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.
Construction of a horse BAC library and cytogenetical assignment of 20 type I and type II markers. A horse BAC library was constructed with about 40,000 clones and mean insert size of 110 kb representing a 1.5 genome equivalent coverage and a probability of finding a single sequence of 0.75. It was characterized by PCR screening of about 130 sequences of horse microsatellites and exonic gene sequences retrieved from databases. BACs containing 8 microsatellites and 12 genes were subsequently localized by fluorescent in situ hybridization (FISH) on chromosomes. Two linkage groups were newly assigned to chromosomes: LG2 to ECA3 and LG5 to ECA24, and five linkage groups were also oriented--LG3,...
A dinucleotide mutation in the endothelin-B receptor gene is associated with lethal white foal syndrome (LWFS); a horse variant of Hirschsprung disease. Lethal white foal syndrome (LWFS) is a congenital anomaly of horses characterized by a white coat colour and aganglionosis of the bowel, which is similar to Hirschsprung disease (HSCR). We decided to investigate possible mutations of the endothelin-B receptor gene ( EDNRB ) in LWFS as recent studies in mutant rodents and some patients have demonstrated EDNRB defects. First, we identified a full-length cDNA for horse EDNRB . This cDNA fragment contained a 1329 bp open reading frame which encoded 443 amino acid residues. The predicted amino acid sequence was 89, 91 and 85% identical to human, bo...
Cloning of equine interleukin 1 receptor antagonist and determination of its full-length cDNA sequence. To clone equine interleukin 1 receptor antagonist (IL-1ra) and determine its full-length cDNA sequence. Methods: A cDNA library derived from lipopolysaccharide-stimulated equine monocytes was screened by means of plaque hybridization to radiolabeled equine IL-1ra DNA probes generated by means of the polymerase chain reaction. The cDNA nucleotide sequence for equine IL-1ra was determined by use of the dideoxy chain termination technique, analyzed by use of computer software for sequence characteristics, and compared with sequences reported for IL-1ra of other species. Results: The cDNA of equin...
A conserved structural element in horse and mouse IGF2 genes binds a methylation sensitive factor. The equine IGF2 gene has been cloned and characterised. It spans a 9 kb region, which is substantially less than the corresponding human gene. Three coding exons and three untranslated leader exons, all highly homologous to those in other species, were identified. Downstream of the polyadenylation site in exon 6, a dinucleotide repeat sequence was identified. Three putative promoters (P1-P3) were localised in the 5' region of the gene. RNase protection analysis revealed two active promoters in fetal tissues, P2 and P3, whereas P3 was the only promoter active in adult tissues. This represents a...
A missense mutation in the endothelin-B receptor gene is associated with Lethal White Foal Syndrome: an equine version of Hirschsprung disease. Lethal White Foal Syndrome is a disease associated with horse breeds that register white coat spotting patterns. Breedings between particular spotted horses, generally described as frame overo, produce some foals that, in contrast to their parents, are all white or nearly all white and die shortly after birth of severe intestinal blockage. These foals have aganglionosis characterized by a lack of submucosal and myenteric ganglia from the distal small intestine to the large intestine, similar to human Hirschsprung Disease. Some sporadic and familial cases of Hirschsprung Disease are due to muta...
A single base transversion in the flanking region of an equine microsatellite locus affects amplification of one allele. 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...
Organization of the equine immunoglobulin constant heavy chain genes. I. c epsilon and c alpha genes. We provide a restriction map of the equine c epsilon and c alpha genes as a molecular basis for isotype classification. Human and murine DNA probes were used for identification of homologous equine DNA sequences and for isolation of the equine c epsilon and c alpha genes from a genomic DNA library. A detailed map of the equine 5'-s epsilon/c epsilon-s alpha/c alpha-3' gene region was obtained. Equine c epsilon and c alpha DNA probes were prepared and used for restriction analysis of immunoglobulin heavy chain gene loci from different horses. This analysis indicated the presence of only one equ...
Equus caballus gelsolin–cDNA sequence and protein structural implications. We have generated and characterized the cDNA from equine smooth muscle that encodes gelsolin, an actin-modulating protein. Overlapping cDNA clones synthesized by the reverse transcriptase/polymerase chain reaction and clones isolated from a horse genomic library provided the complete primary structure for the intracellular isoform of gelsolin, while cDNA complemented with protein sequence data produced the full-length primary transcript of the gelsolin isoform found circulating in equine plasma. The deduced amino acid sequences of the intracellular and secreted versions of equine gelsolin infe...
Tobiano spotting pattern in horses: linkage of To with AlA and linkage disequilibrium. In a study of 2,786 tobiano and non-tobiano horses involved in paint horse breeding programs throughout the United States, the inheritance of the tobiano color pattern gene was tracked in pedigrees using the tightly linked polymorphic albumin gene. The dominant tobiano allele (T(o)), which produces the tobiano spotting pattern in horses, was in coupling with both AIA and AIB alleles at the albumin locus. The frequency of the T(o):AIA linkage phase among all the homozygous tobiano horses in this study including offspring and parents (N = 127), was 0.08. The T(o):AIB linkage phase was the most f...
Horse genome mapping: a new era in horse genetics? This research study discusses the importance of creating a gene map for horses to enhance understanding of horse genetics, improve selective breeding methods, and aid in the diagnosis and treatment […]
[Analysis of the distribution of ribosomal RNA genes on chromosomes of the domestic horse (Equus caballus) using fluorescent in situ hybridization]. Distribution of blocks of ribosomal RNA genes along metaphase chromosomes of 26 horses from five breeds was determined by means of a modified method of fluorescence in situ hybridization (FISH) in combination with simultaneous R- banding. Gene loci coding for rRNA were mapped to the region of secondary constriction on the short arm of chromosome 1, and to the pericentromeric regions of chromosomes 27, 28, and 31. The nucleolar organizer region (NOR) on chromosome 27 was not described earlier. Interindividual and interchromosomal NOR polymorphism was detected With the use of a semiquantitative ...
Comparison of nucleic and amino acid sequences and phylogenetic analysis of open reading frames 3 and 4 of various equine arteritis virus isolates. The genetic variation in equine arteritis virus (EAV) protein-encoding open reading frames (ORFs) 3 and 4 genes was investigated. Nucleic and deduced amino acid sequences from seven different EAV isolates (one European, one American and five Canadian isolates) and the Arvac vaccine strain were compared with those of Bucyrus reference strain. ORF 3 nucleotide and amino acid sequence identities between these isolates (including the Arvac vaccine strain) and the Bucyrus reference strain ranged from 85.6 to 98.8%, and 85.3 to 98.2%, respectively, whereas ORF 4 nucleotide and amino acid sequence id...
Novel and dynamic evolution of equine infectious anemia virus genomic quasispecies associated with sequential disease cycles in an experimentally infected pony. We have investigated the genetic evolution of three functionally distinct regions of the equine infectious anemia virus (EIAV) genome (env, rev, and long terminal repeat) during recurring febrile episodes in a pony experimentally infected with a well-characterized reference biological clone designated EIAV(PV). Viral populations present in the plasma of an EIAV(PV)-infected pony during sequential febrile episodes (18, 34, 80, 106, and 337 days postinfection) were amplified from viral RNA, analyzed, and compared to the inoculated strain. The comparison of the viral quasispecies showed that the ...
Characterization of the equine glycoprotein hormone alpha-subunit gene reveals divergence in the mechanism of pituitary and placental expression. The equine glycoprotein hormone alpha-subunit gene is expressed in both pituitary and placenta, unlike that of all other nonprimate mammals studied, in which expression is limited to pituitary. Previous studies of the 5'-flanking region of the equine alpha-subunit promoter have revealed unique characteristics as well as similarities with the human alpha-subunit promoter, which demonstrates a similar pattern of tissue-specific expression. We have cloned and sequenced the equine alpha-subunit gene and have used tissue culture systems and transgenic mice to characterize its expression. Unlike the...
Mitogenic effects of epidermal growth factor and platelet-derived growth factor on canine and equine mesangial cells in vitro. To evaluate the effects of epidermal growth factor (EGF) and platelet-derived growth factor (PDGF) on canine and equine mesangial cell (MC) proliferation in vitro. Methods: Third- through eighth-passage canine and equine MC were obtained from explant outgrowth after differential sieving of glomeruli isolated from the kidneys of clinically normal dogs and horses. Methods: Mitogenic effects of serum, insulin, EGF, and PDGF were evaluated in MC by induction of DNA synthesis, measured as stimulation of [3H]thymidine incorporation and increase in cell numbers. Results: Epidermal growth factor was a...
An introduction to mammalian interspecific hybrids. Haldane's law states that in interspecific hybrids, it is the heterogametic sex that is likely to be absent, rare, or sterile. In mammals, there is increasing evidence to suggest that this may be due to the high mutation rate of male sex-determining genes on the Y chromosome. The mule, humanity's first successful attempt at genetic engineering, provides some support for this concept. Interspecific hybrids may also shed new light on the importance of the maternal transmission of mitochondrial DNA and the phenomenon of genomic imprinting.
Characterization, genetic and physical mapping analysis of 36 horse plasmid and cosmid-derived microsatellites. Thirty-six new horse microsatellites (11 from plasmid libraries and 25 from a cosmid library) were isolated and characterized on a panel of four horse breeds. Thirty were found to be polymorphic with heterozygosity levels ranging between 0.20 and 0.87. Twenty-two of the cosmids were physically mapped to R-banded single horse Chromosomes (Chrs) 1, 3, 4, 9, 11, 12, 13, 15, 18, 19, 21, 22, 23 and three to pericentromeric regions. Furthermore, linkage analysis between a selection of 42 DNA markers, including those presented in this study, and 16 conventional markers of the horse hemotype was perfo...
FISH mapping of the IGF2 gene in horse and donkey-detection of homoeology with HSA11. Three genomic subclones derived from a phage clone containing the equine IGF2 gene were used to FISH map the gene on horse (ECA) and donkey (EAS) metaphase chromosomes. The gene mapped on ECA 12q13 band and is the first locus mapped to this horse chromosome. In donkey the gene mapped very terminal on the long arm of one small submetacentric chromosome that shows almost identical DAPI-banding pattern with ECA12. This is the first locus mapped in donkey genome. Cross species chromosome painting of equine metaphase chromosomes with human Chromosome (Chr) 11-specific probe showed homoeology of thi...
Profiles of fragments after pulsed-field gel electrophoresis of cleaved genomic DNA from strains of Taylorella equigenitalis isolated from horses in Norway. The genomic DNA of eight strains of Taylorella equigenitalis, isolated from seven Norwegian Trotters and a Norwegian pony with contagious equine metritis in Norway, was examined by pulsed-field gel electrophoresis after separate digestions with two restriction enzymes, namely, ApaI and NotI. The respective electrophoretic profiles of the fragments were essentially identical but differed from those of T. equigenitalis NCTC11184T and Kentucky 188. They also exhibited slight differences from profiles obtained from Japanese isolates. These results may possibly suggest a common genotype and a commo...
Sequence analysis of equine adenovirus 2 hexon and 23K proteinase genes indicates a phylogenetic origin distinct from equine adenovirus 1. We report the first nucleotide sequence data on equine adenovirus 2 (EAdV2) which corroborate on the molecular level that EAdV2 is distinct from equine adenovirus 1 (EAdV1). Based on sequence homology with Eadv1 the hexon gene of Eadv2 was identified. HindIII restriction fragments containing the hexon and eight other viral genes were cloned into the plasmid pUC19 and the nucleotide sequence of the hexon and the 23K proteinase genes completely determined. Amino acid (aa) comparison of sequence fragments with published adenovirus (AdV) proteins identified the genes for the E1B/19K, IVa2, DNA pol...
Immunohistochemical localization in the stallion genital tract, and topography on spermatozoa of seminal plasma protein SSP-7, a member of the spermadhesin protein family. SSP-7 is a protein originally isolated from stallion seminal plasma. It has extensive amino acid sequence homology with boar spermadhesin AWN, and, like its porcine counterpart, SSP-7 displays zona pellucida-binding activity. Strikingly, however, immunohistochemical studies presented here show that the stallion and the boar spermadhesin homologues are secreted at different places of the male genital tract. Furthermore, indirect immunofluorescence shows that the topography of SSP-7 on the surface of stallion spermatozoa is restricted to the equatorial segment, whereas boar AWN epitopes cover th...
Redox regulation of large conductance Ca(2+)-activated K+ channels in smooth muscle cells. The effects of sulfhydryl reduction/oxidation on the gating of large-conductance, Ca(2+)-activated K+ (maxi-K) channels were examined in excised patches from tracheal myocytes. Channel activity was modified by sulfhydryl redox agents applied to the cytosolic surface, but not the extracellular surface, of membrane patches. Sulfhydryl reducing agents dithiothreitol, beta-mercaptoethanol, and GSH augmented, whereas sulfhydryl oxidizing agents diamide, thimerosal, and 2,2'-dithiodipyridine inhibited, channel activity in a concentration-dependent manner. Channel stimulation by reduction and inhibit...
Genetical and physical assignments of equine microsatellites–first integration of anchored markers in horse genome mapping. Twenty equine microsatellites were isolated from a genomic phage library, and their genetical and physical localization was sought by linkage mapping and fluorescent in situ hybridization (FISH). Nineteen of the markers were found to be polymorphic with, in most cases, heterozygosities exceeding 50%. The markers were mapped in a Swedish reference family for gene mapping, comprising eight half-sib families from Standardbred and Icelandic horse sires. Segregation was analyzed against a set of 35 other markers typed in the pedigree. Thirteen of the microsatellites showed linkage to at least one o...
Localization of the U2 linkage group of horses to ECA 3 using chromosome painting. The U2 linkage group of horses includes the genes albumin (ALB), vitamin D binding protein (GC), mitochondrial glutamate oxaloacetate transaminase 2 (GOT2), and haptoglobin (HP) which are found on two human chromosomes, namely, 4 (HSA 4) and 16 (HSA 16). Likewise these genes are also found on two different chromosomes in mice, rats, and cattle. Chromosome painting demonstrated that only horse chromosome 3 (ECA 3) hybridized with whole chromosome paints for both HSA 4 and HSA 16. This indicated that the equine U2 linkage group occurs on ECA 3, spanning the centromere. This technique will be use...