Genotyping in horses involves analyzing the genetic makeup of individual horses to identify specific genetic markers. This process aids in understanding genetic variations that may influence traits such as coat color, disease susceptibility, and performance capabilities. Genotyping can be used in breeding programs to select for desirable traits and manage genetic diversity within populations. Common methods for genotyping include single nucleotide polymorphism (SNP) analysis and microsatellite markers. This page compiles peer-reviewed research studies and scholarly articles that explore the methodologies, applications, and implications of genotyping in equine genetics and breeding.
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...
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...
Science (New York, N.Y.)August 28, 2025
Volume 389, Issue 6763 925-930 doi: 10.1126/science.adp4581
Liu X, Jia Y, Pan J, Zhang Y, Gong Y, Wang X, Ma Y, Alvarez N, Jiang L, Orlando L.Horsepower revolutionized human history through enhanced mobility, transport, and warfare. However, the suite of biological traits that reshaped horses during domestication remains unclear. We scanned an extensive horse genome time series for selection signatures at 266 markers associated with key traits. We detected a signature of positive selection at -known to be a modulator of behavior in mice-occurring ~5000 years ago (ya), suggesting that taming was one of the earliest steps toward domestication of horses. Intensive selection at began ~4750 ya with the domestication bottleneck, leading ...
The Shagya Arabian horse breed was created to address the need of Imperial Hussars (Hungarian light horsemen) for a horse with the intelligence, essential characteristics, and endurance of the Arabian breed, but also of a bigger size and having a better weight-carrying capacity and jumping ability. The present study aimed to explore the genetic variability and population structure of the uninvestigated Shagya Arabian horse population in Bulgaria based on genotyping at 15 equine microsatellite markers. A total of 140 horses belonging to six genealogical lines (Dahoman, Gazal, Ibrahim, Kuhailan ...
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...
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 ...
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...
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...
Bazvand B, Rashidi A, Zandi MB, Moradi MH, Rostamzadeh J, Mahmoudi P.Iran is home to genetically distinct horse breeds shaped by geography and history. Breeds like the Kurdish, Caspian pony, and Turkmen reflect deep-rooted diversity and unique adaptive traits. Objective: This study aimed to identify genomic regions exhibiting signatures of selection and to detect candidate genes and biological pathways related to body size that may influence performance in various Iranian and exotic horse breeds. Methods: Samples were collected from three Iranian native breeds (Caspian pony, Turkmen, and Kurdish) and three exotic breeds (Fell pony, Arabian, and Akhal-Teke) orig...
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D.The core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. However, research on the genetic characteristics within this breed and the genes associated with athletic performance remains relatively limited. We conducted whole-genome resequencing of Grassland-Thoroughbred F1, F2, F3, and the crossbred population (CY) and obtained a total of 4056.23 Gb of high-qual...
Ryan CA, Berry DP, Bugno-Poniewierska M, Burke MK, Raudsepp T, Egan S, Doyle JL.Autosomal trisomy, a genetic disorder characterized by the presence of an extra autosome, is a rare but important chromosomal abnormality in horses, often associated with infertility, developmental abnormalities, and reduced life expectancy. This study represents the largest population-level screening for autosomal trisomy in horses; the analysis used single nucleotide polymorphism (SNP) panel genotype intensity data from 17,078 horses, 6601 of which were juveniles (i.e., ≤12 months of age) when genotyped. Using methodologies adapted from similar screening studies in cattle, the only aneuplo...
Barandalla M, Colleoni S, Perota A, Galli C, Lazzari G.The introduction of ovum pick-up, Intracytoplasmic Sperm Injection (ICSI) and in vitro embryo production in equine reproduction offers significant advantages, including overcoming infertility, high blastocyst yields, embryo cryopreservation, and preimplantation genetic testing (PGT) by collecting few cells extruded spontaneously during embryo growth using a mouth pipette. PGT enables embryo selection before transfer and is particularly useful in breeds with a preference for specific offspring genders, coat color, and detecting genetic diseases. Here, we present the first large-scale validation...
Everts RE, Caron R, Foster G, McLoone K, Martin K, Brooks SA, Lafayette C.The 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 to no white hairs. Previous studies mapped the locus for roan to the KIT region and observed linked variants in a small number of breeds. However, utilizing those linked markers to determine the roan genotype in other breeds has seen limited success. In this communication we identify a second roan allele (RN2) which, in conjunction with a previously observed roan allele (RN1) disc...
Asti V, Summer A, Ablondi M, Sartori C, Giontella A, Pilastro V, Mecocci S, Cappelli K, Mancin E, Oian A, Mantovani R, Capomaccio S, Sabbioni A.Horses have undergone extensive natural and artificial selection, shaping the diversity of breeds observed today. Native Italian breeds present unique traits influenced by natural selection, such as adaptation to harsh climates, or hoof strength, but face challenges due to population declines and the reduction of their original breeding purpose. This study focuses on five local Italian breeds: Bardigiano, Haflinger, Maremmano, Murgese, and Italian Heavy Draught Horse, to understand how selection has shaped their populations. A total of 1620 individuals were genotyped with a medium-density SNP ...
Ziadi C, Valera M, Laseca N, Perdomo-González D, Demyda-Peyrás S, de Los Terreros AR, Molina A. By simultaneously integrating both genotyped and non-genotyped animals into genetic evaluation, the single-step genomic BLUP method enhanced the accuracy of genetic assessments. This study aimed to compare the increase in prediction reliability (R) between restricted maximum likelihood (REML) and single-step genomic REML (ssGREML) in the Pura Raza Española (PRE) horse breed. The dataset comprised reproductive records for seven fertility traits from 47,502 females, with a total of 57,316 animals represented in the pedigree. A total of 4009 animals were genotyped using the EQUIGENE 90K SNP ar...
Vychodilova L, Plasil M, Futas J, Kopecka A, Molinkova D, Wijacki T, Jahn P, Knoll A, Horin P.Although the Major Histocompatibility Complex (MHC) has been repeatedly associated with susceptibility to equine sarcoid, a disease associated with bovine papillomavirus infection, the role of the MHC in the mechanisms of the disease is not fully understood. The objectives of our work were to analyze associations between polymorphic markers of the MHC genomic subregions and of the Natural Killer Complex (NKC) genomic region and the presence of sarcoid in Arabian horses. Microsatellite loci located in the MHC class I, II and III subregions and two MHC class II genes (DRA, DQA1), along with a se...
Aleman M, McCue M, Bellone RR.Fatal anesthesia-induced malignant hyperthermia (MH) and rhabdomyolysis with hyperthermia documented in Quarter Horses (QH) breeds are caused by a missense variant in the ryanodine receptor 1 gene (RYR1: XP_023505430.1.:p.(R2454G), designated as MH). The reported cases to date have all been heterozygous, and the allele frequency is suspected to be low. Objective: To determine an accurate estimate of MH allele frequency in multiple horse breeds and investigate whether homozygous animals exist in the population. Methods: In total, 159 227 horses from 16 breeds who were either submitted for cli...
Bacon EK, Donnelly CG, Finno CJ, Haase B, Velie BD.Multimodal analgesic administration is a promising strategy for mitigating side effects typically associated with analgesia; nevertheless, variation in analgesic effectiveness still poses a considerable safety concern for both horses and veterinarians. Pharmacogenomic studies have started delving into genetic influences on varying drug effectiveness and related side effects. However, current findings have narrow implications and are limited in their ability to individualize analgesic dosages in horses. Hydromorphone and detomidine were administered to a cohort of 48 horses at standardized time...
Sigurðardóttir H, Eriksson S, Niazi A, Rhodin M, Albertsdóttir E, Kristjansson T, Lindgren G.Selection for performance in horse breeding benefits from precise genetic insights at a molecular level, but knowledge remains limited. This study used whole-genome sequences of 39 elite and non-elite Icelandic horses to identify candidate causal variants linked to previously identified haplotypes in the STAU2 and RELN genes affecting pace and other gaits. A frameshift variant in linkage disequilibrium with the previously identified haplotypes in the STAU2 gene (r2 = 0.85) was identified within a predicted STAU2 transcript. This variant alters the amino acid sequence and introduces a prema...
Cullinane A, Garvey M, Dayot L, Lukaseviciute G.Equine rotavirus A (RVA) is a major cause of debilitating diarrhoea in neonatal foals globally. The aim of this study was to characterise RVA viruses currently circulating in Ireland and to identify risk factors associated with disease outbreaks. Of the 377 samples submitted during 2023 and 2024, 48 foals from 36 outbreaks were confirmed to be RVA-positive by real-time PCR. The viruses detected were genotyped by VP7 and VP4 gene sequencing. In 2024, the attending veterinary surgeon was contacted, and epidemiological data were collected. These included the vaccination status of the foal's dam a...
Blohina NV, Khrabrova LA.Russia has a significant pedigree diversity of horse breeds with unique gene pools that are well adapted to a wide variety of harsh natural and climatic conditions, are characterized by universal performance and high productive qualities, and are of significant interest to the world horse breeding. Genetic studies of population diversity in horse breeding are very relevant, since many domestic horse breeds are under threat of extinction. Biomaterials (hair, blood, semen) from horses of 15 local breeds bred in the Russian Federation and neighboring countries (CIS) were selected for the research...
Quatember H, Nell B, Richter B, Rigler D, Dolezal M, Sykora S, Wallner B.A missense mutation in damage-specific DNA binding protein 2 (DDB2 c.1013 C>T; p.Thr338Met) has been described as a risk factor for ocular squamous cell carcinoma (OSCC) in the Haflinger breed. Here, we examined the impact of DDB2 C>T allele status on the development of OSCC, squamous cell carcinoma (SCC) at other localisations, or equine sarcoid (ES) in Haflingers and other breeds with a high incidence of these tumour types. We genotyped affected Haflinger, Noriker, Warmblood, and Icelandic horses. Results based on 56 Haflingers confirmed the significantly higher risk for OSCC in DDB2-TT Hafl...
Obradovic NA, McFadden A, Martin K, Vierra M, McLoone K, Martin E, Thomas A, Everts RE, Brooks SA, Lafayette C.This paper reports three novel KIT variants likely responsible for previously unexplained white patterning phenotypes observed in three groups of horses. White spots and markings may have substantial consequences on the value and health of domesticated horses. This study aims to elucidate the genetic mechanisms underlying depigmented coat colors to aid in producing prosperous herds. Aligned whole genome sequences were manually screened to identify three polymorphisms in a family of Anglo-Arabian horses (N = 7), a family of Warmblood horses (N = 5), and a single stock-type mare with unexplained...
Agbani A, Aminou O, Machmoum M, Germot A, Badaoui B, Petit D, Piro M.This Systematic Literature Review (SLR) consolidates current research on mitochondrial DNA (mtDNA) analysis in horses, focusing on genetic variation, maternal lineage tracing, and haplogroup identification. The article selection process screened 1380 articles, with 76 fulfilling the inclusion criteria. Data extraction covered sampling techniques, studied mtDNA regions, sequencing methods, and haplogroup identification. Following the methodology of the PRISMA guidelines, this review encompasses studies published since 2012, obtained from Scopus, PubMed, Research4Life, Web of Science, and Scienc...
Moroudi RS, Mahboudi H, Mahboudi F.The Dareshouri horse breed is one of Iran's native equine breeds, originating from the Dareshouri tribe, a subgroup of the Qashqai nomads. This breed has a history spanning over 500 years. Horses of this breed have smooth nates, tall stature, raised tails and strong skeletal muscles. This is the first study to investigate the effect of genetics on athletic performance in the Dareshouri breed. For this purpose, in this study, the genotype combination of two important variants, including the rs397152648Single nucleotide polymorphism (SNP) and Short interspersed nuclear element (SINE) insertion, ...
Taha NM, Salem MA, El-Saied MA, Mohammed FF, Kamel M, El-Bahy MM, Ramadan RM.Cystic echinococcosis (CE) is a neglected zoonotic disease that causes significant economic losses in livestock and poses health risks to humans, necessitating improved diagnostic and therapeutic strategies. This study investigates CE in donkeys using a multifaceted approach that includes molecular identification, gene expression analysis, serum biochemical profiling, histopathological and immunohistochemical examination, and in vitro drug efficacy evaluation. Molecular analysis of hydatid cyst protoscolices (HC-PSCs) from infected donkey livers and lungs revealed a high similarity to Echinoco...
Bai F, Cai Y, Qiu M, Liang C, Pan L, Liu Y, Feng Y, Cao X, Yang Q, Ren G, Jiao S, Gao S, Lu M, Wang X, Heller R, Lenstra JA, Jiang Y.Natural variants can significantly improve growth traits in livestock and serve as safe targets for gene editing, thus being applied in animal molecular design breeding. However, such safe and large-effect mutations are severely lacking. Using ancestral recombination graphs, we investigated recent selection signatures in beef cattle breeds, pinpointing sweep-driving variants in the LCORL and STC2 loci with notable effects on body size and growth rate. The ACT-to-A frameshift mutation in LCORL occurs mainly in central-European cattle, and stimulates growth. Remarkably, convergent truncating mut...
Liu X, Peng Y, Zhang X, Chen W, Chen Y, Wei L, Zhu Q, Khan MZ, Wang C.Herbivorous livestock, such as cattle, sheep, goats, horses, and donkeys, play a crucial role in agricultural production and possess remarkable resilience to extreme environmental conditions, driven by complex genetic mechanisms. Recent advancements in high-throughput sequencing, genome assembly, and environmental data integration have enabled a deeper understanding of the genetic basis of their environmental adaptation. This review identifies key genes associated with high-altitude, heat, cold, and drought adaptation, providing insights into the molecular mechanisms underlying these traits. B...
Powers AM, Oberste MS, Brault AC, Rico-Hesse R, Schmura SM, Smith JF, Kang W, Sweeney WP, Weaver SC.Venezuelan equine encephalitis (VEE) epidemics and equine epizootics occurred periodically in the Americas from the 1920s until the early 1970s, when the causative viruses, subtypes IAB and IC, were postulated to have become extinct. Recent outbreaks in Columbia and Venezuela have renewed interest in the source of epidemic/epizootic viruses and their mechanism of interepizootic maintenance. We performed phylogenetic analyses of VEE virus isolates spanning the entire temporal and geographic range of strains available, using 857-nucleotide reverse transcription-PCR products including the E3 and ...
Mammalian centromeres are associated with highly repetitive DNA (satellite DNA), which has so far hindered molecular analysis of this chromatin domain. Centromeres are epigenetically specified, and binding of the CENPA protein is their main determinant. In previous work, we described the first example of a natural satellite-free centromere on Chromosome 11. Here, we investigated the satellite-free centromeres of by using ChIP-seq with anti-CENPA antibodies. We identified an extraordinarily high number of centromeres lacking satellite DNA (16 of 31). All of them lay in LINE- and AT-rich regio...
Laatamna AE, Wagnerová P, Sak B, Květoňová D, Xiao L, Rost M, McEvoy J, Saadi AR, Aissi M, Kváč M.A total of 219 and 124 individual fecal samples of horses and donkeys, respectively, were screened for the presence of Cryptosporidium spp., Encephalitozoon spp., and Enterocytozoon bieneusi DNA by genus-specific nested PCR. Isolates were genotyped by sequence analysis of SSU rRNA, GP60, TRAP-C1, COWP, and HSP70 loci in Cryptosporidium, and the ITS region in microsporidia. Cryptosporidium spp. was detected on 3/18 horse farms and 1/15 farms where donkeys were kept. Overall, five (2.3%) horse and two (1.6%) donkey specimens were PCR positive for Cryptosporidium. Genotyping at SSU and GP60 loci ...
Tirosh-Levy S, Gottlieb Y, Fry LM, Knowles DP, Steinman A.Equine piroplasmosis (EP), caused by the hemoparasites , , and , is an important tick-borne disease of equines that is prevalent in most parts of the world. Infection may affect animal welfare and has economic impacts related to limitations in horse transport between endemic and non-endemic regions, reduced performance of sport horses and treatment costs. Here, we analyzed the epidemiological, serological, and molecular diagnostic data published in the last 20 years, and all DNA sequences submitted to GenBank database, to describe the current global prevalence of these parasites. We demonstrat...
Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G.The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most wi...
McGill S, Malik R, Saul N, Beetson S, Secombe C, Robertson I, Irwin P.A retrospective study of cryptococcosis in domestic animals residing in Western Australia was conducted over an 11-year-period (from 1995 to 2006) by searching the data base of Murdoch University Veterinary Teaching hospital and the largest private clinical pathology laboratory in Perth. Cryptococcosis was identified in 155 animals: 72 cats, 57 dogs, 20 horses, three alpacas, two ferrets and a sheep. There was no seasonal trend apparent from the dates of diagnosis. Taking into account the commonness of accessions to Murdoch University, cats were five to six times more likely to develop this di...
McCue ME, Valberg SJ, Miller MB, Wade C, DiMauro S, Akman HO, Mickelson JR.Polysaccharide storage myopathy (PSSM) is a novel glycogenosis in horses characterized by abnormal glycogen accumulation in skeletal muscle and muscle damage with exertion. It is unlike glycogen storage diseases resulting from known defects in glycogenolysis, glycolysis, and glycogen synthesis that have been described in humans and domestic animals. A genome-wide association identified GYS1, encoding skeletal muscle glycogen synthase (GS), as a candidate gene for PSSM. DNA sequence analysis revealed a mutation resulting in an arginine-to-histidine substitution in a highly conserved region of G...
Anderson MA, Whitlock JE, Harwood VJ.Escherichia coli is the most completely characterized prokaryotic model organism and one of the dominant indicator organisms for food and water quality testing, yet comparatively little is known about the structure of E. coli populations in their various hosts. The diversities of E. coli populations isolated from the feces of three host species (human, cow, and horse) were compared by two subtyping methods: ribotyping (using HindIII) and antibiotic resistance analysis (ARA). The sampling effort required to obtain a representative sample differed by host species, as E. coli diversity was consis...
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...
Brooks SA, Gabreski N, Miller D, Brisbin A, Brown HE, Streeter C, Mezey J, Cook D, Antczak DF.Lavender Foal Syndrome (LFS) is a lethal inherited disease of horses with a suspected autosomal recessive mode of inheritance. LFS has been primarily diagnosed in a subgroup of the Arabian breed, the Egyptian Arabian horse. The condition is characterized by multiple neurological abnormalities and a dilute coat color. Candidate genes based on comparative phenotypes in mice and humans include the ras-associated protein RAB27a (RAB27A) and myosin Va (MYO5A). Here we report mapping of the locus responsible for LFS using a small set of 36 horses segregating for LFS. These horses were genotyped usin...
Gurgul A, Jasielczuk I, Semik-Gurgul E, Pawlina-Tyszko K, Stefaniuk-Szmukier M, Szmatoła T, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M.The genetic differentiation of the current horse population was evolutionarily created by natural or artificial selection which shaped the genomes of individual breeds in several unique ways. The availability of high throughput genotyping methods created the opportunity to study this genetic variation on a genome-wide level allowing detection of genome regions divergently selected between separate breeds as well as among different horse types sharing similar phenotypic features. In this study, we used the population differentiation index (FST) that is generally used for measuring locus-specifi...
Mariat D, Taourit S, Guérin G.In horses, basic colours such as bay or chestnut may be partially diluted to buckskin and palomino, or extremely diluted to cream, a nearly white colour with pink skin and blue eyes. This dilution is expected to be controlled by one gene and we used both candidate gene and positional cloning strategies to identify the "cream mutation". A horse panel including reference colours was established and typed for different markers within or in the neighbourhood of two candidate genes. Our data suggest that the causal mutation, a G to A transition, is localised in exon 2 of the MATP gene leading to an...
de la Fuente J, Torina A, Caracappa S, Tumino G, Furlá R, Almazán C, Kocan KM.Although Anaplasma marginale was known to be endemic in Italy, the diversity of Anaplasma spp. from this area have not been characterized. In this study, the prevalence of Anaplasma spp. antibodies in randomly selected farm animals collected on the island of Sicily was determined by use of a MSP5 cELISA for Anaplasma spp. and an immunofluorescence test specific for Anaplasma phagocytophilum. Genetic variation among strains of Anaplasma spp. from animals and ticks was characterized using the A. marginale msp1alpha and the Anaplasma spp. msp4 genes. Eight species of ticks were collected and test...
Burton AJ, Giguère S, Sturgill TL, Berghaus LJ, Slovis NM, Whitman JL, Levering C, Kuskie KR, Cohen ND.Macrolide and rifampin resistance developed on a horse breeding farm after widespread use was instituted for treatment of subclinical pulmonary lesions in foals. Resistance occurred in 6 (24%) of 25 pretreatment and 8 (62%) of 13 (62%) posttreatment isolates from affected foals. Drug-resistant isolates formed 2 distinct genotypic clusters.
Bower MA, McGivney BA, Campana MG, Gu J, Andersson LS, Barrett E, Davis CR, Mikko S, Stock F, Voronkova V, Bradley DG, Fahey AG, Lindgren G....Selective breeding for speed in the racehorse has resulted in an unusually high frequency of the C-variant (g.66493737C/T) at the myostatin gene (MSTN) in cohorts of the Thoroughbred horse population that are best suited to sprint racing. Here we show using a combination of molecular- and pedigree-based approaches in 593 horses from 22 Eurasian and North-American horse populations, museum specimens from 12 historically important Thoroughbred stallions (b.1764-1930), 330 elite-performing modern Thoroughbreds and 42 samples from three other equid species that the T-allele was ancestral and there...
Haase B, Brooks SA, Schlumbaum A, Azor PJ, Bailey E, Alaeddine F, Mevissen M, Burger D, Poncet PA, Rieder S, Leeb T.White coat color has been a highly valued trait in horses for at least 2,000 years. Dominant white (W) is one of several known depigmentation phenotypes in horses. It shows considerable phenotypic variation, ranging from approximately 50% depigmented areas up to a completely white coat. In the horse, the four depigmentation phenotypes roan, sabino, tobiano, and dominant white were independently mapped to a chromosomal region on ECA 3 harboring the KIT gene. KIT plays an important role in melanoblast survival during embryonic development. We determined the sequence and genomic organization of t...
Hijjawi N, Mukbel R, Yang R, Ryan U.Little is known about the epidemiology of Cryptosporidium in Jordan and to date, only one genotyping study has been conducted on Cryptosporidium isolates from Jordanian children. In the present study, a total of 284 faecal samples from Jordanian cattle, sheep, goats and chicken and 48 human faecal samples were screened for the presence of Cryptosporidium using an 18S quantitative PCR (qPCR) and a C. parvum/C. hominis specific qPCR at a lectin locus. Of these, 37 of 284 animal faecal samples were positive by qPCR at the 18S locus giving an overall prevalence of 11.6%. The point prevalence of Cr...
Haase B, Brooks SA, Tozaki T, Burger D, Poncet PA, Rieder S, Hasegawa T, Penedo C, Leeb T.White coat colour in horses is inherited as a monogenic autosomal dominant trait showing a variable expression of coat depigmentation. Mutations in the KIT gene have previously been shown to cause white coat colour phenotypes in pigs, mice and humans. We recently also demonstrated that four independent mutations in the equine KIT gene are responsible for the dominant white coat colour phenotype in various horse breeds. We have now analysed additional horse families segregating for white coat colour phenotypes and report seven new KIT mutations in independent Thoroughbred, Icelandic Horse, Germ...
Cosgrove EJ, Sadeghi R, Schlamp F, Holl HM, Moradi-Shahrbabak M, Miraei-Ashtiani SR, Abdalla S, Shykind B, Troedsson M, Stefaniuk-Szmukier M....The Arabian horse, one of the world's oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ances...
Loncaric I, Künzel F, Licka T, Simhofer H, Spergser J, Rosengarten R.The aim of this study was to investigate the antimicrobial resistance, resistance gene patterns and genetic relatedness of a collection of Austrian methicillin-resistant Staphylococcus aureus (MRSA) isolates from companion animals and horses. A total of 89 non-repetitive MRSA isolates collected during routine veterinary microbiological examinations from April 2004 to the end of 2012, and one isolate from 2013 were used for this study. The presence of mecA and other resistance genes was confirmed by PCR. Isolates were genotyped by spa typing, two multiple-locus variable-number tandem repeat ana...
Allen WR, Wilsher S, Turnbull C, Stewart F, Ousey J, Rossdale PD, Fowden AL.The interacting influences of maternal size and fetal genotype on placental and fetal development in the mare were assessed by comparing conventional within-breed Thoroughbred (Tb-in-Tb, n = 7) and Pony (P-in-P, n = 7) control pregnancies established by artificial insemination (AI) with between-breed (Tb-in-P, n = 8; deprived in utero condition and P-in-Tb, n = 7; luxurious in utero condition) experimental pregnancies established by embryo transfer. All foals were born spontaneously and the mean (+/- SEM) duration of gestation in the two groups of control mares was significantly different (P <...
Perkins GA, Goodman LB, Tsujimura K, Van de Walle GR, Kim SG, Dubovi EJ, Osterrieder N.A single nucleotide polymorphism in the equine herpesvirus 1 (EHV-1) DNA polymerase gene (ORF30 A(2254) to G) has been associated with clinical signs of equine herpes myeloencephalopathy (EHM). The purpose of our study was to determine the odds ratio for this genetic marker and EHM using a panel of field isolates from North America collected over the past twenty-three years. EHV-1 isolates cultured at the Cornell University Animal Health Diagnostic Laboratory from 1984 to 2007 were retrieved along with their clinical histories. DNA was extracted from these EHV-1 cultures and allelic discrimina...
Binns MM, Boehler DA, Lambert DH.One hundred and eighty-nine Thoroughbred horses that had won Graded Stakes races in North America were genotyped with the Illumina Equine SNP50 bead chip. Association tests using PLINK to determine whether any SNPs were associated with optimum racing distance (7 furlongs and under compared to 8-10 furlongs) identified a locus on ECA18 that was statistically significant (-log 10 EMP2=1.63) at the genome-wide level following permutation analysis (10,000 permutations). Bioinformatic analysis revealed that the two ECA18 SNPs with the highest statistical significance spanned the MSTN (myostatin) lo...
Seo MG, Lee SH, VanBik D, Ouh IO, Yun SH, Choi E, Park YS, Lee SE, Kim JW, Cho GJ, Kwon OD, Kwak D.Coxiella burnetii and Coxiella-like bacteria (CLB) are genetically and ecologically distinct despite some genetic similarities. Furthermore, CLB are exceptionally diverse and widespread in ticks, but rarely detected in domestic animals. Since Coxiella bacteria can be transmitted from infected horses by inhalation or by coming in contact with ticks during activities such as horseback riding, it is necessary to study their prevalence. To the best of our knowledge, this is the first large-scale nationwide investigation of the prevalence of C. burnetii and CLB among horses reared in South Korea. O...
Nolte W, Thaller G, Kuehn C.The study of selection signatures helps to find genomic regions that have been under selective pressure and might host genes or variants that modulate important phenotypes. Such knowledge improves our understanding of how breeding programmes have shaped the genomes of livestock. In this study, 942 stallions were included from four, exemplarily chosen, German warmblood breeds with divergent historical and recent selection focus and different crossbreeding policies: Trakehner (N = 44), Holsteiner (N = 358), Hanoverian (N = 319) and Oldenburger (N = 221). Those breeds are nowadays bred for athlet...
Raudsepp T, Finno CJ, Bellone RR, Petersen JL.The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite-free centromeres provide unique models for mammalian centromer...
Metzger J, Philipp U, Lopes MS, da Camara Machado A, Felicetti M, Silvestrelli M, Distl O.Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses. Results: Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affecte...
Bagcigil FA, Moodley A, Baptiste KE, Jensen VF, Guardabassi L.beta-Lactams and macrolides are important antibiotics for treatment of staphylococcal infections in both humans and animals. The aim of the study was to investigate the occurrence, species distribution and clonality of methicillin- and erythromycin-resistant staphylococci in the nasal cavity of dogs, horses, pigs, and cattle in Denmark. Nasal swabs were collected from a total of 400 animals, including 100 individuals of each species. Methicillin- and erythromycin-resistant staphylococci were isolated on selective media, identified by 16S rDNA sequencing, and typed by pulsed field gel electroph...
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...
Woodward AL, Rash AS, Blinman D, Bowman S, Chambers TM, Daly JM, Damiani A, Joseph S, Lewis N, McCauley JW, Medcalf L, Mumford J, Newton JR, Tiwari A....Equine influenza viruses are a major cause of respiratory disease in horses worldwide and undergo antigenic drift. Several outbreaks of equine influenza occurred worldwide during 2010-2012, including in vaccinated animals, highlighting the importance of surveillance and virus characterisation. Virus isolates were characterised from more than 20 outbreaks over a 3-year period, including strains from the UK, Dubai, Germany and the USA. The haemagglutinin-1 (HA1) sequence of all isolates was determined and compared with OIE-recommended vaccine strains. Viruses from Florida clades 1 and 2 showed c...
