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.
Tew SR, McDermott BT, Fentem RB, Peffers MJ, Clegg PD.Messenger RNA (mRNA) decay rates control not only gene expression levels, but also responsiveness to altered transcriptional input. We undertook this study to examine transcriptome-wide posttranscriptional regulation in both normal and osteoarthritic (OA) human articular chondrocytes. Methods: Human articular chondrocytes were isolated from normal or OA tissue. Equine articular chondrocytes were isolated from young or old horses at a commercial abattoir. RNA decay was measured across the transcriptome in human cells by microarray analysis following an actinomycin D chase. Messenger RNA levels ...
Dong J, Cook FR, Haga T, Horii Y, Norimine J, Misawa N, Goto Y, Zhu W.Although equine infectious anemia virus (EIAV) poses a major threat to the equine industry worldwide, the molecular epidemiology of this virus is poorly understood. Recently, an EIAV strain (EIAVMiyazaki2011-A) representing a new monophyletic group was discovered in feral horses in southern Japan. In the present study, the EIAVMiyazaki2011-A proviral genome is compared with evolutionarily divergent EIAV isolates to investigate conservation of functional elements or motifs within the long terminal repeats (LTRs) and structural genes. This analysis represents a significant step forward in increa...
Leise BS, Watts MR, Roy S, Yilmaz AS, Alder H, Belknap JK.Dysadhesion of laminar basal epithelial cells (LBECs) from the underlying dermis is the central event leading to structural failure in equine laminitis. Although many studies of sepsis-related laminitis have reported multiple events occurring throughout the lamellar tissue, there is minimal information regarding signalling events occurring specifically in LBECs. Objective: To determine signalling events in the LBECs during the early stages of carbohydrate-induced laminitis. Methods: Experimental study. Methods: Eight horses were given an overload of carbohydrate (CHO) consisting of corn starch...
Shinwari MW, Annand EJ, Driver L, Warrilow D, Harrower B, Allcock RJ, Pukallus D, Harper J, Bingham J, Kung N, Diallo IS.In May 2013, the first cases of Australian bat lyssavirus infections in domestic animals were identified in Australia. Two horses (filly-H1 and gelding-H2) were infected with the Yellow-bellied sheathtail bat (YBST) variant of Australian bat lyssavirus (ABLV). The horses presented with neurological signs, pyrexia and progressing ataxia. Intra-cytoplasmic inclusion bodies (Negri bodies) were detected in some Purkinje neurons in haematoxylin and eosin (H&E) stained sections from the brain of one of the two infected horses (H2) by histological examination. A morphological diagnosis of sub-acute m...
Takasu M, Ishihara N, Tozaki T, Kakoi H, Maeda M, Mukoyama H.To determine genetic characteristics of the maternal lineage of the Kiso horse based on polymorphisms of the mitochondrial DNA D-loop region, we collected blood samples from 136 Kiso horses, 91% of the entire population, and sequenced 411 bp from 15,437 to 15,847 in the region. First of all, we estimated the demographic history; by searching homology between the obtained and known sequences using Basic Local Alignment Search Tool, by mismatch analysis to evaluate the mutation processes using Arlequin, and by building a phylogenetic tree showing the relationship of the mtDNA haplotypes for 24 h...
Song KD, Cho HW, Lee HK, Cho BW.The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene (VEGFα) by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog), we constructed a phylogenetic tree which showed that equine VEGFα belonged to the same clade of the pig VEGFα. Analysis for synonymous (Ks) and non-synonymous sub...
Meira CT, Curi RA, Farah MM, de Oliveira HN, Béltran NA, Silva JA, Mota MD.Selection of Quarter Horses for different purposes has led to the formation of lines, including racing and cutting horses. The objective of this study was to identify genomic regions divergently selected in racing line of Quarter Horses in relation to cutting line applying relative extended haplotype homozygosity (REHH) analysis, an extension of extended haplotype homozygosity (EHH) analysis, and the fixation index (F ST) statistic. A total of 188 horses of both sexes, born between 1985 and 2009 and registered at the Brazilian Association of Quarter Horse Breeders, including 120 of the racing ...
Lee JR, Hong CP, Moon JW, Jung YD, Kim DS, Kim TH, Gim JA, Bae JH, Choi Y, Eo J, Kwon YJ, Song S, Ko J, Yang YM, Lee HK, Park KD, Ahn K, Do KT, Ha HS....DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known. Results: We report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA m...
Metzger J, Tonda R, Beltran S, Agueda L, Gut M, Distl O.Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an insight into genetic influences on selective forces. Results: Whole genome sequencing of five horses of four different populations revealed 10,193,421 single nucleotide polymorphisms (SNPs) and 1,361,948 insertion/deletion polymorphisms (indels). In comparison to horse variant databases and previous reports, w...
Finno CJ, Bannasch DL.Genome sequencing of the domestic horse and subsequent advancements in the field of equine genomics have led to an explosion in the development of tools for mapping traits and diseases and evaluating gene expression. The objective of this review is to discuss the current progress in the field of equine genomics, with specific emphasis on assembly and analysis of the reference sequence and subsequent sequencing of a Quarter Horse mare; the genomic tools currently available to researchers and their implications in genomic investigations in the horse; the genomics of Mendelian and non-Mendelian t...
Patterson-Kane JC, Rich T.Superficial digital flexor tendon (SDFT) injury in equine athletes is one of the most well-accepted, scientifically supported companion animal models of human disease (i.e., exercise-induced Achilles tendon [AT] injury). The SDFT and AT are functionally and clinically equivalent (and important) energy-storing structures for which no equally appropriate rodent, rabbit, or other analogues exist. Access to equine tissues has facilitated significant advances in knowledge of tendon maturation and aging, determination of specific exercise effects (including early life), and definition of some of the...
Guo X, Izume S, Okada A, Ohya K, Kimura T, Fukushi H.A strain of equine herpesvirus type 1 (EHV-1) was isolated from zebra. This strain, called "zebra-borne EHV-1", was also isolated from an onager and a gazelle in zoological gardens in U.S.A. The full genome sequences of the 3 strains were determined. They shared 99% identities with each other, while they shared 98% and 95% identities with the horse derived EHV-1 and equine herpesvirus type 9, respectively. Sequence data indicated that the EHV-1 isolated from a polar bear in Germany is one of the zebra-borne EHV-1 and not a recombinant virus. These results indicated that zebra-borne EHV-1 is a ...
Chambers TM, Reedy SE.Equine influenza viruses are cultured in embryonated hen eggs, or in mammalian cells, generally Madin-Darby canine kidney (MDCK) cells, using methods much the same as for other influenza A viruses. Mutations associated with host adaptation occur in both eggs and MDCK cells, but the latter show greater heterogeneity and eggs are the generally preferred host. Both equine-1 H7N7 and equine-2 H3N8 viruses replicate efficiently in 11-day-old eggs, but we find that equine-1 viruses kill the embryos whereas equine-2 viruses do not.
McQueen CM, Doan R, Dindot SV, Bourquin JR, Zlatev ZZ, Chaffin MK, Blodgett GP, Ivanov I, Cohen ND.Pneumonia caused by Rhodococcus equi is a common cause of disease and death in foals. Although agent and environmental factors contribute to the incidence of this disease, the genetic factors influencing the clinical outcomes of R. equi pneumonia are ill-defined. Here, we performed independent single nucleotide polymorphism (SNP)- and copy number variant (CNV)-based genome-wide association studies to identify genomic loci associated with R. equi pneumonia in foals. Foals at a large Quarter Horse breeding farm were categorized into 3 groups: 1) foals with R. equi pneumonia (clinical group [N = ...
Labitzke D, Sieme H, Martinsson G, Distl O.The objectives of this study were to show whether semen traits of 30 Hanoverian stallions regularly used in AI may be useful for breeding purposes. Semen characteristics were studied using 15 149 ejaculates from 30 Hanoverian stallions of the State Stud Celle of Lower Saxony. Semen samples were collected between 2005 and 2009. Traits analysed were gel-free volume, sperm concentration, total and motile sperm number and progressive motility. A linear multivariate animal model was employed to estimate heritabilities and permanent environmental variances for stallions. The same model was used to p...
Dolejska M, Villa L, Minoia M, Guardabassi L, Carattoli A.To determine the structure of two multidrug-resistant IncHI1 plasmids carrying blaCTX-M-1 in Escherichia coli isolates disseminated in an equine clinic in the Czech Republic. Methods: A complete nucleotide sequencing of 239 kb IncHI1 (pEQ1) and 287 kb IncHI1/X1 (pEQ2) plasmids was performed using the 454-Genome Sequencer FLX system. The sequences were compared using bioinformatic tools with other sequenced IncHI1 plasmids. Results: A comparative analysis of pEQ1 and pEQ2 identified high nucleotide identity with the IncHI1 type 2 plasmids. A novel 24 kb module containing an operon involved in ...
da Silveira JC, Carnevale EM, Winger QA, Bouma GJ.Ovarian follicle growth and maturation requires extensive communication between follicular somatic cells and oocytes. Recently, intercellular cell communication was described involving cell-secreted vesicles called exosomes (50-150 nm), which contain miRNAs and protein, and have been identified in ovarian follicular fluid. The goal of this study was to identify a possible role of exosomes in follicle maturation. Methods: Follicle contents were collected from mares at mid-estrous (~35 mm, before induction of follicular maturation) and pre-ovulatory follicles (30-34 h after induction of folli...
Na W, Hong M, Yeom M, Kim S, Kim JK, Song D.We analyzed the complete genome sequence containing the 3' and 5' noncoding regions (NCRs) of the Korean H3N8 equine influenza virus (EIV), which will provide a better understanding of the pathogenesis, transmission, and evolution of EIV.
Begg AP, Todhunter K, Donahoe SL, Krockenberger M, Slapeta J.A case of amoebic placentitis in a mare from eastern Australia was diagnosed postpartum by histopathological examination of the placenta. The identity of the etiological agent was confirmed as Acanthamoeba hatchetti by use of diversity profiling based on a next-generation sequencing approach.
Huang J, Zhao Y, Shiraigol W, Li B, Bai D, Ye W, Daidiikhuu D, Yang L, Jin B, Zhao Q, Gao Y, Wu J, Bao W, Li A, Zhang Y, Han H, Bai H, Bao Y, Zhao L....Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsonian translocation event through the wild horse's chromosomes 23 and 24, which contained sequences th...
Moreton J, Malla S, Aboobaker AA, Tarlinton RE, Emes RD.The immune system of the horse has not been well studied, despite the fact that the horse displays several features such as sensitivity to bacterial lipopolysaccharide that make them in many ways a more suitable model of some human disorders than the current rodent models. The difficulty of working with large animal models has however limited characterisation of gene expression in the horse immune system with current annotations for the equine genome restricted to predictions from other mammals and the few described horse proteins. This paper outlines sequencing of 184 million transcriptome sh...
Bujacz A, Zielinski K, Sekula B.Serum albumin, a protein naturally abundant in blood plasma, shows remarkable ligand binding properties of numerous endogenous and exogenous compounds. Most of serum albumin binding sites are able to interact with more than one class of ligands. Determining the protein-ligand interactions among mammalian serum albumins is essential for understanding the complexity of this transporter. We present three crystal structures of serum albumins in complexes with naproxen (NPS): bovine (BSA-NPS), equine (ESA-NPS), and leporine (LSA-NPS) determined to 2.58 Å (C2), 2.42 Å (P61), and 2.73 Å (P2₁2₁...
Tallmadge RL, Tseng CT, Felippe MJ.To further studies of neonatal immune responses to pathogens and vaccination, we investigated the dynamics of B lymphocyte development and immunoglobulin (Ig) gene diversity. Previously we demonstrated that equine fetal Ig VDJ sequences exhibit combinatorial and junctional diversity levels comparable to those of adult Ig VDJ sequences. Herein, RACE clones from fetal, neonatal, foal, and adult lymphoid tissue were assessed for Ig lambda light chain combinatorial, junctional, and sequence diversity. Remarkably, more lambda variable genes (IGLV) were used during fetal life than later stages and I...
Bigi D, Perrotta G, Zambonelli P.To understand the origin and genetic diversity of Italian horses, mitochondrial DNA D-loop sequences were generated for 163 horses from seven breeds. Sequence analysis of a 480-bp segment revealed a total of 84 haplotypes with 57 polymorphic sites, indicating multiple maternal origins and high genetic diversity. Comparison of the haplotypes with the equine mtDNA haplotype/haplogroup nomenclature showed a haplogroup distribution in the Italian breeds more similar to that found in the Middle East breeds than in the European breeds, probably due to the economic and cultural relationship with the ...
Boyko AR, Brooks SA, Behan-Braman A, Castelhano M, Corey E, Oliveira KC, Swinburne JE, Todhunter RJ, Zhang Z, Ainsworth DM, Robinson NE.Equine recurrent laryngeal neuropathy (RLN) is a bilateral mononeuropathy with an unknown pathogenesis that significantly affects performance in Thoroughbreds. A genetic contribution to the pathogenesis of RLN is suggested by the higher prevalence of the condition in offspring of RLN-affected than unaffected stallions. To better understand RLN pathogenesis and its genetic basis, we performed a genome-wide association (GWAS) of 282 RLN-affected and 268 control Thoroughbreds. Results: We found a significant association of RLN with the LCORL/NCAPG locus on ECA3 previously shown to affect body siz...
Kim MC, Lee SW, Ryu DY, Cui FJ, Bhak J, Kim Y.The role of microRNAs (miRNAs) as a post-transcriptional gene regulator has been elucidated in a broad range of organisms including domestic animals. Characterization of miRNAs in normal tissues is an important step to investigate the functions of miRNAs in various physiological and pathological conditions. Using Illumina Next Generation Sequencing (NGS) technology, we identified a total of 292 known and 329 novel miRNAs in normal horse tissues including skeletal muscle, colon and liver. Distinct sets of miRNAs were differentially expressed in a tissue-specific manner. The miRNA genes were dis...
Song SD, Barker SC, Shao R.The genus Haematopinus contains 21 species of blood-sucking lice, parasitizing both even-toed ungulates (pigs, cattle, buffalo, antelopes, camels and deer) and odd-toed ungulates (horses, donkeys and zebras). The mitochondrial genomes of the domestic pig louse, Haematopinus suis, and the wild pig louse, Haematopinus apri, have been sequenced recently; both lice have fragmented mitochondrial genomes with 37 genes on nine minichromosomes. To understand whether the composition of mitochondrial minichromosomes and the gene content and gene arrangement of each minichromosome are stable within the g...
Sharma R, Livesey MR, Wyllie DJ, Proudfoot C, Whitelaw CB, Hay DC, Donadeu FX.Pluripotent stem cells (PSCs) offer unprecedented biomedical potential not only in relation to humans but also companion animals, particularly the horse. Despite this, attempts to generate bona fide equine embryonic stem cells have been unsuccessful. A very limited number of induced PSC lines have so far been generated from equine fibroblasts but their potential for directed differentiation into clinically relevant tissues has not been explored. In this study, we used retroviral vectors to generate induced pluripotent stem cells (iPSCs) with comparatively high efficiency from equine keratinocy...
Giacomoni EH, Fernández-Stolz GP, Freitas TR.The genetic variability for a sample of 227 animals from three populations of Pantaneiro horses was estimated using data from 10 microsatellite loci. The number of alleles and the proportion of heterozygosity indicated high variability. A total of 91 alleles were found, with a significantly high mean number of alleles. The mean polymorphic information content was 0.7 and the paternity exclusion probability was 99.3%. The inbreeding coefficient (F(IS)) was low for the three populations: Ipiranga (F(IS) = 0.147), Nova Esperança (F(IS) = 0.094) and Promissão (F(IS) = 0.108). Genetic differentia...
Cothran EG, Canelon JL, Luis C, Conant E, Juras R.Various horse populations in the Americas have an origin in Spain; they are remnants of the first livestock introduced to the continent early in the colonial period (16th and 17th centuries). We evaluated genetic variability within the Venezuelan Criollo horse and its relationship with other horse breeds. We observed high levels of genetic diversity within the Criollo breed. Significant population differentiation was observed between all South American breeds. The Venezuelan Criollo horse showed high levels of genetic diversity, and from a conservation standpoint, there is no immediate danger ...
Matéos A, Girardet JM, Mollé D, Corbier C, Gaillard JL, Miclo L.Equine beta-casein is phosphorylated at variable degrees and isoforms carrying 3 to 7 phosphate groups (3P-7P) have been found in milk, but the phosphorylated amino acid residues of each isoform are not yet identified. In the present work, the different phosphorylation variants were first isolated by ion-exchange chromatography and then hydrolysed by trypsin to generate caseinophosphopeptides (CPPs), each containing all the potential phosphorylation sites. The equine CPPs were prepared by metal oxide affinity chromatography, a method based on the affinity of phosphate groups towards titanium d...
Yousefi-Mashouf N, Mehrabani-Yeganeh H, Nejati-Javaremi A, Bailey E, Petersen JL.The present research aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred horses were genotyped across 670,796 markers. After quality control and pruning to eliminate linkage disequilibrium between loci which resulted in 13,554 SNPs in 52 Kurdish, 24 Persian Arabian and 58 Thoroughbred horses, the Kurdish horses were generally distinguished from the Persian Arabian samples by Principal Component Analyses, cluster analyses and calcul...
Nolte W, Alkhoder H, Wobbe M, Stock KF, Kalm E, Vosgerau S, Krattenmacher N, Thaller G, Tetens J, Kühn C.In horses, parentage control is currently performed based on an internationally standardized panel of 17 microsatellite (MS) markers comprising 12 mandatory and five optional markers. Unlike MS, single nucleotide polymorphism (SNP) profiles support a wider portfolio of genomic applications, including parentage control. A transition to SNP-based parentage control is favorable, but requires additional efforts for ensuring generation-overlapping availability of marker genotypes of the same type. To avoid double genotyping of either parents or offspring for changing to SNP technology and enable ef...
Wittwer C, Löhring K, Drögemüller C, Hamann H, Rosenberger E, Distl O.The aim of this study was to identify quantitative trait loci (QTL) for osteochondrosis (OC) and palmar/plantar osseous fragments (POF) in fetlock joints in a whole-genome scan of 219 South German Coldblood horses. Symptoms of OC and POF were checked by radiography in 117 South German Coldblood horses at a mean age of 17 months. The radiographic examination comprised the fetlock and hock joints of all limbs. The genome scan included 157 polymorphic microsatellite markers. All microsatellite markers were equally spaced over the 31 autosomes and the X chromosome, with an average distance of 17.7...
Wijesundera WS, Chandrasekharan NV, Karunanayake EH.A sensitive PCR assay for the detection of Setaria digitata has been developed. Two oligonucleotide primers (17 nt) were designed from a previously cloned and characterized tandemly arranged repetitive sequence of Setaria digitata. Using these primers, it was possible to amplify small quantities (100 fg) of S. digitata genomic DNA. A simple procedure, using proteinase K and non-ionic detergent NP 40, was followed to process the host blood samples and mosquitoes harbouring L3 larvae. The sensitivity of the polymerase chain reaction based assay surpasses the microscopic detection and the previou...
Campana MG, Whitten CM, Edwards CJ, Stock F, Murphy AM, Binns MM, Barker GW, Bower MA.Historic DNA data have the potential to identify phenotypic information otherwise invisible in the historical, archaeological and palaeontological record. In order to determine whether a single nucleotide polymorphism typing protocol based on single based extension (SNaPshot™) could produce reliable phenotypic data from historic samples, we genotyped three coat colour markers for a sample of historic Thoroughbred horses for which both phenotypic and correct genotypic information were known from pedigree information in the General Stud Book. Experimental results were consistent with the pedig...
Macieira S, Lussier J, Bédard C.Glanzmann thrombasthenia (GT) is characterized by a defect of platelet aggregation. This autosomal recessive genetic disorder is caused by an abnormality of the platelet glycoprotein receptors alpha IIb or beta III. Recently, we identified a horse with clinical and pathological features of GT. The aim of this study was to describe this case of GT at the molecular level. A point mutation from G to C in exon 2 of ITGA2B causing a substitution of the expected amino acid arginine 72 (Arg(72)) by a proline (Pro(72)) was encountered. This amino acid change may result in abnormal structural conformat...
Herszberg B, Mata X, Giulotto E, Decaunes P, Piras FM, Chowdhary BP, Chaffaux S, Guérin G.Glycogen debranching enzyme (AGL) is a multifunctional enzyme acting in the glycogen degradation pathway. In humans, the AGL activity deficiency causes a type III glycogen storage disease (Cori-Forbes disease). One particularity of AGL gene expression lies in the multiple alternative splicing in its 5' region. The AGL gene was localized on ECA5q14-q15. The sequence of the equine cDNA was determined to be 7.5 kb in length with an open reading frame of 4602 bp. The gene is 69 kb long and contains 35 exons. The equine AGL gene has an ubiquitous expression and presents five tissue-dependent cDNA v...
Pepin K, Momose F, Ishida N, Nagata K.Heat shock protein 90 (Hsp90), a molecular chaperone, is ubiquitous and involved in numerous cellular processes. To contribute to the relatively small collection of vertebrate Hsp90 sequences in the gene data bank, we cloned and sequenced horse (Equus caballus) Hsp90 alpha and beta cDNAs. This enabled identification of horse-specific primers for development of a convenient PCR-based method that could monitor horse stress tolerance. We analyzed the sequence data comparatively and phylogenetically with other Hsp90 cDNA sequences, and identified vertebrate-specific and isoform-specific conserved ...
Mariat D, Oustry-Vaiman A, Cribiu EP, Raudsepp T, Chowdhary BP, Guérin G.In order to increase the number of markers on the horse cytogenetic map and expand the integration with the linkage map, an equine BAC library was screened for genes and for microsatellites. Eighty-nine intra-exon primers were designed from consensus gene sequences in documented species. After PCR screening, 38 clones containing identified genes were isolated and FISH mapped. These data allowed us to refine the available Zoo-FISH results, to define ten new conserved cytogenetic segments and expand two others, thus leading to the identification of a total of 26 conserved segments between horse ...
Kleiboeker SB, Turnquist SE, Johnson PJ, Kreeger JM.In previous studies, novel putative viral pathogens designated that asinine herpesvirus 4 (AsHV4) and asinine herpesvirus 5 (AsHV5) were associated with fatal interstitial pneumonia in donkeys (Equus asinus). Nucleotide sequence analysis of a portion of the DNA polymerase gene identified these putative pathogens as herpesviruses and possibly as members of the Gammaherpesvirinae subfamily. Although similar to equine herpesvirus 2 (EHV2) and equine herpesvirus 5 (EHV5), sequence diversity was observed among the detected viruses. In this study, novel sequence is reported for a DNA-packaging prote...
Winton CL, McMahon R, Hegarty MJ, McEwan NR, Davies-Morel MCG, Morgan C, Nash DM.The UK and Ireland have many native pony breeds with historical and cultural importance as well as being a source of uncharacterized genetic diversity. However, there is a lack of comprehensive research investigating their genetic diversity and phylogenetic interrelationships. Many studies contain a limited number of pony breeds or small sample sizes for these breeds. This may result in erroneous grouping of pony breeds that otherwise have intricate interrelationships with each other and are not evaluated correctly when placed as a token subset of a larger dataset. This is the first study that...
White RT, Jelocnik M, Klukowski N, Haque MH, Sarker S.Chlamydia psittaci is a zoonotic pathogen that infects birds, humans, and other mammals. Notably, recent studies suggested the human-to-human transmission of C. psittaci, and this pathogen also causes equine reproductive loss in Australia. Molecular studies in Australia to date have focused on and described clonal sequence type (ST)24 strains infecting horses, wild psittacine, and humans. In contrast, the genetic identity of C. psittaci strains from captive psittacine hosts is scarce. In 2022, C. psittaci was detected in the faeces of a healthy captive blue-fronted parrot (Amazona aestiva). Ge...
Wu L, Ou J, Cai S, Ji J, Ren Z, Shao R, Li S.Equine Hepacivirus (EqHV) is a newly discovered equine virus that is classified under the Hepacivirus genus of the Flaviviridae family. There are three sub-types of EqHV worldwide namely; sub-types 1-3. The majority of EqHV sub-type 1 strains were found in China. While different sub-types have been found in Japan and USA, therefore, to investigate whether the other sub-types of EqHV strains were present in China, a total of 60 horse serum samples were collected and screened for EqHV RNA through RT-PCR. The results revealed that 19 serum samples were RNA-positive (19/60) and the EqHV detection ...
Horecky C, Horecka E, Futas J, Janova E, Horin P, Knoll A.Genotyping microsatellite markers represents a standard, relatively easy, and inexpensive method of assessing genetic diversity of complex genomic regions in various animal species, such as the major histocompatibility complex (MHC) and/or natural killer cell receptor (NKR) genes. MHC-linked microsatellite markers have been identified and some of them were used for characterizing MHC polymorphism in various species, including horses. However, most of those were MHC class II markers, while MHC class I and III sub-regions were less well covered. No tools for studying genetic diversity of NKR com...
Zhang B, Huang H, Wang H, Zhang D, Chu H, Ma X, Ge Y, Ente M, Li K.Gasterophilus species are widely distributed around the world. The larvae of these flies parasitize the digestive tract of equids and cause damage, hindering horse breeding and protection of endangered species. However, study of the genetic structure of geographically distinct Gasterophilus populations is lacking. Here, we analyzed the genetic diversity of Gasterophilus pecorum, G. intestinalis, G. nasalis and G. nigricornis from three typical grasslands (meadow, desert and alpine steppes) in China as compared to published sequences from Italy, Poland and China (Daqing and Yili), based on the ...
Rahimi-Mianji G, Nejati-Javaremi A, Farhadi A.The present study was undertaken to genetically evaluate Turkmen horses for genetic diversity and to evaluate whether they have experienced any recent genetic bottlenecks. A total of 565 individuals from Turkmen horses were characterized for within breed diversity using 12 microsatellite markers. The estimated mean allelic diversity was (9.42 ± 1.78) per locus, with a total of 131 alleles in genotyped samples. A high level of genetic variability within this breed was observed in terms of high values of effective number of alleles (4.70 ± 1.36), observed heterozygosity (0.757 ± 0.19), expect...
Peng Z, Shen D, Zhang D, Li X, Wang L, Zhai Q, Hou Z, Li H.The equine Parascaris spp. is large, parasitic nematodes, and predominantly focuses on the intestine of foals and young weanlings. There are two roundworms, Parascaris equorum and Parascaris univalens, recognized among equine hosts. In this study, all fifty-nine Parascaris worms were harvested from three different equine hosts (twenty specimens from Equus zebra, twenty specimens from E. caballus, and nineteen specimens from E. asinus). The ribosomal gene (ITS) and mitochondrial genes (cox1 and nadh1) were amplified to identify and genetically characterize these worms. Analysis of ITS sequences...
Yun J, Oyungerel B, Kong HS.This study aimed to identify the genetic diversity and population structure of Mongolian horse populations according to the province of residence (Khentii, KTP; Uvs, USP; Omnogovi and Dundgovi, GOP; Khovsgol, KGP) using 14 microsatellite (MS) markers. Methods: A total of 269 whole blood samples were obtained from the four populations (KTP, USP, GOP, KGP) geographically distinct provinces. Multiplex polymerase chain reaction (PCR) was conducted using 14 MS markers (AHT4, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, and VHL20), as recommended by the International So...
Głażewska I, Gralak B, Naczk AM, Prusak B.Polish Arabian horses are one of the most important populations of this breed in the world. Their post-war history can be divided into two periods, with the dominant role of state studs until 1989, and the increasing significance of private breeding in the next years. The goal of the study was to evaluate genetic diversity and structure of the population under a new breeding policy. The analyses of breeding and microsatellite data from 1996 to 2012 provide a coherent picture of the population with constant flow of horses only in one direction from state to private studs. An increase in the num...
Swinburne JE, Hopkins A, Binns MM.The dominant grey coat colour gene of horses has been mapped using a whole genome scanning approach. Samples from a large half-sibling pedigree of Thoroughbred horses were utilized in order to map the grey coat colour locus, G. Multiplex groups of microsatellite markers were developed and used to efficiently screen the horse genome at a resolution of approximately 22 cM, based on an estimated map length for the horse genome of 2720 cM. The grey gene was assigned to chromosome 25 (ECA25), one of the smaller acrocentric horse chromosomes. Based on the current state of knowledge of conserved synt...
Podico G, Gray SM, Wang L, Canisso IF.An 8-y-old jenny was presented because of anorexia and mild depression. The jenny had weaned her colt 10 d before the admission. Upon arrival at the University of Illinois Veterinary Teaching Hospital, the heart rate was elevated, and the right udder was painful and swollen on palpation. Milk stripping of the affected side revealed purulent content; the contralateral udder had normal-appearing milk. Cytology of mammary gland secretions from the affected side revealed a large number of hypersegmented reactive neutrophils with phagocytized bacteria. Complete blood count, serum chemistry, and f...
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...
Loux SC, Conley AJ, Scoggin KE, El-Sheikh Ali H, Dini P, Ball BA.Steroid production varies widely among species, with these differences becoming more pronounced during pregnancy. As a result, each species has its own distinct pattern of steroids, steroidogenic enzymes, receptors, and transporters to support its individual physiological requirements. Although the circulating steroid profile is well characterized during equine pregnancy, there is much yet to be explored regarding the factors that support steroidogenesis and steroid signaling. To obtain a holistic view of steroid-related transcripts, we sequenced chorioallantois (45 days, 4 months, 6 months, 1...
Klumplerova M, Splichalova P, Oppelt J, Futas J, Kohutova A, Musilova P, Kubickova S, Vodicka R, Orlando L, Horin P.The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family E...
Polani S, Dean M, Lichter-Peled A, Hendrickson S, Tsang S, Fang X, Feng Y, Qiao W, Avni G, Kahila Bar-Gal G.Juvenile idiopathic epilepsy (JIE) is a self-limiting neurological disorder with a suspected genetic predisposition affecting young Arabian foals of the Egyptian lineage. The condition is characterized by tonic-clonic seizures with intermittent post-ictal blindness, in which most incidents are sporadic and unrecognized. This study aimed to identify genetic components shared across a local cohort of Arabian foals diagnosed with JIE via a combined whole genome and targeted resequencing approach: Initial whole genome comparisons between a small cohort of nine diagnosed foals (cases) and 27 contro...
Dunuwille WMB, YousefiMashouf N, Balasuriya UBR, Pusterla N, Bailey E.Equid herpesvirus (EHV-1) infections in horses can lead to equine herpesvirus myeloencephalopathy (EHM), characterised by neurological clinical signs. The sporadic occurrence of the disease in horse herds suggests a host genetic component. A recent study reported an association between the occurrence of EHM and genetic markers on horse chromosome 6 (ECA6). Objective: To investigate the association of EHM with genetic host factors, especially with reference to the association reported for ECA6. Methods: Genome-wide association study (GWAS) was conducted based on 94 horses that had EHV-1 infecti...
Lee E, Kim EJ, Shin YK, Song JY.The avian influenza A virus causes respiratory infections in animal species. It can undergo genomic recombination with newly obtained genetic material through an interspecies transmission. However, the process is an unpredictable event, making it difficult to predict the emergence of a new pandemic virus and distinguish its origin, especially when the virus is the result of multiple infections. Therefore, identifying a novel influenza is entirely dependent on sequencing its whole genome. Occasionally, however, it can be time-consuming, costly, and labor-intensive when sequencing many influenza...
