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.
A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers. To generate a domestic horse genome map we integrated synteny information for markers screened on a somatic cell hybrid (SCH) panel with published information for markers physically assigned to chromosomes. The mouse-horse SCH panel was established by fusing pSV2neo transformed primary horse fibroblasts to either RAG or LMTk mouse cells, followed by G418 antibiotic selection. For each of the 108 cell lines of the panel, we defined the presence or absence of 240 genetic markers by PCR, including 58 random amplified polymorphic DNA (RAPD) markers and 182 microsatellites. Thirty-three syntenic gr...
Close association between sequence polymorphism in the KIT gene and the roan coat color in horses. The roan coat color in horses is controlled by a dominant allele that is lethal in the homozygous condition. Phenotypic similarities to some pigmentation disorders in human and mouse, combined with comparative mapping data, identified KIT, encoding the mast cell growth factor receptor, as a major candidate gene for the roan locus (Rn). Rn has previously been mapped to equine linkage group (LG) II. In this study, LGII was expanded with KIT and PDGFRA (platelet-derived growth factor receptor alpha) by use of RFLP and linkage analysis. Moreover, highly significant linkage disequilibrium between R...
Two SINE families associated with equine microsatellite loci. BLAST searches of 61 equine microsatellite sequences revealed two related families of retroposons. The first family included seven markers, all of which showed significant homology to the Equine Repetitive Element-1 (ERE-1) Short Interspersed Nucleotide Element (SINE) sequence. Length of homology ranged from 76 to 171 bases with identities to the ERE-1 consensus sequence ranging from 71% to 83%. The second family referred to as Equine Repetitive Element-2 (ERE-2) has a consensus sequence that showed homology to ERE-1 over approximately 60 bases. These 60 bases comprised subunit I. Sequence com...
Polymorphism of Old Kladruber horses, a surviving but endangered baroque breed. Analysis of MHC class I and class II polymorphism, as well as data from other polymorphic systems (non-MHC lymphocyte alloantigen, blood groups systems, biochemical polymorphisms and microsatellite loci), was used to characterize the extent and distribution of the genic polymorphism of Kladruber horses. A breed-characteristic distribution of the MHC polymorphism was found. The repertoire of defined MHC class I specificities was restricted, especially in the grey subpopulation and in stallions, but a high frequency of blanks suggests the possible existence of undetected specificities. Despite t...
Cloning and characterization of the equine F18 gene, which has a novel exon. A genomic clone isolated from an equine genomic library probed with an oligonucleotide (CAG)10 showed high sequence similarity to the human F18 gene and was tentatively named equine F18 gene. Because the human F18 gene is expressed in many tissues, we examined whether this equine clone was also expressed in equine tissues. The cDNA encoding equine F18 was obtained by the reverse transcriptase-polymerase chain reaction (RT-PCR) from equine thymus. The nucleotide sequence of the equine F18 cDNA (1940 bp) was determined and contained both the ATG initiation codon and a poly(A) sequence. The cDNA ...
Genetic variation and phylogenetic analysis of open reading frames 3 and 4 of various equine arteritis virus isolates. The genetic variation in equine arteritis virus (EAV) nonstructural (NS) protein-encoding open reading frames (ORF) 3 and 4 genes was investigated. Nucleotide 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 the Bucyrus reference strain. ORF 3 nucleotide and amino acid sequence identities amongst 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 a...
A primary male autosomal linkage map of the horse genome. A primary male autosomal linkage map of the domestic horse (Equus caballus) has been developed by segregation analysis of 140 genetic markers within eight half-sib families. The family material comprised four Standardbred trotters and four Icelandic horses, with a total of 263 offspring. The marker set included 121 microsatellite markers, eight protein polymorphisms, five RFLPs, three blood group polymorphisms, two PCR-RFLPs, and one single strand conformation polymorphism (SSCP). One hundred markers were arranged into 25 linkage groups, 22 of which could be assigned physically to 18 different...
Equine CRISP-3: primary structure and expression in the male genital tract. Although originally described in the male rodent genital tract, cysteine-rich secretory proteins (CRISPs) are expressed in a variety of mammalian tissue and cell types. The proteins of the male genital tract have been observed associated to spermatozoa and are believed to play a role in mammalian fertilization. Here we describe the identification and primary structure of the first equine member of the CRISP family. Equine CRISP-3 is transcribed and expressed in the stallion salivary gland, in the ampulla and the seminal vesicle. It displays all 16 conserved cysteine residues and shows 82% homo...
Diversity of genomic electropherotypes of naturally occurring equine herpesvirus 1 isolates in Argentina. The genomes of 10 equine herpesvirus 1 (EHV-1) strains isolated in Argentina from 1979 to 1991, and a Japanese HH1 reference strain were compared by restriction endonuclease analysis. Two restriction enzymes, BamHI and BglII, were used and analysis of the electropherotypes did not show significant differences among isolates obtained from horses with different clinical signs. This suggests that the EHV-1 isolates studied, which circulated in Argentina for more than 10 years, belong to a single genotype.
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...