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.
Sátková-Jakabová D, Trandzík J, Hudecová-Kvasnáková L, Hegedüsová-Zetochová E, Bugarský A, Buleca J, Zöldág L, Jakab F, Fl'ak P.Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the obse...
Miller I, Friedlein A, Tsangaris G, Maris A, Fountoulakis M, Gemeiner M.We constructed a reference two-dimensional protein map for horse (Equus caballus) serum. The serum proteins were separated by two-dimensional electrophoresis (2-DE); 29 different gene products were identified. Proteins represented by 25 spots/spot groups were identified by tandem nanoelectrospray mass spectrometry (MS), four by matrix-assisted laser desorption ionization time-of-flight (TOF) MS and one was sequenced by TOF-TOF technology. The identities of four proteins were deduced by similarity to the human plasma protein database. In selected cases, i.e. the immunoglobulins, immunoblotting ...
Ward TL, Valberg SJ, Adelson DL, Abbey CA, Binns MM, Mickelson JR.Comparative biochemical and histopathological evidence suggests that a deficiency in the glycogen branching enzyme, encoded by the GBE1 gene, is responsible for a recently identified recessive fatal fetal and neonatal glycogen storage disease (GSD) in American Quarter Horses termed GSD IV. We have now derived the complete GBE1 cDNA sequences for control horses and affected foals, and identified a C to A substitution at base 102 that results in a tyrosine (Y) to stop (X) mutation in codon 34 of exon 1. All 11 affected foals were homozygous for the X34 allele, their 11 available dams and sires w...
May JP, Walker CA, Maskell DJ, Slater JD.Streptococcus equi subsp. equi is the causative agent of the equine disease strangles. In this study we describe the development of an in vivo Himar1 transposon system for the random mutagenesis of S. equi and, potentially, other Gram-positive bacteria. We demonstrate efficient and random transposition of a modified mini-transposon onto the chromosome by Southern blot analysis and insertion site sequencing. Non-haemolytic mutants were isolated at a frequency of 0.2%, and acapsular mutants at a frequency of 0.04%. Taken together, these data demonstrate that in vivo Himar1 mutagenesis can be use...
Watson ED, Bae SE, Thomassen R, Thomson SR, Woad K, Armstrong DG.The period between seasonal anoestrus and cyclicity is characterized in many mares by cyclical growth and regression of large dominant follicles. The insulin-like growth factor (IGF) system plays a key role in follicular growth and regression; therefore, we hypothesized that changes in the IGF system and its binding proteins would modulate onset of cyclicity in mares. Ovaries were obtained from pony mares on the day after detection of an actively growing 30 mm transitional anovulatory follicle, and also at the second or third oestrus of the breeding season on the day after the preovulatory fol...
Wagner B, Miller DC, Lear TL, Antczak DF.This report contains the first map of the complete Ig H chain constant (IGHC) gene region of the horse (Equus caballus), represented by 34 overlapping clones from a new bacterial artificial chromosome library. The different bacterial artificial chromosome inserts containing IGHC genes were identified and arranged by hybridization using overgo probes specific for individual equine IGHC genes. The analysis of these IGHC clones identified two previously undetected IGHC genes of the horse. The newly found IGHG7 gene, which has a high homology to the equine IGHG4 gene, is located between the IGHG3 ...
Brown JJ, Thomson W, Clegg P, Eyre S, Kennedy LJ, Matthews J, Carter S, Ollier WE.The full extent of the polymorphism of ELA-DRA in Equidae is not yet known. Given the apparent differences in DRA polymorphisms between Equidae and other species, the aims of this study were to more fully characterize ELA-DRA, determine the extent of gene polymorphism and establish the allele-frequency distribution. An allele reference panel for the second exon of ELA-DRA was established by sequence-based typing of 69 equine DNA samples consisting of various breeds of domestic horse (Equus caballus), together with donkeys (Equus asinus), Grant's zebras (Equus boehmi) and one onager (Equus hemi...
Timoney JF.Streptococci pathogenic for the horse include S. equi (S. equi subsp. equi), S. zooepidemicus (S. equi subsp. zooepidemicus), S. dysgalactiae subsp. equisimilis and S. pneumoniae capsule Type III. S. equi is a clonal descendent or biovar of an ancestral S. zooepidemicus strain with which it shares greater than 98% DNA homology and therefore expresses many of the same proteins and virulence factors. Rapid progress has been made in identification of virulence factors and proteins uniquely expressed by S. equi. Most of these are expressed either on the bacterial surface or are secreted. Notable e...
Raudsepp T, Santani A, Wallner B, Kata SR, Ren C, Zhang HB, Womack JE, Skow LC, Chowdhary BP.We herein report a detailed physical map of the horse Y chromosome. The euchromatic region of the chromosome comprises approximately 15 megabases (Mb) of the total 45- to 50-Mb size and lies in the distal one-third of the long arm, where the pseudoautosomal region (PAR) is located terminally. The rest of the chromosome is predominantly heterochromatic. Because of the unusual organization of the chromosome (common to all mammalian Y chromosomes), a number of approaches were used to crossvalidate the results. Analysis of the 5,000-rad horse x hamster radiation hybrid panel produced a map spannin...
Paulis M, Moralli D, Bensi M, De Carli L, Raimondi E.Tigger elements are human DNA transposons homologous to the pogo element of Drosophila melanogaster. They contain an open reading frame for a transposase very similar to the major mammalian centromere protein CENP-B. We found in the horse genome a DNA element ( Ecatig3) sharing 88% homology with human Tigger3. The presence of Tigger elements in the horse genome confirms previous data that date these elements before the divergence between Perissodactyla and Primates (80-90 Myr ago). Copy number evaluation indicates that the horse element is much more abundant than its human counterpart. Souther...
Chikuni K, Muroya S, Nakajima I.Nucleotide sequences which included the full coding region for three types of myosin heavy chain (MyHC) isoforms were determined from equine skeletal muscles. The deduced amino acid sequences were 1937, 1938, and 1935 residues for the MyHC-2a, -2x, and -slow, respectively. No MyHC-2b isoform was amplified from the equine muscle cDNA except for one pseudogene fragment. One nucleotide was inserted in the coding region of the equine pseudogene product, a minute amount of which was expressed in the skeletal muscle. The 596 bp sequence of the equine MyHC pseudogene was categorized into the MyHC-2b ...
Wallner B, Piumi F, Brem G, Müller M, Achmann R.Y chromosome polymorphisms such as microsatellites or single nucleotide polymorphisms represent a paternal counterpart to mitochondrial DNA (mtDNA) for evolutionary and phylogeographic studies. The use of Y chromosome haplotyping in natural populations of species other than humans is still hindered by the lack of sequence information necessary for polymorphism screening. Here we used representational difference analysis (RDA) followed by a screen of a bacterial artificial chromosome (BAC) library for repetitive sequences to obtain polymorphic Y-chromosomal markers. The procedure was performed ...
Belousova IP, Orlov VN, Kudriavtsev IV.The current condition of the megapopulation of the Przhevalsky horse was assessed using genetic indices of biological diversity of species and genealogical analysis and taking into account both nuclear and non-nuclear (mitochondrial), maternally inherited components of hereditary information.
Di Bernardo G, Galderisi U, Del Gaudio S, D'Aniello A, Lanave C, De Robertis MT, Cascino A, Cipollaro M.DNA extracted from the skeletons of five equids discovered in a Pompeii stable and of a horse found in Herculaneum was investigated. Amino acid racemization level was consistent with the presence of DNA. Post-mortem base modifications were excluded by sequencing a 146 bp fragment of the 16S rRNA mitochondrial gene. Sequencing of a 370 bp fragment of mitochondrial (mt)DNA control region allowed the construction of a phylogenetic tree that, along with sequencing of nuclear genes (epsilon globin, gamma interferon, and p53) fragments, gave us the possibility to address some questions puzzling arch...
Lindgren G, Backström N, Swinburne J, Hellborg L, Einarsson A, Sandberg K, Cothran G, Vilà C, Binns M, Ellegren H.Genetic studies using mitochondrial DNA (mtDNA) have identified extensive matrilinear diversity among domestic horses. Here, we show that this high degree of polymorphism is not matched by a corresponding patrilinear diversity of the male-specific Y chromosome. In fact, a screening for single-nucleotide polymorphisms (SNPs) in 14.3 kb of noncoding Y chromosome sequence among 52 male horses of 15 different breeds did not identify a single segregation site. These observations are consistent with a strong sex-bias in the domestication process, with few stallions contributing genetically to the do...
Yang F, Fu B, O'Brien PC, Nie W, Ryder OA, Ferguson-Smith MA.We have made a complete set of painting probes for the domestic horse by degenerate oligonucleotide-primed PCR amplification of flow-sorted horse chromosomes. The horse probes, together with a full set of those available for human, were hybridized onto metaphase chromosomes of human, horse and mule. Based on the hybridization results, we have generated genome-wide comparative chromosome maps involving the domestic horse, donkey and human. These maps define the overall distribution and boundaries of evolutionarily conserved chromosomal segments in the three genomes. Our results shed further lig...
Raudsepp T, Lee EJ, Kata SR, Brinkmeyer C, Mickelson JR, Skow LC, Womack JE, Chowdhary BP.Development of a dense map of the horse genome is key to efforts aimed at identifying genes controlling health, reproduction, and performance. We herein report a high-resolution gene map of the horse (Equus caballus) X chromosome (ECAX) generated by developing and typing 116 gene-specific and 12 short tandem repeat markers on the 5,000-rad horse x hamster whole-genome radiation hybrid panel and mapping 29 gene loci by fluorescence in situ hybridization. The human X chromosome sequence was used as a template to select genes at 1-Mb intervals to develop equine orthologs. Coupled with our previou...
Kleiboeker SB, Turnquist SE, Johnson PJ, Kreeger JM.In previous studies, novel putative viral pathogens designated that asinine herpesvirus 4 (AsHV4) and asinine herpesvirus 5 (AsHV5) were associated with fatal interstitial pneumonia in donkeys (Equus asinus). Nucleotide sequence analysis of a portion of the DNA polymerase gene identified these putative pathogens as herpesviruses and possibly as members of the Gammaherpesvirinae subfamily. Although similar to equine herpesvirus 2 (EHV2) and equine herpesvirus 5 (EHV5), sequence diversity was observed among the detected viruses. In this study, novel sequence is reported for a DNA-packaging prote...
Myka JL, Lear TL, Houck ML, Ryder OA, Bailey E.The genus Equus is unusual in that five of the ten extant species have documented centric fission (Robertsonian translocation) polymorphisms within their populations, namely E. hemionus onager, E. hemionus kulan, E. kiang, E. africanus somaliensis, and E. quagga burchelli. Here we report evidence that the polymorphism involves the same homologous chromosome segments in each species, and that these chromosome segments have homology to human chromosome 4 (HSA4). Bacterial artificial chromosome clones containing equine genes SMARCA5 (ECA2q21 homologue to HSA4q31. 21) and UCHL1 (ECA3q22 homologue ...
Chowdhary BP, Bailey E.Analysis of the horse genome is proceeding at a rapid pace. Within a short span of 6-7 years, approximately 1,500 markers have been mapped in horse, of which at least half are genes/ESTs. Health, performance and phenotypic characteristic are of major concern/interest to horse breeders and owners. Current efforts to analyze the equine genome are primarily aimed at developing critical resources (including an advanced gene map) that could readily be used in the near future to i) identify genes and mutations responsible for inherited equine diseases/disorders and to formulate approaches for accura...
Myka JL, Lear TL, Houck ML, Ryder OA, Bailey E.Przewalski's wild horse (E. przewalskii, EPR) has a diploid chromosome number of 2n = 66 while the domestic horse (E. caballus, ECA) has a diploid chromosome number of 2n = 64. Discussions about their phylogenetic relationship and taxonomic classification have hinged on comparisons of their skeletal morphology, protein and mitochondrial DNA similarities, their ability to produce fertile hybrid offspring, and on comparison of their chromosome morphology and banding patterns. Previous studies of GTG-banded karyotypes suggested that the chromosomes of both equids were homologous and the differenc...
Gustafson AL, Tallmadge RL, Ramlachan N, Miller D, Bird H, Antczak DF, Raudsepp T, Chowdhary BP, Skow LC.A physical map of ordered bacterial artificial chromosome (BAC) clones was constructed to determine the genetic organization of the horse major histocompatibility complex. Human, cattle, pig, mouse, and rat MHC gene sequences were compared to identify highly conserved regions which served as source templates for the design of overgo primers. Thirty-five overgo probes were designed from 24 genes and used for hybridization screening of the equine USDA CHORI 241 BAC library. Two hundred thirty-eight BAC clones were assembled into two contigs spanning the horse MHC region. The first contig contain...
Park HB, Marklund S, Jeon JT, Mickelson JR, Valberg SJ, Sandberg K, Andersson L.The PRKAG3 gene encodes a muscle-specific isoform of the regulatory gamma subunit of AMP-activated protein kinase (AMPK). A major part of the coding PRKAG3 sequence was isolated from horse muscle cDNA using reverse-transcriptase (RT)-PCR analysis. Horse-specific primers were used to amplify genomic fragments containing 12 exons. Comparative sequence analysis of horse, pig, mouse, human, Fugu, and zebrafish was performed to establish the exon/intron organization of horse PRKAG3 and to study the homology among different isoforms of AMPK gamma genes in vertebrates. The results showed conclusively...
Aberle K, Wrede J, Distl O.Gene contributions of foreign populations as well as coefficients of inbreeding and relationship were calculated in 1918 South German Coldblood horses registered in Bavaria in 2003. Based on nearly complete 8-generation-pedigrees (index of pedigree completeness: 76%) the mean coefficient of inbreeding was 23%. After considering missing pedigree data, the mean coefficient of inbreeding was 3%. The rates of inbreeding per generation in the current population amount to about 0.43% over the last eight generations and to about 0.15% in the forthcoming generation. In the total current population, th...
Payne SL, Pei XF, Jia B, Fagerness A, Fuller FJ.The molecular clones pSPeiav19 and p19/wenv17 of equine infectious anemia virus (EIAV) differ in env and long terminal repeats (LTRs) and produce viruses (EIAV(19) and EIAV(17), respectively) of dramatically different virulence phenotypes. These constructs were used to generate a series of chimeric clones to test the individual contributions of LTR, surface (SU), and transmembrane (TM)/Rev regions to the disease potential of the highly virulent EIAV(17). The LTRs of EIAV(19) and EIAV(17) differ by 16 nucleotides in the transcriptional enhancer region. The two viruses differ by 30 amino acids i...
Frazer KA, Tao H, Osoegawa K, de Jong PJ, Chen X, Doherty MF, Cox DR.Cross-species DNA sequence comparison is a fundamental method for identifying biologically important elements, because functional sequences are evolutionarily conserved, wheres nonfunctional sequences drift. A recent genome-wide comparison of human and mouse DNA discovered over 200,000 conserved noncoding sequences with unknown function. Multispecies DNA comparison has been proposed as a method to prioritize these conserved noncoding sequences for functional analysis based on the hypothesis that elements present in many species are more likely to be functional than elements present in limited ...
Balasuriya UBR, Hedges JF, Smalley VL, Navarrette A, McCollum WH, Timoney PJ, Snijder EJ, MacLachlan NJ.Equine arteritis virus (EAV) causes a persistent infection of the reproductive tract of carrier stallions. The authors determined the complete genome sequences of viruses (CW96 and CW01) that were present 5 years apart in the semen of a carrier stallion (CW). The CW96 and CW01 viruses respectively had only 85.6 % and 85.7 % nucleotide identity to the published sequence of EAV (EAV030). The CW96 and CW01 viruses had two 1 nt insertions and a single 1 nt deletion in the leader sequence, and a 3 nt coding insertion in ORF1a; thus their genomes included 12 708 nt as compared to the 12 704 nt in EA...
Solberg OD, Jackson KA, Millon LV, Stott JL, Vandenplas ML, Moore JN, Watson JL.Three overlapping fragments of the equine interleukin-4 receptor alpha chain gene (IL4R) were cloned and sequenced. The resulting 3553 bp cDNA sequence exhibited homology to human, murine and bovine IL4R. The equine IL4R exhibits many conserved features when compared to other species, including intron-exon boundary positions and amino acid sequence motifs characteristic of type I cytokine receptors. The IL4R gene was localized to horse chromosome ECA13 by synteny mapping on a somatic cell hybrid panel. Evidence for an alternative splice variant of IL4R was found in the genomic sequence and sub...
Farber CR, Medrano JF.In this study the flanking sequences of 1534 horse microsatellites were used in a BLAST search to identify putative human-horse homologies. BLAST searches revealed 129 flanking sequences with significant blastn matches [alignment scores (S) > or = 60 and sum probability values (E) < or = 3.0E-6], also, 25 of these produced significant blastx matches. To provide a reference point in the human genome the flanking sequences with matches were subjected to a BLAT search of the University of California Santa Cruz (UCSC) human genome assembly (July 2003 freeze). Eighty-three of the flanking seq...
van den Heuvel LP, Veerkamp JH, Monnens LA, Schröder CH.1. Proteoglycans were isolated from human and equine glomeruli or tubules by guanidine extraction and anion exchange chromatography. 2. These proteoglycan preparations contained about equal amounts of heparan sulfate and chondroitin sulfates. 3. During the preparation of glomerular or tubular basement membranes the main part of proteoglycans (greater than 50%) was extracted in the salt extract. Chondroitin sulfate proteoglycan was mainly found in the water and salt extracts of glomeruli and tubules, heparan sulfate proteoglycan in the deoxycholate extracts and the basement membranes. 4. The gl...
Kalinowski M, Grądzki Z, Jarosz Ł, Adaszek Ł.Rhodococcus equi (R. hoagii) is an opportunistic pathogen commonly found in foals up to 6 months old and animal environment. The R. equi genome contains genetically stable chromosomal DNA and an 80-90 kb plasmid containing vapA gene, responsible for virulence. Most reports from around the world focus on the determination of R. equi plasmid profiles. Few studies have attempted to determine differences in nucleotide sequences between virulent strains of R. equi isolated from foals and breeding environment. The aim of the study was to perform a molecular analysis of a fragment of the chromosomal ...
Tezuka A, Takasu M, Tozaki T, Nagano AJ.Taishu horses are a native Japanese breed, of which only 41 individuals remained on Tsushima Island in 2018. Their genetic diversity is considered lower than that of other Japanese native horse breeds; thus, it needs to be investigated for sustainable conservation of this breed. Historical records revealed that several Taishu individuals were released areas off-Tsushima Island in mid-1980s. At present, Taishu horses living outside of Tsushima Island, hereafter referred to as Non-Tsushima Taishus (NTTs), are tagged. However, the genetic structure of the NTT individuals remains unclear, and such...
Autry JM, Karim CB, Perumbakkam S, Finno CJ, McKenzie EC, Thomas DD, Valberg SJ.Ca regulation in equine muscle is important for horse performance, yet little is known about this species-specific regulation. We reported recently that horse encode unique gene and protein sequences for the sarcoplasmic reticulum (SR) Ca-transporting ATPase (SERCA) and the regulatory subunit sarcolipin (SLN). Here we quantified gene transcription and protein expression of SERCA and its inhibitory peptides in horse gluteus, as compared to commonly-studied rabbit skeletal muscle. RNA sequencing and protein immunoblotting determined that horse gluteus expresses the gene (SERCA1) as the predomin...
Collinder E, Lindholm A, Rasmuson M.The equine rhabdomyolysis syndrome (RHA) is believed to be multifactorial in origin; and could be caused by an interaction between genetic and environmental factors. In order to analyse its genetic background an association study was undertaken. Two sample groups of Standardbreds (Stb) which had suffered from RHA were compared to the total population of Swedish Standardbred trotters using recorded polymorphic genetic markers. The results showed that gene frequencies for several markers in the RHA groups differed significantly from those estimated for the total population. A rhabdomyolysis risk...
Yang J, Wang Y, Cui X, Zhang Y, Yu Z.Huge numbers of microorganisms reside in livestock faeces and constitute one of the most complex microbial ecosystems. Here, faecal microbial communities of three typical livestock in Xilingol steppe grassland, i.e. sheep, cattle, and horse, were investigated by Illumina MiSeq sequencing and quantitative real-time polymerase chain reaction (qPCR). Firmicutes and Bacteroidetes comprised the majority of bacterial communities in three livestock faeces. Sordariomycetes, Leotiomycetes, and Dothideomycetes were dominant in fungal communities, as well as Methanobacteria and Methanomicrobia were domin...
Wnuk M, Oklejewicz B, Lewinska A, Zabek T, Bartosz G, Slota E, Bugno-Poniewierska M.The fluorescence in situ hybridization (FISH) technique is widely used in animal cytogenetics. Contrary to FISH procedure, primed in situ DNA synthesis (PRINS) does not require the DNA probe preparation (design, synthesis, gel purification of PCR products and labeling). The PRINS method with primers used as 'DNA probes' is both PCR-sensitive and allows for chromosomal localization of DNA sequences. Here, we show the application of PRINS reaction with one unlabeled oligonucleotide pair to identify 18S rDNA loci in three different animal species: domestic pig (Sus scrofa), red fox (Vulpes vulpes...
Al-Jaru A, Goodwin W, Skidmore J, Raudsepp T, Khazanehdari K.Chromosome configurations and chiasma frequency during the metaphase I stage of spermatogenesis in the male horse are characterized in this work. The genome-wide frequency and distribution of chiasmata was detected as 49.45 ± 2.07 for 14 fertile stallions. All X and Y chromosomes shared a single chiasma at their pseudoautosomal region, while 1-4 chiasmata were observed in autosomal chromosomes. The chiasma frequency and distribution were further studied for 8 different bivalents identified by FISH in 5 fertile stallions. Genetic length was calculated from chiasmata data for the whole genome a...
Norton E, McCue ME.A role for a genetic contribution to equine metabolic syndrome (EMS) and pars pituitary intermedia dysfunction (PPID) has been hypothesized. Heritability estimates of EMS biochemical measurements were consistent with moderately to highly heritable traits. Further, genome-wide association analyses have identified hundreds of regions of the genome contributing to EMS and candidate variants have been identified. The genetics of PPID has not yet been proven. Continued research for the specific genetic risk factors for both EMS and PPID is crucial for gaining a better understanding of the pathophys...
O'Donnell MM, Harris HM, O'Toole PW, Ross RP.We report the draft genome sequence of Lactobacillus equi strain DPC6820, isolated from equine feces. L. equi is a predominant Lactobacillus species in the horse hindgut microbiota. An examination of the genome identified genes and enzymes highlighting L. equi adaptations to the herbivorous gastrointestinal tract of the horse, including fructan hydrolases. This genome sequence may help us further understand the microbial ecology of the equine hindgut and the influence lactobacilli have on it.
Amano T, Tozaki T, Takasu M, Onogi A, Yamada F, Kawai M, Ueda J.We investigated whether regular changes of the sire in a breeding farm of Hokkaido Native Horses (HKDs) enables the DNA-level genetic variation of the produced animals to be maintained. The genotypes of 31 microsatellite markers were identified and analyzed in 207 animals produced in a breeding farm in which the sire was replaced every 3 to 5 years. The mean allele number indicating the degree of genetic variation was 5.97 and was similar to those reported previously. The mean observed heterozygosity was 0.74 and was higher than the expected heterozygosity, 0.69; F was -0.07, indicating that ...
Lu G, Huang J, Li S.Theiler's disease-associated virus (TDAV) could be the aetiological agent of Theiler's disease. Horses experimentally inoculated with equine plasma containing TDAV develop acute and chronic infections with viraemia. Since its first identification in 2013, TDAV has not been detected in equines in the epidemiological studies that have been conducted. Until now, only one genome sequence of TDAV (HorseA1_serum) had been obtained. In this study, we sequenced the genome of four TDAV strains (A/China, F/China, H/USA and I/USA) in commercial equine sera used for cell culture propagation in China using...
Richer CL, Romagnano A.Both dynamic G-banding and cell synchronization produced by bromodeoxyuridine (BrdU), were applied to equine chromosomes. BrdU incorporated during the first half of the S-phase is taken up into the R-bands that are early replicating. These bands, which have incorporated BrdU, cannot contract as usual and remain elongated; only the other regions of the chromosome, i.e., the G-bands, contract normally and are sharply defined. BrdU also can be used for cell synchronization. The addition of BrdU in a high concentration, 15 hours before harvest, and its removal 11 hours later, has two effects: init...
Ishige T, Kikuchi M, Kakoi H, Hirota KI, Ohnuma A, Tozaki T, Hirosawa Y, Tanaka S, Nagata SI.We evaluated the utility of single nucleotide polymorphism (SNP) markers for parentage testing in Breton (BR) and Percheron (PR) horses in Japan using the proposed International Society for Animal Genetics (P-ISAG) 147 SNP panel and 414 autosomal SNPs. Genomic DNA was extracted from 98 horses of two breeds, BR (n = 47) and PR (n = 51), and sequenced using next-generation sequencing. The average minor allele frequencies for the P-ISAG panel for BR and PR were 0.306 and 0.301, respectively. The combined probabilities of exclusion (PEs) given two parents and one offspring: exclude a relat...
Tozaki T, Hirota K, Hasegawa T, Ishida N, Tobe T.The identification of candidate genes for significant traits is crucial. In this study, we developed and tested effective and systematic methods based on linkage disequilibrium (LD) for the identification of candidate regions for genes with Mendelian inheritance and those associated with complex traits. Our approach entailed the combination of primary screening using pooled DNA samples based on DeltaTAC, secondary screening using an individual typing method and tertiary screening using a permutation test based on the differences in the haplotype frequency between two neighbouring microsatellit...
Smith RM, Kotzé A, Grobler JP, Dalton DL.Toll-like receptors (TLR) are a family of proteins that signal activation of the innate immune response through the recognition of a variety of pathogen molecular compounds. Here, we characterized the complete TLR9 gene in Cape mountain zebra (Equus zebra zebra) from three populations in South Africa and compared sequences to a variety of horse and donkey breeds. Overall, we identified six single nucleotide polymorpHisms (SNPs). A single SNP (G586S) was non-synonymous, whereas the remaining SNPs were synonymous. The G586S alteration was detected in Cape mountain zebra populations with varying ...
Song KD, Cho HW, Lee HK, Cho BW.The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene (VEGFα) by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog), we constructed a phylogenetic tree which showed that equine VEGFα belonged to the same clade of the pig VEGFα. Analysis for synonymous (Ks) and non-synonymous sub...
Zhou H, Liu C, Wang W.This study was conducted to reconstruct heterogeneous embryos using equine skin fibroblast cells as donor karyoplasts and the bovine oocytes as recipient cytoplast for investigating the reprogramming of equine somatic cell nuclear in bovine oocyte cytoplasm and the developmental potential of the reconstructed embryos. Adult horse skin fibroblast cells serum-starved were used as donor somatic cells. Bovine oocytes matured in vitro were employed as recipient cytoplasts. The fusion of fibroblast cells into recipient cytoplasm was induced by electofusion. The fused eggs were activated by inomycin ...
Dugarjaviin M, Yang H.Mongolian horse is a kind of important breed resource of local horses in our country. It has a lot of advantages such as powerful endurance, rough feeding resistance, and strong disease resistance. These advantages have become driving force for in-depth study on Mongolian horse. Genetic diversity can reflect all the genetic information of a species or a variety, namely, it reflects the richness of genetic diversity and confirms the degree of uniqueness of genetic resources through genetic markers. This paper introduces the progress in the study on genetic diversity of Mongolian horse in many a...
Perrocheau M, Boutreux V, Chadi-Taourit S, Di Meo GP, Perucatti A, Incarnato D, Cribiu EP, Guérin G, Iannuzzi L.The INRA and the CHORI-241 horse BAC libraries were screened by hybridization with DNA probes and/or directly by PCR with primers designed in consensus sequences of genes localized at the end of each human chromosome. BAC clones were retrieved and 36 could be FISH mapped after the expected gene was confirmed in each BAC by sequencing. Our results show that 16 BACs can be considered to be at telomeric or centromeric positions in the horse and 15 were found at the boundary of actually defined conserved segments even-though often located within conserved syntenic fragments between horse and human...
Shen Y, Ren H, Davshilt T, Tian S, Wang X, Yi M, Ulaangerel T, Li B, Dugarjav M, Bou G.During equine early gestation, trophectoderm forms chorion tissue, which is composed of two parts that one is covering allantoin, called allantochorion (AC) and another is covering yolk sac, which here we call vitelline-chorion (VC). Given that little is known about the equine trophoblast-derived chorion differentiation at an early stage, we first compared the transcriptome of AC and VC of day 30 equine conceptus based on RNA-sequencing. As a result, we found that compared to VC, there are 484 DEGs, including 305 up- and 179 down-regulated genes in AC. GO and KEGG analysis indicated that up-re...
Brooks SA.The sheer diversity of heritable physiological traits, and the ingenuity of genome derived research technologies, extends the study of genetics to impact diverse scientific fields. Equine science is no exception, experiencing a number of genome-enabled discoveries that spur further research in areas like nutrition, reproduction, and exercise physiology. Yet unexpected findings, especially those that over-turn commonly held beliefs in the horse industry, can create challenges in outreach, education and communication with stakeholders. For example, studies of ancient DNA revealed that the oldest...
Cappelli A, Capone A, Valzano M, Bozic J, Preziuso S, Mensah P, Varotto Boccazzi I, Rinaldi L, Favia G, Ricci I.Tick-borne diseases are an increasing problem for the community. Ticks harbor a complex microbial population acquired while feeding on a variety of animals. Profiling the bacterial population by 16S rDNA amplification and denaturing gradient gel electrophoresis enables detection of the broad spectrum of bacteria that settles in the ticks. This study identified known and unknown tick-infecting bacteria in samples from Italy. Seven adult ticks from different hosts and origins were analyzed: two ticks from dogs (Lombardia), two ticks from bovines (Lazio), and three ticks from humans (Marche). ...
Simonin EM, Wagner B.IgE-binding monocytes are a rare peripheral immune cell type involved in the allergic response through binding of IgE on their surface. IgE-binding monocytes are present in both healthy and allergic individuals. We performed RNA sequencing to ask how the function of IgE-binding monocytes differs in the context of allergy. Using a large animal model of allergy, equine Culicoides hypersensitivity, we compared the transcriptome of IgE-binding monocytes in allergic and non-allergic horses at two seasonal timepoints: (i) when allergic animals were clinical healthy, in the winter "Remission Phase", ...
Gurgul A, Szmatoła T, Ocłoń E, Jasielczuk I, Semik-Gurgul E, Finno CJ, Petersen JL, Bellone R, Hales EN, Ząbek T, Arent Z, Kotula-Balak M....In recent years, a vast amount of sequencing data has been generated and large improvements have been made to reference genome sequences. Despite these advances, significant portions of reads still do not map to reference genomes and these reads have been considered as junk or artificial sequences. Recent studies have shown that these reads can be useful, e.g., for refining reference genomes or detecting contaminating microorganisms present in the analyzed biological samples. A special case of this is RNA sequencing (RNA-Seq) reads that come from tissue transcriptomes. Unmapped reads from RNA-...
Patterson Rosa L, Whitaker B, Allen K, Peters D, Buchanan B, McClure S, Honnas C, Buchanan C, Martin K, Lundquist E, Vierra M, Foster G, Brooks SA....Commonly known as "Kissing Spines" (KS), the pathological mechanisms underlying impingement and overriding of spinous processes (ORSPs) in horses are poorly understood. Thoroughbreds, Warmbloods, and stock-type breeds, including Paint Horses and Quarter Horses are at increased risk for developing clinical signs of KS. A total of 155 stock-type and Warmblood horses presented at collaborating veterinary clinics and hospitals were examined using a strict clinical and radiographical phenotyping scheme to grade each horse from 0 for unaffected controls to 4 for severe KS. Following genotyping with ...
Farmerie TA, Abbud RA, Budworth PR, Clay CM, Keri RA, McDowell KJ, Wolfe MW, Nilson JH.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...
Douet C, Parodi O, Martino NA, Lacalandra GM, Nicassio M, Reigner F, Deleuze S, Dell'Aquila ME, Goudet G.Most wild equids and many domestic horse breeds are at risk of extinction, so there is an urgent need for genome resource banking. Embryos cryopreservation allows the preservation of genetics from male and female and is the fastest method to restore a breed. In the equine, embryo production in vitro would allow the production of several embryos per cycle. Intracytoplasmic sperm injection (ICSI) is used to generate horse embryos, but it requires expensive equipment and expertise in micromanipulation, and blastocyst development rates remain low. No conventional in vitro fertilization (IVF) techn...
Tada M, Kobashigawa Y, Mizuguchi M, Miura K, Kouno T, Kumaki Y, Demura M, Nitta K, Kawano K.Equine lysozyme is a calcium-binding lysozyme and an evolutional intermediate between non-calcium binding c-type lysozyme and alpha-lactalbumin. We constructed a chimeric protein by substituting the fluctuating loop of bovine alpha-lactalbumin with the D-helix of equine lysozyme. The substitution affects the protection factors not only in the fluctuating loop but also in the antiparallel beta-sheet, the A- and B-helices, and the loop between the B-helix and the beta-sheet. Amide protons in these regions of the chimera are more protected from exchange than are those of bovine alpha-lactalbumin....
De Paolis L, De Ciucis CG, Peletto S, Cappelli K, Mecocci S, Nervo T, Guardone L, Crescio MI, Pietrucci D, Fruscione F, Gabbianelli F, Turco S....Papillomavirus (PV) infections may be related to anogenital lesions and cancer development in humans and several other animal species. To date, 11 different PVs have been reported in horses. Among them, a newly described PV named Papillomavirus Type9 (EcPV9) was thus far only reported in the semen of a stallion with penile lesions in Australia. This study reports for the first time the presence of EcPV9 in asymptomatic Italian horses. From July 2020 to January 2022, genital brush samples were collected from 209 horses with no apparent signs of neoplastic disease and no PV-associated lesions, ...
