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.
The Journal of heredityNovember 25, 2009
Volume 101, Issue 2 246-250 doi: 10.1093/jhered/esp091
Mittmann EH, Lampe V, Mömke S, Zeitz A, Distl O.The availability of a high-quality draft sequence of the horse makes known the physical location of microsatellites. The aim of the present study was to establish a highly polymorphic minimal screening set of microsatellite markers for horses (MSSH) annotated on the horse genome assembly EquCab2.0. We have used the previously reported linkage and radiation hybrid maps and have extended these marker sets by filling in gaps as noted from annotation on the horse sequence. This MSSH covers all autosomes and the X chromosome with 322 evenly spaced microsatellites whose positions were determined on ...
Rieder S.Colour phenotypes may have played a major role during early domestication events and initial selection among domestic animal species. As coat colours mostly follow a relatively simple mode of Mendelian inheritance, they have been among the first traits to be systematically analysed at the molecular level. As a result of the number of genetic tools developed during the past decade, horse coat colour tests have been designed and are now commercially available for some of the basic phenotypes. These tests enable breeders to verify segregation within particular pedigrees, to select specific colour...
Kakoi H, Tozaki T, Nagata S, Gawahara H, Kijima-Suda I.In order to develop a genotyping method that can be used in the registration procedure for Thoroughbreds, we developed a method for simultaneously genotyping multiple coat colour genes on the basis of single nucleotide polymorphism typing by using the SNaPshot(TM) technique. This method enabled precise and reasonable detection of causal mutations; it was effective for genotyping of MC1R, ASIP, and SLC45A2 at the Extension (E), Agouti (A), Cream dilution (C) loci, and the possibility of identification of rare variants of MC1R, EDNRB and KIT at the E, Overo (O) and Sabino 1 (SB1) loci, respectiv...
Burocziova M, Riha J.Genetic relationships and population structure of 8 horse breeds in the Czech and Slovak Republics were investigated using classification methods for breed discrimination. To demonstrate genetic differences among these breeds, we used genetic information - genotype data of microsatellite markers and classification algorithms - to perform a probabilistic prediction of an individual's breed. In total, 932 unrelated animals were genotyped for 17 microsatellite markers recommended by the ISAG for parentage testing (AHT4, AHT5, ASB2, HMS3, HMS6, HMS7, HTG4, HTG10, VHL20, HTG6, HMS2, HTG7, ASB17, AS...
Stanley RL, McCue ME, Valberg SJ, Mickelson JR, Mayhew IG, McGowan C, Hahn CN, Patterson-Kane JC, Piercy RJ.A glycogen synthase (GYS1) mutation has been described in horses with histopathological evidence of polysaccharide storage myopathy (PSSM) in the USA. It is unknown whether the same mutation is present in horses from the UK. Objective: To determine whether the GYS1 mutation occurs in UK horses with histopathological evidence of PSSM and exertional rhabdomyolysis. Objective: The R309H GYS1 mutation is present in a variety of UK horse breeds and that the mutation is commonly associated with exertional rhabdomyolysis. Methods: DNA was extracted from 47 muscle or blood samples from UK horses with ...
Santín M, Vecino JA, Fayer R.This is the first report of Enterocytozoon bieneusi in an equid species. Feces from 195 horses from 4 locations in Colombia were examined for E. bieneusi by polymerase chain reaction. Of these, 21 horses (10.8%) were found positive for E. bieneusi . The prevalence of E. bieneusi in horses 1 yr of age (2.5%). No significant differences in prevalence were observed between male (13.7%) and female horses (9%). Sequencing of the internal transcribed spacer region of the SSUrRNA locus identified 3 genotypes. Two genotypes appear to be unique to horses and were named Horse 1 and Horse 2. A third geno...
Lake SL, Matthews JB, Kaplan RM, Hodgkinson JE.Genetic resistance against benzimidazole (BZ) anthelmintics is widespread in cyathostomins, the commonest group of intestinal parasitic nematodes of horses. Studies of BZ-resistant nematodes of sheep, particularly Haemonchus contortus, have indicated that an anthelmintic resistance-conferring T/A polymorphism, encoding an F (phenylalanine) to Y (tyrosine) substitution, in beta-tubulin isotype 1 is present at two loci, codons 167 and 200 (F167Y, F200Y). Recent studies using complementary (c) DNA derived from BZ-susceptible and -resistant cyathostomins identified statistical differences in the f...
Swinburne JE, Bogle H, Klukowska-Rötzler J, Drögemüller M, Leeb T, Temperton E, Dolf G, Gerber V.Recurrent airway obstruction (RAO), or heaves, is a naturally occurring asthma-like disease that is related to sensitisation and exposure to mouldy hay and has a familial basis with a complex mode of inheritance. A genome-wide scanning approach using two half-sibling families was taken in order to locate the chromosome regions that contribute to the inherited component of this condition in these families. Initially, a panel of 250 microsatellite markers, which were chosen as a well-spaced, polymorphic selection covering the 31 equine autosomes, was used to genotype the two half-sibling familie...
Chen JW, Uboh CE, Soma LR, Li X, Guan F, You Y, Liu Y.Proper identification of racehorses competing in an official race and maintenance of defensible chain of custody are important in doping control regulations. The purpose of this study was to develop a reliable multiplex PCR method for providing genetic evidence for matching donors to test samples by using short tandem repeat (STR) loci. Amplification of 21 STR loci from blood, urine or hair root was achieved in a single tube and STR length polymorphism was analyzed using fluorescent labeled capillary electrophoresis. This novel approach showed an allele confidence interval of 0.19-0.43 bp and ...
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...
Lampe V, Dierks C, Komm K, Distl O.In this study we present a newly detected QTL associated with osteochondrosis in Hanoverian warmblood horses on equine chromosome 18 (ECA18). We developed a highly polymorphic and evenly distributed marker set on ECA18 employing the horse genome assembly EquCab2. The marker set included 11 newly developed microsatellites. Average polymorphism information content was 62.1% at an average spacing of 3 Mb. For genotyping of this marker set comprising a total of 27 highly polymorphic microsatellites, we used the same 14 paternal half-sib families as in the previous whole genome scan. The chromosome...
Barrey E, Mucher E, Jeansoule N, Larcher T, Guigand L, Herszberg B, Chaffaux S, Guérin G, Mata X, Benech P, Canale M, Alibert O, Maltere P, Gidrol X.Several cases of myopathies have been observed in the horse Norman Cob breed. Muscle histology examinations revealed that some families suffer from a polysaccharide storage myopathy (PSSM). It is assumed that a gene expression signature related to PSSM should be observed at the transcriptional level because the glycogen storage disease could also be linked to other dysfunctions in gene regulation. Thus, the functional genomic approach could be conducted in order to provide new knowledge about the metabolic disorders related to PSSM. We propose exploring the PSSM muscle fiber metabolic disorder...
Astakhova NM, Perelygin AA, Zharkikh AA, Lear TL, Coleman SJ, MacLeod JN, Brinton MA.Toll-like receptors 3, 7, and 8 (TLR3, TLR7, and TLR8) were studied in the genomes of the domestic horse and several other mammals. The messenger RNA sequences and exon/intron structures of these TLR genes were determined. An equine bacterial artificial chromosome clone containing the TLR3 gene was assigned by fluorescent in situ hybridization to the horse chromosomal location ECA27q16-q17 and this map location was confirmed using an equine radiation hybrid panel. Direct sequencing revealed 13 single-nucleotide polymorphisms in the coding regions of the equine TLR 3, 7, and 8 genes. Of these p...
Tazumi A, Maeda Y, Buckley T, Millar B, Goldsmith C, Dooley J, Elborn J, Matsuda M, Moore J.Clinical isolates (n = 63) of Pseudomonas aeruginosa obtained from various sites in 63 horses were compared using ERIC2 RAPD PCR to determine their genetic relatedness. Resulting banding patterns (n = 24 genotypes) showed a high degree of genetic heterogeneity amongst all isolates examined, indicating a relative non-clonal relationship between isolates from these patients, employing this genotyping technique. This study characterised 63 clinical isolates into 24 distinct genotypes, with the largest cluster (genotype E) accounting for 10/63 (15.9%) of the isolates. ERIC2 RAPD PCR proved to be a...
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...
Janova E, Matiasovic J, Vahala J, Vodicka R, Van Dyk E, Horin P.The major histocompatibility complex genes coding for antigen binding and presenting molecules are the most polymorphic genes in the vertebrate genome. We studied the DRA and DQA gene polymorphism of the family Equidae. In addition to 11 previously reported DRA and 24 DQA alleles, six new DRA sequences and 13 new DQA alleles were identified in the genus Equus. Phylogenetic analysis of both DRA and DQA sequences provided evidence for trans-species polymorphism in the family Equidae. The phylogenetic trees differed from species relationships defined by standard taxonomy of Equidae and from trees...
Vissani MA, Becerra ML, Olguín Perglione C, Tordoya MS, Miño S, Barrandeguy M.Infection with Equid Herpesvirus type 1 (EHV-1) leads to respiratory disease, abortion, and neurological disorders in horses. Molecular epidemiology studies have demonstrated that a single nucleotide polymorphism (A(2254)/G(2254)) in the genome region of the open reading frame 30 (ORF30), which results in an amino acid variation (N(752)/D(752)) of the EHV-1 DNA polymerase, is significantly associated with the neuropathogenic potential of naturally occurring strains. In order to estimate the prevalence of the EHV-1 neuropathogenic genotype in our country, we analyzed the ORF30 genome region of ...
Lopes MS, Diesterbeck U, da Câmara Machado A, Distl O.Navicular disease or podotrochlosis is one of the main causes of progressive forelimb lameness in warmblood horses. The objective of this study was to refine a quantitative trait locus on horse chromosome 2 for radiological alterations in the contour of the navicular bone (RAC) in Hanoverian warmblood horses. Genotyping was performed in 192 Hanoverian warmblood horses from 17 paternal half-sib groups. The marker set was extended to 58 informative microsatellites including nine newly developed microsatellites. QTL for RAC could be delineated at 32.50-43.13 Mb and a further new QTL for RAC could...
Bomcke E, Gengler N.Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data, but in case of incomplete or inexistent pedigrees they are replaced by coefficients calculated from molecular data. The main objective of this study was to develop a new method to estimate relationship coefficients by combining molecular with pedigree data, which is useful for specific situations where neither pedigree nor molecular data are complete. The developed method was applied to contribute to the conservation of the Skyr...
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...
Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He T, Zheng Y.The importance of microRNAs at the post-transcriptional regulation level has recently been recognized in both animals and plants. We used the simple but effective sequential method of first Blasting known animal miRNAs against the horse genome and then using the located candidates to search for novel miRNAs by RNA folding method in the vicinity (+ -500 bp) of the candidates. Here, a total of 407 novel horse miRNA genes including 354 mature miRNAs were identified, of these, 75 miRNAs were grouped into 32 families based on seed sequence identity. MiRNA genes tend to be present as clusters in som...
Chen JW, Uboh CE, Soma LR, Li X, Guan F, You Y.To evaluate whether urine supernatant contains amplifiable DNA and to determine factors that influence genotyping of samples from racehorses after storage and transportation. Methods: 580 urine, 279 whole blood, and 40 plasma samples obtained from 261 Thoroughbreds and Standardbreds. Methods: Genomic DNA was isolated from stored blood and urine samples collected from racehorses after competition. Quantified DNA was evaluated to determine whether 5 equine microsatellite loci (VHL20, HTG4, AHT4, HMS6, and HMS7) could be amplified by use of PCR techniques. Fragment size of each amplified locus wa...
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...
Lampe V, Dierks C, Distl O.In this report, we provide 29 new informative microsatellites distributed over a region of 21 Mb on horse chromosome (ECA) 5 and refine a quantitative trait locus (QTL) for fetlock osteochondrosis dissecans (OCD) to a genome-wide significant interval between 78.03 and 90.23 Mb on ECA5. Genotyping was performed in 211 Hanoverian warmblood horses from 14 paternal half-sib groups. Within this OCD-QTL, collagen type XXIV alpha 1 was identified as a potential functional candidate gene for equine osteochondrosis. This report is a further step towards unravelling the genes that cause equine osteochon...
The Journal of heredityMarch 20, 2009
Volume 100, Issue 4 481-486 doi: 10.1093/jhered/esp006
Wittwer C, Hamann H, Distl O.A whole-genome scan for radiological signs of osteochondrosis (OC) and osteochondrosis dissecans (OCD) in South German Coldblood (SGC) horses using 250 microsatellite markers identified a genome-wide significant quantitative trait locus (QTL) for fetlock OCD and a chromosome-wide QTL for hock OC on Equus caballus chromosome (ECA) 18 at a relative position of 45.9-78.2 cM. The aim of this study was to analyze associations of single-nucleotide polymorphisms (SNPs) in candidate genes for OC in this QTL region using 96 SGC horses. The OC-QTL on ECA18 could be confirmed and narrowed down to an inte...
Zeman P, Jahn P.Anaplasma phagocytophilum is a tick-borne rickettsial pathogen that has measurable genetic heterogeneity across its geographical range and reservoir spectrum. In the present study, publicly available sequences of the genes that have prevailingly been used for typing A. phagocytophilum were analysed to identify the segments giving the highest resolution with respect to the predictability of host and geographical provenances of the strains. Selected partial sequences of 16S rRNA, groL, msp4 and ank genes were then employed in a tentative multilocus typing scheme used to characterize the strains ...
Nieto JE, Aleman M.Anesthetic-induced malignant hyperthermia has been documented in Quarter Horses and is caused by a single-point mutation in the ryanodine receptor 1 gene at nucleotide C7360G generating a R2454G amino acid substitution. An accurate, faster molecular test that is less prone to contamination would facilitate screening for the mutation in horses intended for breeding, in those undergoing surgical procedures, and in those with clinical signs compatible with malignant hyperthermia. Objective: To report a rapid and accurate method for the detection of the ryanodine receptor 1 C7360G mutation. Method...
Zaayman D, Human S, Venter M.In recent years, West Nile virus has been responsible for outbreaks in regions where it has not previously been found. Five genetic lineages with specific geographic distributions exist. Recent outbreaks of WNV associated with the introduction of lineage 1 strains into the western hemisphere, together with the emergence of lineage 2 WNV in Central Europe, has highlighted the potential for spread of pathogenic WNV strains beyond their expected geographical boundaries. Therefore, genotyping of WNV strains may have important applications in surveillance and epidemiology. We report here the develo...
Díaz S, Echeverría MG, It V, Posik DM, Rogberg-Muñoz A, Pena NL, Peral-García P, Vega-Pla JL, Giovambattista G.The polymorphism of equine lymphocyte antigen (ELA) class II DRA gene had been detected by polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) and reference strand-mediated conformation analysis. These methodologies allowed to identify 11 ELA-DRA exon 2 sequences, three of which are widely distributed among domestic horse breeds. Herein, we describe the development of a pyrosequencing-based method applicable to ELA-DRA typing, by screening samples from eight different horse breeds previously typed by PCR-SSCP. This sequence-based method would be useful in high-throug...
Ryder OA, Sparkes RS, Sparkes MC, Clegg JB.1. Through the use of isoelectric focusing and peptide analysis, the hemoglobins of Przewalski's horse. Equus przewalskii and the domestic horse, E. caballus have been compared. 2. Przewalski's horses have two separate alpha-globin chain polymorphisms similar to domestic horses. Each hemoglobin phenotype could be accurately determined by isoelectric focusing. 3. Confirmation of the electrofocusing hemoglobin determinations was made by comparison to amino acid composition analyses of purified tryptic peptides and by analysis of the rare hemoglobins phenotypes observed in a family of Norwegian t...
Lieto LD, Cothran EG.Epitheliogenesis imperfecta (EI) is a hereditary junctional mechanobullous disease that occurs in newborn American Saddlebred foals. The pathological signs of epitheliogenesis imperfecta closely match a similar disease in humans known as Herlitz junctional epidermolysis bullosa, which is caused by a mutation in one of the genes (LAMA3, LAMB3 and LAMC2) coding for the subunits of the laminin 5 protein (laminin alpha3, laminin beta3 and laminin gamma2). The LAMA3 gene has been assigned to equine chromosome 8 and LAMB3 and LAMC2 have been mapped to equine chromosome 5. Linkage disequilibrium betw...
Stock KF, Distl O, Hoeschele I.Requirements for successful implementation of multivariate animal threshold models including phenotypic and genotypic information are not known yet. Here simulated horse data were used to investigate the properties of multivariate estimators of genetic parameters for categorical, continuous and molecular genetic data in the context of important radiological health traits using mixed linear-threshold animal models via Gibbs sampling. The simulated pedigree comprised 7 generations and 40000 animals per generation. Additive genetic values, residuals and fixed effects for one continuous trait and ...
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...
Al-Ghamdi GM, Kapur V, Ames TR, Timoney JF, Love DN, Mellencamp MA.To determine whether repetitive sequence-based polymerase chain reaction (rep-PCR) could be used to differentiate Streptococcus equi isolates, to examine S equi isolates from throughout the world, and to determine whether a horse had > 1 subtype of S equi during an outbreak of disease. Methods: An initial group of 32 S equi isolates, 63 S equi isolates from various geographic areas, and 17 S equi isolates obtained during outbreaks of disease. Methods: An aliquot of S equi genomic DNA was amplified, using enterobacterial repetitive intergenic consensus primers. Gel electrophoresis was perfor...
Hack Y, Henriksen ML, Pihl TH, Nielsen RK, Dwyer AE, Bellone RR.Equine recurrent uveitis (ERU) is an autoimmune disease defined by inflammation of the uveal tract of the eye. The cause of ERU is thought to be complex, involving both genetic and environmental factors. The purpose of this study was to investigate potential genetic risk factors for ERU in the Icelandic horse. Fifty-six Icelandic horses (11 affected with ERU and 45 controls) living in Denmark and the USA, eight years or older, were included in the study. A case-control GWAS was performed using the GGP Equine 80K array on the Illumina Infinium HD Beadchip using 40 horses. A mixed linear model a...
Esdaile E, Kallenberg A, Avila F, Bellone RR.Coat color is a trait of economic significance in horses. Variants in seven genes have been documented to cause white patterning in horses. Of the 34 variants that have been identified in KIT proto-oncogene, receptor tyrosine kinase (), 27 have only been reported in a single individual or family and thus not all are routinely offered for genetic testing. Therefore, to enable proper use of marker-assisted selection, determining breed specificity for these alleles is warranted. Screening 19 unregistered all-white Shetland ponies for 16 white patterning markers identified 14 individuals whose phe...
Hatai H, Hatazoe T, Seo H, Tozaki T, Ishikawa S, Miyoshi N, Misumi K, Hobo S.A 27-y-old Anglo-Arabian gelding with bay coat color was presented with a swelling of the left maxillary region. Fenestration on the left maxilla revealed that the left maxillary sinus was filled with black-red tissue. A portion of the tissue was excised and diagnosed histologically as malignant melanoma. Genotyping of the STX17 gene for gray coat color revealed that the horse did not have the "gray" factor. The horse was euthanized ~3 mo after first presentation. During autopsy, a black-to-gray mass extended from the left nasal cavity to the surrounding paranasal sinus and invaded the hard ...
Eggleston-Stott ML, Delvalle A, Dileanis S, Wictum E, Bowling AT.The equine dinucleotide microsatellite HMS7 is part of a microsatellite panel utilized in a parentage verification programme at the Veterinary Genetics Laboratory (Davis, California, USA). Apparent non-Mendelian inheritance was noted when a Quarter Horse mare was excluded as the parent of two offspring based on analysis of the HMS7 locus. The mare's DNA type qualified her as a parent of the offspring at an additional 20 microsatellite loci. The three animals appeared homozygous for HMS7 with each possessing an allele different from that of the other two animals. Polymerase chain reaction prime...
Leon PM, Campos VF, Thurow HS, Hartwig FP, Selau LP, Dellagostin OA, Neto JB, Deschamps JC, Seixas FK, Collares T.Single nucleotide polymorphisms (SNPs) in the p53 gene have been studied extensively in humans. The aims of this study were to determine the frequency of the Arg/Pro SNP in p53 in Thoroughbred mares on one stud in Brazil and to correlate p53 genotypes with reproductive performance. SNPs were detected by PCR-restriction fragment length polymorphism in blood samples from 105 horses and confirmed by sequencing. The allele frequency in Thoroughbred mares at codon 72 in exon 4 was 73.3% Arg/Pro, 17.1% Arg/Arg and 9.6% Pro/Pro. The presence of Arg/Pro was significantly associated with abortion (P=0....
Clark BL, Bamford NJ, Stewart AJ, McCue ME, Rendahl A, Bailey SR, Bertin FR, Norton EM.The HMGA2:c.83G>A variant was identified in Welsh ponies having pleiotropic effects on height and insulin concentration. Objective: Determine whether the HMGA2:c.83G>A variant is associated with decreased height and higher basal insulin concentrations across pony breeds. Methods: Two hundred thirty-six ponies across 6 breeds. Methods: Cross-sectional study. Ponies were genotyped for the HMGA2:c.83G>A variant and phenotyped for height and basal insulin concentrations. Stepwise regression was performed for model analysis using a linear regression model for height and mixed linear model ...
Bellone RR.Advances in equine genetics and genomics resources have enabled the understanding of some inherited ocular disorders and ocular manifestations. These ocular disorders include congenital stationary night blindness, equine recurrent uveitis, multiple congenital ocular anomalies, and squamous cell carcinoma. Genetic testing can identify horses with or at risk for disease and thus can assist in clinical management. In addition, genetic testing can identify horses that are carriers and thus can inform breeding decisions. Use of genetic tests in management and breeding decisions should aid in reduci...
Wagner B, Siebenkotten G, Radbruch A, Leibold W.IgE is the dominant immunoglobulin isotype involved in type I hypersensitivities in mammals. The heavy chain constant region domains of equine IgE are encoded by a single gene, the Cvarepsilon gene. By restriction analysis of cDNA from 15 unrelated horses, we have now identified two Cvarepsilon alleles, characterised by a Sma I restriction fragment length polymorphism, which we designated Cvarepsilon(a) and Cvarepsilon(b). Sequence analysis of both, Cvarepsilon(a) and Cvarepsilon(b) cDNA, showed in addition two single base exchanges resulting in two amino acid substitutions. Both sequences hav...
Moloney E, Kavanagh KS, Buckley TC, Cooney JC.Streptococcus equi ssp. equi is the causative agent of 'Strangles' in horses. This is a debilitating condition leading to economic loss, yard closures and cancellation of equestrian events. There are multiple genotypes of S. equi ssp. equi which can cause disease, but to date there has been no systematic study of strains which are prevalent in Ireland. This study identified and classified Streptococcus equi ssp. equi strains isolated from within the Irish equine industry. Results: Two hundred veterinary isolates were subjected to SLST (single locus sequence typing) based on an internal sequenc...
Hijazin M, Ulbegi-Mohyla H, Alber J, Lämmler C, Hassan AA, Prenger-Berninghoff E, Weiss R, Zschöck M.An Arcanobacterium haemolyticum strain isolated from a postcastrational lesion of a horse was identified phenotypically and genotypically. The latter was performed by sequencing the 16S-23S rDNA intergenic spacer region (ISR), by amplification of the gene encoding A. haemolyticum phospholipase D, by amplification of A. haemolyticum specific parts of ISR-23S rDNA and by amplification of the newly described CAMP factor family protein encoding gene of A. haemolyticum. This indicates (as described previously for seven additional A. haemolyticum strains; Hassan et al. 2009) that A. haemolyticum see...
Padilha FGF, El-Jaick KB, de Castro L, Moreira ADS, Ferreira AMR.Polymorphisms in MSTN have previously been associated with equine performance. Therefore, the aim of this study was to identify variants in intron 1 in 16 Brazilian Sport Horses selected for competition in eventing and their possible effects of selection on performance. Among the nine variants identified, eight had already been reported in previous studies or genomic databases, although they showed differences in frequencies when compared with other horse breeds. Moreover, a new mutation was identified in two horses, both in heterozygous form. Considering the absence of molecular studies in t...
Liu C, Lei H, Ran X, Wang J.The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including , , and and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. had the lowest / ratio (0.560) compared with the other three loci, indicating that was conserved and could be conserved after undergoing selective processes. Nine , five , nine and seven codons were under significant positive selection at the antigen b...
Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Takahashi Y, Nagata SI.Thoroughbreds are some of the most famous racehorses worldwide and are currently animals of high economic value. To understand genomic variability in Thoroughbreds, we identified genome-wide insertions and deletions (INDELs) and obtained their allele frequencies in this study. INDELs were obtained from whole-genome sequencing data of 101 Thoroughbred racehorses by mapping sequence reads to the horse reference genome. By integrating individual data, 1,453,349 and 113,047 INDELs were identified in the autosomal (1-31) and X chromosomes, respectively, while 18 INDELs were identified on the mitoch...
de Faria DA, do Prado Paim T, Dos Santos CA, Paiva SR, Nogueira MB, McManus C.Since domestication, horse breeds have adapted to their environments and differentiated from one another. This paper uses two methods to detect selection signatures in 23 horse breeds, eight of which are Brazilian (610 animals), both cold-blooded and warm-blooded, from temperate and tropical regions. These animals were genotyped using the GGP Equine BeadChip and we analysed the data by Principal Component Analysis (PCA). The samples were separated into groups based on their geographical area of origin and PCA results studied. The genomic regions under selection were detected by hapFLK and PCAd...
Liu X, Zhang Y, Pu Y, Ma Y, Jiang L.Transposable elements (TEs) are diverse, abundant, and complicated in genomes. They not only can drive the genome evolution process but can also act as special resources for adaptation. However, little is known about the evolutionary processes that shaped horses. In this work, 126 horse assemblages involved in most horse breeds in China were used to investigate the patterns of TE variation for the first time. By using RepeatMasker and melt software, we found that the horse-specific short interspersed repetitive elements family, equine repetitive elements (ERE1), exhibited polymorphisms in hors...
Reeben M, Koho NM, Raekallio M, Hyyppä S, Pösö AR.Transport of lactate across membranes is facilitated by proton-monocarboxylate transporters (MCT). The most widely distributed isoform is MCT1, which needs an ancillary protein CD147. Studies on erythrocytes have shown that high activity of MCT1 is inherited as the dominant allele and that activity is regulated through CD147. Mutations of human MCT1 have been described that appear to impair lactate transport in muscles and cause exertional rhabdomyolysis. There are no reports of this potential relationship in the horse. Objective: To obtain sequences of equine MCT1 and CD147 to examine differe...
Shnaiderman-Torban A, Navon-Venezia S, Paitan Y, Archer H, Abu Ahmad W, Bonder D, Hanael E, Nissan I, Zizelski Valenci G, Weese SJ, Steinman A.We aimed to investigate the prevalence, molecular epidemiology and prevalence factors for Extended Spectrum β-Lactamase-producing Enterobacteriaceae (ESBL-E) shedding by race horses. A cross-sectional study was performed involving fecal samples collected from 169 Thoroughbred horses that were housed at a large racing facility in Ontario, Canada. Samples were enriched, plated on selective plates, sub-cultured to obtain pure cultures and ESBL production was confirmed. Bacterial species were identified and antibiotic susceptibility profiles were assessed. E. coli sequence types (ST) and ESBL gen...
Ayala-Valdovinos MA, Galindo-García J, Sánchez-Chiprés D, Duifhuis-Rivera T, Anguiano-Estrella R.The 'Gait keeper' mutation in the DMRT3 gene alters locomotion and gait patterns in horses. This mutation (C>A) has been found in all gaited breeds of horses analyzed but is absent in most non-gaited breeds. We developed a new mutagenically separated polymerase chain reaction (MS-PCR) based method for simple detection of horse DMRT3 genotype. Our method was applied in a preliminary study to determine DMRT3 allele frequencies in 78 Azteca horses (AZ) and 53 Costa Rican Saddle Horses (CRSH). We found a wild-type C allele frequency of 100% in the AZ horses. For the CRSH, the wild-type C freque...
Bowling AT, Gordon L, Penedo MC, Wictum E, Beebout J.We describe a method for agarose IEF under acid conditions in which a single gel can be used to diagnose from equine red cell lysates genetic variants for carbonic anhydrase (CA) and catalase (Cat). Family and population data for 4801 horses of 27 breeds and seven trap sites of Great Basin feral horses are presented to support the presence of a sixth CA allele, CAE, which has been recognized previously, but not described by published data. Allelic frequencies for the two systems suggest it may be appropriate to use this gel for parentage verification programmes or to obtain population data for...
Diesterbeck US, Hertsch B, Distl O.The aim of this study was to identify quantitative trait loci (QTLs) for pathologic changes in the navicular bone in Hanoverian warmblood horses. Seventeen paternal half-sib groups comprising 192 individuals were analyzed in a whole-genome scan. These families included 144 progeny and grandchildren, which were randomly chosen from the Hanoverian warmblood. Three different traits were considered: deformed canales sesamoidales and radiographic changes in the contour and in the structure of the navicular bone. The genome scan included in total 214 highly polymorphic microsatellite markers. The pu...
de Almeida Campos AC, Cicolo S, de Oliveira CM, Molina CV, Navas-Suárez PE, Poltronieri Dos Santos T, da Silveira VB, Barbosa CM, Baccarin RYA....Equid herpesvirus (EHV) commonly affects horses causing neurologic and respiratory symptoms beside spontaneous abortions, meaning huge economic losses for equine industry worldwide. In foals, the virus can facilitate secondary infections by Rhodococcus equi, important in morbidity and mortality in equines. A total of five genotypes of EHV were previously described in Brazil including EHV-1, EHV-2, EHV-3, EHV-4, and EHV-5. EHV-2 genotype had only been previously described in Brazil in asymptomatic animals. We report the investigation of the dead of 11 foals in Middle-west region of Brazil showi...
Bustos CP, Retamar G, Leiva R, Frosth S, Ivanissevich A, Demarchi ME, Walsh S, Frykberg L, Guss B, Mesplet M, Waller A.Streptococcus dysgalactiae subsp. equisimilis (Sde) is a commensal bacterium of horses that causes opportunistic infections. The aim of the work was to study genotypic and phenotypic properties of the Sde strain related to equine neonatal mastitis. Sde was isolated from an 8 day-old filly and sequenced for genome analysis, antibiotic susceptibility tests and virulence factor (VF) assays. The Sde strain presented the novel emm-subtype stC839.12 and the novel multilocus-sequence type ST-670, which belonged to a specific equine genotype group. Although no specific genotypic mechanisms related to ...
Braend M.During the routine parentage control of Norwegian Trotter horses with 10 000 parent offspring combinations two irregular transmissions of Pr alleles were found. The allele products were provisionally named D1 and D2. They appeared in two stallions which were typed as D1I and D2N respectively. The first stallion transmitted PrD1 to seven out of 10 offspring and the second stallion PrD2 to two of four offspring. Photographs of seven new Pr phenotypes are presented.
Ouragh L, Mériaux JC, Braun JP.Gene frequencies at 16 blood group and protein polymorphism loci (A, C, D, K, P, Q, U, Al, Gc, Es, A1B, Tf, PGD, PGM, GPI and Pi) are given for three horse breeds in Morocco (Arabian, Arab-Barb and Barb). These data are used to calculate average heterozygosity (h), Nei's standard genetic distance (DN) and probability of exclusion (PE). Variability expressed as the average heterozygosity was lower in the Arabian (0.330 +/- 0.066), while it was higher and almost the same in the Arab-Barb (0.413 +/- 0.071) and the Barb (0.414 +/- 0.070). The shortest genetic distance was found between Barb and Ar...
