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.
Kubacki J, Lechmann J, Fraefel C, Bachofen C.We present the genome sequence of equid alphaherpesvirus 1 (EHV-1) sequenced directly from the nasal swab of a Swiss horse that attended an international equestrian event in Valencia, Spain, the origin of an outbreak of neurological disorders in horses in several European countries in February 2021.
Higuera A, Herrera G, Jimenez P, García-Corredor D, Pulido-Medellín M, Bulla-Castañeda DM, Pinilla JC, Moreno-Pérez DA, Maloney JG, Santín M.... is frequently reported in fecal samples from animals and humans worldwide, and a variety of subtypes (STs) have been observed in wild and domestic animals. In Colombia, few studies have focused on the transmission dynamics and epidemiological importance of in animals. In this study, we characterized the frequency and subtypes of in fecal samples of domestic animals including pigs, minipigs, cows, dogs, horses, goats, sheep, and llama from three departments of Colombia. Of the 118 fecal samples included in this study 81.4% ( = 96) were positive for using a PCR that amplifies a fragment of t...
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 ...
Hu D, Yang J, Qi Y, Li B, Li K, Mok KM.Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to dete...
Altan E, Hui A, Li Y, Pesavento P, Asín J, Crossley B, Deng X, Uzal FA, Delwart E.Six foals with interstitial pneumonia of undetermined etiology from Southern California were analyzed by viral metagenomics. Spleen, lung, and colon content samples obtained during necropsy from each animal were pooled, and nucleic acids from virus-like particles enriched for deep sequencing. The recently described equine copiparvovirus named eqcopivirus, as well as three previously uncharacterized viruses, were identified. The complete ORFs genomes of two closely related protoparvoviruses, and of a bocaparvovirus, plus the partial genome of a picornavirus were assembled. The parvoviruses were...
Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Kusano K, Nagata SI.The Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) revealed 11,570,312 and 602,756 SNVs in autosomal (1-31) and X chromosomes, respectively, yielding a total of 12,173,068 SNVs. About 6.9% of identified SNVs were rare variants observed only in one allele in 101 horses. The number of SNVs detected in individual horses ranged from 4.8 to 5.3 million. Individual...
Paul LJ, Ericsson AC, Andrews FM, Keowen ML, Morales Yniguez F, Garza F, Banse HE.The role of the gastric microbiome in development or persistence of equine glandular gastric disease (EGGD) remains to be investigated. Objective: The objective was to characterize the glandular mucosal and gastric fluid microbiomes of horses with and without EGGD. It was hypothesized that differences in the mucosal microbiome are associated with EGGD. Methods: Twenty-four horses were enrolled. Methods: Gastroscopy was performed and EGGD scores recorded (score 0, n = 6; score 1, n = 8; score ≥2, n = 10). Gastric fluid and pinch biopsies of healthy glandular mucosa and EGGD lesions were...
Little SV, Hillhouse AE, Lawhon SD, Bryan LK.While Staphylococcus aureus is associated with significant morbidity and mortality in equids (horses, donkeys, and mules), few studies have performed whole-genome sequencing to fully categorize large collections of equine isolates. Such sequencing allows for a comprehensive analysis of the genetic lineage and relationships of isolates, as well as the virulence genes present in each, which can be important for understanding the epidemiology of strains and their range of infections. Seventy-two clinical Staphylococcus aureus isolates from equids were collected at the Texas A&M University Veterin...
Fernandes KA, Gee EK, Rogers CW, Kittelmann S, Biggs PJ, Bermingham EN, Bolwell CF, Thomas DG.Seasonal variation in the faecal microbiota of forage-fed horses was investigated over a 12-month period to determine whether the bacterial diversity fluctuated over time. Horses ( = 10) were maintained on pasture for one year, with hay supplemented from June to October. At monthly intervals, data were recorded on pasture availability and climate (collected continuously and averaged on monthly basis), pasture and hay samples were collected for nutrient analysis, and faecal samples were collected from all horses to investigate the diversity of faecal microbiota using next-generation sequencing ...
The Journal of heredityAugust 4, 2021
Volume 112, Issue 5 443-446 doi: 10.1093/jhered/esab037
Hammons V, Ribeiro L, Munyard K, Sadeghi R, Miller D, Antczak D, Brooks SA.Chestnut coat color in horses is determined by a missense mutation within the MC1R gene. However, the intensity of the chestnut color can vary widely within individuals possessing this genotype. Here, we investigated this variation using standardized photographs of 96 horses. Each horse was ranked lightest to darkest within the cohort for phenotype by 3 blinded observers. A genome-wide association study utilizing the relative shade ranking as the phenotype and using 268 487 single-nucleotide polymorphisms (SNPs) genotyped using the Affymetrix Equine 670k array identified a single significantly...
Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota K, Kusano K, Nagata S.Gene doping is prohibited in horseracing. In a previous study, we developed a method for non-targeted transgene detection using DELLY, which is based on split-read (SR) and paired-end (PE) algorithms to detect structural variants, on WGS data. In this study, we validated the detection sensitivity of DELLY using artificially generated sequence data of 12 target genes. With DELLY, at least one intron was detected as a deletion in eight targeted genes using the 150 bp PE read WGS data, whereas all targeted genes were detected by DELLY using the 100 bp PE read data. The detection sensitivity was h...
Bunpapong N, Charoenkul K, Nasamran C, Chamsai E, Udom K, Boonyapisitsopa S, Tantilertcharoen R, Kesdangsakonwut S, Techakriengkrai N, Suradhat S....To investigate an outbreak of African horse sickness (AHS) on a horse farm in northeastern Thailand, we used whole-genome sequencing to detect and characterize the virus. The viruses belonged to serotype 1 and contained unique amino acids (95V,166S, 660I in virus capsid protein 2), suggesting a single virus introduction to Thailand.
Maniego J, Pesko B, Habershon-Butcher J, Huggett J, Taylor P, Scarth J, Ryder E.Throughout the history of horse racing, doping techniques to suppress or enhance performance have expanded to match the technology available. The next frontier in doping, both in the equine and human sports areas, is predicted to be genetic manipulation; either by prohibited use of genome editing, or gene therapy via transgenes. By using massively-parallel sequencing via a two-step PCR method we can screen for multiple doping targets at once in pooled primer sets. This method has the advantages of high scalability through combinational indexing, and the use of reference standards with altered ...
Jakobsen JR, Schjerling P, Svensson RB, Buhl R, Carstensen H, Koch M, Krogsgaard MR, Kjær M, Mackey AL.The myotendinous junction (MTJ) is a specialized interface for transmitting high forces between the muscle and tendon and yet the MTJ is a common site of strain injury with a high recurrence rate. The aim of this study was to identify previously unknown MTJ components in mature animals and humans. Samples were obtained from the superficial digital flexor (SDF) muscle-tendon interface of 20 horses, and the tissue was separated through a sequential cryosectioning approach into muscle, MTJ (muscle tissue enriched in myofiber tips attached to the tendon), and tendon fractions. RT-PCR was performed...
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 ...
Uprety T, Sreenivasan CC, Hause BM, Li G, Odemuyiwa SO, Locke S, Morgan J, Zeng L, Gilsenan WF, Slovis N, Metcalfe L, Carter CN, Timoney P, Horohov D....Equine rotavirus group A (ERVA) is one of the most common causes of foal diarrhea. Starting in February 2021, there was an increase in the frequency of severe watery to hemorrhagic diarrhea cases in neonatal foals in Central Kentucky. Diagnostic investigation of fecal samples failed to detect evidence of diarrhea-causing pathogens including ERVA. Based on Illumina-based metagenomic sequencing, we identified a novel equine rotavirus group B (ERVB) in fecal specimens from the affected foals in the absence of any other known enteric pathogens. Interestingly, the protein sequence of all 11 segment...
Patterson Rosa L, Martin K, Vierra M, Foster G, Lundquist E, Brooks SA, Lafayette C.Over 30 polymorphisms in the KIT Proto-Oncogene Receptor Tyrosine Kinase (KIT) gene have been implicated in white spotting patterns ranging from small areas to full dermal depigmentation in the horse. We performed a candidate-gene exon sequencing approach on KIT and MITF, 2 known causatives of white spotting patterns, within 2 families of horses of unknown white spotting. Family 1 (Fam1, N = 5) consisted of a Quarter Horse stallion and 4 offspring with white spotting pattern ranging from legs, lower ventral, and head regions with jagged borders, to almost complete white. The second family (Fam...
Monteiro de Barros MR, Davies-Morel MCG, Mur LAJ, Creevey CJ, Alison RH, Nash DM.Persistent mating-induced endometritis is a major cause of poor fertility rates in the mare. Endometritis can be investigated using an ex vivo equine endometrial explant system which measures uterine inflammation using prostaglandin F2α as a biomarker. However, this model has yet to undergo a wide-ranging assessment through transcriptomics. In this study, we assessed the transcriptomes of cultured endometrial explants and the optimal temporal window for their use. Endometrium harvested immediately post-mortem from native pony mares (n = 8) were sampled (0 h) and tissue explants were cultured ...
Lee W, Mun S, Choi SY, Oh DY, Park YS, Han K.The Jeju horse is a native Korean species that has been breeding on Jeju Island since the 13th century. Their shape has a distinct appearance from the representative species, Thoroughbred. Here, we performed a comparison of the Jeju horse and Thoroughbred horse for the identification of genome-wide structure variation by using the next-generation sequencing (NGS) technique. We generated an average of 95.59 Gb of the DNA sequence, resulting in an average of 33.74 X sequence coverage from five Jeju horses. In addition, reads obtained from WGRS data almost covered the horse reference genome (mapp...
Pavulraj S, Eschke K, Theisen J, Westhoff S, Reimers G, Andreotti S, Osterrieder N, Azab W.Equine herpesvirus type 4 (EHV-4) is enzootic in equine populations throughout the world. A large outbreak of EHV-4 respiratory infection occurred at a Standardbred horse-breeding farm in northern Germany in 2017. Respiratory illness was observed in a group of in-housed foals and mares, which subsequently resulted in disease outbreak. Out of 84 horses in the stud, 76 were tested and 41 horses were affected, including 20 foals, 10 stallions, and 11 mares. Virological investigations revealed the involvement of EHV-4 in all cases of respiratory illness, as confirmed by virus isolation, qPCR, and/...
O'Shaughnessy-Hunter LC, Yu A, Rousseau JD, Foster RA, Weese JS.Next-generation sequencing techniques have revealed that human and animal skin is colonised by a rich and diverse population of bacteria, and that microbial composition varies between different body sites and individuals. Very little is known about the normal microbiota of healthy equine skin. Objective: To describe the taxonomic distributions of cutaneous bacterial microbiota in a population of healthy horses in Ontario, Canada, and to evaluate the effects of body site, individual and time of year on microbial diversity and community composition. Methods: Samples were collected from four body...
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...
Arnold C, Pilla R, Chaffin K, Lidbury J, Steiner J, Suchodolski J.Diarrhea is an adverse effect of antimicrobial therapy in horses. This matched, case-controlled study compared the fecal microbiome and metabolome of horses on antibiotics that developed diarrhea (AAD, = 17) to those that did not develop diarrhea (ABX, = 15) and to a control population not exposed to antibiotics (CON, = 31). Fecal samples were collected from horses that were matched for diet and antimicrobial agent (including dose, route, and duration of therapy). Illumina sequencing of 16S rRNA genes was performed, and QIIME 2.0 was used to generate alpha and beta diversity metrics. Untarg...
Park T, Cheong H, Yoon J, Kim A, Yun Y, Unno T.(1) Background: The intestinal microbiota plays an essential role in maintaining the host's health. Dysbiosis of the equine hindgut microbiota can alter the fermentation patterns and cause metabolic disorders. (2) Methods: This study compared the fecal microbiota composition of horses with intestinal disease and their healthy counterparts living in Korea using 16S rRNA sequencing from fecal samples. A total of 52 fecal samples were collected and divided into three groups: horses with large intestinal disease (n = 20), horses with small intestinal disease (n = 8), and healthy horses (n = 24). (...
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...
Theelen MJP, Luiken REC, Wagenaar JA, Sloet van Oldruitenborgh-Oosterbaan MM, Rossen JWA, Zomer AL.Several studies have described the faecal microbiota of horses and the factors that influence its composition, but the variation in results is substantial. This study aimed to investigate the microbiota composition in healthy equids in The Netherlands under standard housing and management conditions and to evaluate the effect of age, gender, horse type, diet, pasture access, the season of sampling and location on it. Spontaneously produced faecal samples were collected from the stall floor of 79 healthy horses and ponies at two farms. The validity of this sampling technique was evaluated in a ...
Subbiah M, Thirumalapura N, Thompson D, Kuchipudi SV, Jayarao B, Tewari D.Metagenomic sequencing of clinical diagnostic specimens has a potential for unbiased detection of infectious agents, diagnosis of polymicrobial infections and discovery of emerging pathogens. Herein, next generation sequencing (NGS)-based metagenomic approach was used to investigate the cause of illness in a subset of horses recruited for a tick-borne disease surveillance study during 2017-2019. Blood samples collected from 10 horses with suspected tick-borne infection and five apparently healthy horses were subjected to metagenomic analysis. Total genomic DNA extracted from the blood samples ...
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...
Park T, Yoon J, Kim A, Unno T, Yun Y.(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoro...
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...
O'Nion VL, Montilla HJ, Qurollo BA, Maggi RG, Hegarty BC, Tornquist SJ, Breitschwerdt EB.Ehrlichia sp. DNA was amplified from 4 Ehrlichia-seroreactive horses from Mérida, Nicaragua. Sequencing of 16S rDNA, sodB, and groEL genes indicated that the bacterium is most likely a novel Ehrlichia species. The tick vector and the potential for canine and human infection remain unknown.
Nemoto M, Oue Y, Murakami S, Kanno T, Bannai H, Tsujimura K, Yamanaka T, Kondo T.Equine coronavirus has been responsible for several outbreaks of disease in the United States and Japan. Only one complete genome sequence (NC99 isolated in the US) had been reported for this pathogenic RNA virus. Here, we report the complete genome sequences of three equine coronaviruses isolated in 2009 and 2012 in Japan. The genome sequences of Tokachi09, Obihiro12-1 and Obihiro12-2 were 30,782, 30,916 and 30,916 nucleotides in length, respectively, excluding the 3'-poly (A) tails. All three isolates were genetically similar to NC99 (98.2-98.7%), but deletions and insertions were observed i...
Walker RL, Read DH, Hayes DC, Nordhausen RW.Direct amplification and sequencing of the 16S rRNA gene and a variable region of the flagellin gene from fetal liver-associated spirochetes belonging to the Borrelia parkeri-B. turicatae tick-borne relapsing fever spirochete group with a late-term abortion in a mare are described.
Bao T, Han H, Li B, Zhao Y, Bou G, Zhang X, Du M, Zhao R, Mongke T, Laxima , Ding W, Jia Z, Dugarjaviin M, Bai D.Skeletal muscle is the largest organ system in the mammalian body and plays a key role in locomotion of horses. Fast and slow muscle fibers have different abilities and functions to adapt to exercises. To investigate the RNA and miRNA expression profiles in the muscles with different muscle fiber compositions on Mongolian horses. We examined the muscle fiber type population and produced deep RNA sequencing for different parts of skeletal muscles. And chose two of them with the highest difference in fast and slow muscle fiber population (splenius and gluteus medius) for comparing the gene expre...
Mott J, Muramatsu Y, Seaton E, Martin C, Reed S, Rikihisa Y.Upon ingestion of adult aquatic insects, horses developed clinical signs of Potomac horse fever, and Neorickettsia risticii was isolated from the blood. 16S rRNA and 51-kDa antigen gene sequences from blood, isolates, and caddis flies fed to the horses were identical, proving oral transmission of N. risticii from caddis flies to horses.
Lwin KO, Matsui H.Comparative analysis of methanogen compositions in the feces of horse and pony was carried out by constructing the α -subunit of methyl coenzyme-M reductase (mcrA) gene and 16S ribosomal RNA gene (16S rRNA) clone libraries. The mcrA clone library analysis indicated that Methanomicrobiales was predominant in both horse and pony. Furthermore, most of the clones of the 16S rRNA gene library showed that Methanomicrobiales was also predominant in horse and pony, but the LIBSHUFF analysis showed that the horse and pony libraries were significantly different (P < 0.05). Most of operational taxono...
Jun J, Cho YS, Hu H, Kim HM, Jho S, Gadhvi P, Park KM, Lim J, Paek WK, Han K, Manica A, Edwards JS, Bhak J.The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. Results: We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The seq...
Al-Kass Z, Guo Y, Vinnere Pettersson O, Niazi A, Morrell JM.Bacteria colonize stallion semen during collection and processing which may cause disease in inseminated females or negatively affect sperm quality during storage prior to insemination. Antibiotics are added to semen extenders to control the growth of these bacteria but may induce antimicrobial resistance. Research into alternatives to antibiotics for this purpose requires knowledge of which bacteria are present in semen. Not all bacteria in semen, however, can be identified by conventional microbiological techniques. The objectives of the study were to: i) determine which bacteria are present...
Klohonatz KM, Coleman SJ, Islas-Trejo AD, Medrano JF, Hess AM, Kalbfleisch T, Thomas MG, Bouma GJ, Bruemmer JE.Equine maternal recognition of pregnancy (MRP) is a process whose signal remains unknown. During MRP the conceptus and endometrium communicate to attenuate prostaglandin F (PGF) secretion, sparing the corpus luteum and maintaining progesterone production. Recognition of a mobile conceptus by the endometrium is critical by days 14-16 post-ovulation (PO), when endometrium produces PGF, initiating luteolysis. The objective of this study was to evaluate endometrial gene expression changes based upon pregnancy status via RNA sequencing. This experiment utilized a cross-over design with each mare se...
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...
Smits K, Gansemans Y, Tilleman L, Van Nieuwerburgh F, Van De Velde M, Gerits I, Ververs C, Roels K, Govaere J, Peelman L, Deforce D, Van Soom A.The signal for maternal recognition of pregnancy (MRP) has still not been identified in the horse. High-throughput molecular biology at the embryo-maternal interface has substantially contributed to the knowledge on pathways affected during MRP, but an integrated study in which proteomics, transcriptomics and miRNA expression can be linked directly is currently lacking. The aim of this study was to provide such analysis. Endometrial biopsies, uterine fluid, embryonic tissues, and yolk sac fluid were collected 13 days after ovulation during pregnant and control cycles from the same mares. Micro...
Almagro JC, Martinez L, Smith SL, Alagon A, Estevez J, Paniagua J.We have constructed a chimeric antibody single-chain Fv (scFv) fragments phage-displayed library that combines an invariant human V(L) chain with the repertoire of V(H) domains amplified from a horse immunized against scorpion venom. To gain insight into the equine V(H) repertoire, the V(H) sequences of 46 unique clones randomly chosen from the library prior to antigenic selection were analyzed. Comparisons with previously reported equine V(H) sequences, as well as with the repertoire of human IGHV germline genes and known V(H) sequences of sheep, cattle and pig, suggest that the equine IGH lo...
Leclere M, Costa MC.Gastrointestinal microbiota can be influenced by several factors, including diet and systemic inflammation, and in turn could act as a modulator of the allergic response. Fecal microbiota of horses with asthma has not been described. Objective: Analyze the bacterial fecal microbiota of horses with and without asthma under different environment and diet conditions, during both remission and exacerbation. Methods: Prospective observational study. Feces from 6 asthmatic and 6 healthy horses were collected under 3 different conditions: on pasture, housed indoors receiving good quality hay ("good h...
Ruiz-López MJ, Muñoz-Chimeno M, Figuerola J, Gavilán AM, Varona S, Cuesta I, Martínez-de la Puente J, Zaballos Á, Molero F, Soriguer RC....Emerging infectious diseases are one of the most important global health challenges because of their impact on human and animal health. The vector-borne West Nile virus (WNV) is transmitted between birds by mosquitos, but it can also infect humans and horses causing disease. The local circulation of WNV in Spain has been known for decades, and since 2010, there have been regular outbreaks in horses, although only six cases were reported in humans until 2019. In 2020, Spain experienced a major outbreak with 77 human cases, which was followed by 6 additional cases in 2021, most of them in the An...
Mansour TA, Scott EY, Finno CJ, Bellone RR, Mienaltowski MJ, Penedo MC, Ross PJ, Valberg SJ, Murray JD, Brown CT.Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome. This equine transcriptome integrates eight d...
Moon S, Lee JW, Shin D, Shin KY, Kim J, Choi IY, Kim J, Kim H.Using next-generation sequencing, we conducted a genome-wide scan of selective sweeps associated with selection toward genetic improvement in Thoroughbreds. We investigated potential phenotypic consequence of putative candidate loci by candidate gene association mapping for the finishing time in 240 Thoroughbred horses. We found a significant association with the trait for Ral GApase alpha 2 (RALGAP2) that regulates a variety of cellular processes of signal trafficking. Neighboring genes around RALGAP2 included insulinoma-associated 1 (INSM1), pallid (PLDN), and Ras and Rab interactor 2 (RIN2)...
Rash A, Woodward A, Bryant N, McCauley J, Elton D.H3N8 equine influenza virus (EIV) has caused disease outbreaks in horses across the world since its first isolation in 1963. However, unlike human, swine and avian influenza, there is relatively little sequence data available for this virus. The majority of published sequences are for the segment encoding haemagglutinin (HA), one of the two surface glycoproteins, making it difficult to study the evolution of the other gene segments and determine the level of reassortment occurring between sub-lineages. Methods: To facilitate the generation of full genome sequences for EIV, we developed a simpl...
Bond SL, Workentine M, Hundt J, Gilkerson JR, Léguillette R.Prolonged exposure to environmental antigens or allergens elicits an immune response in both healthy horses and those with mild asthma. Corticosteroids often are used to treat lower airway inflammation. Objective: To investigate the changes in equine herpesvirus (EHV)-1,2,4,5 glycoprotein B gene expression and changes in respiratory bacterial and fungal communities after nebulized dexamethasone treatment of horses with asthma. Methods: Horses with naturally occurring mild asthma (n = 16) and healthy control horses (n = 4). Methods: Prospective, randomized, controlled, blinded clinical trial. P...
Blitvich BJ, Fernández-Salas I, Contreras-Cordero JF, Loroño-Pino MA, Marlenee NL, Díaz FJ, González-Rojas JI, Obregón-Martínez N....West Nile virus RNA was detected in brain tissue from a horse that died in June 2003 in Nuevo Leon State, Mexico. Nucleotide sequencing and phylogenetic analysis of the premembrane and envelope genes showed that the virus was most closely related to West Nile virus isolates collected in Texas in 2002.
Tyma JF, Epstein KL, Whitfield-Cargile CM, Cohen ND, Giguère S.OBJECTIVE To determine the effects of oral omeprazole administration on the fecal and gastric microbiota of healthy adult horses. ANIMALS 12 healthy adult research horses. PROCEDURES Horses were randomly assigned to receive omeprazole paste (4 mg/kg, PO, q 24 h) or a sham (control) treatment (tap water [20 mL, PO, q 24 h]) for 28 days. Fecal and gastric fluid samples were collected prior to the first treatment (day 0), and on days 7, 28, 35, and 56. Sample DNA was extracted, and bacterial 16S rRNA gene sequences were amplified and sequenced to characterize α and β diversity and differential ...
Sekizuka T, Niwa H, Kinoshita Y, Uchida-Fujii E, Inamine Y, Hashino M, Kuroda M.MRSA is a known pathogen that affects horses. We investigated an equine MRSA isolate for potential antimicrobial resistance genes, classified the staphylococcal cassette chromosome mec (SCCmec) and identified the strain-specific dissemination in the horse community based on WGS. WGS, using short-read sequencing, and subsequent long-read sequencing by hybrid assembly, was conducted to obtain a complete genome sequence. Pairwise sequence alignment of relative SCCmec sequences and core-genome phylogenetic analysis were performed to highlight transmission routes of the SCCmec and MRSA strain-speci...
Pawlina K, Gurgul A, Szmatoła T, Koch C, Mählmann K, Witkowski M, Bugno-Poniewierska M.Equine sarcoids are the most common neoplasms occurring in horses. Despite frequent occurrence, they are still not well described at the molecular level. Thus, in the present study, we performed a comprehensive comparative analysis of sarcoid miRNAome profile to identify aberrantly expressed microRNAs, along with their structural variants, potentially useful as biomarkers and, in a wider perspective, broaden the knowledge about this tumor and underlying mechanisms. To this end, we conducted next generation sequencing and as a result we identified both known and potentially novel miRNAs. Differ...
Gharsa H, Slama KB, Gómez-Sanz E, Gómez P, Klibi N, Zarazaga M, Boudabous A, Torres C.Staphylococcus intermedius group (SIG) bacteria can colonise the nares of some animals but are also emerging pathogens in humans and animals. Objective: To analyse SIG nasal carriage in healthy donkeys destined for food consumption in Tunisia and to characterise recovered isolates. Methods: Nasal swabs from 100 healthy donkeys were tested for SIG recovery, and isolates were identified by biochemical and molecular methods. Antimicrobial susceptibility of isolates was tested and detection of antimicrobial resistance and virulence genes was performed. Isolates were typed at the clonal level by mu...
Guarino H, Castilho JG, Souto J, Oliveira Rde N, Carrieri ML, Kotait I.After 25 years without any reported cases of rabies in Uruguay, the northern region of the country experienced an epizootic of bovine paralytic rabies in October 2007. The outbreak affected bovines and equines, and the main source of infection was the bat Desmodus rotundus, the only hematophagous species in the country. From October 2007 to July 2008, 42 bovine, 3 equine and 120 chiropteran samples were submitted to the National Veterinary Diagnostic Laboratory for rabies testing. A total of 12 samples (7 bovine, 2 equine and 3 from D. rotundus) were positive by the fluorescent antibody test, ...
Xing J, Liu G, Zhang X, Bai D, Yu J, Li L, Wang X, Su S, Zhao Y, Bou G, Dugarjaviin M.The community of microorganisms inhabiting the gastrointestinal tract of monogastric herbivores played critical roles in the absorption of nutrients and keeping the host healthy. However, its establishment at different age groups has not been quantitatively and functionally examined. The knowledge of microbial colonization and its function in the intestinal tract of different-age donkeys is still limited. By applying the V3-V4 region of the bacterial 16S rRNA gene and functional prediction on fecal samples from different-age donkeys, we characterized the gut microbiota during the different age...
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 ...
Frischknecht M, Neuditschko M, Jagannathan V, Drögemüller C, Tetens J, Thaller G, Leeb T, Rieder S.A cost-effective strategy to increase the density of available markers within a population is to sequence a small proportion of the population and impute whole-genome sequence data for the remaining population. Increased densities of typed markers are advantageous for genome-wide association studies (GWAS) and genomic predictions. Methods: We obtained genotypes for 54 602 SNPs (single nucleotide polymorphisms) in 1077 Franches-Montagnes (FM) horses and Illumina paired-end whole-genome sequencing data for 30 FM horses and 14 Warmblood horses. After variant calling, the sequence-derived SNP geno...
Dhorne-Pollet S, Barrey E, Pollet N.Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochondrial genomes using nanopore long-read sequencing. Our method relies on the selective elimination of nuclear DNA using an exonuclease treatment and on the amplification of circular mitochondrial DNA using a multiple displacement amplification step. Results: We optimized each preparative step to obtain a 100 million-fold enrichment of horse mitochondrial DNA relative to nuclear DNA. We sequ...
Chowdhary BP, Raudsepp T.The map of the horse genome has undergone unprecedented expansion during the past six years. Beginning from a modest collection of approximately 300 mapped markers scattered on the 31 pairs of autosomes and the X chromosome in 2001, today the horse genome is among the best-mapped in domestic animals. Presently, high-resolution linearly ordered gene maps are available for all autosomes as well as the X and the Y chromosome. The approximately 4350 mapped markers distributed over the approximately 2.68 Gbp long equine genome provide on average 1 marker every 620 kb. Among the most remarkable deve...
