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.
Pirault P, Danvy S, Verrier E, Leroy G.Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average [Formula: see text] of -0.07% when considering the 55 origins, showing that most horse ...
Kapoor A, Simmonds P, Cullen JM, Scheel TK, Medina JL, Giannitti F, Nishiuchi E, Brock KV, Burbelo PD, Rice CM, Lipkin WI.The recent identification of nonprimate hepaciviruses in dogs and then in horses prompted us to look for pegiviruses (GB virus-like viruses) in these species. Although none were detected in canines, we found widespread natural infection of horses by a novel pegivirus. Unique genomic features and phylogenetic analyses confirmed that the tentatively named equine pegivirus (EPgV) represents a novel species within the Pegivirus genus. We also determined that EPgV causes persistent viremia whereas its clinical significance is undetermined.
Kim H, Lee T, Park W, Lee JW, Kim J, Lee BY, Ahn H, Moon S, Cho S, Do KT, Kim HS, Lee HK, Lee CK, Kong HS, Yang YM, Park J, Kim HM, Kim BC, Hwang S....The modern horse (Equus caballus) is the product of over 50 million yrs of evolution. The athletic abilities of the horse have been enhanced during the past 6000 yrs under domestication. Therefore, the horse serves as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. The structure and function of skeletal muscle show remarkable plasticity to the physical and metabolic challenges following exercise. Here, we reveal an evolutionary layer of responsiveness to exercise-stress in the skeletal muscle of the racing horse. We analysed differentia...
Binder AK, Rodriguez KF, Hamilton KJ, Stockton PS, Reed CE, Korach KS.Determining the spatial and temporal expression of genes involved in the ovulatory pathway is critical for the understanding of the role of each estrogen receptor in the modulation of folliculogenesis and ovulation. Estrogen receptor (ER)-β is highly expressed in ovarian granulosa cells, and mice lacking ER-β are subfertile due to inefficient ovulation. Previous work has focused on isolated granulosa cells or cultured follicles and, although informative, provides confounding results due to the heterogeneous cell types present including granulosa and theca cells and oocytes and exposure to in...
Tallmadge RL, Tseng CT, King RA, Felippe MJ.Humoral immunity is a critical component of the immune system that is established during fetal life and expands upon exposure to pathogens. The extensive humoral immune response repertoire is generated in large part via immunoglobulin (Ig) heavy chain variable region diversity. The horse is a useful model to study the development of humoral diversity because the placenta does not transfer maternal antibodies; therefore, Igs detected in the fetus and pre-suckle neonate were generated in utero. The goal of this study was to compare the equine fetal Ig VDJ repertoire to that of neonatal, foal, an...
Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G.The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most wi...
Musilova P, Kubickova S, Vahala J, Rubes J.Equidae is a small family which comprises horses, African and Asiatic asses, and zebras. Despite equids having diverged quite recently, their karyotypes underwent rapid evolution which resulted in extensive differences among chromosome complements in respective species. Comparative mapping using whole-chromosome painting probes delineated genome-wide chromosome homologies among extant equids, enabling us to trace chromosome rearrangements that occurred during evolution. In the present study, we performed subchromosomal comparative mapping among seven Equidae species, representing the whole fam...
Chandriani S, Skewes-Cox P, Zhong W, Ganem DE, Divers TJ, Van Blaricum AJ, Tennant BC, Kistler AL.Theiler's disease is an acute hepatitis in horses that is associated with the administration of equine blood products; its etiologic agent has remained unknown for nearly a century. Here, we used massively parallel sequencing to explore samples from a recent Theiler's disease outbreak. Metatranscriptomic analysis of the short sequence reads identified a 10.5-kb sequence from a previously undescribed virus of the Flaviviridae family, which we designate "Theiler's disease-associated virus" (TDAV). Phylogenetic analysis clusters TDAV with GB viruses of the recently proposed Pegivirus genus, altho...
Lange CE, Vetsch E, Ackermann M, Favrot C, Tobler K.Papillomaviruses appear to be species-specific pathogens, and it was suggested that each animal species might harbour its own set of papillomaviruses. However, all approaches addressing the underlying evolutionary phenomena still suffer from very limited data about animal papillomaviruses. In case of the horse for example, only three equine papillomaviruses (EcPVs) have been identified. To further address the situation in this host, suspected papillomavirus-associated lesions were tested for EcPV DNA. Four novel EcPV types were detected and their genomes entirely cloned and sequenced. They dis...
Moyo NA, Marchi E, Steinbach F.Dendritic cells (DC) are the main immune mediators inducing primary immune responses. DC generated from monocytes (MoDC) are a model system to study the biology of DC in vitro, as they represent inflammatory DC in vivo. Previous studies on the generation of MoDC in horses indicated that there was no distinct difference between immature and mature DC and that the expression profile was distinctly different from humans, where CD206 is expressed on immature MoDC whereas CD83 is expressed on mature MoDC. Here we describe the kinetics of equine MoDC differentiation and activation, analysing both ph...
Robinson C, Steward KF, Potts N, Barker C, Hammond TA, Pierce K, Gunnarsson E, Svansson V, Slater J, Newton JR, Waller AS.The detection of anti-Streptococcus equi antibodies in the blood serum of horses can assist with the identification of apparently healthy persistently infected carriers and the prevention of strangles outbreaks. The aim of the current study was to use genome sequencing data to develop an indirect enzyme linked immunosorbent assay (iELISA) that targets two S. equi-specific protein fragments. The sensitivity and specificity of the antigen A and antigen C iELISAs were compared to an SeM-based iELISA marketed by IDvet - diagnostic Vétérinaire (IDvet). Individually, each assay compromised specifi...
The Journal of heredityFebruary 28, 2013
Volume 104, Issue 3 386-398 doi: 10.1093/jhered/est003
Khanshour A, Conant E, Juras R, Cothran EG.The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was ...
Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM....The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further charact...
Tetens J, Widmann P, Kühn C, Thaller G.A genome-wide association scan for loci affecting withers height was conducted in 782 German Warmblood stallions, which were genotyped using the Illumina EquineSNP50 Bead Chip. A principal components approach was applied to correct for population structure. The analysis revealed a single major QTL on ECA3 explaining ~18 per cent of the phenotypic variance, which is in concordance with recent reports from other horse populations. The LCORL/NCAPG locus represents a strong candidate gene for this QTL. This locus is among a small number that have consistently been identified to influence human hei...
Metzger J, Schrimpf R, Philipp U, Distl O.Body size is an important characteristic for horses of various breeds and essential for the classification of ponies concerning the limit value of 148 cm (58.27 inches) height at the withers. Genome-wide association analyses revealed the highest associated quantitative trait locus for height at the withers on horse chromosome (ECA) 3 upstream of the candidate gene LCORL. Using 214 Hanoverian horses genotyped on the Illumina equine SNP50 BeadChip and 42 different horse breeds across all size ranges, we confirmed the highly associated single nucleotide polymorphism BIEC2-808543 (-log(10)P = ...
Hamilton NA, Tammen I, Raadsma HW.Angiotensin converting enzyme (ACE) is essential for control of blood pressure. The human ACE gene contains an intronic Alu indel (I/D) polymorphism that has been associated with variation in serum enzyme levels, although the functional mechanism has not been identified. The polymorphism has also been associated with cardiovascular disease, type II diabetes, renal disease and elite athleticism. We have characterized the ACE gene in horses of breeds selected for differing physical abilities. The equine gene has a similar structure to that of all known mammalian ACE genes. Nine common single nuc...
Curik I, Druml T, Seltenhammer M, Sundström E, Pielberg GR, Andersson L, Sölkner J.The dominant phenotype of greying with age in horses, caused by a 4.6-kb duplication in intron 6 of STX17, is associated with a high incidence of melanoma and vitiligo-like skin depigmentation. However, the progressive greying and the incidence of melanoma, vitiligo-like depigmentation, and amount of speckling in these horses do not follow a simple inheritance pattern. To understand their inheritance, we analysed the melanoma grade, grey level, vitiligo grade, and speckling grade of 1,119 Grey horses (7,146 measurements) measured in six countries over a 9-year period. We estimated narrow sense...
Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Distl O....Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and dista...
Petersen JL, Mickelson JR, Rendahl AK, Valberg SJ, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A....Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle...
Boldbaatar B, Bazartseren T, Koba R, Murakami H, Oguma K, Murakami K, Sentsui H.In the current study, primers described previously and modified versions of these primers were evaluated for amplification of full-length gag genes from different equine infectious anemia virus (EIAV) strains from several countries, including the USA, Germany and Japan. Each strain was inoculated into a primary horse leukocyte culture, and the full-length gag gene was amplified by reverse transcription polymerase chain reaction. Each amplified gag gene was cloned into a plasmid vector for sequencing, and the detectable copy numbers of target DNA were determined. Use of a mixture of two forward...
Vychodilova L, Matiasovic J, Bobrova O, Futas J, Klumplerova M, Stejskalova K, Cvanova M, Janova E, Osickova J, Vyskocil M, Sedlinska M, Dusek L....Equine insect bite hypersensitivity (IBH) is a seasonal IgE-mediated dermatosis caused by bites of insects of the genus Culicoides. A familial predisposition for the disease has been shown but, except for the MHC, the genes involved have not been identified so far. An immunogenomic analysis of IBH was performed in a model population of Old Kladruby horses, all living in the same environment. Clinical signs of IBH were used as phenotypic manifestation of IBH. Furthermore, total serum IgE levels were determined in the sera of these horses and used as an independent phenotypic marker for the immu...
Zaniboni A, Merlo B, Zannoni A, Bernardini C, Lavitrano M, Forni M, Mari G, Bacci ML.Sperm mediated gene transfer (SMGT) has been reported to be a powerful tool for producing transgenic livestock with applications in biomedicine and agriculture. To date, two studies have reported the production of transgenic equine embryo with, however, low efficiency in blastocyst production and transgene expression. The aim of the present study was to develop a method which allowed the efficient production of transgene-expressing embryos of the equine species through SMGT. To overcome problems due to in vitro fertilization (IVF) in horses, the ICSI procedure was associated with SMGT. The upt...
Orr N, Hill EW, Gu J, Govindarajan P, Conroy J, van Grevenhof EM, Ducro BJ, van Arendonk JA, Knaap JH, van Weeren PR, Machugh DE, Ennis S, Brama PA.Equine osteochondrosis is a developmental joint disease that is a significant source of morbidity affecting multiple breeds of horse. The genetic variants underlying osteochondrosis susceptibility have not been established. Here, we describe the results of a genome-wide association study of osteochondrosis using 90 cases and 111 controls from a population of Dutch Warmblood horses. We report putative associations between osteochondrosis and loci on chromosome 3 (BIEC2-808543; P = 5.03 × 10(-7) ) and chromosome 10 (BIEC2-121323; P = 2.62 × 10(-7) ).
Raudsepp T, McCue ME, Das PJ, Dobson L, Vishnoi M, Fritz KL, Schaefer R, Rendahl AK, Derr JN, Love CC, Varner DD, Chowdhary BP.Impaired acrosomal reaction (IAR) of sperm causes male subfertility in humans and animals. Despite compelling evidence about the genetic control over acrosome biogenesis and function, the genomics of IAR is as yet poorly understood, providing no molecular tools for diagnostics. Here we conducted Equine SNP50 Beadchip genotyping and GWAS using 7 IAR-affected and 37 control Thoroughbred stallions. A significant (PA and g.11040379C>A (p.166H>N) in exon 4 that were significantly associated with the IAR phenotype both in the GWAS cohort (n = 44) and in a large multi-breed cohort of 265 ho...
Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, Elton D, Newton JR, Kellam P, Wood JL, Holmes EC, Murcia PR.The ability of influenza A viruses (IAVs) to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales - from the individual to the population - are essential for devising effective measures to predict, prevent or contain influenza emergence. Understanding how IAVs spread and evolve during outbreaks is critical for the management of epidemics. Reconstructing the transmission network during a single outbreak by sampling viral genetic data in time and space can generate insights about these processes. Here, we ob...
Grubaugh ND, Petz LN, Melanson VR, McMenamy SS, Turell MJ, Long LS, Pisarcik SE, Kengluecha A, Jaichapor B, O'Guinn ML, Lee JS.Highly multiplexed assays, such as microarrays, can benefit arbovirus surveillance by allowing researchers to screen for hundreds of targets at once. We evaluated amplification strategies and the practicality of a portable DNA microarray platform to analyze virus-infected mosquitoes. The prototype microarray design used here targeted the non-structural protein 5, ribosomal RNA, and cytochrome b genes for the detection of flaviviruses, mosquitoes, and bloodmeals, respectively. We identified 13 of 14 flaviviruses from virus inoculated mosquitoes and cultured cells. Additionally, we differentiate...
Gebhardt S, Merkl M, Herbach N, Wanke R, Handler J, Bauersachs S.The equine endometrium exhibits characteristic morphological and functional changes during the estrous cycle controlled by the interplay of progesterone and estradiol. A microarray analysis of endometrial tissue samples derived from five time points of the estrous cycle (Day [D] 0, D3, D8, D12, and D16) was performed to study the dynamics of equine endometrial gene expression. Statistical analysis revealed 4996 genes differentially expressed during the estrous cycle. Clustering of similar expression profiles was performed to find groups of coregulated genes. This revealed eight major profiles:...
Ricard A, Danvy S, Legarra A.Genomic evaluations often use as pseudo-phenotypes corrected means of progeny performances, like daughter yield deviations (DYD) in dairy species. In horse breeding, own performances are also available and performances from other relatives (as half sibs) may play an important part in the EBV because the number of progeny remains low, even for stallions. The first step for genomic selection in horses is therefore to generate pseudo-phenotypes for genomic analysis when parental or own information is considered. This work presents an easy method to compute deregressed EBV from regular pedigree-ba...
Ramos RT, Carneiro AR, Soares Sde C, dos Santos AR, Almeida S, Guimarães L, Figueira F, Barbosa E, Tauch A, Azevedo V, Silva A.New sequencing platforms have enabled rapid decoding of complete prokaryotic genomes at relatively low cost. The Ion Torrent platform is an example of these technologies, characterized by lower coverage, generating challenges for the genome assembly. One particular problem is the lack of genomes that enable reference-based assembly, such as the one used in the present study, Corynebacterium pseudotuberculosis biovar equi, which causes high economic losses in the US equine industry. The quality treatment strategy incorporated into the assembly pipeline enabled a 16-fold greater use of the seque...
Soares SC, Trost E, Ramos RT, Carneiro AR, Santos AR, Pinto AC, Barbosa E, Aburjaile F, Ali A, Diniz CA, Hassan SS, Fiaux K, Guimarães LC....Corynebacterium pseudotuberculosis is the causative agent of several veterinary diseases in a broad range of economically important hosts, which can vary from caseous lymphadenitis in sheep and goats (biovar ovis) to ulcerative lymphangitis in cattle and horses (biovar equi). Existing vaccines against C. pseudotuberculosis are mainly intended for small ruminants and, even in these hosts, they still present remarkable limitations. In this study, we present the complete genome sequence of C. pseudotuberculosis biovar equi strain 258, isolated from a horse with ulcerative lymphangitis. The genome...
Hollanders B, Mougin A, N'Diaye F, Hentz E, Aude X, Girard A.A new two-step gradient technique has been used in the separation of the different classes of lipoproteins from the serum of cows, horses, dogs, pigs, rabbits and rats. Total lipoproteins were first isolated at d 1.21 then floated through a d 1.006 to d 1.21 gradient. Collection by mean of a gradient fractionator provided directly comparable lipoprotein profiles, allowed the determination of the exact density range of each lipoprotein class and the fraction by fraction analysis of composition. Cholesterol and apo AI recoveries were high. Horse, dog, rabbit and pig exhibited three distinct lipo...
Carpenter MA, Broad TE.The cDNA sequence of horse transferrin was determined by sequencing clones isolated from a horse liver cDNA library and clones obtained by PCR. The 2305 bp horse transferrin cDNA sequence included part of the 5' untranslated region and extended to the poly(A) tail. It had 80% sequence identity with the human transferrin cDNA, and encoded a protein of 706 residues, including a signal sequence of 19 amino acids. The horse transferrin sequence had the duplicated structure and conserved iron binding and cysteine residues which are characteristic of the transferrin family.
Elschner MC, Thomas P, Melzer F.Burkholderia mallei is a zoonotic agent causing glanders, a notifiable disease in equines. During the past decades glanders emerged, and the Kingdom of Bahrain reported outbreaks to the World Organization of Animal Health in 2010 and 2011. This paper presents the complete genome sequence of the Burkholderia mallei strain 11RR2811 Bahrain1.
Munday JS, Gedye K, Daudt C, Chaves Da Silva F.Bovine papillomavirus (BPV) types 1 and 2 are recognized as the main cause of equine sarcoids. However, some studies report that up to a quarter of these tumors do not contain detectible BPV1 or BPV2 DNA. The absence of detectible BPV1 or BPV2 in these sarcoids suggests the possible involvement of other papillomavirus types. Currently, five are recognized to cause mesenchymal neoplasia after cross-species infection. In addition to BPV1 and BPV2, BPV13 has been associated with equine sarcoids in Brazil, BPV14 has been associated with feline sarcoids, and Ovis aries papillomavirus 2 caused a sa...
Vegas AR, Podico G, Canisso IF, Bollwein H, Fröhlich T, Bauersachs S, Almiñana C.During initial maternal recognition of pregnancy (MRP), the equine embryo displays a series of unique events characterized by rapid blastocyst expansion, secretion of a diverse array of molecules, and transuterine migration to interact with the uterine surface. Up to date, the intricate transcriptome and proteome changes of the embryo underlying these events have not been critically studied in horses. Thus, the objective of this study was to perform an integrative transcriptomic (including mRNA, miRNAs, and other small non-coding RNAs) and proteomic analysis of embryos collected from days 10 t...
Santos Alves J, da Silva Anjos M, Silva Bastos M, Sarmento Martins de Oliveira L, Pereira Pinto Oliveira I, Batista Pinto LF....Equid breeds originating from the Iberian Peninsula and North Africa are believed to have genetically contributed to the formation of breeds and ecotypes from Brazil. The country has numerous breeds and ecotypes of horses and donkeys but there are no extensive studies on maternal genetic diversity and their origins. This study reports the results of the first genetic analysis of all horse and donkey breeds/ecotypes from Brazil based on sequences of the mitochondrial DNA control region (D-loop) whose main objective was to characterize the genetic variation in these animals. These analyses will ...
Raudsepp T.Reproductive disorders are genetically heterogeneous and complex; available genetic tests are limited to chromosome analysis and 1 susceptibility gene. Cytogenetic analysis should be the first test to confirm or rule out chromosomal aberrations. No causative genes/mutations are known. The only available genetic test for stallion subfertility is based on a susceptibility gene FKBP6. The ongoing progress in equine genomics will improve the status of genetic testing. However, because subfertile phenotypes do not facilitate collection of large numbers of samples or pedigrees, and clinical causes o...
Posnett ES, Ambrosio RE.This report describes DNA probes for the identification of Babesia equi. A genomic library of B. equi was constructed in pUC13. Several clones were identified that hybridized strongly to B. equi DNA. Clone pBE33 hybridized specifically to B. equi DNA and did not hybridize to horse DNA nor to DNA from Babesia caballi, Babesia bovis or Babesia bigemina. Two subclones of pBE33 (pSB20 and pEH21) containing B. equi repetitive sequences, could detect 0.49 ng and 0.97 ng B. equi DNA, respectively.
Zhu C, Li Q, Guo W, Lu G, Yin X, Qi T, Xiang W, Ran D, Qu J.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.
Tesena P, Kingkaw A, Phaonakrop N, Roytrakul S, Limudomporn P, Vongsangnak W, Kovitvadhi A.Equine melanocytic neoplasm (EMN) is a common disease in older grey horses. The purpose of this study was to examine the potential proteins throughout EMN stages from faecal proteomic outlining using functional analysis. Faecal samples were collected from the rectum of 25 grey horses divided into three groups; normal group without EMN ( = 10), mild EMN ( = 6) and severe EMN ( = 9). Based on the results, 5910 annotated proteins out of 8509 total proteins were assessed from proteomic profiling. We observed differentially expressed proteins (DEPs) between the normal group and the EMN group, and 1...
Blott S, Cunningham H, Malkowski L, Brown A, Rauch C.Exercise-induced pulmonary haemorrhage (EIPH) occurs in horses performing high-intensity athletic activity. The application of physics principles to derive a 'physical model', which is coherent with existing physiology and cell biology data, shows that critical parameters for capillary rupture are cell-cell adhesion and cell stiffness (cytoskeleton organisation). Specifically, length of fracture in the capillary is a ratio between the energy involved in cell-cell adhesion and the stiffness of cells suggesting that if the adhesion diminishes and/or that the stiffness of cells increases EIPH is ...
Ding L, Wang Y, Zhang L, Luo C, Wu F, Huang Y, Zhen Y, Chen N, Wang L, Song L, Pool K, Blache D, Maloney SK, Liu D, Yang Z, Huang X, Li C, Yu X....Here, we describe the Herbivore Transcriptome Integrated Resource Database (HTIRDB, https://yanglab.hzau.edu.cn/HTIRDB#/). The HTIRDB comprises the self-generated transcriptomic data from 100 to 105 tissues from two female domestic herbivores from six species (cattle, donkey, goat, horse, rabbit, and sika deer) and two breeds of sheep, and an extra 28,710 related published datasets. The HTIRDB user-friendly interface provides tools and functionalities that facilitate the exploration of gene expression between tissues and species. The tools for comparative transcriptomics can be used to identif...
Ryder OA, Hansen SK.A (G + C)-rich density satellite DNA (rho = 1.713 gm/cc) has been purified from splenic DNA of Przewalski's horse, Equus przewalskii, by successive equilibrium density gradient centrifugations. The purified satellite, which may comprise as much as 29% of the total DNA, renatures rapidly; however, analyses of native, single-stranded, and reassociated molecules by analytical ultracentrifugation and melting properties suggest that some sequence heterogeniety exists in the 1.713 gm/cc satellite. Complementary RNA (cRNA) transcribed from satellite DNA has been utilized for in situ hybridization stu...
Hernández-Quiroz F, Murugesan S, Flores-Rivas C, Piña-Escobedo A, Juárez-Hernández JI, García-Espitia M, Chávez-Carbajal A, Nirmalkar K....Horses are non-ruminant, herbivorous mammals, been used through history for various purposes, with a gut microbiota from cecum to the colon, possessing remarkable fermentative capacity. We studied the fecal microbiota of Azteca, Criollo, Frisian, Iberian, Pinto, Quarter and Spanish horse breeds living in Mexico by next-generation DNA sequencing of 16S rRNA gene libraries. Dominant phyla Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, Fibrobacteres, Actinobacteria and Verrucomicrobia have different relative abundances among breeds, with contrasted alpha and beta diversities as well. He...
Kinoshita Y, Niwa H, Katayama Y, Hariu K.Obligate anaerobes are important etiological agents in pneumonia or pleuropneumonia in horses, because they are isolated more commonly from ill horses that have died or been euthanized than from those that survive. We performed bacterial identification and antimicrobial susceptibility testing for obligate anaerobes to establish effective antimicrobial therapy. We used 16S rRNA gene sequencing to identify 58 obligate anaerobes and compared the results with those from a phenotypic identification kit. The identification results of 16S rRNA gene sequencing were more reliable than those of the comm...
Hagen A, Niebert S, Brandt VP, Holland H, Melzer M, Wehrend A, Burk J.Successful translation of multipotent mesenchymal stromal cell (MSC)-based therapies into clinical reality relies on adequate cell production procedures. These should be available not only for human MSC, but also for MSC from animal species relevant to preclinical research and veterinary medicine. The cell culture medium supplementation is one of the critical aspects in MSC production. Therefore, we previously established a scalable protocol for the production of buffy-coat based equine platelet lysate (ePL). This ePL proved to be a suitable alternative to fetal bovine serum (FBS) for equine a...
Desjardin C, Riviere J, Vaiman A, Morgenthaler C, Diribarne M, Zivy M, Robert C, Le Moyec L, Wimel L, Lepage O, Jacques C, Cribiu E, Schibler L.Osteochondrosis (OC(D)) is a juvenile osteo-articular disorder affecting several mammalian species. In horses, OC(D) is considered as a multifactorial disease and has been described as a focal disruption of endochondral ossification leading to the development of osteoarticular lesions. Nevertheless, OC(D) physiopathology is poorly understood. Affected horses may present joint swelling, stiffness and lameness. Thus, OC(D) is a major concern for the equine industry. Our study was designed as an integrative approach using omics technologies for the identification of constitutive defects in epiphy...
Fernandez-Fuente M, Ames EG, Wagner ML, Zhou H, Strom M, Zammit PS, Mickelson JR, Muntoni F, Brown SC, Piercy RJ.To develop a reliable method for converting cultured equine skin-derived fibroblasts into muscle cells. Methods: Equine skin-derived fibroblasts. Methods: The equine myogenic differentiation 1 (eqMyoD) genomic sequence was obtained by use of equine bacterial artificial chromosome screening and PCR sequencing. Total mRNA was extracted from foal skeletal muscle, and eqMyoD cDNA was cloned into a plasmid vector with an internal ribosomal entry site to express bicistronic eqMyoD or enhanced green fluorescent protein (EGFP). Transient expression was confirmed by immunocytochemical analysis and west...
Dube S, Chionuma H, Matoq A, Alshiekh-Nasany R, Abbott L, Poiesz BJ, Dube DK.In order to better understand the training and athletic activity of horses, we must have complete understanding of the isoform diversity of various myofibrillar protein genes like tropomyosin. Tropomyosin (TPM), a coiled-coil dimeric protein, is a component of thin filament in striated muscles. In mammals, four TPM genes (TPM1, TPM2, TPM3, and TPM4) generate a multitude of TPM isoforms via alternate splicing and/or using different promoters. Unfortunately, our knowledge of TPM isoform diversity in the horse is very limited. Hence, we undertook a comprehensive exploratory study of various TPM i...
Li S, Zhao G, Han H, Li Y, Li J, Wang J, Cao G, Li X.It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field. Results: Using the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 leng...
Puppione DL, Whitelegge JP, Yam LM, Bassilian S, Schumaker VN, MacDonald MH.In pigs, humans, chimpanzees and probably other great apes, a cysteine at residue 6 enables apolipoprotein A-II to form a homodimer. However, the apoA-IIs of other primates, lacking a cysteine residue, are monomeric. We have already reported that horse apoA-IIs form homodimers due also to a cysteine at residue 6. In this study, we wanted to determine whether other equine apoA-IIs might be monomeric. The high density lipoproteins were ultracentrifugally isolated from the plasmas of a horse (Equus caballus), a donkey (Equus asinus) and five wild equines: two types of zebras (Equus zebra hartmann...
Jinglong X, Xiaobin L, Fang Z, Chenchen W, Kailun Y.The aim of this research was to isolate bacteria capable of biotransforming daidzein from fresh feces from pregnant horses. A Hungate anaerobic roller tube was used for anaerobic culture. Single colonies were picked at random and incubated with daidzein. High performance liquid chromatography was used to detect whether the isolated bacteria were able to biotransform the substrate. A strain capable of reducing daidzein was selected and characterized using sequence analysis of 16S rDNA, and a phylogenetic tree was constructed. The morphological physiological and biochemical characteristics of th...
Maeda K, Kai K, Matsumura T.Infection with equine herpesvirus-4 (EHV-4) is a major cause of respiratory tract disease, equine rhinopneumonitis, in horses. Although the full sequence of EHV-4 has been reported, genomic differences among EHV-4 field isolates have not yet been characterized. In this study, the genomic diversity between 23 Japanese EHV-4 isolates was analyzed by digestion with restriction endonucleases (BamHI, BgIII, EcoRI, SacI, and SalI) and polymerase chain reaction (PCR). The restriction endonuclease digestion patterns of the EHV-4 field isolates showed distinct differences which included mobility shifts...
Godovac-Zimmermann J, Conti A, James L, Napolitano L.The complete primary structure of donkey beta-lactoglobulin I was determined by pulsed-liquid phase microsequencing of tryptic peptides. The protein has been isolated in monomeric form and it corresponds to monomeric beta-lactoglobulin of type I. With the inclusion of donkey beta-lactoglobulin I there are 13% common residues amongst the members of the beta-lactoglobulin family. Donkey beta-lactoglobulin I is homologous to the retinol-binding protein, bilin-binding protein and five other proteins belonging to the new superfamily of hydrophobic molecule transporters. A rapid method for peptide i...
Suchan T, Chauvey L, Poullet M, Tonasso-Calvière L, Schiavinato S, Clavel P, Clavel B, Lepetz S, Seguin-Orlando A, Orlando L.Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post-mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have rec...
Fornal A, Radko A, Piestrzyńska-Kajtoch A.Short tandem repeat (STR) loci, i.e. microsatellites are a class of genetic markers commonly used for population studies and parentage control. This study determined the usefulness of microsatellite markers recommended by International Society for Animal Genetics (ISAG) for identification and pedigree analysis in horses based on the example of Polish Hucul horse population (Equus caballus). The set of seventeen microsatellites loci was tested (AHT4, AHT5, ASB2, HMS2, HMS3, HMS6, HMS7, HTG10, HTG4, HTG6, HTG7, VHL20, ASB17, ASB23, CA425, HMS1, LEX3) for 216 individuals. All samples were genotyp...
Jones CJP, Allen WRT, Wilsher S.In this study, we compare glycosylation at the fetomaternal interface in 3 equine species: horse, donkey and zebra, all of which can interbreed to produce hybrids, to assess their glycan similarities and differences. Methods: Sections cut from 3 specimens of horse (Equus caballus) placenta (50, 200 and 280 days gestation), one donkey (Equus asinus) placenta (65 cm crown-rump length) and 5 specimens of zebra (Equus quagga) placentae (81-239 days gestation) were stained with a panel of 24 biotinylated lectins using an avidin-peroxidase revealing system. Results: There were only slight quantitat...
Cieslak J, Pawlak P, Wodas L, Borowska A, Stachowiak A, Puppel K, Kuczynska B, Luczak M, Marczak L, Mackowski M.Currently, research interest is increasing in horse milk composition and its effect on human health. Despite previously published studies describing the presence of intra- and interbreed variability of equine milk components, no investigations have focused on the genetic background of this variation. Among horse caseins and the genes encoding them, least is known about the structure and expression of the α-S2 casein gene, CSN1S2. Herein, based on direct sequencing of the equine CSN1S2 coding sequence, we describe the presence of 51-bp insertion-deletion (in/del) polymorphism, which significan...
Tallmadge RL, Lear TL, Johnson AK, Guérin G, Millon LV, Carpenter SL, Antczak DF.A clone containing beta(2)-microglobulin (beta(2)-m), the light chain of the major histocompatibility complex class I cell surface molecule, was isolated from an equine bacterial artificial chromosome library. This clone was used as a template for polymerase chain reaction (PCR) and unidirectional sequencing to elucidate the genomic sequence and intron/exon boundaries. We obtained 7,000 bases of sequence, extending from 1,100 nucleotides (nt) upstream of the coding region start through 1,698 nt downstream of the stop codon. The sequence contained regulatory elements in the region upstream of t...
Hansen M, Knorr C, Hall AJ, Broad TE, Brenig B.The solute carrier family 26, member 2 (SLC26A2) gene belongs to a family of multifunctional anion exchangers. Mutations in the human SLC26A2 gene are associated with autosomal recessively inherited chondrodysplasias. Hence, we postulate that the equine SLC26A2 could be a candidate gene for conformational traits in horses. An equine BAC clone harboring the SLC26A2 gene was isolated. The complete 142,625 bp insert sequence of this clone was determined by transposon sequencing. Together with the SLC26A2 gene the BAC clone contains four genes, i.e. the macrophage colony stimulating factor 1 recep...
