the EqHV evolutionary history within equid sister species, we analyzed 829 donkeys and 53 mules sampled in nine European, Asian, African, and American countries by molecular and serologic tools for EqHV infection. Antibodies were found in...
Almarzook S, Reissmann M, Brockmann GA.Arabian horse registries classify Arabian horses based on their dam lineages into five main strains. To test the maternal origin of Syrian Arabian horses, 192 horses representing the three major strains Saglawi, Kahlawi, and Hamdani were sequenced for 353 bp of their mitochondrial displacement loop (D-loop) region. Sequencing revealed 28 haplotypes comprising 38 sequence variations. The haplotype diversity values were 0.95, 0.91, and 0.90 in Kahlawi, Hamdani, and Saglawi strains, respectively. The pair-wise population differentiation estimates (Fst) between strains were low, ranging between 0...
Metzger J, Gast AC, Schrimpf R, Rau J, Eikelberg D, Beineke A, Hellige M, Distl O.The Miniature Shetland pony represents a horse breed with an extremely small body size. Clinical examination of a dwarf Miniature Shetland pony revealed a lowered size at the withers, malformed skull and brachygnathia superior. Computed tomography (CT) showed a shortened maxilla and a cleft of the hard and soft palate which protruded into the nasal passage leading to breathing difficulties. Pathological examination confirmed these findings but did not reveal histopathological signs of premature ossification in limbs or cranial sutures. Whole-genome sequencing of this dwarf Miniature Shetland p...
Elschner MC, Thomas P, Melzer F.Burkholderia mallei is a zoonotic agent causing glanders, a notifiable disease in equines. During the past decades glanders emerged, and the Kingdom of Bahrain reported outbreaks to the World Organization of Animal Health in 2010 and 2011. This paper presents the complete genome sequence of the Burkholderia mallei strain 11RR2811 Bahrain1.
Peripolli E, Munari DP, Silva MVGB, Lima ALF, Irgang R, Baldi F.This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping t...
Goodman LB, Anderson RR, Slater M, Ortenberg E, Renshaw RW, Chilson BD, Laverack MA, Beeby JS, Dubovi EJ, Glaser AL.Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of combining reactions together. We designed and evaluated a panel based on this principle to rapidly identify the presence of common disease agents in dogs and horses with acute respiratory illness. This manuscript describes a nanoscale diagnostic PCR workflow for sample preparation, amplification, and analysis of target pathogen sequences, focusing on procedures that are different from microliter scale reactions. In the respiratory panel prese...
Miller D, Tallmadge RL, Binns M, Zhu B, Mohamoud YA, Ahmed A, Brooks SA, Antczak DF.The polymorphism of major histocompatibility complex (MHC) class II DQ and DR genes in five common equine leukocyte antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine bacterial artificial chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci. Next generation...
Woo PC, Teng JL, Bai R, Wong AY, Martelli P, Hui SW, Tsang AK, Lau CC, Ahmed SS, Yip CC, Choi GK, Li KS, Lam CS, Lau SK, Yuen KY.In a molecular epidemiology study using 791 fecal samples collected from different terrestrial and marine mammals in Hong Kong, genogroup I picobirnaviruses (PBVs) were positive by RT-PCR targeting the partial RdRp gene in specimens from five cattle, six monkeys, 17 horses, nine pigs, one rabbit, one dog, and 12 California sea lions, with 11, 9, 23, 17, 1, 1, and 15 sequence types in the positive specimens from the corresponding animals, respectively. Phylogenetic analysis showed that the PBV sequences from each kind of animal were widely distributed in the whole tree with high diversity, shar...
Seo JH, Park KD, Lee HK, Kong HS.Currently about 26,000 horses are breeding in Korea and 57.2% (14,776 horses) of them are breeding in Jeju island. According to the statistics published in 2010, the horses breeding in Jeju island are subdivided into Jeju horse (6.1%), Thoroughbred (18.8%) and Halla horse (75.1%). Halla horses are defined as a crossbreed between Jeju and Thoroughbred horses and are used for horse racing, horse riding and horse meat production. However, little research has been conducted on Halla horses because of the perception of crossbreed and people's weighted interest toward Jeju horses. Methods: Using 17 ...
Payne CL, Dark MJ, Conway JA, Farina LL.Fungi in the genus Aspergillus are some of the most common fungal pathogens in veterinary species, primarily affecting the respiratory tract. In both human and veterinary cases, calcium oxalate crystals have been documented in sites of Aspergillus infection. Cases in multiple species (16 birds, 15 horses, 5 dogs, 1 ox, and 1 dolphin) were identified that had either positive cultures for Aspergillus sp., or had conidiophores present that could be identified as belonging to the genus Aspergillus. Histologic slides were examined to confirm the presence of oxalate crystals and how often they were ...
Izume S, Kirisawa R, Ohya K, Ohnuma A, Kimura T, Omatsu T, Katayama Y, Mizutani T, Fukushi H.Equine herpesvirus type 4 (EHV-4) is one of the most important pathogens in horses. To clarify the key genes of the EHV-4 genome that cause abortion in female horses, we determined the whole genome sequences of a laboratory strain and 7 Japanese EHV-4 isolates that were isolated from 2 aborted fetuses and nasal swabs of 5 horses with respiratory disease. The full genome sequences and predicted amino acid sequences of each gene of these isolates were compared with of the reference EHV-4 strain NS80567 and Australian isolates that were reported in 2015. The EHV-4 isolates clustered in 2 groups w...
Loux SC, Scoggin KE, Troedsson MH, Squires EL, Ball BA.The cervical mucus plug (CMP) is believed to play an integral role in the maintenance of pregnancy in the mare, primarily by inhibiting microbial entry. Unfortunately, very little is known about its composition or origin. To determine the proteomic composition of the CMP, we collected CMPs from mares (n = 4) at 9 months of gestation, and proteins were subsequently analyzed by nano-LC-MS/MS. Results were searched against EquCab2.0, and proteomic pathways were predicted by Ingenuity Pathway Analysis. Histologic sections of the CMP were stained with H&E and PAS. To identify the origin of ...
Jahdasani R, Jamnani FR, Behdani M, Habibi-Anbouhi M, Yardehnavi N, Shahbazzadeh D, Kazemi-Lomedasht F.The venom of the Hemiscorpius lepturus scorpion contains mixtures of bioactive compounds that disturb biochemical and physiological functions of the victims. Hemiscorpius lepturus envenomation is recognized as a serious health concern in tropical regions. So far, there is no preventive procedure, and the main focus is on treatment of victims with an antiserum purified from hyper-immunized horses. Although antisera can neutralize the venom, they, in some cases, lead to anaphylactic shock and even death. Selection of peptides mimicking antigenic and immunogenic epitopes of toxins from random pep...
Alzan HF, Knowles DP, Suarez CE.Apicomplexa tick-borne hemoparasites, including Babesia bovis, Babesia microti, and Theileria equi are responsible for bovine and human babesiosis and equine theileriosis, respectively. These parasites of vast medical, epidemiological, and economic impact have complex life cycles in their vertebrate and tick hosts. Large gaps in knowledge concerning the mechanisms used by these parasites for gene regulation remain. Regulatory genes coding for DNA binding proteins such as members of the Api-AP2, HMG, and Myb families are known to play crucial roles as transcription factors. Although the reperto...
Kobayashi D, Isawa H, Ejiri H, Sasaki T, Sunahara T, Futami K, Tsuda Y, Katayama Y, Mizutani T, Minakawa N, Ohta N, Sawabe K.Getah virus (GETV; genus Alphavirus, family Togaviridae) is a mosquito-borne virus known to cause disease in horses and pigs. In 2014, for the first time in ∼30 years, a sudden GETV outbreak occurred among racehorses in Ibaraki, Japan. Two years before this outbreak, we obtained multiple GETV isolates from Culex tritaeniorhynchus mosquitoes collected in Nagasaki, Japan and determined the whole genome sequence of GETV isolate 12IH26. Our phylogenetic analysis of GETV strains revealed that the isolate 12IH26 forms a robust clade with the epidemic strains 14-I-605-C1 and 14-I-605-C2 isolated fr...
Sharma M, Nunez-Garcia J, Kearns AM, Doumith M, Butaye PR, Argudín MA, Lahuerta-Marin A, Pichon B, AbuOun M, Rogers J, Ellis RJ, Teale C, Anjum MF.In recent years, there has been an increase in the number of livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 recovered from S. aureus isolated animals in the UK. To determine possible origins of 12 LA-MRSA CC398 isolates collected after screening more than a thousand S. aureus animal isolates from the UK between 2013 and 2015, whole genome sequences (WGS) of CC398 European, including UK, and non-European isolates from diverse animal hosts were compared. Phylogenetic reconstruction applied to WGS data to assess genetic relatedness of all 89 iso...
Leegwater PA, Vos-Loohuis M, Ducro BJ, Boegheim IJ, van Steenbeek FG, Nijman IJ, Monroe GR, Bastiaansen JW, Dibbits BW, van de Goor LH, Hellinga I....Inbreeding and population bottlenecks in the ancestry of Friesian horses has led to health issues such as dwarfism. The limbs of dwarfs are short and the ribs are protruding inwards at the costochondral junction, while the head and back appear normal. A striking feature of the condition is the flexor tendon laxity that leads to hyperextension of the fetlock joints. The growth plates of dwarfs display disorganized and thickened chondrocyte columns. The aim of this study was to identify the gene defect that causes the recessively inherited trait in Friesian horses to understand the disease proce...
Pacholewska A, Mach N, Mata X, Vaiman A, Schibler L, Barrey E, Gerber V.MiRNAs regulate multiple genes at the post-transcriptional level and therefore play an important role in many biological processes. It has been suggested that miRNA exported outside the cells contribute to inter-cellular communication. Consequently, circulating miRNAs are of particular interest and are promising biomarkers for many diseases. The number of miRNAs annotated in the horse genome is much lower compared to model organisms like human and mouse. We therefore aimed to identify novel equine miRNAs for tissue types and breed in serum. We analysed 71 small RNA-seq libraries derived from n...
Semik E, Gurgul A, Ząbek T, Ropka-Molik K, Koch C, Mählmann K, Bugno-Poniewierska M.Equine sarcoids are the most commonly detected skin tumours in Equidae. In the present research, a comparative transcriptomic analysis was performed which aimed at looking inside a tumour biology and identification of the expression profile as a potential source of cancer specific genes useful as biomarkers. We have used Horse Gene Expression Microarray data from matched equine sarcoids and tumour-distant skin samples. In total, 901 significantly differentially expressed genes (DEGs) between lesional and healthy skin samples have been identified (fold change ≥ 2; P < 0.05). The la...
Finno CJ, Bordbari MH, Valberg SJ, Lee D, Herron J, Hines K, Monsour T, Scott E, Bannasch DL, Mickelson J, Xu L.Specific spontaneous heritable neurodegenerative diseases have been associated with lower serum and cerebrospinal fluid α-tocopherol (α-TOH) concentrations. Equine neuroaxonal dystrophy (eNAD) has similar histologic lesions to human ataxia with vitamin E deficiency caused by mutations in the α-TOH transfer protein gene (TTPA). Mutations in TTPA are not present with eNAD and the molecular basis remains unknown. Given the neuropathologic phenotypic similarity of the conditions, we assessed the molecular basis of eNAD by global transcriptome sequencing of the cervical spinal cord. Differential...
Librado P, Fages A, Gaunitz C, Leonardi M, Wagner S, Khan N, Hanghøj K, Alquraishi SA, Alfarhan AH, Al-Rasheid KA, Der Sarkissian C, Schubert M....The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds...
Scott EY, Penedo MCT, Murray JD, Finno CJ.Equine cerebellar abiotrophy (CA) is a hereditary neurodegenerative disease that affects the Purkinje neurons of the cerebellum and causes ataxia in Arabian foals. Signs of CA are typically first recognized either at birth to any time up to 6 months of age. CA is inherited as an autosomal recessive trait and is associated with a single nucleotide polymorphism (SNP) on equine chromosome 2 (13074277G>A), located in the fourth exon of TOE1 and in proximity to MUTYH on the antisense strand. We hypothesize that unraveling the functional consequences of the CA SNP using RNA-seq will elucidate the m...
Gemingguli M, Iskhan KR, Li Y, Qi A, Wunirifu W, Ding LY, Wumaierjiang A.The Kazakh horse is an important old horse breed in Xinjiang. They have contributed greatly to the breeding and improvement of other local horse breeds, yet their genetic diversity and population structure are not well understood. In the present study, we evaluated the genetic diversity of Kazakh horses and their relationship with other horse breeds using the mtDNA D-loop region, Cyt b gene, and a DNA fragment (nps 7974-9963, containing COX3, tRNA-Gly, ND3, and tRNA-Arg). A total of 130 Kazakh horses from 8 populations in China and Kazakhstan were analyzed. A total of 88 haplotypes (haplotype ...
Fedorka CE, Scoggin KE, Woodward EM, Squires EL, Ball BA, Troedsson M.In the horse, breeding induces a transient endometrial inflammation. A subset of mares are unable to resolve this inflammation, and they are considered susceptible to persistent mating-induced endometritis PMIE Select seminal plasma proteins cysteine-rich secretory protein-3 (CRISP-3) and lactoferrin have been shown to affect the innate immune response to sperm in vitro. The objective of this study was to determine whether the addition of CRISP-3 and lactoferrin at the time of insemination had an effect on the mRNA expression of endometrial cytokines in susceptible mares after breeding. Six ma...
Franco MM, Santos JB, Mendonça AS, Silva TC, Antunes RC, Melo EO.The domestication of the Equus genus 5000-6000 years ago has influenced the history of human civilization. As soon as horse and donkey species had been domesticated, they were crossbred, producing humanity's first documented attempt at animal genome manipulation. Since then, the mule (male donkey x female horse) and the reciprocal cross (the hinny, male horse x female donkey) have been the most common equine hybrids in the world. Due to their hybrid vigor, mules and hinnies have been intensively used for carrying loads and people and for tilling the land. Despite their importance, visual disti...
Yang Y, Zheng N, Wang W, Zhao X, Zhang Y, Han R, Ma L, Zhao S, Li S, Guo T, Zang C, Wang J.Glycosylation of proteins has been implicated in various biological functions and has received much attention; however, glycoprotein components and inter-species complexity have not yet been elucidated fully in milk proteins. N-linked glycosylation sites and glycoproteins in milk fat globule membrane (MFGM) fractions were investigated by combining N-glycosylated peptides enrichment and high-accuracy Q Exactive identification, to map the N-glycoproteome profiles in Holstein and Jersey cows, buffaloes, yaks, goats, camels, horses, and humans. A total of 399 N-glycoproteins with 677 glycosylation...
Murgiano L, Waluk DP, Towers R, Wiedemar N, Dietrich J, Jagannathan V, Drögemüller M, Balmer P, Druet T, Galichet A, Penedo MC, Müller EJ....We investigated a family of horses exhibiting irregular vertical stripes in their hair coat texture along the neck, back, hindquarters, and upper legs. This phenotype is termed "brindle" by horse breeders. We propose the term "brindle 1 (BR1)" for this specific form of brindle. In some BR1 horses, the stripes were also differentially pigmented. Pedigree analyses were suggestive of a monogenic X-chromosomal semidominant mode of inheritance. Haplotype analyses identified a 5 Mb candidate region on chromosome X. Whole genome sequencing of four BR1 and 60 nonbrindle horses identified 61 private v...
Charbonneau ARL, Taylor E, Mitchell CJ, Robinson C, Cain AK, Leigh JA, Maskell DJ, Waller AS.The availability of next-generation sequencing techniques provides an unprecedented opportunity for the assignment of gene function. subspecies is the causative agent of strangles in horses, one of the most prevalent and important diseases of equids worldwide. However, the live attenuated vaccines that are utilized to control this disease cause adverse reactions in some animals. Here, we employ transposon-directed insertion-site sequencing (TraDIS) to identify genes that are required for the fitness of in whole equine blood or in the presence of HO to model selective pressures exerted by th...
Lykkjen S, Dolvik NI, McCue ME, Rendahl AK, Mickelson JR, Røed KH.Palmar/plantar osteochondral fragments (POF) in fetlock joints commonly affect and influence the athletic performance of horses. In this study, we used the Equine SNP50 BeadChip® to perform a genome-wide association study of metatarsophalangeal POF in 176 Norwegian Standardbred trotter yearlings. Putative quantitative trait loci (QTL) for medial and/or lateral POF, and medial POF only were identified on ECA1, 2, 7, 9 and 31, whereas for lateral POF, only on ECA7, 11, 27 and X. The moderate number of QTL evidences a complex inheritance and suggests various genes controlling POF development in ...
Zhang FL, Zhang XY, Zhao JX, Zhu KX, Liu SQ, Zhang T, Sun YJ, Wang JJ, Shen W.Mongolian horses have been bred and used for labor and transport for centuries. Nevertheless, traits of testicular development in Mongolian horses have rarely been studied; particularly, studies regarding the transcriptional regulation characteristics of testicular development are lacking. In this paper, transcription specificity during testicular development in Mongolian horses is highlighted via a multispecies comparative analysis and weighted gene co-expression network analysis (WGCNA). Interestingly, the results showed that most genes were up-regulated in the testes after sexual maturity, ...
Sletten K, Husebekk A, Husby G.The amino acid sequence of the amyloid fibril protein AA from horse was established from characterization of cyanogen bromide fragments, tryptic peptides, and a peptide derived from a digest with Staphylococcus aureus V8 proteinase. The protein was found to consist of 80 amino acid residues. Sequence homologies with protein AA from other species were very striking, and revealed an insertion of two amino acid residues between positions 72 and 73. In position 44, two amino acid residues were found which provide further evidence for a polymorphism in the amyloid fibril protein AA.
Boshuizen B, Moreno de Vega CV, De Maré L, de Meeûs C, de Oliveira JE, Hosotani G, Gansemans Y, Deforce D, Van Nieuwerburgh F, Delesalle C.Aleurone, a layer of the bran fraction, is deemed to be responsible for the positive health effects associated with the consumption of whole-grain products. Studies on rodents, pigs, and humans report beneficial effects of aleurone in five main areas: the reduction of oxidative stress, immunomodulatory effects, modulation of energy management, digestive health, and the storage of vitamins and minerals. Our study is the first aleurone supplementation study performed in horses. The aim of this study was to investigate the effect of an increase in the dose levels of aleurone on the postprandial g...
Jindra C, Hainisch EK, Brandt S.Horses and other equid species are frequently affected by bovine papillomavirus type 1 and/or 2 (BPV1, BPV2)-induced skin tumors termed sarcoids. Although sarcoids do not metastasize, they constitute a serious health problem due to their BPV1/2-mediated resistance to treatment and propensity to recrudesce in a more severe, multiple form following accidental or iatrogenic trauma. This review provides an overview on BPV1/2 infection and associated immune escape in the equid host and presents early and recent immunotherapeutic approaches in sarcoid management.
Nazari F, Seyedabadi HR, Noshary A, Emamjomeh-Kashan N, Banabazi MH.The genetic diversity and genomic regions being under putative natural selection in Kurdish horse population were studied. The samples from 72 horses were genotyped by using GGP Equine 70K SNP arrays. The Ne Slope (NeS) analyses revealed that a sharp decline in Ne has probably occurred around four generations ago, and high frequency of ROH with 2-4 Mbp in length suggested that the inbreeding has probably occurred around 20 generations ago. The effective population size (Ne) was 104 horses up to three generations ago and the average inbreeding (FROH) was 0.047(± 0.045). Using de-correlated com...
Yue XP, Qin F, Campana MG, Liu DH, Mao CC, Wang XB, Lan XY, Chen H, Lei CZ.Previous mitochondrial DNA (mtDNA) D-loop and microsatellite studies have shown that Chinese horses have multiple maternal origins and high genetic diversity. To better characterize maternal genetic origins and diversity of Chinese domestic horses, we conducted a comprehensive analysis of 407 complete 1140 bp sequences of the horse mitochondrially encoded cytochrome b (CYTB) gene, including 323 horses from 13 Chinese indigenous breeds and 84 reference sequences from GenBank. A total of 114 haplotypes were identified, of which 73 appeared among the 13 Chinese horse breeds. The high mitochondria...
Ehmann R, Brandes K, Antwerpen M, Walter M, V Schlippenbach K, Stegmaier E, Essbauer S, Bugert J, Teifke JP, Meyer H.Cases of pox-like lesions in horses and donkeys have been associated with poxviruses belonging to different genera of the family . These include the orthopoxviruses vaccinia virus (VACV), horsepoxvirus (HPXV) and cowpoxvirus (CPXV), as well as a potentially novel parapoxvirus and molluscum contagiosum virus (MOCV). However, with the exception of VACV, HPXV and CPXV, the genomic characterization of the causative agents remains largely elusive with only single short genome fragments available. Here we present the first full-length genome sequence of an equine molluscum contagiosum-like virus (EM...
Ning T, Li J, Lin K, Xiao H, Wylie S, Hua S, Li H, Zhang YP.The domestic horse is the most widely used and important stock and recreational animal, valued for its strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria via oxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horse mitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. To understand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencing approach to obtain the complete sequences of 15 mitochondrial genomes, and fo...
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...
Yamashita-Kawanishi N, Chambers JK, Uchida K, Tobari Y, Yoshimura H, Yamamoto M, Yumoto N, Aoki H, Sugiura K, Higuchi T, Saito S, Haga T.Bovine papillomavirus types 1 and 2 (BPV1/2) infection in horses has been associated with the development of equine sarcoids. Previous findings revealed the presence of sarcoid-associated BPV sequence variants that have been proposed as a key factor of cross-species infection in horses. To verify this hypothesis, sarcoid-associated BPV variants should be identified regardless of geographic location. Objective: Sequence analyses of BPV1/2 derived from both horses and cattle were conducted to clarify the sarcoid-associated sequence variants. The aim of this study was to clarify the correlation b...
Ramos RT, Silva A, Carneiro AR, Pinto AC, Soares Sde C, Santos AR, Almeida SS, Guimarães LC, Aburjaile FF, Barbosa EG, Dorella FA, Rocha FS....The bacterium Corynebacterium pseudotuberculosis is of major veterinary importance because it affects livestock, particularly sheep, goats, and horses, in several countries, including Australia, Brazil, the United States, and Canada, resulting in significant economic losses. In the present study, we describe the complete genome of the Corynebacterium pseudotuberculosis Cp316 strain, biovar equi, isolated from the abscess of a North American horse.
Fukai K, Saito T, Fukuda O, Hagiwara A, Inoue K, Sato M.In this study, equine group A rotavirus (RV-A), Nasuno, isolated from foal diarrhoea in Tochigi Prefecture, Japan was characterised genetically by sequence analysis of the genome segments encoding VP4 and VP7. The nucleotide and deduced amino acid sequences revealed high homology with P[12] RV-As (94.0-99.3% and 94.9-99.4%) and G3 RV-As (86.9-99.5% and 91.1-99.4%). Nasuno was also classified into P[12] and G3 in the phylogenetic analysis of the nucleotide sequences of the genome segments encoding VP4 and VP7.
Hokke CH, Roosenboom MJ, Thomas-Oates JE, Kamerling JP, Vliegenthart JF.The disialylated poly-(N-acetyllactosamine)-containing O-linked oligosaccharide alditols, released by alkaline borohydride treatment of the enzymically N-deglycosylated beta-subunit of equine chorionic gonadotropin, were purified by fast protein liquid chromatography (FPLC) on Mono Q and analysed by fast ion bombardment mass spectrometry (FAB-MS) and 1H-NMR spectroscopy. The identified oligosaccharide alditols have the following structure: [Formula: see text]
Epe C, Bienioschek S, Rehbein S, Schnieder T.Genomic DNA isolated from the four Dictyocaulus species D. viviparus, D. eckerti, D. filaria and D. arnfieldi was compared by random amplified polymorphic DNA polymerase chain reaction (RAPD)-PCR to get additional information whether lungworms from fallow deer belong to a separate species (D. eckerti) or have to be regarded as an isolate of D. viviparus in wild ruminants. The resulting banding patterns of the electrophoresed PCR products were compared to assess the degree of genetic differences between the different lungworms. For the two D. viviparus isolates a similarity coefficient of 93.4%...
Hristov P, Yordanov G, Ivanova A, Mitkov I, Sirakova D, Mehandzyiski I, Radoslavov G.It is believed that population structure of mountain horse breeds is preserved from any genetic introgression, because of their geographical isolation and specific semi-wild life style of husbandry. Till date there are no molecular data for the Balkan horses. In this study we try to give information about some autochthonous mountain horse breeds from Bulgaria. A total of 121 horses from three different mountain massifs are presented: Stara Planina (the Balkan mountain), the Rhodopes and Rila-Pirin massif were genotyped according to mitochondrial D-loop region. The results showed huge diversity...
Locke MM, Ruth LS, Millon LV, Penedo MC, Murray JD, Bowling AT.The colour locus historically referred to as C in the horse is linked to microsatellites markers on horse chromosome 21. Preliminary results demonstrated linkage of Ccr, thought to be the cream dilution variant of the C locus, to HTG10. An analysis of horse chromosome 21 using additional families confirmed and established a group of markers linked to Ccr. This work also improved the resolution of previously reported linkage maps for this chromosome. Linkage analysis unambiguously produced the map order: SGCV16-(19.1 cM)-HTG10-(3.8 cM)-LEX60/COR73-(1.3 cM)-COR68-(4.5 cM)- Ccr-(11.9 cM)-LEX31. C...
Cwiklinski K, Merga JY, Lake SL, Hartley C, Matthews JB, Paterson S, Hodgkinson JE.Clade V nematodes comprise several parasitic species that include the cyathostomins, primary helminth pathogens of horses. Next generation transcriptome datasets are available for eight parasitic clade V nematodes, although no equine parasites are included in this group. Here, we report next generation transcriptome sequencing analysis for the common cyathostomin species, Cylicostephanus goldi. A cDNA library was generated from RNA extracted from 17 C. goldi male and female adult parasites. Following sequencing using a 454 GS FLX pyrosequencer, a total of 475,215 sequencing reads were generate...
Wong KS, Cheung HW, Szeto CWL, Tsang CYN, Wan TSM, Ho ENM.Illicit administration of transgene into horses is a form of gene doping that has been a key concern in equine sports. The large number of potential performance-enhancing transgenes has demanded a cost-effective and reliable detection method. Multiplex qPCR is a relevant technique, but the cross-talking between fluorophores and high background noise limits the method sensitivity and specificity. This study reports a simpler multiplexing approach by using the same fluorophore for four hydrolysis probes each targeting one of the four transgenes: human growth hormone, insulin-like growth factor 1...
Lee EJ, Raudsepp T, Kata SR, Adelson D, Womack JE, Skow LC, Chowdhary BP.Comparative genomics has served as a backbone for the rapid development of gene maps in domesticated animals. The integration of this approach with radiation hybrid (RH) analysis provides one of the most direct ways to obtain physically ordered comparative maps across evolutionarily diverged species. We herein report the development of a detailed RH and comparative map for horse chromosome 17 (ECA17). With markers distributed at an average interval of every 1.4 Mb, the map is currently the most informative among the equine chromosomes. It comprises 75 markers (56 genes and 19 microsatellites),...
Jindra C, Kamjunke AK, Jones S, Brandt S.Bovine papillomavirus types 1 and 2 (BPV1 and BPV2) are accepted aetiological agents of equine sarcoids. Recently, genetically similar BPV13 has been identified from equine sarcoids in Brazil. Objective: To determine whether BPV13 DNA can be also found in sarcoid-affected horses in Austria, and donkeys in Northern Italy and the UK, and should hence be considered in the context of vaccine-mediated sarcoid prevention. Methods: Cross sectional study. Methods: A total of 194 archival, equine and asinine DNA isolates derived from confirmedly delta-BPV-positive tumours were subjected to quality cont...
Winton CL, Plante Y, Hind P, McMahon R, Hegarty MJ, McEwan NR, Davies-Morel MC, Morgan CM, Powell W, Nash DM.Most species exist as subdivided ex situ daughter population(s) derived from a single original group of individuals. Such subdivision occurs for many reasons both natural and manmade. Traditional British and Irish pony breeds were introduced to North America (U.S.A. and Canada) within the last 150 years, and subsequently equivalent breed societies were established. We have analyzed selected U.K. and North American equivalent pony populations as a case study for understanding the relationship between putative source and derived subpopulations. Diversity was measured using mitochondrial DNA and ...
Akula S, Riihimäki M, Waern I, Åbrink M, Raine A, Hellman L, Wernersson S.Asthma is a chronic inflammatory airway disease and a serious health problem in horses as well as in humans. In humans and mice, mast cells (MCs) are known to be directly involved in asthma pathology and subtypes of MCs accumulate in different lung and airway compartments. The role and phenotype of MCs in equine asthma has not been well documented, although an accumulation of MCs in bronchoalveolar lavage fluid (BALF) is frequently seen. To characterize the phenotype of airway MCs in equine asthma we here developed a protocol, based on MACS Tyto sorting, resulting in the isolation of 92.9% pur...
Norton E, Schultz N, Geor R, McFarlane D, Mickelson J, McCue M.Equine metabolic syndrome (EMS) is a complex trait for which few genetic studies have been published. Our study objectives were to perform within breed genome-wide association analyses (GWA) to identify associated loci in two high-risk breeds, coupled with meta-analysis to identify shared and unique loci between breeds. GWA for 12 EMS traits identified 303 and 142 associated genomic regions in 264 Welsh ponies and 286 Morgan horses, respectively. Meta-analysis demonstrated that 65 GWA regions were shared across breeds. Region boundaries were defined based on a fixed-size or the breakdown of li...
Ren X, Liu Y, Zhao Y, Li B, Bai D, Bou G, Zhang X, Du M, Wang X, Bou T, Shen Y, Dugarjaviin M.Interspecific hybridization often shows negative effects on hybrids. However, only a few multicellular species, limited to a handful of plants and animals, have shown partial genetic mechanisms by which hybridization leads to low fitness in hybrids. Here, to explore the outcome of combining the two genomes of a horse and donkey, we analyzed the whole-genome sequences from an parent-offspring trio using Illumina platforms. We generated 41.39× and 46.21× coverage sequences for the horse and mule, respectively. For the donkey, a 40.38× coverage sequence was generated and stored in our laborat...
Kim DS, Kim DW, Kim MY, Nam SH, Choi SH, Kim RN, Kang A, Kim A, Park HS.A conjoined gene is defined as one formed at the time of transcription by combining at least part of one exon from each of two or more distinct genes that lie on the same chromosome, in the same or opposite orientation, which translate independently into different proteins. We comparatively studied the extent of conjoined genes in thirteen genomes by analyzing the public databases of expressed sequence tags and mRNA sequences using a set of computational tools designed to identify conjoined genes on the same DNA strand or opposite DNA strands of the same genomic locus. The CACG database, avail...
Lee K, Pusterla N, Barnum SM, Lee DH, Martínez-López B.Equine influenza virus (EIV) is a major infectious pathogen causing significant respiratory signs in equids worldwide. Voluntary surveillances in the United States recently reported EIV detection in horses with respiratory signs even with adequate vaccine protocols and biosecurity programs and posed a concern about suboptimal effectiveness of EIV vaccine in the United States. This study aims to determine the genetic characteristics of 58 field EIV H3N8 strains in the United States from 2012 to 2017 using the phylogenetic analysis based on the haemagglutinin (HA) gene. Amino acid substitution a...
The Journal of heredityAugust 26, 2021
Volume 112, Issue 5 436-442 doi: 10.1093/jhered/esab034
Cieslak J, Brooks SA, Wodas L, Mantaj W, Borowska A, Sliwowska JH, Ziarniak K, Mackowski M.Only the blue dun coat color, produced by the action of the dun allele on the background of a black base coat, is officially permitted in the Polish primitive horse (PPH, Konik) breed, yet the population is not visually homogenous and various coat color shades occur. Herein, the molecular background of PPH coat color was studied based on genotyping of known causative variants in equine coat color-related genes (ASIP, MC1R, TBX3, SLC36A1, SLC45A2, PMEL17, and RALY). Additionally, screening for the new polymorphisms was conducted for the ASIP gene coding sequence and the TBX3 1.6-kb insert (asso...
