DNA in horses refers to the genetic material that carries the hereditary information necessary for the growth, development, functioning, and reproduction of equine species. It consists of sequences of nucleotides that encode the genetic instructions used in the development and functioning of horses. DNA analysis in horses can provide insights into genetic diversity, lineage, and breed characteristics. It is also utilized in identifying genetic disorders, understanding hereditary traits, and assisting in selective breeding programs. This page compiles peer-reviewed research studies and scholarly articles that explore the structure, function, and applications of DNA analysis in equine genetics and breeding.
Steensma MJ, Doekes HP, Derks MFL, Ducro BJ.In Friesian horses, withers height is an important trait as a minimum has been set to be eligible to the studbook. Several loci for withers height have been identified in horses. However, withers height has not been studied in the Friesian horse. Therefore, our aim was to identify loci associated with withers height in the Friesian horse population. We performed a genome-wide association study using 70 K SNP data of 2192 Friesian horses. We found ECA1 and ECA9 to be significantly associated with withers height, explaining 19.6% and 3.5% of the phenotypic variance, respectively. In other hors...
Kingsley NB, Sandmeyer L, Dwyer A, Langefeld CD, McMullen RJ, McCue M, Lassaline M, Bellone RR.Equine recurrent uveitis (ERU), an inflammatory eye disease, is the leading cause of blindness among horses. Insidious uveitis, a form of ERU, is especially pervasive within the Appaloosa breed and is highly heritable (h = 0.68-1.0). To date only one risk locus, leopard complex (LP), has been identified, and it explained 0.16-0.33 of the heritability estimate, suggesting that insidious uveitis is a complex genetic disease within the Appaloosa horse breed with multiple unknown predisposing loci. Results: A genome-wide association study (GWAS) using relatedness, LP genotype, sex, and age as ...
Klass LG, Diekmann I, Andreotti S, Mbedi S, Sparmann S, Schenk T, Anderson HP, Bellaw J, Nielsen MK, Krücken J, von Samson-Himmelstjerna G.Strongyles, especially non-migratory Strongylidae, are the most common equine gut parasites, and typically occur in mixed infections with 10 - 20 species per host. Current knowledge on strongyle species prevalence and within-host tropism is sparse. Herein species composition of mixed strongyle infections of 12 naturally infected untreated young horses, based on strongyle eggs extracted from faeces, cultured third stage larva and luminal worms collected from ventral and dorsal colon was examined. Species were identified using a cytochrome c oxidase I (COI) metabarcoding approach allowing differ...
Huang Q, Ren W, Shan D, Su Y, Li Z, Li L, Wang R, Ma S, Wang J.This study aimed to compare blood samples from Yili horses with outstanding and average performance in 5000 m races through transcriptome sequencing, identify key differentially expressed genes, lncRNAs, and circRNAs, as well as related enriched pathways, and elucidate their regulatory networks. This study used six healthy four-year-old Yili stallions as subjects, divided into an excellent group (E group, = 3) and an ordinary group (O group, = 3) based on their 5000-m race performance. Blood RNA-Seq technology was used to analyze differentially expressed mRNAs, lncRNAs, and circRNAs. A total...
Krücken J, Diekmann I, Andreotti S, Bredtmann CM, Mbedi S, Sparmann S, Schmidt JS, de Almeida Borges F, de Freitas MG, Sallé G, Hofer H....Equines are parasitized by complex communities of Strongylidae (Nematoda) comprising multi-species infections. Currently, Cyathostominae are most prevalent, while Strongylus species are only rarely detected. Since eggs and, in most cases, infective larvae cannot be differentiated to species level, except for Strongylus spp., species-specific knowledge of the pathology, epidemiology and ecology of these parasitic nematodes is limited. Reference sequence data for several cyathostomin species are limited or missing. Deep amplicon sequencing of internal transcribed spacer 2 (ITS-2) regions of nema...
Lewczuk D, Wypchło M, Hecold M, Buczkowska R, Korwin-Kossakowska A.Finding the causative mutations for musculoskeletal system development and health status is of a higher priority for all sport horse breeders' associations. Of the regulating proteins involved in animal ossification, 15 gene polymorphisms were chosen to be identified as connected with the nine fetlock and 14 hock bone structures measurements of 198 horses. All measurements were taken using X-rays of the limbs, which were available at the beginning and end of the horse training. The analysis of variance (GLM, SAS program) was performed taking into account identified training and horse-connected...
Weingarten A, Häusler M, Serangeli J, Verheijen I, Reiter E, Radzevičiūtė R, Stoessel A, Krause J, Spyrou MA, Conard NJ, Nieselt K, Posth C.Deep-time palaeogenomics offers rare insights into macroevolutionary events for both extant and extinct species. Aside from a Middle Pleistocene genome from North American permafrost (780-560 ka) and a number of Late Pleistocene specimens, most ancient horse DNA studies have focused on tracing the origins of domestication and subsequent periods. Here we present mitochondrial genomes from two Equus mosbachensis specimens from Schöningen, Germany, a Middle Pleistocene archaeological site complex with direct and repeated evidence of hominin-horse interactions on the shore of a palaeolake. Usin...
Vasconcelos AB, França DA, Prado ACD, Yamauchi DH, Silva ACAD, Barros IO, Valença SRFA, Lucheis SB, Bosco SMG.Pythiosis is an underestimated and neglected disease in Brazil, both in horse breeders and in horses. The molecular detection of in horses in the Brazilian Northeast represents a milestone in the epidemiology of equine pythiosis in the country. This study reports novel cases of equine pythiosis, diagnosed by molecular methods, in five states of Northeastern Brazil. Clinical samples were submitted to microbiological culture, DNA extraction, and nested-PCR for molecular detection of . The nested-PCR successfully detected in four out of five equine lesion samples, demonstrating higher sensitivi...
Brito LFC, Linardi RL, Rosales LAS, Balamurugan NS, Hernández-Avilés C, Ramírez-Agámez L.Efficient use of stallion semen in liquid state is limited by its relatively short shelf-life. A chemically defined extender (Beyond) is now available for long-term liquid semen preservation. The objectives of the present study were to compare Beyond with milk extenders for the preservation of semen at two temperatures, and to evaluate fertility of semen cooled for 4-8 days before artificial insemination. Semen was processed using different extenders: milk, cholesterol (BotuSemen Special); milk-based (INRA 96); and Beyond. Sperm motility, membrane and acrosome integrity, and chromatin struct...
Motta D, Pedrosa J, Lilenbaum W.Leptospirosis is a zoonotic disease caused by pathogenic bacteria of the genus Leptospira. A lesser-known form, equine genital leptospirosis (EGL), has been identified as a chronic and often silent infection involving the colonisation of the mare's genital tract. Despite its potential impact, EGL remains underdiagnosed and poorly understood, particularly in its association with reproductive inefficiency. This study showed the presence of Leptospira spp. DNA by lipL32-PCR in the genital tract of mares with a history of reproductive disturbances. Cervicovaginal mucus samples were collected from ...
Zhou Y, Yao X, Meng J, Wang J, Zeng Y, Li L, Ren W.The Kazakh horse is a highly valuable indigenous Chinese breed known for its use in both milk and meat production. However, the mechanisms underlying color variation in the abdominal adipose tissue of this breed remain poorly understood. In this study, the sequencing of non-coding RNAs (ncRNAs) was conducted on abdominal adipose tissue of different colors from Kazakh horses, with the aim of investigating the molecular mechanisms responsible for this variation. A total of 205 differentially expressed long non-coding RNAs (DELncRNAs) including , , and ; 52 differentially expressed microRNAs (DEm...
Hou L, Sulayman A, Zeng Y, Zhou L, Aimaier A, Kader A, Shi L.The study of horse genetic diversity is imperative for informing conservation strategies, safeguarding ancestral lineages, and enhancing breed adaptability to environmental and disease pressures. This study employed 13 microsatellite markers with fluorescent-labeled capillary electrophoresis to analyze the genetic diversity of the Kyrgyz horse ( = 30) and Barkol horse ( = 30) for the first time, comparing them with three other indigenous horse breeds ( = 30 per breed) from Xinjiang, China. A total of 208 alleles were detected. The Polymorphic Information Content (PIC) results from GenAlEx 6.51...
Kassymbekova SN, Bimenova ZZ, Iskhan KZ, Sobiech P, Jastrzebski JP, Brym P, Babis W, Kalykova AS, Otebayev ZM, Kabylbekova DI, Baneh H, Romanov MN.Mugalzhar horses are a relatively young native breed of Kazakhstan, prized for meat and milk production and adaptation. This study was conducted to investigate genetic diversity and pinpoint genomic regions associated with selection signatures in this breed using whole-genome sequence data. Variant calling yielded a total of 21,722,393 high-quality variants, including 19,495,163 SNPs and 2,227,230 indels. Most variants were located in introns and intergenic regions, while only 1.94% were exonic. Estimates of genetic diversity were moderate, with expected and observed heterozygosity and nucleot...
Duderstadt S, Distl O.Dülmen wild horses are kept in a fenced wooden and marsh area around Dülmen in Westphalia, Germany, since 1856. Previous analyses supported early genetic divergence from other domesticated horse populations and the Przewalski horse. Therefore, the objective of this study was to evaluate genetic diversity using high-density genomic data. Methods: We collected 337 one-year-old male Dülmen wild horses, captured at 12 annual auctions, for genotyping on the Illumina GGP Equine Plus Beadchip. All analyses were performed for 63,123 autosomal SNPs. Results: On average, each horse had 27.96 ROH with...
Mughal MAS, Khan MK, Lan H, Abbas RZ, Imran M, Abbas Z, Mehmood MS, Ali S.Parasitic diseases caused by Leishmania spp. create considerable health concerns in animals, resulting in a considerable financial impact. They causes a complex infection in equines, affecting weight gain, skin, liver, and spleen. To date, there is a lack of reports on the occurrence of Leishmania in equines in Southern Punjab, Pakistan, highlighting the need for molecular epidemiological surveillance. The current study focused on determining the prevalence of Leishmania in the equine population from District Rahim Yar Khan, Southern Punjab, Pakistan, through amplification of mitochondrial (Cy...
Steensma MJ, Ducro BJ, Dibbits B, Doekes HP, van Schipstal JGC, Kalblfleisch T, Groenen MAM, Derks MFL.In horses, genetic diversity is predominantly observed between breeds, with little variation within breeds. The studbooks of the two largest horse populations in the Netherlands, the Dutch Warmblood horse and Friesian horse population, have ongoing conservation projects including collecting large-scale genotype and sequence data. The current reference genome, derived from a Thoroughbred horse can lead to bias in genetic analyses of other horse breeds. Therefore, the aim of this study was to create high-quality breed-specific reference genomes of Dutch Warmblood and Friesian horses. We performe...
Furukawa R, Tozaki T, Mizukami K, Iwasaki Y, Kawate K, Kikuchi M, Ishige T, Momozawa Y, Fukui E, Kakoi H.Thoroughbreds have been maintained as a closed breed for over 300 years since the crossbreeding between Arabian stallions and English mares. Despite interest in germline de novo mutations across species, their frequency in horses, particularly in Thoroughbreds, remains largely unexplored. Objective: This study aimed to identify de novo mutations in Thoroughbreds and estimate their frequency within a genetically closed population. Methods: We performed deep whole-genome sequencing (≥230× depth, 150 bp paired-end reads) and Sanger validation in a Thoroughbred trio (sire, dam, and foal). Reads...
Dos Santos Gomes V, Dos Santos Marques JV, da Silva GN, Marmett B, Dallegrave E.The inhalation of pollutants from fossil fuel combustion increases oxidative stress and may cause genotoxic damage, a risk heightened during physical exercise due to increased respiratory rates. This concern extends to equines engaged in intense activities like show jumping. Antioxidant supplementation with vitamin E and selenium may mitigate oxidative stress induced by exercise in polluted environments. This study evaluated the effects of oral supplementation on show jumping horses subjected to physical exertion in urban (n = 10) and peri-urban (n = 10) areas with varying pollution le...
Toda J, Miyasaka J, Osako H, Murata K, Yunus M, Amalia R, Soe BK, Sato H.Food poisoning caused by consuming raw horsemeat contaminated with Sarcocystis is a significant public health concern. Two morphotypes of sarcocysts in horsemeat, characterized by upright and folded villar protrusions, are typically identified as Sarcocystis fayeri and S. bertrami, respectively. However, recent molecular studies focusing on the ribosomal RNA gene (rDNA) and mitochondrial cytochrome c oxidase subunit I gene (cox1) have indicated a conspecific relationship between these two morphotypes using a limited number of specimens. To explore further genetic diversity in equid sarcocysts,...
Van Buren SL, Petersen JL, Brown CT, Finno CJ.With advancing genomic technologies, single-nucleotide polymorphism (SNP) arrays and whole genome sequencing (WGS) have become essential tools in equine genetic research. In this study, we assessed the concordance in SNP calls and trait-mapping efficacy by comparing data of 21 horses both genotyped on the Equine 670 K SNP array and sequenced at either ~12× or ~30× depth. Our analysis revealed that higher sequencing depths were significantly associated with fewer discordant calls between platforms. Additionally, we investigated the most frequent no-call and discordant positions and identifi...
Aboelmaaty AM, El-Seadawy IE, Kotp MS, Mohamed AA, El-Debaky HA, El-Badry DA, Anwer AM, Tsvetkov T, Daneva T, Elgabry MA.Alpha-tocopherol is one of the non-enzymatic lipophilic antioxidants. Butylated hydroxytoluene (BHT) is a synthetic analog with similar modes of action in protecting the cryopreserved sperms. Objective: This study hypothesized that a certain concentration of any antioxidant is suitable for improving the post-thaw semen quality of stallions. Methods: To determine the optimum BHT concentration, a synthetic antioxidant similar to vitamin E in potency and scavenging oxidative stress power in concentrations of 0.0, 0.25, 0.50, 1.0, 2.0, and 4.0 mM/ml were added to semen extender. The post-thaw sper...
Everts RE, Caron R, Foster G, McLoone K, Simiele L, Martin K, Brooks SA, Lafayette C.Roan coat color is described as the dispersion of white hairs within an otherwise solid background-color coat. This phenotype is primarily expressed on the body of the horse, with the head and legs exhibiting few or no white hairs. Previous studies mapped the locus for roan to the region and observed linked variants in a small number of breeds. Recently, we reported evidence for two independent haplotypes, and , in the region, which account for approximately 38% and 36% of roan horses, respectively. In the current report, using whole genome sequencing for unknown roan samples. We present a ...
Sharif MB, Mohaseb AF, Orlando L, Saliari K, Kunst GK, Czeika S, Mashkour M, Cucchi T, Peters J, Trixl S, Mohandesan E.The Roman conquest of the northern Alpine foreland in 15 BCE introduced larger-sized horses and hybrid mules to the region. To investigate their genetic profiles and influence on local breeding, we analyzed our previously generated shallow shotgun DNA data from 402 Late Iron Age and Roman equids, supplemented with mitochondrial and nuclear capture data from 40 to 31 equids from the same regions and periods. Late Iron Age and Roman horses exhibit high matrilineal diversity, with unique haplogroups in the latter indicating exogenous animals. The preferred use of male mounts in army service menti...
Cutarelli A, Buonavoglia A, Fusco G, Pellicanò R, Napoletano M, Brandt S, Roperto S.Sarcoids are benign and locally aggressive skin lesions that commonly affect horses and other equid species. Sarcoids are generally considered to be caused by bovine delta-papillomaviruses (δPVs) types 1 and 2 (BPV1 and BPV2, respectively). Moreover, while bovine δPV types 13 and 14 (BPV13 and BPV14, respectively) are also suspected to induce sarcoids, information regarding this possibility and the occurrence of multiple bovine δPV infections in sarcoids is scarce. This study aimed, for the first time, to assess BPV1, BPV2, BPV13, and BPV14 infections and co-infections in equine sarcoid sam...
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D.Speed is not only the primary objective of racehorse breeding but also a crucial indicator for evaluating racehorse performance. This study investigates a newly developed racehorse breed in China. Through whole-genome resequencing, we selected 60 offspring obtained from the crossbreeding of Thoroughbred horses and Xilingol horses for this study. This breed is tentatively named "Grassland-Thoroughbred", and the samples were divided into two groups based on racing ability: 30 racehorses and 30 non-racehorses. Based on whole-genome sequencing data, the study achieved an average sequencing depth o...
Ramírez-Agámez L, Hernández-Avilés C, Samper JC, Love CC.Intracytoplasmic sperm injection (ICSI) using frozen/thawed (F/T) stallion sperm is a common procedure in the equine breeding industry. Historically, sex-sorted (SS) F/T stallion sperm has yielded lower cleavage (<30 %) and blastocyst rates (<5 %) after ICSI when compared to non-sorted (NS) F/T sperm. Recently, a new technology for sperm sex-sorting (Genesis III) has been validated by a commercial company. In Experiment 1, the post-thaw quality between NS-F/T and SS-F/T stallion sperm produced with this technology was compared. The post-thaw sperm motility was higher in NS-F/T (41 %) than i...
Horses have inhabited Iberia (present-day Spain and Portugal) since the Middle Pleistocene, shaping a complex history in the region. Iberia has been proposed as a potential domestication centre and is renowned for producing world-class bloodlines. Here, we generate genome-wide sequence data from 87 ancient horse specimens (median coverage = 0.97X) from Iberia and the broader Mediterranean to reconstruct their genetic history over the last ~26,000 years. Here, we report that wild horses of the divergent IBE lineage inhabited Iberia from the Late Pleistocene, while domesticated DOM2 horses, nati...
Xu X, Arnason U.The sequence of the mitochondrial (mt) DNA of the horse (Equus caballus) was determined. The length of the sequence presented is 16,660 bp. This figure, however, is not absolute due to pronounced heteroplasmy caused by variable numbers of the motif GTGCACCT in the control region of different molecules. Boundaries of the 13 peptide-coding genes were determined by the presence of start and stop codons, and by analogy with other eutherian mtDNAs. Three genes (COIII, NADH3 and NADH4) were not terminated by a stop codon. Comparison among the peptide-coding genes of the horse and eight other mammals...
Schmiedel J, Falgenhauer L, Domann E, Bauerfeind R, Prenger-Berninghoff E, Imirzalioglu C, Chakraborty T.Multiresistant Gram-negative bacteria producing extended-spectrum β-lactamases (ESBLs) are an emerging problem in human and veterinary medicine. This study focused on comparative molecular characterization of β-lactamase and ESBL-producing Enterobacteriaceae isolates from central Hesse in Germany. Isolates originated from humans, companion animals (dogs and cats) and horses. Results: In this study 153 (83.6%) of the human isolates (n = 183) and 163 (91.6%) of the animal isolates (n = 178) were confirmed as ESBL producers by PCR and subsequent sequencing of the PCR amplicons. Predomin...
Shepherd ML, Swecker WS, Jensen RV, Ponder MA.The diversity of the equine fecal bacterial community was evaluated using pyrosequencing of 16S rRNA gene amplicons. Fecal samples were obtained from horses fed cool-season grass hay. Fecal bacteria were characterized by amplifying the V4 region of bacterial 16S rRNA gene. Of 5898 mean unique sequences, a mean of 1510 operational taxonomic units were identified in the four fecal samples. Equine fecal bacterial richness was higher than that reported in humans, but lower than that reported in either cattle feces or soil. Bacterial classified sequences were assigned to 16 phyla, of which 10 were ...
Worster AA, Brower-Toland BD, Fortier LA, Bent SJ, Williams J, Nixon AJ.This study evaluated chondrogenesis of mesenchymal progenitor stem cells (MSCs) cultured initially under pre-confluent monolayer conditions exposed to transforming growth factor-beta1 (TGF-beta1), and subsequently in three-dimensional cultures containing insulin-like growth factor I (IGF-I). Bone marrow aspirates and chondrocytes were obtained from horses and cultured in monolayer with 0 or 5 ng of TGF-beta 1 per ml of medium for 6 days. TGF-beta 1 treated and untreated cultures were distributed to three-dimensional fibrin disks containing 0 or 100 ng of IGF-I per ml of medium to establish fou...
Dougal K, de la Fuente G, Harris PA, Girdwood SE, Pinloche E, Geor RJ, Nielsen BD, Schott HC, Elzinga S, Newbold CJ.Faecal samples were collected from seventeen animals, each fed three different diets (high fibre, high fibre with a starch rich supplement and high fibre with an oil rich supplement). DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the faecal microbiome of the horse. The effect of age was also considered by comparing mature (8 horses aged 5-12) versus elderly horses (9 horses aged 19-28). A reduction in diversity was found in the elderly horse group. Significant differences between diets were found at an OTU level (52 OTUs at corrected Q<0.1). The ma...
Hauswirth R, Haase B, Blatter M, Brooks SA, Burger D, Drögemüller C, Gerber V, Henke D, Janda J, Jude R, Magdesian KG, Matthews JM, Poncet PA....During fetal development neural-crest-derived melanoblasts migrate across the entire body surface and differentiate into melanocytes, the pigment-producing cells. Alterations in this precisely regulated process can lead to white spotting patterns. White spotting patterns in horses are a complex trait with a large phenotypic variance ranging from minimal white markings up to completely white horses. The "splashed white" pattern is primarily characterized by an extremely large blaze, often accompanied by extended white markings at the distal limbs and blue eyes. Some, but not all, splashed white...
Tetens J, Widmann P, Kühn C, Thaller G.A genome-wide association scan for loci affecting withers height was conducted in 782 German Warmblood stallions, which were genotyped using the Illumina EquineSNP50 Bead Chip. A principal components approach was applied to correct for population structure. The analysis revealed a single major QTL on ECA3 explaining ~18 per cent of the phenotypic variance, which is in concordance with recent reports from other horse populations. The LCORL/NCAPG locus represents a strong candidate gene for this QTL. This locus is among a small number that have consistently been identified to influence human hei...
Bosch G, van Schie HT, de Groot MW, Cadby JA, van de Lest CH, Barneveld A, van Weeren PR.Tendon injuries are notorious for their slow and functionally inferior healing. Intratendinous application of platelet-rich plasma (PRP) has been reported to stimulate the repair process of tendon injuries, but there is little conclusive evidence for its effectiveness. A placebo-controlled experimental trial was performed to test the hypothesis that a single intratendinous PRP treatment enhances the quality of tendon repair, as evidenced by improved biochemical, biomechanical, and histological tissue properties. In six horses, tendon lesions were created surgically in the Superficial Digital F...
Tulman ER, Delhon G, Afonso CL, Lu Z, Zsak L, Sandybaev NT, Kerembekova UZ, Zaitsev VL, Kutish GF, Rock DL.Here we present the genomic sequence of horsepox virus (HSPV) isolate MNR-76, an orthopoxvirus (OPV) isolated in 1976 from diseased Mongolian horses. The 212-kbp genome contained 7.5-kbp inverted terminal repeats and lacked extensive terminal tandem repetition. HSPV contained 236 open reading frames (ORFs) with similarity to those in other OPVs, with those in the central 100-kbp region most conserved relative to other OPVs. Phylogenetic analysis of the conserved region indicated that HSPV is closely related to sequenced isolates of vaccinia virus (VACV) and rabbitpox virus, clearly grouping to...
Cieslak M, Pruvost M, Benecke N, Hofreiter M, Morales A, Reissmann M, Ludwig A.Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population r...
Wu DD, Yang CP, Wang MS, Dong KZ, Yan DW, Hao ZQ, Fan SQ, Chu SZ, Shen QS, Jiang LP, Li Y, Zeng L, Liu HQ, Xie HB, Ma YF, Kong XY, Yang SL, Dong XX....Abundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution and genetic convergence. Here, we used 327 genomes from horses, sheep, goats, cattle, pigs and dogs living at both high and low altitudes, including 73 genomes generated for this study, to disentangle the genetic mechanisms underlying local adaptation of domestic mammals. Although molecular convergence is comparatively rare at the DNA sequence level, we found convergent signature of positive selection at the gene level, particularly the gene in these Tibetan domest...
Hill EW, McGivney BA, Gu J, Whiston R, Machugh DE.Thoroughbred horses have been selected for traits contributing to speed and stamina for centuries. It is widely recognized that inherited variation in physical and physiological characteristics is responsible for variation in individual aptitude for race distance, and that muscle phenotypes in particular are important. Results: A genome-wide SNP-association study for optimum racing distance was performed using the EquineSNP50 Bead Chip genotyping array in a cohort of n = 118 elite Thoroughbred racehorses divergent for race distance aptitude. In a cohort-based association test we evaluated geno...
Schroeder DI, Jayashankar K, Douglas KC, Thirkill TL, York D, Dickinson PJ, Williams LE, Samollow PB, Ross PJ, Bannasch DL, Douglas GC, LaSalle JM.Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylated domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of hu...
Telford EA, Watson MS, Aird HC, Perry J, Davison AJ.The complete DNA sequence of equine herpesvirus 2 (EHV-2) strain 86/67 was determined. The genome is 184,427 bp in size and has a base composition of 57.5% G + C. Unusually for a herpesvirus, about a third of the sequence distributed in several large blocks appears not to encode proteins. The 79 open reading frames that were identified as probably polypeptide-coding are predicted to encode 77 distinct proteins. Amino acid sequence comparisons confirmed that EHV-2 is a gamma-herpesvirus that is genetically collinear with herpesvirus saimiri (HVS; a gamma 2-herpesvirus) and Epstein-Barr virus (E...
Ericsson AC, Johnson PJ, Lopes MA, Perry SC, Lanter HR.Horses are exquisitely sensitive to non-specific gastrointestinal disturbances as well as systemic and extraintestinal conditions related to gut health, yet minimal data are available regarding the composition of the microbiota present in the equine stomach, small intestine, and cecum and their relation to fecal microbiota. Moreover, there is minimal information regarding the concordance of the luminal and mucosal microbial communities throughout the equine gut. Illumina-based 16S rRNA gene amplicon sequencing of the luminal and mucosal microbiota present in seven regions of the gastrointestin...
Warmuth V, Eriksson A, Bower MA, Barker G, Barrett E, Hanks BK, Li S, Lomitashvili D, Ochir-Goryaeva M, Sizonov GV, Soyonov V, Manica A.Despite decades of research across multiple disciplines, the early history of horse domestication remains poorly understood. On the basis of current evidence from archaeology, mitochondrial DNA, and Y-chromosomal sequencing, a number of different domestication scenarios have been proposed, ranging from the spread of domestic horses out of a restricted primary area of domestication to the domestication of numerous distinct wild horse populations. In this paper, we reconstruct both the population genetic structure of the extinct wild progenitor of domestic horses, Equus ferus, and the origin and...
Fernandes KA, Kittelmann S, Rogers CW, Gee EK, Bolwell CF, Bermingham EN, Thomas DG.The effects of abrupt dietary transition on the faecal microbiota of forage-fed horses over a 3-week period were investigated. Yearling Thoroughbred fillies reared as a cohort were exclusively fed on either an ensiled conserved forage-grain diet ("Group A"; n = 6) or pasture ("Group B"; n = 6) for three weeks prior to the study. After the Day 0 faecal samples were collected, horses of Group A were abruptly transitioned to pasture. Both groups continued to graze similar pasture for three weeks, with faecal samples collected at 4-day intervals. DNA was isolated from the faeces and microbial 16S ...
Ehlers B, Borchers K, Grund C, Frölich K, Ludwig H, Buhk HJ.A consensus primer PCR approach was used to (i) investigate the presence of herpesviruses in wild and zoo equids (zebra, wild ass, tapir) and to (ii) study the genetic relationship of the herpesvirus of pigeons (columbid herpesvirus 1) to other herpesvirus species. The PCR assay, based on degenerate primers targeting highly conserved regions of the DNA polymerase gene of herpesviruses, was modified by using a mixture of degenerate and deoxyinosine-substituted primers. The applicability of the modification was validated by amplification of published DNA polymerase genes of 16 herpesvirus specie...
Lindgren G, Backström N, Swinburne J, Hellborg L, Einarsson A, Sandberg K, Cothran G, Vilà C, Binns M, Ellegren H.Genetic studies using mitochondrial DNA (mtDNA) have identified extensive matrilinear diversity among domestic horses. Here, we show that this high degree of polymorphism is not matched by a corresponding patrilinear diversity of the male-specific Y chromosome. In fact, a screening for single-nucleotide polymorphisms (SNPs) in 14.3 kb of noncoding Y chromosome sequence among 52 male horses of 15 different breeds did not identify a single segregation site. These observations are consistent with a strong sex-bias in the domestication process, with few stallions contributing genetically to the do...
Carbone L, Nergadze SG, Magnani E, Misceo D, Francesca Cardone M, Roberto R, Bertoni L, Attolini C, Francesca Piras M, de Jong P, Raudsepp T....Centromere repositioning (CR) is a recently discovered biological phenomenon consisting of the emergence of a new centromere along a chromosome and the inactivation of the old one. After a CR, the primary constriction and the centromeric function are localized in a new position while the order of physical markers on the chromosome remains unchanged. These events profoundly affect chromosomal architecture. Since horses, asses, and zebras, whose evolutionary divergence is relatively recent, show remarkable morphological similarity and capacity to interbreed despite their chromosomes differing co...
Turton JF, Baklan H, Siu LK, Kaufmann ME, Pitt TL.A multiplex PCR using targets within the serotype-specific region of the capsular polysaccharide synthesis gene cluster of serotypes K1, K2 and K5 was evaluated using the 77 reference serotype strains of Klebsiella, and a panel of clinical isolates subjected previously to conventional serotyping. The PCR was highly specific for these serotypes, which are those most associated with virulence in humans and horses. PCR confirmed that isolates of the K5 serotype had cross-reacted with antiserum for other serotypes, particularly for K7. K5 isolates received by our laboratory were almost exclusively...
Malda J, Benders KE, Klein TJ, de Grauw JC, Kik MJ, Hutmacher DW, Saris DB, van Weeren PR, Dhert WJ.Articular cartilage defects are common after joint injuries. When left untreated, the biomechanical protective function of cartilage is gradually lost, making the joint more susceptible to further damage, causing progressive loss of joint function and eventually osteoarthritis (OA). In the process of translating promising tissue-engineering cartilage repair approaches from bench to bedside, pre-clinical animal models including mice, rabbits, goats, and horses, are widely used. The equine species is becoming an increasingly popular model for the in vivo evaluation of regenerative orthopaedic ap...
Brunberg E, Andersson L, Cothran G, Sandberg K, Mikko S, Lindgren G.The Silver coat color, also called Silver dapple, in the horse is characterized by dilution of the black pigment in the hair. This phenotype shows an autosomal dominant inheritance. The effect of the mutation is most visible in the long hairs of the mane and tail, which are diluted to a mixture of white and gray hairs. Herein we describe the identification of the responsible gene and a missense mutation associated with the Silver phenotype. Results: Segregation data on the Silver locus (Z) were obtained within one half-sib family that consisted of a heterozygous Silver colored stallion with 34...
Schraiber JG, Evans SN, Slatkin M.The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such direct observations of allele frequency dynamics are expected to be more powerful than inferences made using patterns of linked neutral variation obtained from modern individuals. We developed a Bayesian method to make use of allele frequency time series data and infer the parameters of general diploid selection, along with allele age, in nonequilibrium populati...
Haile J, Froese DG, Macphee RD, Roberts RG, Arnold LJ, Reyes AV, Rasmussen M, Nielsen R, Brook BW, Robinson S, Demuro M, Gilbert MT, Munch K....Causes of late Quaternary extinctions of large mammals ("megafauna") continue to be debated, especially for continental losses, because spatial and temporal patterns of extinction are poorly known. Accurate latest appearance dates (LADs) for such taxa are critical for interpreting the process of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000-13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinc...
Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V....To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, ...
McNulty SN, Tort JF, Rinaldi G, Fischer K, Rosa BA, Smircich P, Fontenla S, Choi YJ, Tyagi R, Hallsworth-Pepin K, Mann VH, Kammili L, Latham PS....Food borne trematodes (FBTs) are an assemblage of platyhelminth parasites transmitted through the food chain, four of which are recognized as neglected tropical diseases (NTDs). Fascioliasis stands out among the other NTDs due to its broad and significant impact on both human and animal health, as Fasciola sp., are also considered major pathogens of domesticated ruminants. Here we present a reference genome sequence of the common liver fluke, Fasciola hepatica isolated from sheep, complementing previously reported isolate from cattle. A total of 14,642 genes were predicted from the 1.14 GB gen...
Knowles DP, Kappmeyer LS, Haney D, Herndon DR, Fry LM, Munro JB, Sears K, Ueti MW, Wise LN, Silva M, Schneider DA, Grause J, White SN, Tretina K....A novel apicomplexan parasite was serendipitously discovered in horses at the United States - Mexico border. Phylogenetic analysis based on 18S rDNA showed the erythrocyte-infective parasite to be related to, but distinct from, Theileria spp. in Africa, the most similar taxa being Theileria spp. from waterbuck and mountain zebra. The degree of sequence variability observed at the 18S rDNA locus also suggests the likely existence of additional cryptic species. Among described species, the genome of this novel equid Theileria parasite is most similar to that of Theileria equi, also a pathogen of...
Kubickova S, Cernohorska H, Musilova P, Rubes J.Laser microbeam microdissection and laser pressure catapulting procedure were used for the construction of chromosome-specific painting probes, arm-specific probes and probes for chromosomal subfragments. We report on a method for generation of fluorescence in-situ hybridization probes from laser dissected chromosomes of farm animals. So far, using the described method, a set of chromosome-specific painting probes has been obtained for all porcine chromosomes, 17 chromosomes of cattle and selected equine chromosomes. It is concluded that the laser technology appears to be a useful and powerful...
Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM....The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further charact...
