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.
Dong J, Gao N, Waller AS, Cook FR, Fan S, Yuan D, Du Y, Li F, Norimine J, Zhu W.Strangles is a highly contagious respiratory disease of equids caused by the bacterium Streptococcus equi subspecies equi. Objective: To identify the cause of an outbreak of strangles that occurred on donkey farms within the Shandong Province of China and determine the prevalence of the disease. Methods: Cross-sectional. Methods: Samples were taken from clinically affected animals to measure the prevalence of strangles within the population of donkeys at six intensive farms in China and identify the SeM type of isolate recovered from affected animals. Diagnosis was confirmed by bacterial isola...
Stejskalova K, Cvanova M, Oppelt J, Janova E, Horecky C, Horecka E, Knoll A, Leblond A, Horin P.West Nile virus (WNV) is a mosquito-borne zoonotic neurotropic virus capable to cause lethal meningoencephalitis (WNE) in infected hosts such as birds, horses, and humans. Due to their sensitivity, horses serve as sentinel species in areas at risk. We studied a population of Camargue horses living in Southern France in two zones with endemic WNV circulation where WNV outbreaks were recorded in 2000 and 2003-4. Two sets of microsatellite markers located in MHC and Ly49 genomic regions were genotyped as well as multiple SNPs in ten immunity-related candidate gene regions. Associations between ge...
Sevane N, Sanz CR, Dunner S.Four loci seem responsible for the dilution of the basic coat colours in horse: Dun (D), Silver Dapple (Z), Champagne (CH) and Cream (C). Apart from the current phenotypes ascribed to these loci, pearl has been described as yet another diluted coat colour in this species. To date, this coat colour seems to segregate only in the Iberian breeds Purebred Spanish horse and Lusitano and has also been described in breeds of Iberian origin, such as Quarter Horses and Paint Horse, where it is referred to as the 'Barlink Factor'. This phenotype segregates in an autosomal recessive manner and resembles ...
Putnová L, Štohl R.Considering the extensive data sets and statistical techniques, animal breeding embodies a branch of machine learning that has a constantly increasing impact on breeding. In our study, information regarding the potential of machine learning and data mining within a large set of horses and breeds is presented. The individual assignment methods and factors influencing the success rate of the procedure are compared at the Czech population scale. The fixation index values ranged from 0.057 (HMS1) to 0.144 (HTG6), and the overall genetic differentiation amounted to 8.9% among the breeds. The highes...
Seong HS, Kim NY, Kim DC, Hwang NH, Son DH, Shin JS, Lee JH, Chung WH, Choi JW.The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds. The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski's horse). Using the equine reference genome assembly (EquCab 2.0), more than ~ 6.5 billion sequence reads were successfully mapped, which generated an average of 40.87-fold coverage throughout the genome. Using these data, we detected a total of 12.88 million SNPs, of w...
Ren WX, Zhang XX, Long CY, Zhao Q, Cheng T, Ma JG, Xu P, Hou G, Ni HB.Horse meat and milk are an important source of nutrition for many Chinese. Previous studies have shown a fairly high prevalence of infection in horses. However, there is no data concerning the molecular characterization of in horses in China. The present study tested 231 cervical lymph node samples of horses from northern China (97 from Jilin, 54 from Liaoning, and 80 from Xinjiang) for the presence of the B1 gene by seminested PCR. The B1-positive samples were genotyped at nine nuclear loci, that is, SAG1, alternative SAG2, SAG3, BTUB, c22-8, GRA6, c29-2, PK1, and an apicoplast locus, usin...
Ma H, Wang S, Zeng G, Guo J, Guo M, Dong X, Hua G, Liu Y, Wang M, Ling Y, Ding X, Zhao C, Wu C. The Jinjiang horse is a unique Chinese indigenous horse breed distributed in the southern coastal areas, but the ancestry of Jinjiang horses is not well understood. Here, we used Equine SNP70 Bead Array technology to genotype 301 horses representing 10 Chinese indigenous horse breeds, and we integrated the published genotyped data of 352 individuals from 14 foreign horse breeds to study the relationships between Jinjiang horses and horse breeds from around the world. Principal component analysis (PCA), linkage disequilibrium (LD), runs of homozygosity (ROH) analysis, and ancestry estimating m...
Kobayashi I, Akita M, Takasu M, Tozaki T, Kakoi H, Nakamura K, Senju N, Matsuyama R, Horii Y.The Misaki horse is a Japanese native horse, known as the "feral horse of Cape Toi". In this study, we acquired the genetic information to establish their studbook, and analyzed their genetic characteristics for conservation. We genotyped 32 microsatellites and a mitochondrial D-loop region in 77 Misaki horses (80.2% of the population). The average number of alleles, observed heterozygosity, and expected heterozygosity were 3.4, 0.509, and 0.497, respectively. A neighbor-joining phylogenetic tree of individuals was constructed. Moreover, the results suggested that Misaki horses experienced a b...
Grilz-Seger G, Druml T, Neuditschko M, Dobretsberger M, Horna M, Brem G.The sample ascertainment bias due to complex population structures remains a major challenge in genome-wide investigations of complex traits. In this study we derived the high-resolution population structure and levels of autozygosity of 377 Lipizzan horses originating from five different European stud farms utilizing the SNP genotype information of the high density 700 k Affymetrix Axiom™ Equine genotyping array. Scanning the genome for overlapping runs of homozygosity (ROH) shared by more than 50% of horses, we identified homozygous regions (ROH islands) in order to investigate the gene ...
Vitari GLV, Costa RL, Abreu APM, Peckle M, Silva CB, Paulino PG, Pires MS, Massard CL, Santos HA.Equine piroplasmosis stands out among the diseases that affect Equidae in Brazil and the world. It is caused by the protozoa Theileria equi and Babesia caballi. The objective of the present study was to carry out the molecular characterization of T. equi using equine blood samples collected in the 5 geographic regions of Brazil. Samples from all over the country were tested for the presence of T. equi by real-time PCR. The 18S rRNA sequences (∼1,600 bp) obtained from 23 samples taken from naturally infected horses were characterized by sequencing and analyzed to identify the genotypes and th...
Brister H, Barnum SM, Reedy S, Chambers TM, Pusterla N.We validated 2 multiplex real-time PCR (rtPCR) assays based on single nucleotide polymorphisms (SNPs) of the hemagglutinin-1 ( HA1) gene of H3N8 equine influenza A virus (EIV) to determine clade affiliation of prototype and field isolates. Initial validation of the 2 multiplex rtPCR assays (SNP1 and SNP2) was performed using nucleic acid from 14 EIV Florida sublineage clade 1 and 2 prototype strains. We included in our study previously banked EIV rtPCR-positive nasal secretions from 341 horses collected across the United States in 2012-2017 to determine their clade affiliation. All 14 EIV prot...
Shang S, Yu Y, Zhao Y, Dang W, Zhang J, Qin X, Irwin DM, Wang Q, Liu F, Wang Z, Zhang S, Wang Z.Through domestication and human selection, horses have acquired various coat colors, including seven phenotypes: black, brown, dark bay, bay, chestnut, white, and gray. Here we determined the genotypes for melanocortin-1 receptor (MC1R) and agouti signaling protein (ASIP) in 709 horses from 15 breeds. We found that the EEEE genotype frequency at MC1R decreased from dark to light colors (black = 64.5%, brown = 67.5%, dark bay = 47.0%, bay = 16.5%, and chestnut = 0.0%), whereas the AAAA genotype frequency at ASIP increased as coat color lightened (black = 0.0%, brown = 22.9%, dark bay = 69.2%, a...
Sant C, Allicock OM, d'Abadie R, Charles RA, Georges K.The agents of equine piroplasmosis, Theileria equi and Babesia caballi, are endemic in Trinidad, West Indies. While transmission is mainly by ixodid ticks, transplacental transmission of T. equi has also been reported. This disease has contributed to foetal losses as well as morbidity and mortality of neonatal foals and adult horses. Previous 18S rRNA-based phylogenetic studies indicated a noticeable degree of variation within and among B. caballi and T. equi isolates from different geographical regions. The objective of this study was to evaluate the diversity of T. equi and B. caballi obtain...
Copy number variation (CNV) has been proved to be widespread in human, animal and plant genomes. Together with single nucleotide polymorphisms (SNPs), CVNs play a key role in genetic diversity. In this study, genome-wide detection of CNVs was performed based on SNP data from 24 Criollo Argentino horses genotyped with the GGP Equine70k array. Overall, 165 CNVs meeting stringent quality control criteria were identified and then aggregated into 87 CNV regions (CNVRs), representing a horse genome coverage of 13.69 Mb. Functional analysis of CNVRs allowed the identification of 337 genes implicate...
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...
Pereira GL, Malheiros JM, Ospina AMT, Chardulo LAL, Curi RA.Among horses selected for speed, the racing line of Quarter Horses is characterized by high performance in sprint races, with these animals being considered the fastest horses in the world. However, few studies have investigated in more detail the polymorphisms and genes that act on this trait. The objective of this study was to analyze exomes and UTRs in regions previously associated with this trait by GWAS in Quarter Horse racehorses with contrasting maximum speed index (SImax), prospecting causal gene polymorphisms that are related to or are in strong linkage disequilibrium with racing perf...
Wang J, Liu J, Yang J, Wang X, Li Z, Jianlin X, Li X, Xiang Q, Li Y, Liu Z, Luo J, Guan G, Yin H.Equine piroplasmosis, caused by Theileria equi and Babesia caballi, is an economically important tick-borne disease worldwide. In the current study, 242 blood samples were randomly collected from horses in Zhangye city of Gansu province, China. The presence and genetic diversity of piroplasms were evaluated with a nested PCR assay, gene sequencing and phylogenetic analysis. The results showed that seventy-five (31.0%) samples were positive for piroplasms. Sequences analysis showed that seventy-three (30.2%) were positive for T. equi, and seven (2.9%) for B. caballi, five of which (2.1%) were i...
Henkel J, Lafayette C, Brooks SA, Martin K, Patterson-Rosa L, Cook D, Jagannathan V, Leeb T.White spotting phenotypes in horses are highly valued in some breeds. They are quite variable and may range from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for white spotting phenotypes in horses. For the present study, we investigated an American Paint Horse family segregating a phenotype involving white spotting and blue eyes. Six of eight horses with the white-spotting phenotype were deaf. We obtained whole-genome sequence data from an affected horse and specifically searched for structural variants in the known ...
Gianino GM, Valberg SJ, Perumbakkam S, Henry ML, Gardner K, Penedo C, Finno CJ.Immune-mediated myositis (IMM) in American Quarter Horses (QHs) causes acute muscle atrophy and lymphocytic infiltration of myofibers. Recently, an E321G mutation in a highly conserved region of the myosin heavy chain 1 (MYH1) gene was associated with susceptibility to IMM and nonexertional rhabdomyolysis. Objective: To estimate prevalence of the E321G MYH1 variant in the QH breed and performance subgroups. Methods: Three-hundred seven elite performance QHs and 146 random registered QH controls. Methods: Prospective genetic survey. Elite QHs from barrel racing, cutting, halter, racing, reining...
Mackowski M, Wodas L, Brooks SA, Cieslak J.Although only a few specific pigmentation types are allowed within the Hucul horse registry, accurate determination of particular coat colors can be uncertain due to the presence of variation in color shades and segregation of multiple dun dilution variants. Herein, we genotyped the previously identified polymorphisms within two coat color loci TBX3 (T-box 3) and ASIP (Agouti Signaling Protein) in 462 Hucul individuals and compared the genotype predicted phenotypes with observed pigmentation types provided in the Polish Horse Breeders Association database. We identified disagreement between th...
Hill EW, McGivney BA, Rooney MF, Katz LM, Parnell A, MacHugh DE.Race distance aptitude in Thoroughbred horses is highly heritable and is influenced largely by variation at the myostatin gene (MSTN). Objective: In addition to MSTN, we hypothesised that other modifying loci contribute to best race distance. Methods: Using 3006 Thoroughbreds, including 835 'elite' horses, which were >3Â years old, had race records and were sampled from Europe/Middle-East, Australia/New Zealand, North America and South Africa, we performed genome-wide association (GWA) tests and separately developed a genomic prediction algorithm to comprehensively catalogue additive geneti...
The Journal of heredityDecember 28, 2018
Volume 110, Issue 2 173-182 doi: 10.1093/jhered/esy061
Sadeghi R, Moradi-Shahrbabak M, Miraei Ashtiani SR, Schlamp F, Cosgrove EJ, Antczak DF.The principal aims of this study were to explore genetic diversity and genome-wide selection signatures in Persian Arabian horses and to determine genetic relationship of Persian Arabians with other Iranian horse breeds. We evaluated 71 horses from 8 matrilineal strains tracing to 47 mares from the mid to late 19th century, using the equine 670k single nucleotide polymorphism (SNP) BeadChip. Mean observed and expected heterozygosity were (0.43) and (0.45), respectively, average inbreeding measures (inbreeding estimates based on runs of homozygosity and pedigree information) were low, indicatin...
Shang S, Zhang M, Zhao Y, Dang W, Hua P, Zhang S, Wang Z.Due to the thriving development of the modern horse industry and the occurrence of horse related crimes, the demand for methods of individual horse identification, parentage tests and other genetic analyses is increasing. Previous methods had disadvantages that decreased the accuracy of the results, lacked the inclusion of all commonly used short tandem repeats (STR) or increased the experimental cost and time. Objective: We aimed to develop a novel 13-plex STR typing system to resolve the above issues. Methods: Experimental study. Methods: Twelve autosomal and most commonly used di-nucleotide...
Senokuchi A, Ishikawa S, Tozaki T, Takasu M, Kakoi H, Misumi K, Hobo S.In order to promote conservation of the traditional Tokara horse in its remaining three breeding areas in Japan (Nakanoshima, Kaimondake, and Iriki), we genotyped 123 horses using 31 microsatellite markers and determined their genetic diversity. On average, the number of alleles (N), observed heterozygosity (H), expected heterozygosity (H), and inbreeding coefficient (F) among all horses were 3.0, 0.424, 0.481, and 0.108, respectively. Compared with other endangered horse breeds, we found that, even though the size of the Tokara horse population has recently increased, the N, H, and H of Tokar...
Senju N, Tozaki T, Kakoi H, Matsuyama R, Nakamura K, Takasu M.The Miyako and Yonaguni horses are native horses in Okinawa. Here, we evaluated their genetic relationship using microsatellite data and Kiso horses, which have four subpopulations, as a reference population for evaluating this relationship. Microsatellite data from 35 Miyako, 78 Yonaguni, and 172 Kiso horses were evaluated using the STRUCTURE software for analyzing multilocus genotype data to investigate the population structures and their underlying relationship. The results of the STRUCTURE analysis were stable when ΔK was 2, suggesting that the Okinawan horses are different from the Kiso ...
Kakoi H, Kikuchi M, Tozaki T, Hirota KI, Nagata SI.The integrity of thoroughbreds is maintained under strict regulation involving DNA parentage testing, which is robust in a population with high genetic variability. The genetic variability of the thoroughbred population is possibly fluctuating because of selective breeding that has focused on adaptations for racing performance. To monitor genetic variability within the population and the effectiveness of short tandem repeat (STR) parentage testing, we investigated allele frequencies and the exclusion probability (PE) of 16-17 loci of a parentage panel in the Japanese thoroughbred population ov...
Brosnahan MM, Al Abri MA, Brooks SA, Antczak DF, Osterrieder N.Equine herpesvirus type 1 (EHV-1)-induced myeloencephalopathy (EHM) is a neurologic disease of horses that represents one outcome of infection. The neurologic form of disease occurs in a subset of infected horses when virus-induced endothelial cell damage triggers vasculitis and subsequent ischemic insult to the central nervous system. EHM causes considerable animal suffering and economic loss for the horse industry. Virus polymorphisms have been previously associated with disease outcome but cannot fully explain why only some horses develop EHM. This study investigated the role of host geneti...
Jagannathan V, Gerber V, Rieder S, Tetens J, Thaller G, Drögemüller C, Leeb T.Whole-genome sequencing studies are vital to gain a thorough understanding of genomic variation. Here, we summarize the results of a whole-genome sequencing study comprising 88 horses and ponies from diverse breeds at 19.1× average coverage. The paired-end reads were mapped to the current EquCab3.0 horse reference genome assembly, and we identified approximately 23.5 million single nucleotide variants and 2.3 million short indel variants. Our dataset included at least 7 million variants that were not previously reported. On average, each individual horse genome carried ∼5.7 million single n...
Matczuk AK, Skarbek M, Jackulak NA, Bażanów BA.Equid alphaherpesvirus 1 (EHV-1) is one of the main infectious causative agents of abortion in mares and can also be associated with stillbirth, neonatal foal death, rhinopneumonitis in young horses and a neurological disorder called equine herpesvirus myeloencephalopathy (EHM). The neuropathogenicity of the virus was shown to be significantly higher in EHV-1 strains that carry a single nucleotide point (SNP) mutation in the ORF30, which encodes a catalytic subunit of viral DNA polymerase (ORF30 D). Another gene, ORF68 is frequently used for phylogenetic analysis of EHV-1. 27 EHV-1 strains iso...
Miyata H, Itoh R, Sato F, Takebe N, Hada T, Tozaki T.Variants of the Myostatin gene have been shown to have an influence on muscle hypertrophy phenotypes in a wide range of mammalian species. Recently, a Thoroughbred horse with a C-Allele at the g.66493737C/T single-nucleotide polymorphism (SNP) has been reported to be suited to short-distance racing. In this study, we examined the effect of the Myostatin SNP on muscle fiber properties in young Thoroughbred horses during a training period. To investigate the effect of the Myostatin SNP on muscle fiber before training, several mRNA expressions were relatively quantified in biopsy samples from the...
Tirosh-Levy S, Steinman A, Levy H, Katz Y, Shtilman M, Gottlieb Y.Equine piroplasmosis is a highly endemic protozoan disease of horses worldwide, caused by Theileria equi and Babesia caballi. While most horses in endemic areas are subclinically infected, the mechanisms leading to clinical outcome are vastly unknown. Moreover, since clinical signs of disease are not specific, and the prevalence in endemic areas is high, it is difficult to determine if equine piroplasmosis is the cause of disease. To identify possible mechanisms leading to the clinical outcome in an endemic area, we compared parasite loads and genotypes in clinically and subclinically infected...
van Duijkeren E, van Asten AJ, Gaastra W.In the present study E. coli strains isolated from the faeces of ten horses with diarrhoea and 14 horses without diarrhoea were characterized. All horses were culture negative for Salmonella species. Nine colonies of E. coli from each faecal sample were picked at random and a DNA fingerprint was made by means of a polymerase chain reaction (PCR) using Enterobacterial Repetitive Intergenic Consensus (ERIC) primers. The number of E. coli genotypes did not differ significantly between horses with and without diarrhoea. In addition, all E. coli strains with different DNA fingerprints were tested b...
Rotinsulu DA, Ewers C, Kerner K, Amrozi A, Soejoedono RD, Semmler T, Bauerfeind R.Strangles, caused by ssp. (), is a highly infectious and frequent disease of equines worldwide. No data are available regarding the molecular epidemiology of strangles in Indonesia. This study aimed to characterize isolates obtained from suspected strangles cases in Indonesia in 2018. Isolates originated from seven diseased horses on four different farms located in three provinces of Indonesia. Whole genome sequences of these isolates were determined and used for typing, multilocus sequence typing (MLST), and core genome MLS typing (cgMLST). Genomes were also screened for known antimicrobi...
Laseca N, Molina A, Valera M, Antonini A, Demyda-Peyrás S.Copy number variations (CNVs) are a new-fangled source of genetic variation that can explain changes in the phenotypes in complex traits and diseases. In recent years, their study has increased in many livestock populations. However, the study and characterization of CNVs in equines is still very limited. Our study aimed to investigate the distribution pattern of CNVs, characterize CNV regions (CNVRs), and identify the biological pathways affected by CNVRs in the Pura Raza Española (PRE) breed. To achieve this, we analyzed high-density SNP genotyping data (670,804 markers) from a large cohort...
Behl R, Behl J, Gupta N, Gupta SC.The genetic relationships of five Indian horse breeds, namely Marwari, Spiti, Bhutia, Manipuri and Zanskari were studied using microsatellite markers. The DNA samples of 189 horses of these breeds were amplified by polymerase chain reaction using 25 microsatellite loci. The total number of alleles varied from five to 10 with a mean heterozygosity of 0.58 ± 0.05. Spiti and Zansakari were the most closely related breeds, whereas, Marwari and Manipuri were most distant apart with Nei's DA genetic distance of 0.071 and 0.186, respectively. In a Nei's DA genetic distances based neighbour joining...
The Journal of heredityApril 27, 2017
Volume 108, Issue 4 361-368 doi: 10.1093/jhered/esx025
Al Abri MA, König von Borstel U, Strecker V, Brooks SA.Horse breeders rely heavily on pedigrees for identification of ancestry in breeding stock. Inaccurate pedigrees may erroneously assign individuals to false lineages or breed memberships resulting in wrong estimates of inbreeding and coancestry. Moreover, discrepancies in pedigree records can lead breeders seeking to limit inbreeding into making misguided breeding decisions. Genome-wide SNPs provide a quantitative tool to aid in the resolution of lineage assignments and the calculation of genomic measures of relatedness. The aim of this project was to pilot a comparison between pedigree and gen...
Gemingguli M, Iskhan KR, Li Y, Qi A, Wunirifu W, Ding LY, Wumaierjiang A.The Kazakh horse is an important old horse breed in Xinjiang. They have contributed greatly to the breeding and improvement of other local horse breeds, yet their genetic diversity and population structure are not well understood. In the present study, we evaluated the genetic diversity of Kazakh horses and their relationship with other horse breeds using the mtDNA D-loop region, Cyt b gene, and a DNA fragment (nps 7974-9963, containing COX3, tRNA-Gly, ND3, and tRNA-Arg). A total of 130 Kazakh horses from 8 populations in China and Kazakhstan were analyzed. A total of 88 haplotypes (haplotype ...
Liu S, Fu C, Yang Y, Zhang Y, Ma H, Xiong Z, Ling Y, Zhao C.To investigate the genetic diversity of Chinese indigenous horses and determine the genetic status of extant horse breeds, novel Y chromosomal microsatellite markers and known Y chromosomal SNPs and mtDNA loop sequences, were employed to study the genetic diversity levels of 13 Chinese indigenous horse populations and four introduced breeds. Sixteen Y-chromosomal microsatellite markers, including seven newly identified loci, were used in the genotyping. The results showed that 4 out of the 16 loci were highly polymorphic in Chinese indigenous horse populations, in which the polymorphisms of 3 ...
Farries G, McGettigan PA, Gough KF, McGivney BA, MacHugh DE, Katz LM, Hill EW.Adaptation to early training and racing (i.e. precocity), which is highly variable in racing Thoroughbreds, has implications for the selection and training of horses. We hypothesised that precocity in Thoroughbred racehorses is heritable. Age at first sprint training session (work day), age at first race and age at best race were used as phenotypes to quantify precocity. Using high-density SNP array data, additive SNP heritability (hSNP2) was estimated to be 0.17, 0.14 and 0.17 for the three traits respectively. In genome-wide association studies (GWAS) for age at first race and age at best ra...
Roczo-Farkas S, Kirkwood CD, Bines JE.The Australian Rotavirus Surveillance Program, together with collaborating laboratories Australia-wide, reports the rotavirus genotypes responsible for the hospitalisation of children with acute gastroenteritis during the period 1 January to 31 December 2015. During the survey period, 1,383 faecal samples were referred for rotavirus G and P genotype analysis, and of these, 1,031 were confirmed as rotavirus positive. A total of 634 specimens had been collected from children under 5 years of age, while 397 were from older children and adults. Genotype analysis of samples from both children an...
Bleumink-Pluym N, ter Laak EA, van der Zeijst BA.Contagious equine metritis (CEM), a sexually transmitted bacterial disease, was first described in thoroughbred horses. It also occurs in nonthoroughbred horses, in which it produces isolated, apparently unrelated outbreaks. Thirty-two strains of Taylorella equigenitalis, the causative agent of CEM, from all over the world were characterized by field inversion gel electrophoresis of fragments of genomic DNA obtained by digestion with low-cleavage-frequency restriction enzymes. This resulted in a division into five clearly distinct groups. Strains from thoroughbred horses from all continents be...
Hirota K, Kakoi H, Gawahara H, Hasegawa T, Tozaki T.We characterized the SNP 53 JPN System for parentage verification during horse registry. The SNP 53 JPN System was constructed using 53 highly polymorphic single nucleotide polymorphisms (SNPs), which were amplified and genotyped with 2 multiplex assays. The SNP 53 JPN System showed good resolution for 95 unrelated thoroughbreds, and the exclusion probability (PE01) for each SNP ranged from 11.5 to 23.0%, resulting in a total PE01 value of 99.996%. These results indicate that the SNP 53 JPN System is useful for parentage testing of thoroughbreds. Of the 53 SNPs, 8 SNPs could be used to exclude...
Chassier M, Barrey E, Robert C, Duluard A, Danvy S, Ricard A.Genotype imputation is now a key component of genomic analyses as it increases the density of available genotypes within a population. However, many factors can influence imputation accuracy. The aim of this study was to assess and compare the accuracy of imputation of high-density genotypes (Affymetrix Axiom Equine genotyping array, 670,806 SNPs) from two moderate-density genotypes (Illumina Equine SNP50 BeadChip, 54,602 SNPs and Illumina Equine SNP70 BeadChip, 65,157 SNPs), using single-breed or multiple-breed reference sets. Genotypes were available from five groups of horse breeds: Arab (A...
Knickelbein KE, Lassaline ME, Singer-Berk M, Reilly CM, Clode AB, Famula TR, Michau TM, Bellone RR.Belgian horses are commonly affected with ocular squamous cell carcinoma (SCC), the most common cancer of the equine eye. A missense mutation in damage-specific DNA binding protein 2 (DDB2 c.1013C>T, p.Thr338Met) has been established as a recessive genetic risk factor for ocular SCC in the Haflinger breed. A sample of Belgian horses with unknown SCC phenotype was shown to possess this variant at a similar frequency to the Haflinger breed. Retrospective studies indicate that chestnut coat colour may predispose to the development of SCC. Objective: To determine if DDB2 c.1013C>T is a risk ...
Ketter-Ratzon D, Tirosh-Levy S, Nachum-Biala Y, Saar T, Qura'n L, Zivotofsky D, Abdeen Z, Baneth G, Steinman A.Equine theileriosis caused by Theileria equi is endemic in the Middle East, where it causes a severe disease as well as widespread subclinical infection. The aim of this study was to evaluate the diversity of T. equi genotypes in Israel and the neighboring Palestinian Authority and Jordan. Blood samples from 355 horses from Israel, the Palestinian Authority and Jordan were tested for the prevalence of T. equi DNA. Two hundred and fourteen (60%) were found positive for T. equi infection by PCR. Of those, the 18S rRNA (1458bp) and the EMA-1 (745bp) genes of T. equi were sequenced from 15 horse s...
Lampe V, Dierks C, Distl O.Osteochondrosis (OC) is an inherited developmental disease in young horses most frequently observed in thoroughbreds, trotters, warmblood and coldblood horses. Quantitative trait loci (QTL) for equine OC have been identified in Hanoverian warmblood horses employing a whole genome scan with microsatellites. A QTL on ECA16 reached the genome-wide significance level for hock osteochondrosis dissecans (OCD). The aim of this study was to refine this QTL on ECA16 using an extended marker set of 34 newly developed microsatellites and 15 single nucleotide polymorphisms (SNPs). We used the same 14 pate...
Hori Y, Tozaki T, Nambo Y, Sato F, Ishimaru M, Inoue-Murayama M, Fujita K.Tractability, or how easily animals can be trained and controlled, is an important behavioural trait for the management and training of domestic animals, but its genetic basis remains unclear. Polymorphisms in the serotonin receptor 1A gene (HTR1A) have been associated with individual variability in anxiety-related traits in several species. In this study, we examined the association between HTR1A polymorphisms and tractability in Thoroughbred horses. We assessed the tractability of 167 one-year-old horses reared at a training centre for racehorses using a questionnaire consisting of 17 items....
Choi SK, Cho CY, Yeon SH, Cho BW, Cho GJ.Genetic characterization of the Jeju horse (JH) was performed to construct a correct pedigree of the JH family. A total of 111 horses including 79 JH were genotyped using 20 microsatellite loci. The number of alleles varied from 5 to 11 (mean 7.45) in the JH. The observed heterozygosity and expected heterozygosity ranged from 0.293 to 0.891 and from 0.357 to 0.841, respectively. The polymorphic information contents (PIC) ranged from 0.335 to 0.816. AHT4, ASB2, ASB17, ASB23, CA425, HMS2, HMS3, HTG10, LEX3 and VHL20 loci had relatively high PIC values (> 0.7). The total exclusion probability ...
Singha H, Gulati BR, Kumar P, Singh BK, Virmani N, Singh RK.The complete genome of the Japanese encephalitis virus (JEV) strain JEV/eq/India/H225/2009(H225), isolated from an infected horse in India, was sequenced and compared to previously published JEV genomes. H225 genome was 10,977-nucleotides long, comprising a single ORF of 10,299-nucleotides, a 5'-UTR of 95 nucleotides and a 3'-UTR of 582 nucleotides. The H225 genome showed high levels of sequence identity with 47 fully sequenced JEV genomes, ranging from 99.3 % to 75.5 % for nucleotides and 99.2 % to 91.5 % for amino acid sequences. Phylogenetic analysis of the full-length sequence indicated th...
Li R, Liu DH, Cao CN, Wang SQ, Dang RH, Lan XY, Chen H, Zhang T, Liu WJ, Lei CZ.The myostatin gene (MSTN) is a genetic determinant of skeletal muscle growth. Single nucleotide polymorphisms (SNP) in MSTN are of importance due to their strong associations with horse racing performances. In this study, we screened the SNPs in MSTN gene in 514 horses from 15 Chinese horse breeds. Six SNPs (g.26T>C, g.156T>C, g.587A>G, g.598C>T, g.1485C>T, g.2115A>G) in MSTN gene were detected by sequencing and genotyped using PCR-RFLP method. The g.587A>G and g.598C>T residing in the 5'UTR region were novel SNPs identified by this study. The g.2115A>G which have pr...
Venner M, Meyer-Hamme B, Verspohl J, Hatori F, Shimizu N, Sasaki Y, Kakuda T, Tsubaki S, Takai S.Pulsotypes of VapA positive Rhodococcus equi isolated from foals and soil on a farm in Germany were characterized on the basis of nasal and tracheal samples simultaneously collected in 2003 from 217 foals with sonographic evidence of pneumonia or pulmonary abscesses. Of the 217 double samples, R. equi was isolated in 118 (54%) of the tracheal samples and in 52 of the nasal swab samples (24%) (P<0.001). Furthermore, 37 and 55 isolates were also randomly selected from nasal swabs and the tracheal samples, respectively, and further processed to determine the presence of VapA by colony blot enz...
Patterson Rosa L, Martin K, Vierra M, Foster G, Lundquist E, Brooks SA, Lafayette C.Over 30 polymorphisms in the KIT Proto-Oncogene Receptor Tyrosine Kinase (KIT) gene have been implicated in white spotting patterns ranging from small areas to full dermal depigmentation in the horse. We performed a candidate-gene exon sequencing approach on KIT and MITF, 2 known causatives of white spotting patterns, within 2 families of horses of unknown white spotting. Family 1 (Fam1, N = 5) consisted of a Quarter Horse stallion and 4 offspring with white spotting pattern ranging from legs, lower ventral, and head regions with jagged borders, to almost complete white. The second family (Fam...
Broström H, Fahlbrink E, Dubath ML, Lazary S.The distribution of equine leucocyte antigens (ELA) in Swedish Halfbreds affected by sarcoid tumors was determined and compared with that of control horses of the same breed. ELA-haplotype A3W13 appeared more frequently in affected horses, resulting in a chi 2 value of 4.45 (P = 0.034) for A3 and 9.05 (P = 0.0026) for W13, respectively. The relative risk factor (RR) could be estimated to 2.13 and 3.00 for A3 and W13, respectively. The etiology fraction (EF) was calculated to 28% and 37% for A3 and W13, respectively. Thus, in the population of Swedish Halfbreds approximately 40% (at least) of t...
Sant C, Allicock OM, d'Abadie R, Charles RA, Georges K.The agents of equine piroplasmosis, Theileria equi and Babesia caballi, are endemic in Trinidad, West Indies. While transmission is mainly by ixodid ticks, transplacental transmission of T. equi has also been reported. This disease has contributed to foetal losses as well as morbidity and mortality of neonatal foals and adult horses. Previous 18S rRNA-based phylogenetic studies indicated a noticeable degree of variation within and among B. caballi and T. equi isolates from different geographical regions. The objective of this study was to evaluate the diversity of T. equi and B. caballi obtain...
Bellone RR, Ocampo NR, Hughes SS, Le V, Arthur R, Finno CJ, Penedo MCT.Catastrophic fractures are among the most common cause of fatalities in racehorses. Several factors, including genetics, likely contribute to increased risk for fatal injuries. A variant in the procollagen-lysine, 2-oxoglutarate 5-dioxygenase1 gene (PLOD1 c.2032G>A) was shown to cause Warmblood fragile foal syndrome type 1 (WFFS), a fatal recessive defect of the connective tissue. Screening of multiple horse breeds identified the presence of the WFFS allele in the Thoroughbred. PLOD1 is involved in cross-linking of collagen fibrils and thus could potentially increase the risk of catastrophic b...
Kaiser-Thom S, Gerber V, Collaud A, Hurni J, Perreten V.Many contributing factors are involved in the development of equine pastern dermatitis (EPD). Among the most frequently suspected is Staphylococcus aureus, known for its pathogenic potential in skin and soft tissue infections. We therefore investigated the association between S. aureus carriage and EPD. Results: One hundred five EPD-affected horses and 95 unaffected controls were examined for the presence of methicillin-resistant and -susceptible Staphylococcus aureus (MRSA and MSSA) on the pastern skin and in the nostrils. S. aureus isolates were cultivated from swab samples on selective MSSA...
Komáromy AM, Rowlan JS, La Croix NC, Mangan BG.To describe the clinical phenotype and genetics of equine Multiple Congenital Ocular Anomalies (MCOA) syndrome in PMEL17 (Silver) mutant ponies. Methods: Five presumably unrelated ponies. Methods: The ponies were examined under field conditions in their barn by slit lamp biomicroscopy, indirect ophthalmoscopy, and applanation tonometry. Blood was collected and genomic DNA extracted for MCOA genotyping using the PMEL17ex11 marker. Results: One pony solely presented with temporal ciliary body cysts, suggestive of the less severe Cyst phenotype of MCOA; the animal was heterozygous at the MCOA loc...
Reshadi P, Heydari F, Ghanbarpour R, Bagheri M, Jajarmi M, Amiri M, Alizade H, Badouei MA, Sahraei S, Adib N.Transmission of antimicrobial resistant and virulent Escherichia coli (E. coli) from animal to human has been considered as a public health concern. This study aimed to determine the phylogenetic background and prevalence of diarrheagenic E. coli and antimicrobial resistance in healthy riding-horses in Iran. In this research, the genes related to six main pathotypes of E. coli were screened. Also, genotypic and phenotypic antimicrobial resistance against commonly used antibiotics were studied, then phylo-grouping was performed on all the isolates. Results: Out of 65 analyzed isolates, 29.23â€...
He HY, Liu LL, Chen B, Xiao HX, Liu WJ.Donkey milk has high nutritional and medicinal value, but there are few researches in donkey milk traits, especially on genome. The whole lactation of 89 donkeys was recorded and it was found that Xinjiang donkey had good lactation performance while great differences among individuals. In our previous study, four genes including , , and were identified as milk-associated with Chinese Kazakh house, based on Equine 670k Chip genomic analysis. And then 15 SNPs of the four key genes were conducted for genotyping in Xinjiang donkey in this study, one of Chinese indigenous breed, 14 SNPs were succ...
