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Topic:Genomics

Genomics in horses involves the study and analysis of the horse genome to understand genetic variations and their implications for equine health, performance, and breeding. This field encompasses the identification and mapping of genes associated with specific traits, diseases, and conditions in horses. Techniques such as whole-genome sequencing and genome-wide association studies (GWAS) are employed to explore genetic diversity and inheritance patterns among different horse breeds. Genomics provides insights into hereditary disorders, informs selective breeding practices, and aids in the development of personalized veterinary care. This page compiles peer-reviewed research studies and scholarly articles that explore the applications, methodologies, and findings of genomic research in equine science.
DNA testing in the equine.
The Veterinary clinics of North America. Equine practice    December 1, 1995   Volume 11, Issue 3 525-542 doi: 10.1016/s0749-0739(17)30314-0
Malyj W.No abstract available
Cloning of a DNA repeat element from horse: DNA sequence and chromosomal localization.
Genome    December 1, 1995   Volume 38, Issue 6 1132-1138 doi: 10.1139/g95-150
Broad TE, Forrest JW, Lewis PE, Pearce PD, Phua SH, Pugh PA, Stewart-Scott IA.A DNA repeat element, revealed initially by digestion of horse DNA with TaqI, was cloned and characterized by Southern and in situ hybridization studies and nucleotide sequencing. The clone, e4/1, consisted of 32 tandem reiteration of a unit repeat of 21-22 bp, and produced multilocus DNA fingerprinting profiles that were useful for parentage analysis in horses. The tandem repeat element was shown by in situ hybridization to be localized in the centromeres of the acrocentric but not metacentric classes of horse chromosomes.
Families of tandemly repeated DNA elements from horse: cloning, nucleotide sequence, and organization.
Genome    December 1, 1995   Volume 38, Issue 6 1285-1289 doi: 10.1139/g95-169
Broad TE, Ede AJ, Forrest JW, Lewis PE, Phua SH, Pugh PA.DNA repeats, revealed initially by digestion of horse DNA with restriction enzymes, were cloned and characterized by cross-hybridization studies and nucleotide sequencing. The Sau-like family of tandem repeats contained two classes of repetitive elements with unit repeats of about 80 bp that shared no sequence similarity. Both unit repeats were present, frequently in tandem, in cloned segments of horse DNA of less than 600 bp. Evidence is presented, based on their ladderlike patterns of hybridization to horse DNA and their high level of similarity to published sequences of satellites from equi...
Genetics and disease in the horse.
Equine veterinary journal    November 1, 1995   Volume 27, Issue 6 400-401 doi: 10.1111/j.2042-3306.1995.tb04416.x
Gerber V, Bailey E.No abstract available
Amino acid sequence of HSP-1, a major protein of stallion seminal plasma: effect of glycosylation on its heparin- and gelatin-binding capabilities.
The Biochemical journal    September 1, 1995   Volume 310 ( Pt 2), Issue Pt 2 615-622 doi: 10.1042/bj3100615
Calvete JJ, Mann K, Schäfer W, Sanz L, Reinert M, Nessau S, Raida M, Töpfer-Petersen E.We report the complete amino acid sequence of HSP-1, a major protein isolated from stallion seminal plasma or acid extracts of ejaculated spermatozoa. The protein consists of 121 amino acids organized in two types of homologous repeats arranged in the pattern AA'BB'. Each of the 13-15-residue A-type repeats contains two O-linked oligosaccharide chains. The B-type repeats span 44-47 amino acids each, are not glycosylated, and have the consensus pattern of the gelatin-binding fibronectin type-II module. This domain also occurs in the major bovine seminal plasma heparin-binding proteins PDC-109 (...
An equine microsatellite repeat at the VIAS-H64 locus.
Animal genetics    August 1, 1995   Volume 26, Issue 4 282 doi: 10.1111/j.1365-2052.1995.tb03263.x
Ewen KR, Matthews ME.No abstract available
Mitochondrial DNA sequences of various species of the genus Equus with special reference to the phylogenetic relationship between Przewalskii’s wild horse and domestic horse.
Journal of molecular evolution    August 1, 1995   Volume 41, Issue 2 180-188 doi: 10.1007/BF00170671
Ishida N, Oyunsuren T, Mashima S, Mukoyama H, Saitou N.The noncoding region between tRNAPro and the large conserved sequence block is the most variable region in the mammalian mitochondrial DNA D-loop region. This variable region (ca. 270 bp) of four species of Equus, including Mongolian and Japanese native domestic horses as well as Przewalskii's (or Mongolian) wild horse, were sequenced. These data were compared with our recently published Thoroughbred horse mitochondrial DNA sequences. The evolutionary rate of this region among the four species of Equus was estimated to be 2-4 x 10(-8) per site per year. Phylogenetic trees of Equus species demo...
The DNA sequence of equine herpesvirus 2.
Journal of molecular biology    June 9, 1995   Volume 249, Issue 3 520-528 doi: 10.1006/jmbi.1995.0314
Telford EA, Watson MS, Aird HC, Perry J, Davison AJ.The complete DNA sequence of equine herpesvirus 2 (EHV-2) strain 86/67 was determined. The genome is 184,427 bp in size and has a base composition of 57.5% G + C. Unusually for a herpesvirus, about a third of the sequence distributed in several large blocks appears not to encode proteins. The 79 open reading frames that were identified as probably polypeptide-coding are predicted to encode 77 distinct proteins. Amino acid sequence comparisons confirmed that EHV-2 is a gamma-herpesvirus that is genetically collinear with herpesvirus saimiri (HVS; a gamma 2-herpesvirus) and Epstein-Barr virus (E...
Extensive mtDNA diversity in horses revealed by PCR-SSCP analysis.
Animal genetics    June 1, 1995   Volume 26, Issue 3 193-196 doi: 10.1111/j.1365-2052.1995.tb03162.x
Marklund S, Chaudhary R, Marklund L, Sandberg K, Andersson L.The hypervariable D-loop region of mitochondrial DNA (mtDNA) was amplified with the polymerase chain reaction using total horse DNA samples. Analysis of single strand conformation polymorphism (SSCP) of denatured amplification products was carried out by native polyacrylamide (8%) gel electrophoresis followed by silver staining. As many as 15 distinct SSCP variants were revealed when screening a total of 78 maternally unrelated horses representing five different breeds. All breeds showed a high degree of polymorphism and the estimated probability (PImt) that two maternally unrelated individual...
Comparative RAPD-PCR analysis of lungworms (Dictyocaulidae) from fallow deer, cattle, sheep, and horses.
Zentralblatt fur Veterinarmedizin. Reihe B. Journal of veterinary medicine. Series B    May 1, 1995   Volume 42, Issue 3 187-191 doi: 10.1111/j.1439-0450.1995.tb00699.x
Epe C, Bienioschek S, Rehbein S, Schnieder T.Genomic DNA isolated from the four Dictyocaulus species D. viviparus, D. eckerti, D. filaria and D. arnfieldi was compared by random amplified polymorphic DNA polymerase chain reaction (RAPD)-PCR to get additional information whether lungworms from fallow deer belong to a separate species (D. eckerti) or have to be regarded as an isolate of D. viviparus in wild ruminants. The resulting banding patterns of the electrophoresed PCR products were compared to assess the degree of genetic differences between the different lungworms. For the two D. viviparus isolates a similarity coefficient of 93.4%...
Sodium channel inactivation is impaired in equine hyperkalemic periodic paralysis.
Journal of neurophysiology    May 1, 1995   Volume 73, Issue 5 1892-1899 doi: 10.1152/jn.1995.73.5.1892
Cannon SC, Hayward LJ, Beech J, Brown RH.1. Equine hyperkalemic periodic paralysis (E-HPP) is a dominantly inherited disorder of muscle that causes recurrent episodes of stiffness (myotonia) and weakness in association with elevated serum K+. Affected horses carry a mutant allele of the skeletal muscle isoform of the Na channel alpha-subunit. To understand how this mutation may cause the disease phenotype, the functional defect in Na channel behavior was defined physiologically by recording unitary currents from cell-attached patches on normal and affected equine myotubes. 2. The presence of the mutation was confirmed in our cell lin...
Equine parentage testing by microsatellite locus at chromosome 1q2.1.
Animal genetics    April 1, 1995   Volume 26, Issue 2 123-124 doi: 10.1111/j.1365-2052.1995.tb02647.x
Sakagami M, Tozaki T, Mashima S, Hirota K, Mukoyama H.No abstract available
Delineating minimal protein domains and promoter elements for transcriptional activation by lentivirus Tat proteins.
Journal of virology    April 1, 1995   Volume 69, Issue 4 2605-2610 doi: 10.1128/JVI.69.4.2605-2610.1995
Southgate CD, Green MR.Lentivirus Tat proteins comprise a novel class of RNA-binding transcriptional activators that are essential for viral replication. In this study, we performed a series of protein fusion experiments to delineate the minimal protein domains and promoter elements required for Tat action. We show that a 15-amino-acid region of equine infectious anemia virus (EIAV) Tat protein, when fused to the GAL4 or LexA DNA binding domain, can activate transcription in appropriate promoter contexts. In the natural human immunodeficiency virus type 1 long terminal repeat, activation by Tat is dependent on multi...
Differences in a ribosomal DNA sequence of Strongylus species allows identification of single eggs.
International journal for parasitology    March 1, 1995   Volume 25, Issue 3 359-365 doi: 10.1016/0020-7519(94)00116-6
Campbell AJ, Gasser RB, Chilton NB.In the current study, molecular techniques were evaluated for the species identification of individual strongyle eggs. Adult worms of Strongylus edentatus, S. equinus and S. vulgaris were collected at necropsy from horses from Australia and the U.S.A. Genomic DNA was isolated and a ribosomal transcribed spacer (ITS-2) amplified and sequenced using polymerase chain reaction (PCR) techniques. The length of the ITS-2 sequence of S. edentatus, S. equinus and S. vulgaris ranged between 217 and 235 nucleotides. Extensive sequence analysis demonstrated a low degree (0-0.9%) of intraspecific variation...
Unusual D system inheritance in Anglo-Arab horse.
Animal genetics    February 1, 1995   Volume 26, Issue 1 53-54 doi: 10.1111/j.1365-2052.1995.tb02622.x
Kakoi H, Gawahara H, Miura N.An unusual D system phenogroup appeared in one family line of Anglo-Arab horse. This phenogroup probably originated from inheritance with an apparent absence of factors and was transmitted through successive generations.
A new GC allele in horses.
Hereditas    January 1, 1995   Volume 122, Issue 1 91-93 doi: 10.1111/j.1601-5223.1995.00091.x
Ouragh L, Juneja RK, Bengtsson S.No abstract available
Equine parentage testing and DNA technology–the route forward?
The British veterinary journal    January 1, 1995   Volume 151, Issue 1 1-3 doi: 10.1016/s0007-1935(05)80054-5
Knapp MR, Goelet P.No abstract available
The complete cDNA and deduced amino acid sequence of equine IgE.
Molecular immunology    January 1, 1995   Volume 32, Issue 1 1-8 doi: 10.1016/0161-5890(94)00143-o
Navarro P, Barbis DP, Antczak D, Butler JE.The cDNA from a transcript encoding the complete heavy chain of the equine immunoglobulin IgE has been cloned and sequenced. A fragment of the equine epsilon gene was amplified from cDNA using PCR and this fragment was then used to probe a horse cDNA library prepared from peripheral blood lymphocytes. A recombinant clone containing the cDNA encoding the complete horse epsilon chain and its associated V-D-J and leader, was subsequently isolated and sequenced. Comparison of the deduced amino acid sequence of equine IgE with the C epsilon heavy chains of other species indicates it to be most simi...
Nucleotide sequence of exons 5 to 9 of the p53 tumour-suppressor gene of the donkey (Equus asinus).
DNA sequence : the journal of DNA sequencing and mapping    January 1, 1995   Volume 6, Issue 1 61-63 doi: 10.3109/10425179509074702
Nasir L, Reid SW.The evolutionary conserved region of the equine homologue of the p53 gene from the donkey genome was PCR amplified and cloned. The 1380 bp fragment consisted of exons 5 to 9 and the intervening introns. The exonic and intronic DNA sequences showed a variable but high level of homology with previously published human sequences. The aminoacid sequences corresponding to the evolutionary conserved domains II, III, and V were identical to the human regions, whilst domain IV was 96% homologous.
The identification of polymorphic microsatellite loci in the horse and their use in thoroughbred parentage testing.
The British veterinary journal    January 1, 1995   Volume 151, Issue 1 9-15 doi: 10.1016/s0007-1935(05)80057-0
Binns MM, Holmes NG, Holliman A, Scott AM.Six new horse microsatellite loci were identified by sequencing M13 clones containing horse genomic inserts which gave positive signals when probed with a CA/GT repeat probe. Oligonucleotide primer pairs were synthesized for these loci and for two previously described horse microsatellites, HTG4 and HTG6. Polymerase chain reaction assays were then carried out on a panel of 20 different unrelated Thoroughbred horse DNAs. DNAs from eight cases of double covering which could not be solved by conventional blood typing were also examined. Several of the loci amplified were found to be polymorphic a...
The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region.
Gene    October 21, 1994   Volume 148, Issue 2 357-362 doi: 10.1016/0378-1119(94)90713-7
Xu X, Arnason U.The sequence of the mitochondrial (mt) DNA of the horse (Equus caballus) was determined. The length of the sequence presented is 16,660 bp. This figure, however, is not absolute due to pronounced heteroplasmy caused by variable numbers of the motif GTGCACCT in the control region of different molecules. Boundaries of the 13 peptide-coding genes were determined by the presence of start and stop codons, and by analogy with other eutherian mtDNAs. Three genes (COIII, NADH3 and NADH4) were not terminated by a stop codon. Comparison among the peptide-coding genes of the horse and eight other mammals...
Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms.
Nucleic acids research    October 11, 1994   Volume 22, Issue 20 4167-4175 doi: 10.1093/nar/22.20.4167
Nikiforov TT, Rendle RB, Goelet P, Rogers YH, Kotewicz ML, Anderson S, Trainor GL, Knapp MR.A new method for typing single nucleotide polymorphisms in DNA is described. In this method, specific fragments of genomic DNA containing the polymorphic site(s) are first amplified by the polymerase chain reaction (PCR) using one regular and one phosphorothioate-modified primer. The double-stranded PCR product is rendered single-stranded by treatment with the enzyme T7 gene 6 exonuclease, and captured onto individual wells of a 96 well polystyrene plate by hybridization to an immobilized oligonucleotide primer. This primer is designed to hybridize to the single-stranded target DNA immediately...
Multiple genotypes of mitochondrial DNA within a horse population from a small region in Yunnan Province of China.
Biochemical genetics    October 1, 1994   Volume 32, Issue 9-10 371-378 doi: 10.1007/BF02426899
Wang W, Liu AH, Lin SY, Lan H, Su B, Xie DW, Shi LM.mtDNA genotypes of six domestic horses (three adult short horses whose heights are under 1 m and three common domestic horses) from a small region of 15 km2 in Malipo county of Yunnan province of China were investigated by the technique of restriction fragment length polymorphism (RFLP) with 16 restriction endonucleases which recognize 6-bp sequences. An average of 56 fragments for an individual was obtained. Unlike other domestic animals, this population of horses exhibits high mtDNA genetic diversity. Each of the six horses has a specific mtDNA genotype showing a pattern of multiple maternal...
Equine dinucleotide repeat polymorphism at the VIAS-H7 locus.
Animal genetics    August 1, 1994   Volume 25, Issue 4 292 doi: 10.1111/j.1365-2052.1994.tb00221.x
Ewen KR, Matthews ME.No abstract available
Polymorphic sequence in the D-loop region of equine mitochondrial DNA.
Animal genetics    August 1, 1994   Volume 25, Issue 4 215-221 doi: 10.1111/j.1365-2052.1994.tb00196.x
Ishida N, Hasegawa T, Takeda K, Sakagami M, Onishi A, Inumaru S, Komatsu M, Mukoyama H.The D-loop regions in equine mitochondrial DNA were cloned from three thoroughbred horses by polymerase chain reaction (PCR). The total number of bases in the D-loop region were 1114 bp, 1115 bp and 1146 bp. The equine D-loop region is A/T rich like many other mammalian D-loops. The large central conserved sequence block and small conserved sequence blocks 1, 2 and 3, that are common to other mammals, were observed. Between conserved sequence blocks 1 and 2 there were tandem repeats of an 8 bp equine-specific sequence TGTGCACC, and the number of tandem repeats differed among individual horses....
Pregnancy-associated endometrial expression of antileukoproteinase gene is correlated with epitheliochorial placentation.
Molecular reproduction and development    August 1, 1994   Volume 38, Issue 4 357-363 doi: 10.1002/mrd.1080380402
Badinga L, Michel FJ, Fields MJ, Sharp DC, Simmen RC.Uterine expression of the mRNA encoding antileukoproteinase (ALP) is highest in pig uterus during mid- to late pregnancy, suggesting a stage of pregnancy-dependent role for this elastase/cathepsin G protease inhibitor in feto-maternal interactions. To examine a potential relationship between uterine synthesis of ALP and the type of placentation in mammalian species, the expression of ALP mRNA and/or protein in pregnant mares, cows, rats, and mice was evaluated. Genomic DNA and mRNA hybridization analyses were performed using a porcine ALP cDNA as probe. The concentration of ALP protein in repr...
Genomic sequences of bovine papillomaviruses in formalin-fixed sarcoids from Australian horses revealed by polymerase chain reaction.
Veterinary microbiology    July 1, 1994   Volume 41, Issue 1-2 163-172 doi: 10.1016/0378-1135(94)90145-7
Bloch N, Breen M, Spradbrow PB.Seventy six formalin-fixed paraffin-embedded sarcoids from 62 Australian horses, collected over a ten year period, were examined for the presence of genomic sequences from bovine papillomavirus 1 and 2 (BPV1, BPV2) with the polymerase chain reaction (PCR). Sequences that could be amplified by primers specific for BPV1 and BPV2 were present in 56 of the 76 sarcoids (73%). A restriction site present in BPV1 and absent from BPV2 was detected in 28 of 34 amplified products that were treated with endonuclease.
A highly polymorphic horse microsatellite locus: VHL20.
Animal genetics    June 1, 1994   Volume 25, Issue 3 207 doi: 10.1111/j.1365-2052.1994.tb00129.x
van Haeringen H, Bowling AT, Stott ML, Lenstra JA, Zwaagstra KA.No abstract available
Comparative genetic analysis of Swiss and Spanish isolates of Echinococcus granulosus by southern hybridization and Random Amplified Polymorphic DNA technique.
Applied parasitology    June 1, 1994   Volume 35, Issue 2 107-117 
Siles-Lucas M, Felleisen R, Cuesta-Bandera C, Gottstein B, Eckert J.Swiss and Spanish isolates of Echinococcus granulosus were compared using different molecular biological techniques: Genomic DNAs isolated from parasites originating from various intermediate hosts were subjected to Southern hybridization with different probes, the same source of DNA was used for DNA amplification using the Random Amplified Polymorphic DNA (RAPD) technique. With both methods the various isolates (metacestodes) of E. granulosus exhibited characteristic banding patterns which allowed us to assign them to the following groups of homologous profiles: (a) isolates of horse and donk...
Comparison of thoroughbred and Arabian horses using RAPD markers.
Animal genetics    June 1, 1994   Volume 25 Suppl 1 105-108 doi: 10.1111/j.1365-2052.1994.tb00414.x
Bailey E, Lear TL.We compared pools of DNA from 10 Thoroughbred horses and 10 Arabian horses for the presence of randomly amplified polymorphic DNA (RAPD) markers which might be useful in distinguishing between the breeds. Using 212 decamer oligonucleotides and our polymerase chain reaction (PCR) conditions, 173 of the primers produced scoreable bands. The number of bands ranged from 0 to 9 with an average of 3.6. In family studies using 11 arbitrarily selected primers, five of the 11 primers produced polymorphic bands which exhibited Mendelian inheritance as dominant markers. When comparing the pooled DNA from...
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