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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.
Streptococcus zooepidemicus and Streptococcus equi evolution: the role of CRISPRs. The host-restricted bacterium Streptococcus equi is the causative agent of equine strangles, the most frequently diagnosed infectious disease of horses worldwide. The disease is characterized by abscessation of the lymph nodes of the head and neck, leading to significant welfare and economic cost. S. equi is believed to have evolved from an ancestral strain of Streptococcus zooepidemicus, an opportunistic pathogen of horses and other animals. Comparison of the genome of S. equi strain 4047 with those of S. zooepidemicus identified examples of gene loss due to mutation and deletion, and gene ga...
Identification of equine influenza virus infection in Asian wild horses (Equus przewalskii). An outbreak of equine influenza was observed in the Asian wild horse population in Xinjiang Province, China, in 2007. Nasal swabs were collected from wild horses and inoculated into 9-10-day SPF embryonated eggs. The complete genome of the isolate was sequenced. A comparison of the amino acid sequence revealed that the isolate was an equine influenza virus strain, which we named A/equine/Xinjiang/4/2007. Each gene of the virus was found to have greater than 99 % homology to equine influenza virus strains of the Florida-2 sublineage, which were circulating simultaneously in China, and a lesser ...
Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse. Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ(2)=1022.00, p<<...
Sarcoid-derived fibroblasts: links between genomic instability, energy metabolism and senescence. Bovine papillomavirus 1 (BPV-1) is a well recognized etiopathogenetic factor in a cancer-like state in horses, namely equine sarcoid disease. Nevertheless, little is known about BPV-1-mediated cell transforming effects. It was shown that BPV-1 triggers genomic instability through DNA hypomethylation and oxidative stress. In the present study, we further characterized BPV-1-positive fibroblasts derived from sarcoid tumors. The focus was on cancer-like features of sarcoid-derived fibroblasts, including cell cycle perturbation, comprehensive DNA damage analysis, end-replication problem, energy me...
Identification of potential platelet alloantigens in the Equidae family by comparison of gene sequences encoding major platelet membrane glycoproteins. Platelet alloantigens in horses may play an important role in the development of neonatal alloimmune thrombocytopenia (NAIT). Objective: The objective of this study was to evaluate genes encoding major platelet glycoproteins within the Equidae family in an effort to identify potential alloantigens. Methods: DNA was isolated from blood samples obtained from Equidae family members, including a Holsteiner-Oldenburg cross, a Quarter horse, a donkey, and a Plains zebra (Equus burchelli). Gene sequences encoding equine platelet membrane glycoproteins IIb, IIIa (integrin subunits αIIb and β3), Ia (...
An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction. Laminitis is a chronic, crippling disease triggered by the sudden influx of dietary starch. Starch reaches the hindgut resulting in enrichment of lactic acid bacteria, lactate accumulation, and acidification of the gut contents. Bacterial products enter the bloodstream and precipitate systemic inflammation. Hindgut lactate levels are normally low because specific bacterial groups convert lactate to short chain fatty acids. Why this mechanism fails when lactate levels rapidly rise, and why some hindgut communities can recover is unknown. Fecal samples from three adult horses eating identical di...
Accumulating mutations in series of haplotypes at the KIT and MITF loci are major determinants of white markings in Franches-Montagnes horses. Coat color and pattern variations in domestic animals are frequently inherited as simple monogenic traits, but a number are known to have a complex genetic basis. While the analysis of complex trait data remains a challenge in all species, we can use the reduced haplotypic diversity in domestic animal populations to gain insight into the genomic interactions underlying complex phenotypes. White face and leg markings are examples of complex traits in horses where little is known of the underlying genetics. In this study, Franches-Montagnes (FM) horses were scored for the occurrence of white fac...
Molecular phylogeny of Indian horse breeds with special reference to Manipuri pony based on mitochondrial D-loop. Manipuri pony is the geographically distant breed of horse from the five recognized horse breeds found in the Indian subcontinent. The phylogenetic relationship of Manipuri pony with the other breeds is unknown. The diversity in the mitochondrial (mt) DNA D-loop region is employed as an important tool to understand the origin and genetic diversification of domestic horses and to examine genetic relationships among breeds around the world. This study was carried out to understand the maternal lineages of Manipuri pony using the 247 bp region of the mtDNA D-loop. The dataset comprised of eleven ...
Equine multiple congenital ocular anomalies and silver coat colour result from the pleiotropic effects of mutant PMEL. Equine Multiple Congenital Ocular Anomalies (MCOA) syndrome is a heritable eye disorder mainly affecting silver colored horses. Clinically, the disease manifests in two distinct classes depending on the horse genotype. Horses homozygous for the mutant allele present with a wide range of ocular defects, such as iris stromal hypoplasia, abnormal pectinate ligaments, megaloglobus, iridociliary cysts and cataracts. The phenotype of heterozygous horses is less severe and predominantly includes iridociliary cysts, which occasionally extend into the temporal retina. In order to determine the genetic ...
Isolation of RNA from equine peripheral blood cells: comparison of methods. Gene expression studies in equine research involve the use of whole blood samples as a vital source of RNA. To determine the optimal method for RNA isolation from equine whole blood, we compared three RNA isolation strategies using different commercially available kits to evaluate the yield and quality of equine RNA. All 3 methods produced RNA with high quality. Though it did not produce the highest yield, combining the quality, yield and the need for the downstream application in our project, LeukoLOCK™ total RNA isolation system was the best RNA extraction method.
Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing. Maternal inheritance is an essential point in Arabian horse population genetics and strains classification. The mitochondrial DNA (mtDNA) sequencing is a highly informative tool to investigate maternal lineages. We sequenced the whole mtDNA D-loop of 251 Arabian horses to study the genetic diversity and phylogenetic relationships of Arabian populations and to examine the traditional strain classification system that depends on maternal family lines using native Arabian horses from the Middle East. Results: The variability in the upstream region of the D-loop revealed additional differences amo...
Indicators of replicative damage in equine tendon fibroblast monolayers. Superficial digital flexor tendon (SDFT) injuries of horses usually follow cumulative matrix microdamage; it is not known why the reparative abilities of tendon fibroblasts are overwhelmed or subverted. Relevant in vitro studies of this process require fibroblasts not already responding to stresses caused by the cell culture protocols. We investigated indicators of replicative damage in SDFT fibroblast monolayers, effects of this on their reparative ability, and measures that can be taken to reduce it. Results: We found significant evidence of replicative stress, initially observing consistent...
From glanders to Hendra virus: 125 years of equine infectious diseases. Josh Slater looks back at the past 125 years of developments in equine infectious disease, including landmark discoveries in microbiology and genomics, and considers what the future may hold.
Family of melanocortin receptor (MCR) genes in mammals-mutations, polymorphisms and phenotypic effects. The melanocortin receptor gene family consists of five single-exon members, which are located on autosomes. Three genes (MC2R, MC4R and MC5R) are syntenic in the human, mouse, cattle and dog genomes, while in the pig, the syntenic group comprises MC1R, MC2R and MC5R. Two genes (MC1R and MC4R) have been extensively studied due to their function in melanogenesis (MC1R) and energy control (MC4R). Conservative organisation of these genes in five mammalian species (human, mouse, cattle, pig and dog), in terms of the encoded amino acid sequence, is higher in the case of MC4R compared to MC1R. Polymo...
Genomic selection: Status in different species and challenges for breeding. Technical advances and development in the market for genomic tools have facilitated access to whole-genome data across species. Building-up on the acquired knowledge of the genome sequences, large-scale genotyping has been optimized for broad use, so genotype information can be routinely used to predict genetic merit. Genomic selection (GS) refers to the use of aggregates of estimated marker effects as predictors which allow improved individual differentiation at young age. Realizable benefits of GS are influenced by several factors and vary in quantity and quality between species. General cha...
Transcriptomic signatures in cartilage ageing. Age is an important factor in the development of osteoarthritis. Microarray studies provide insight into cartilage aging but do not reveal the full transcriptomic phenotype of chondrocytes such as small noncoding RNAs, pseudogenes, and microRNAs. RNA-Seq is a powerful technique for the interrogation of large numbers of transcripts including nonprotein coding RNAs. The aim of the study was to characterise molecular mechanisms associated with age-related changes in gene signatures. Methods: RNA for gene expression analysis using RNA-Seq and real-time PCR analysis was isolated from macroscopicall...
Complete Genomic Sequences of an H3N8 Equine Influenza Virus Strain Isolated in China. We report the complete genomic sequence of A/equine/Heilongjiang/1/2010, a strain of Florida sublineage clade 2 of H3N8 subtype equine influenza virus (EIV) isolated in northern China. This is the first announcement of a complete genomic sequence of EIV of such a clade in China.
Papillomavirus associated diseases of the horse. The Papillomaviridae family comprises a large number of viruses that can infect a broad range of hosts including mammals, birds and reptiles giving rise to benign lesions of the skin or mucosal membranes. They are characterized by great genetic diversity yet adhere to common biological principles. In this review, we first describe the structure and function of the viral proteins encoded by papillomaviruses (PVs), with a particular emphasis on bovine papillomaviruses (BPV). We then discuss the role of BPV types 1 and 2 in the pathogenesis of equine sarcoids and present recent evidence implicati...
A genome-wide association study identifies risk loci to equine recurrent uveitis in German warmblood horses. Equine recurrent uveitis (ERU) is a common eye disease affecting up to 3-15% of the horse population. A genome-wide association study (GWAS) using the Illumina equine SNP50 bead chip was performed to identify loci conferring risk to ERU. The sample included a total of 144 German warmblood horses. A GWAS showed a significant single nucleotide polymorphism (SNP) on horse chromosome (ECA) 20 at 49.3 Mb, with IL-17A and IL-17F being the closest genes. This locus explained a fraction of 23% of the phenotypic variance for ERU. A GWAS taking into account the severity of ERU, revealed a SNP on ECA18 n...
Equine oviduct explant culture: a basic model to decipher embryo-maternal communication. Equine embryos remain for 6 days in the oviduct and thus there is a need for an in vitro model to study embryo-oviductal interactions in the horse, since this subtle way of communication is very difficult to analyse in vivo. Until now, no equine oviduct explant culture model has been characterised both morphologically and functionally. Therefore, we established a culture system for equine oviduct explants that maintained epithelial morphology during 6 days of culture, as revealed by light microscopy and transmission electron microscopy. We demonstrated the presence of highly differentiated, ta...
Transcriptome analysis of a parasitic clade V nematode: comparative analysis of potential molecular anthelmintic targets in Cylicostephanus goldi. Clade V nematodes comprise several parasitic species that include the cyathostomins, primary helminth pathogens of horses. Next generation transcriptome datasets are available for eight parasitic clade V nematodes, although no equine parasites are included in this group. Here, we report next generation transcriptome sequencing analysis for the common cyathostomin species, Cylicostephanus goldi. A cDNA library was generated from RNA extracted from 17 C. goldi male and female adult parasites. Following sequencing using a 454 GS FLX pyrosequencer, a total of 475,215 sequencing reads were generate...
Analysis of unannotated equine transcripts identified by mRNA sequencing. Sequencing of equine mRNA (RNA-seq) identified 428 putative transcripts which do not map to any previously annotated or predicted horse genes. Most of these encode the equine homologs of known protein-coding genes described in other species, yet the potential exists to identify novel and perhaps equine-specific gene structures. A set of 36 transcripts were prioritized for further study by filtering for levels of expression (depth of RNA-seq read coverage), distance from annotated features in the equine genome, the number of putative exons, and patterns of gene expression between tissues. From ...
Whole genomic analyses of equine group A rotaviruses from Japan: evidence for bovine-to-equine interspecies transmission and reassortment events. Equine group A rotaviruses (RVA) are a major cause of severe diarrhea in foals. The whole genomes of only six common and three unusual equine RVA strains have been analyzed so far. To date, there are no reports on whole genomic analyses of equine RVAs from Asian countries. We report here the whole genomic analyses of three common (strains RVA/Horse-tc/JPN/BI/1981/G3P[12], RVA/Horse-tc/JPN/HH-22/1989/G3P[12] and RVA/Horse-tc/JPN/CH-3/1987/G14P[12]) and an unusual (RVA/Horse-tc/JPN/OH-4/1982/G6P[5]) equine RVA strains isolated from diarrheic foals in Japan. Strains BI, HH-22 and CH-3 shared a la...
Analysis of copy number variants by three detection algorithms and their association with body size in horses. Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses. Results: Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affecte...
Equine herpesvirus 1 (EHV-1) nucleotide polymorphism determination using formalin fixed tissues in EHV-1 induced abortions and myelopathies with real-time PCR and pyrosequencing. Equine herpesvirus-1 (EHV-1) strains with a single point mutation at the 2254 nucleotide position with a G2254 constitution within the DNA polymerase gene are associated strongly with equine myeloencephalopathies. Infections with non-neuropathogenic EHV-1 strains without the G2254 nucleotide but with an A2254 nucleotide are associated less frequently with equine neurologic disease. A retrospective study utilizing DNA extracted from formalin fixed paraffin embedded tissues was conducted with real time PCR and pyrosequencing, to determine the infecting EHV-1 strains. Infection with EHV-1 A2254 a...
Lawsonia intracellularis infection and proliferative enteropathy in foals. Equine proliferative enteropathy (EPE) is a disease of foals caused by the obligate intracellular organism Lawsonia intracellularis. This organism is unique in that it causes proliferation of infected enterocytes, resulting in thickening of the intestinal epithelium, most often the small intestine. This disease affects mainly weanling foals and causes fever, lethargy, peripheral edema, diarrhea, colic and weight loss. The diagnosis of EPE may be challenging and relies on the presence of hypoproteinemia, thickening of segments of the small intestinal wall observed on abdominal ultrasonography, ...
Rhodococcus equi: the many facets of a pathogenic actinomycete. Rhodococcus equi is a soil-dwelling pathogenic actinomycete that causes pulmonary and extrapulmonary pyogranulomatous infections in a variety of animal species and people. Young foals are particularly susceptible and develop a life-threatening pneumonic disease that is endemic at many horse-breeding farms worldwide. R. equi is a facultative intracellular parasite of macrophages that replicates within a modified phagocytic vacuole. Its pathogenicity depends on a virulence plasmid that promotes intracellular survival by preventing phagosome-lysosome fusion. Species-specific tropism of R. equi fo...
Comparative genome sequencing identifies a prophage-associated genomic island linked to host adaptation of Lawsonia intracellularis infections. Lawsonia intracellularis is an obligate intracellular bacterium and the causative agent of proliferative enteropathy (PE). The disease is endemic in pigs, emerging in horses and has also been reported in a variety of other animal species, including nonhuman primates. Comparing the whole genome sequences of a homologous porcine L. intracellularis isolate cultivated for 10 and 60 passages in vitro, we identified a 18-kb prophage-associated genomic island in the passage 10 (pathogenic variant) that was lost in the passage 60 (non-pathogenic variant). This chromosomal island comprises 15 genes dow...
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that ...
