Bioinformatics in horses involves the application of computational tools and techniques to analyze and interpret biological data related to equine species. This interdisciplinary field integrates biology, computer science, and information technology to study genetic, genomic, and proteomic information in horses. Bioinformatics can be used to investigate genetic variations, understand disease mechanisms, and assist in the development of targeted therapies and breeding programs. Key areas of focus include genome sequencing, gene expression analysis, and the identification of genetic markers associated with specific traits or conditions. This page compiles peer-reviewed research studies and scholarly articles that explore the application and impact of bioinformatics on equine genetics, health, and breeding.
Palomino Lago E, Baird A, Blott SC, McPhail RE, Ross AC, Durward-Akhurst SA, Guest DJ.Fractures caused by bone overloading are a leading cause of euthanasia in Thoroughbred racehorses. The risk of fatal fracture has been shown to be influenced by both environmental and genetic factors but, to date, no specific genetic mechanisms underpinning fractures have been identified. In this study, we utilised a genome-wide polygenic risk score to establish an in vitro cell system to study bone gene regulation in horses at high and low genetic risk of fracture. Candidate gene expression analysis revealed differential expression of and genes in osteoblasts derived from high- and low-risk...
Maniego J, Pesko B, Habershon-Butcher J, Hincks P, Taylor P, Stewart G, Proudman C, Ryder E.Gene doping in horses is a threat to the fairness in sport and has serious implications for animal welfare. To investigate the effect of long-term storage on the detection of AAV in plasma and whole blood, samples from an administration study using an adeno-associated virus serotype 6 expressing green fluorescence protein (AAV6-GFP) were stored at -20°C for 8 months before analysis. The AAV vector was detected in stored plasma samples, following the same detection profile as the fresh plasma samples. The stored blood showed lower overall DNA detection but followed the same detection profile ...
Song X, Jiang H, Lv P, Cui K, Liu Q, Yin S, Liu H, Li Z.Oocyte in vitro maturation is necessary for the study and application of animal-assisted reproduction technology in animal reproduction and breeding. The comprehensive transcriptional profile of equine oocyte maturated in vitro has not been fully mined yet, which makes many key transcriptional events still unidentified. Here, Smart-seq2 was performed to analyse the gene expression pattern and the underlying regulatory mechanism of horse germinal vesicle (GV) and in vitro metaphase II (MII) oocytes. The results showed that 6402 genes (2640 up-regulated and 3762 down-regulated in MII samples com...
Xing J, Xie L, Qi X, Liu G, Akhtar MF, Li X, Bou G, Bai D, Zhao Y, Dugarjaviin M, Zhang X.The proliferation and differentiation of skeletal muscle satellite cells (SCs) are necessary for the development of mature skeletal muscle. Leucine (Leu) is both an essential amino acid (EAA) and a branched-chain amino acid (BCAA), which has attracted worldwide attention due to its ability to repair and become new fibers. We separated the equine SCs into the control group (CON) and the Leu-supplemented group (LEU), which the cells were cultured in Leu-deprived and Leu-supplemented media respectively. We combined the transcriptome (RNA-Seq) and quantitative proteome (TMT) profiling analyses on ...
Pelkola K, Heinikainen S, Pohjanvirta T.In Finland, Taylorella equigenitalis, the causative agent of contagious equine metritis (CEM), was first detected in 1992. The aim of this study was to genotype Finnish T. equigenitalis isolates to investigate the epidemiology of the infection in the Finnish horse population. A total of 34 T. equigenitalis isolates from 24 horses obtained during 1992-2021 were subjected to whole genome sequencing (WGS) and subsequent local ad hoc core genome multi-locus sequence typing (cgMLST) targeting 1259 loci. Classical MLST profiles were extracted from the whole-genome sequence data. Three novel MLST ty...
Foury A, Mach N, Ruet A, Lansade L, Moisan MP.The improvement of horse welfare through housing conditions has become a real issue in recent years and have highlighted the detrimental effect of individual housing of horses on their health and behaviour. In this new study, we analysed the blood transcriptome of 45 sport horses housed individually that were previously examined for their behaviour and gut microbiota. We performed differential and regression analyses of gene expression, followed by downstream bioinformatic analyses, to unveil the molecular pathways related to the behavioural changes associated with welfare impairment in these ...
Laseca N, Cánovas Á, Valera M, Id-Lahoucine S, Perdomo-González DI, Fonseca PAS, Demyda-Peyrás S, Molina A.The phenomenon in which the expected Mendelian inheritance is altered is known as transmission ratio distortion (TRD). The TRD analysis relies on the study of the transmission of one of the two alleles from a heterozygous parent to the offspring. These distortions are due to biological mechanisms affecting gametogenesis, embryo development and/or postnatal viability, among others. In this study, TRD phenomenon was characterized in horses using SNP-by-SNP model by TRDscan v.2.0 software. A total of 1,041 Pura Raza Español breed horses were genotyped with 554,634 SNPs. Among them, 277 horses ge...
Semik-Gurgul E, Gurgul A, Szmatoła T.Recent publications confirmed that long non-coding RNAs (lncRNAs) perform an essential function in gene-specific transcription regulation. Nevertheless, despite its important role, lncRNA has not yet been described in equine sarcoids, the skin neoplasia of horses. Therefore, the aim of this study is to deepen the knowledge about lncRNA expression in the pathogenesis of equine sarcoids and provide new insight into the regulatory function of lncRNA in the bovine papillomavirus-dependent neoplasia of horse dermal tissues. RNA sequencing (RNA-seq) data from 12 equine sarcoid samples and the corres...
Liu L, Yu W, Cai K, Ma S, Wang Y, Ma Y, Zhao H. () is a zoonotic opportunistic pathogen that can cause life-threatening infections. The rapid evolution of multidrug-resistant and the fact that there is no currently licensed effective vaccine against warrant the need for vaccine development. Reverse vaccinology (RV), which involves screening a pathogen's entire genome and proteome using various web-based prediction tools, is considered one of the most effective approaches for identifying vaccine candidates. Here, we performed a pangenome analysis to determine the core proteins of . We then used the RV approach to examine the subcellular l...
Sheikh A.The Arabian horse breed is well known for its purity and played a key role in the genetic improvement of other horses worldwide. The mitochondrial genome plays a vital role in maternal inheritance and it's helpful to evaluate its genetic diversity and conservation. It has higher mutation rates than nuclear DNA in vertebrates and therefore reveals phylogenetic relationships and haplotypes. In this study, the mitochondrial genome mutations in two Saudi horse strains, Kehilan and Hamdani demonstrated various changes in the gene and amino acid levels and included two other Saudi horses (Hadban and...
Manzoori S, Farahani AHK, Moradi MH, Kazemi-Bonchenari M.The assignment of an individual to the true population of origin using a low-panel of discriminant SNP markers is one of the most important applications of genomic data for practical use. The aim of this study was to evaluate the potential of different Artificial Neural Networks (ANNs) approaches consisting Deep Neural Networks (DNN), Garson and Olden methods for feature selection of informative SNP markers from high-throughput genotyping data, that would be able to trace the true breed of unknown samples. The total of 795 animals from 37 breeds, genotyped by using the Illumina SNP 50k Bead ch...
Triant DA, Walsh AT, Hartley GA, Petry B, Stegemiller MR, Nelson BM, McKendrick MM, Fuller EP, Cockett NE, Koltes JE, McKay SD, Green JA, Murdoch BM....Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for...
Vasoya D, Tzelos T, Benedictus L, Karagianni AE, Pirie S, Marr C, Oddsdóttir C, Fintl C, Connelley T.The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and app...
Gurgul A, Jasielczuk I, Szmatoła T, Sawicki S, Semik-Gurgul E, Długosz B, Bugno-Poniewierska M.Nanopore sequencing is a third-generation biopolymer sequencing technique that relies on monitoring the changes in an electrical current that occur as nucleic acids are passed through a protein nanopore. Increasing quality of reads generated by nanopore sequencing systems encourages their application in genome-wide polymorphism detection and genotyping. In this study, we employed nanopore sequencing to identify genome-wide polymorphisms in the horse genome. To reduce the size and complexity of genome fragments for sequencing in a simple and cost-efficient manner, we amplified random DNA fragme...
McFadden A, Martin K, Foster G, Vierra M, Lundquist EW, Everts RE, Martin E, Volz E, McLoone K, Brooks SA, Lafayette C.Mutations causing depigmentation are relatively common in Equus caballus (horse). Over 40 alleles in multiple genes are associated with increased white spotting (as of February 2023). The splashed white phenotype, a coat spotting pattern described as appearing like the horse has been splashed with white paint, was previously associated with variants in the PAX3 and MITF genes. Both genes encode transcription factors known to control melanocyte migration and pigmentation. We report two novel mutations, a stop-gain mutation in PAX3 (XM_005610643.3:c.927C>T, ECA6:11,196,181, EquCab3.0) and a m...
Górski K, Borowska M, Stefanik E, Polkowska I, Turek B, Bereznowski A, Domino M.Incorrect Reference: In the original article [1], the reference [43] was incorrectly written as Padhye, N.; Rios, D.; Fay, V.; Hanneman, S.K. Pressure Injury Link to Entropy of Abdominal Temperature; Cizik School of Nursing, The University of Texas Health Science Center at Houston: Houston, TX, USA, 2022; Preprint. It should be Flood, M.W.; Grimm, B. EntropyHub: An open-source toolkit for entropic time series analysis. PLoS ONE 2021, 16, e0259448.
With this correction, the order of references has not been changed. The authors state that the scientific conclusions are unaffected. This correcti...
Ohnuma A, Tozaki T, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Takahashi Y, Nagata SI.To ensure fair competition and sports integrity, gene doping is prohibited in horseracing and equine sports. One gene doping method is by administering exogenous genes, called transgenes, to postnatal animals. Although several transgene detection methods have been developed for horses, many are unsuitable for multiplex detection. In this proof-of-concept study, we developed a highly sensitive and multiplex transgene detection method using multiple πCode with identification patterns printed on the surface. The following steps were employed: (1) multiplex polymerase chain reaction amplification...
Lee J, Kang YJ, Kim YK, Choi JY, Shin SM, Shin MC.The influences of diet and environmental factors on gut microbial profiles have been widely acknowledged; however, the specific roles of host genetics remain uncertain. To unravel host genetic effects, we raised 47 Jeju crossbred (Jeju × Thoroughbred) foals that exhibited higher genetic diversity. Foals were raised under identical environmental conditions and diets. Microbial composition revealed that Firmicutes, Bacteroidetes, and Spirochaetes were the predominant phyla. We identified 31 host-microbiome associations by utilizing 47,668 single nucleotide polymorphisms (SNPs) and 734 taxa with...
Krishnan BS, Jones LR, Elmore JA, Samiappan S, Evans KO, Pfeiffer MB, Blackwell BF, Iglay RB.Visible and thermal images acquired from drones (unoccupied aircraft systems) have substantially improved animal monitoring. Combining complementary information from both image types provides a powerful approach for automating detection and classification of multiple animal species to augment drone surveys. We compared eight image fusion methods using thermal and visible drone images combined with two supervised deep learning models, to evaluate the detection and classification of white-tailed deer (Odocoileus virginianus), domestic cow (Bos taurus), and domestic horse (Equus caballus). We cla...
Bou T, Ding W, Ren X, Liu H, Gong W, Jia Z, Zhang X, Dugarjaviin M, Bai D.Traditional Mongolian endurance training is an effective way to improve the athletic ability of the horse for endurance events and is widely used. This incorporates aerobic exercise and intermittent fasting and these altered physiologic conditions are associated with switches between muscle fibre types. Objective: To better understand the adaption of horse skeletal muscle to traditional Mongolian endurance training from muscle fibre characteristics and transcriptional levels and to explore possible molecular mechanisms associated with the endurance performance of horses. Methods: Before-after ...
Aguilar-Lazcano CA, Espinosa-Curiel IE, Ríos-Martínez JA, Madera-Ramírez FA, Pérez-Espinosa H.The development of technology, such as the Internet of Things and artificial intelligence, has significantly advanced many fields of study. Animal research is no exception, as these technologies have enabled data collection through various sensing devices. Advanced computer systems equipped with artificial intelligence capabilities can process these data, allowing researchers to identify significant behaviors related to the detection of illnesses, discerning the emotional state of the animals, and even recognizing individual animal identities. This review includes articles in the English langu...
Machmoum M, Badaoui B, Petit D, Germot A, El Alaoui MA, Boujenane I, Piro M.Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin cultur...
Beaumont RE, Smith EJ, Zhou L, Marr N, Thorpe CT, Guest DJ.We investigated how Interleukin 1 beta (IL-1β) impacts equine tenocyte function and global gene expression in vitro and determined if these effects could be rescued by pharmacologically inhibiting nuclear factor-κB (NF-B) or interleukin 1 signalling. Equine superficial digital flexor tenocytes were cultured in three-dimensional (3D) collagen gels and stimulated with IL-1β for two-weeks, with gel contraction and interleukin 6 (IL6) measured throughout and transcriptomic analysis performed at day 14. The impact of three NF-B inhibitors on gel contraction and IL6 secretion were measured in 3D ...
Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T....Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with high...
Sánchez-Guerrero MJ, Ripollés-Lobo M, Bartolomé E, Perdomo-González DI, Valera M.The Arabian horse is a generally reliable sport horse, and continues to be a remarkable endurance horse, so the relevance of the expected value of the proportion of Arabian genes (EV%AG) in horses participating in eventing could be a relevant factor. A total of 1089 horses participating in eventing (8866 records) were used. A GLM revealed that the EV%AG was significant in dressage, show jumping and cross-country. A BLUP genetic evaluation was computed with five genetic models (without the EV%AG (0) using as a covariate (A), as a fixed effect (B), with variance heterogeneity, and in genetic gro...
Mousavi SF, Razmkabir M, Rostamzadeh J, Seyedabadi HR, Naboulsi R, Petersen JL, Lindgren G.Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Ar...
Maniego J, Giles O, Hincks P, Stewart G, Proudman C, Ryder E.We present here the use of targeted, long-read sequencing of the myostatin (MSTN) gene as a model to detect potential gene editing events in Thoroughbred horses. MSTN is a negative regulator of muscle development, making the gene a prime candidate target for gene doping. By sequencing the complete gene in one PCR product, we can catalogue all mutations without the need to produce short-fragment libraries. A panel of reference material fragments with defined mutations was constructed and successfully sequenced by both Oxford Nanopore and Illumina-based methods, showing that gene doping editing ...
Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D.LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant peris...
Valberg SJ, Williams ZJ, Henry ML, Finno CJ.Shivers in horses is characterized by abnormal hindlimb movement when walking backward and is proposed to be caused by a Purkinje cell (PC) axonopathy based on histopathology. Objective: Define region-specific differences in gene expression within the lateral cerebellar hemisphere and compare cerebellar protein expression between Shivers horses and controls. Methods: Case-control study of 5 Shivers and 4 control geldings ≥16.2 hands in height. Methods: Using spatial transcriptomics, gene expression was compared between Shivers and control horses in PC soma and lateral cerebellar hemisphere w...
Bi X, Li G, Doty SB, Camacho NP.The orientation of collagen molecules is an important determinant of their functionality in connective tissues. The objective of the current study is to establish a method to determine the alignment of collagen molecules in histological sections of cartilage by polarized Fourier transform infrared imaging spectroscopy (FT-IRIS), a method based on molecular vibrations. Methods: Polarized FT-IRIS data obtained from highly oriented tendon collagen were utilized to calibrate the derived spectral parameters. The ratio of the integrated areas of the collagen amide I/II absorbances was used as an ind...
Doud MB, Ashenberg O, Bloom JD.Evolution drives changes in a protein's sequence over time. The extent to which these changes in sequence lead to shifts in the underlying preference for each amino acid at each site is an important question with implications for comparative sequence-analysis methods, such as molecular phylogenetics. To quantify the extent that site-specific amino acid preferences shift during evolution, we performed deep mutational scanning on two homologs of human influenza nucleoprotein with 94% amino acid identity. We found that only a modest fraction of sites exhibited shifts in amino acid preferences tha...
Lab on a chipApril 26, 2020
Volume 20, Issue 9 1621-1627 doi: 10.1039/d0lc00304b
Sun F, Ganguli A, Nguyen J, Brisbin R, Shanmugam K, Hirschberg DL, Wheeler MB, Bashir R, Nash DM, Cunningham BT.Rapid, sensitive and specific detection and reporting of infectious pathogens is important for patient management and epidemic surveillance. We demonstrated a point-of-care system integrated with a smartphone for detecting live virus from nasal swab media, using a panel of equine respiratory infectious diseases as a model system for corresponding human diseases such as COVID-19. Specific nucleic acid sequences of five pathogens were amplified by loop-mediated isothermal amplification on a microfluidic chip and detected at the end of reactions by the smartphone. Pathogen-spiked horse nasal swab...
Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I....Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9 Mb and 76.9 Mb of DNA sequences from a permafrost-...
Wilson AM, McGuigan MP, Su A, van Den Bogert AJ.The muscular work of galloping in horses is halved by storing and returning elastic strain energy in spring-like muscle-tendon units.These make the legs act like a child's pogo stick that is tuned to stretch and recoil at 2.5 strides per second. This mechanism is optimized by unique musculoskeletal adaptations: the digital flexor muscles have extremely short fibres and significant passive properties, whereas the tendons are very long and span several joints. Length change occurs by a stretching of the spring-like digital flexor tendons rather than through energetically expensive length changes...
Thorpe CT, Peffers MJ, Simpson D, Halliwell E, Screen HR, Clegg PD.Tendon is a simple aligned fibre composite, consisting of collagen-rich fascicles surrounded by a softer interfascicular matrix (IFM). The composition and interactions between these material phases are fundamental in ensuring tissue mechanics meet functional requirements. However the IFM is poorly defined, therefore tendon structure-function relationships are incompletely understood. We hypothesised that the IFM has a more complex proteome, with faster turnover than the fascicular matrix (FM). Using laser-capture microdissection and mass spectrometry, we demonstrate that the IFM contains more ...
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 = ...
Schenkman KA, Marble DR, Burns DH, Feigl EO.Multiwavelength optical spectroscopy was used to determine the oxygen-binding characteristics for equine myoglobin. Oxygen-binding relationships as a function of oxygen tension were determined for temperatures of 10, 25, 35, 37, and 40 degrees C, at pH 7.0. In addition, dissociation curves were determined at 37 degrees C for pH 6.5, 7.0, and 7.5. Equilibration was achieved with a myoglobin solution, at the desired temperature and pH, and 16 oxygen-nitrogen gas mixtures of known oxygen fraction. Correction for the inevitable presence of metmyoglobin was made by using a three-component least squ...
Evans SV, Brayer GD.The three-dimensional structure of horse heart metmyoglobin has been refined to a final R-factor of 15.5% for all observed data in the 6.0 to 1.9 A resolution range. The final model consists of 1242 non-hydrogen protein atoms, 154 water molecules and one sulfate ion. This structure has nearly ideal bonding and bond angle geometry. A Luzzati plot of the variation in R-factor with resolution yields an estimated mean co-ordinate error of 0.18 A. An extensive analysis of the pattern of hydrogen bonds formed in horse heart metmyoglobin has been completed. Over 80% of the polypeptide chain is involv...
Morrison PK, Newbold CJ, Jones E, Worgan HJ, Grove-White DH, Dugdale AH, Barfoot C, Harris PA, Argo CM.Gastrointestinal microbial communities are increasingly being implicated in host susceptibilities to nutritional/metabolic diseases; such conditions are more prevalent in obese and/or older horses. This controlled study evaluated associations between host-phenotype and the fecal microbiome / metabolome. Thirty-five, Welsh Mountain pony mares were studied across 2 years (Controls, = 6/year, 5-15 years, Body Condition Score (BCS) 4.5-6/9; Obese, = 6/year, 5-15 years, BCS > 7/9; Aged, = 6 Year 1; = 5 Year 2, ≥19 years old). Animals were individually fed the same hay to maintenance (2% bo...
Peffers M, Liu X, Clegg P.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...
The Journal of hereditySeptember 1, 1991
Volume 82, Issue 5 369-377 doi: 10.1093/oxfordjournals.jhered.a111106
Wichman HA, Payne CT, Ryder OA, Hamilton MJ, Maltbie M, Baker RJ.We describe a molecular model for rapid chromosomal evolution that proposes tandemly repeated DNA sequences as a driving force. A prediction of this model is that when extensive rearrangements of euchromatin have been facilitated by heterochromatin, genomes will be characterized by tandemly repeated sequences that have actively changed chromosomal fields by intragenomic movement. Alternatively, it is proposed that in conservative chromosomal lineage each class of tandemly repeated sequences will be restricted to a specific chromosomal field. To provide baseline data to test this model we exami...
McCue ME, Valberg SJ, Miller MB, Wade C, DiMauro S, Akman HO, Mickelson JR.Polysaccharide storage myopathy (PSSM) is a novel glycogenosis in horses characterized by abnormal glycogen accumulation in skeletal muscle and muscle damage with exertion. It is unlike glycogen storage diseases resulting from known defects in glycogenolysis, glycolysis, and glycogen synthesis that have been described in humans and domestic animals. A genome-wide association identified GYS1, encoding skeletal muscle glycogen synthase (GS), as a candidate gene for PSSM. DNA sequence analysis revealed a mutation resulting in an arginine-to-histidine substitution in a highly conserved region of G...
Doan R, Cohen N, Harrington J, Veazey K, Juras R, Cothran G, McCue ME, Skow L, Dindot SV.Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a whole-exome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein- and...
Xu S, Luosang J, Hua S, He J, Ciren A, Wang W, Tong X, Liang Y, Wang J, Zheng X.To investigate genetic mechanisms of high altitude adaptations of animals living in the Tibetan Plateau, three mitochondrial genomes (mt-genome) of Tibetan horses living in Naqu (4,500 m) of Tibetan, Zhongdian (3,300 m) and Deqin (3,100 m) of Yunnan province were sequenced. The structures and lengths of these three mt-genomes are similar to the Cheju horse, which is related to Tibetan horses, but little shorter than the Swedish horse. The pair-wise identity of these three horses on nucleotide level is more than 99.3%. When the gene encoding the mitochondrial protein of Tibetan horses was analy...
Su TW, Choi I, Feng J, Huang K, McLeod E, Ozcan A.We report the discovery of an entirely new three-dimensional (3D) swimming pattern observed in human and horse sperms. This motion is in the form of 'chiral ribbons', where the planar swing of the sperm head occurs on an osculating plane creating in some cases a helical ribbon and in some others a twisted ribbon. The latter, i.e., the twisted ribbon trajectory, also defines a minimal surface, exhibiting zero mean curvature for all the points on its surface. These chiral ribbon swimming patterns cannot be represented or understood by already known patterns of sperms or other micro-swimmers. The...
Marycz K, Kornicka K, Grzesiak J, Śmieszek A, Szłapka J.Equine metabolic syndrome (EMS) is mainly characterized by insulin resistance, obesity, and local or systemic inflammation. That unfriendly environment of adipose tissue has huge impact on stem cells population (ASC) residing within. In the present study, using molecular biology techniques and multiple imaging techniques (SEM, FIB-SEM, and confocal microscopy), we evaluated the impact of EMS on ASC viability and chondrogenic differentiation. Moreover, we visualized the mitochondrial network and dynamics in ASC and ASC during control and chondrogenic conditions. In control conditions, ASC were ...
Lunn DP, Holmes MA, Antczak DF, Agerwal N, Baker J, Bendali-Ahcene S, Blanchard-Channell M, Byrne KM, Cannizzo K, Davis W, Hamilton MJ, Hannant D....The final assignment of antibody clusters for leucocyte antigens and immunoglobulins, as described in detail in Sections 3 and 4, is summarized in Table 4. Together with other mAbs developed outside of ELAW II (Table 9) this pool of reagents represent a powerful array of tools for the study of equine immunity. The Second Equine Leucocyte Antigen Workshop made considerable advances in pursuing the objectives of establishing the specificities of mAbs and achieving consensus on the nomenclature for equine leucocyte and immunoglobulin molecules. Of equal importance, several productive collaboratio...
Imsland F, McGowan K, Rubin CJ, Henegar C, Sundström E, Berglund J, Schwochow D, Gustafson U, Imsland P, Lindblad-Toh K, Lindgren G, Mikko S....Dun is a wild-type coat color in horses characterized by pigment dilution with a striking pattern of dark areas termed primitive markings. Here we show that pigment dilution in Dun horses is due to radially asymmetric deposition of pigment in the growing hair caused by localized expression of the T-box 3 (TBX3) transcription factor in hair follicles, which in turn determines the distribution of hair follicle melanocytes. Most domestic horses are non-dun, a more intensely pigmented phenotype caused by regulatory mutations impairing TBX3 expression in the hair follicle, resulting in a more circu...
Baer A, Lundberg L, Swales D, Waybright N, Pinkham C, Dinman JD, Jacobs JL, Kehn-Hall K.Venezuelan equine encephalitis virus (VEEV) is a previously weaponized arthropod-borne virus responsible for causing acute and fatal encephalitis in animal and human hosts. The increased circulation and spread in the Americas of VEEV and other encephalitic arboviruses, such as eastern equine encephalitis virus and West Nile virus, underscore the need for research aimed at characterizing the pathogenesis of viral encephalomyelitis for the development of novel medical countermeasures. The host-pathogen dynamics of VEEV Trinidad donkey-infected human astrocytoma U87MG cells were determined by car...
Mach N, Plancade S, Pacholewska A, Lecardonnel J, Rivière J, Moroldo M, Vaiman A, Morgenthaler C, Beinat M, Nevot A, Robert C, Barrey E.The adaptive response to extreme endurance exercise might involve transcriptional and translational regulation by microRNAs (miRNAs). Therefore, the objective of the present study was to perform an integrated analysis of the blood transcriptome and miRNome (using microarrays) in the horse before and after a 160 km endurance competition. A total of 2,453 differentially expressed genes and 167 differentially expressed microRNAs were identified when comparing pre- and post-ride samples. We used a hypergeometric test and its generalization to gain a better understanding of the biological functio...
McGivney BA, McGettigan PA, Browne JA, Evans AC, Fonseca RG, Loftus BJ, Lohan A, MacHugh DE, Murphy BA, Katz LM, Hill EW.Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of exercise training. The study cohort comprised seven Thoroughbred racehorses from a single training yard. Skeletal muscle biopsies were collected at rest from the gluteus medius at two time points: T(1) - untrained, (9 +/- 0.5 months old) and T(2) - trained (20 +/- 0.7 months old). Results: The most abundant mRNA transcripts in the muscle transcriptome were those involved in mus...
Stewart MC, Stewart AA.This article provides an overview of mesenchymal stem cell (MSC) biology. In the first section, the characteristics that are routinely used to define MSCs-adherence, proliferation, multi-lineage potential, and "cluster of differentiation" marker profiles-are discussed. In the second section, the major tissues and body fluids that are used as sources for equine MSCs are presented, along with the comparative biologic activities of MSCs from specific locations. Finally, the current understanding of the mechanisms by which MSCs influence repair and regeneration are discussed, with an emphasis on t...
Spaas JH, De Schauwer C, Cornillie P, Meyer E, Van Soom A, Van de Walle GR.Although the use of mesenchymal stromal cells (MSCs) for the treatment of orthopaedic injuries in horses has been reported, no official guidelines exist that classify a particular cell as an equine MSC. Given the limited characterisation of peripheral blood (PB)-derived equine MSCs in particular, this study aimed to provide more detailed information in relation to this cell type. Mesenchymal stromal cells were isolated from equine PB samples and colony forming unit (CFU) assays as well as population doubling times (PDTs) (from P(0) to P(10)) were performed. Two types of colonies, 'fingerprint'...
Park KD, Park J, Ko J, Kim BC, Kim HS, Ahn K, Do KT, Choi H, Kim HM, Song S, Lee S, Jho S, Kong HS, Yang YM, Jhun BH, Kim C, Kim TH, Hwang S, Bhak J....Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes. Results: We present a large-scale analysis of whole transcriptome data. We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current genome annotations, we identified 32,361 unigene cluster...
Cosgrove EJ, Sadeghi R, Schlamp F, Holl HM, Moradi-Shahrbabak M, Miraei-Ashtiani SR, Abdalla S, Shykind B, Troedsson M, Stefaniuk-Szmukier M....The Arabian horse, one of the world's oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ances...
Mariat D, Taourit S, Guérin G.In horses, basic colours such as bay or chestnut may be partially diluted to buckskin and palomino, or extremely diluted to cream, a nearly white colour with pink skin and blue eyes. This dilution is expected to be controlled by one gene and we used both candidate gene and positional cloning strategies to identify the "cream mutation". A horse panel including reference colours was established and typed for different markers within or in the neighbourhood of two candidate genes. Our data suggest that the causal mutation, a G to A transition, is localised in exon 2 of the MATP gene leading to an...
Sedykh SE, Purvinish LV, Monogarov AS, Burkova EE, Grigor'eva AE, Bulgakov DV, Dmitrenok PS, Vlassov VV, Ryabchikova EI, Nevinsky GA.Exosomes are 40-100 nm nanovesicles containing RNA and different proteins. Exosomes containing proteins, lipids, mRNAs, and microRNAs are important in intracellular communication and immune function. Exosomes from different sources are usually obtained by combination of centrifugation and ultracentrifugation and according to published data can contain from a few dozens to thousands of different proteins. Crude exosome preparations from milk of eighteen horses were obtained for the first time using several standard centrifugations. Exosome preparations were additionally purified by FPLC gel fi...
Binns MM, Boehler DA, Lambert DH.One hundred and eighty-nine Thoroughbred horses that had won Graded Stakes races in North America were genotyped with the Illumina Equine SNP50 bead chip. Association tests using PLINK to determine whether any SNPs were associated with optimum racing distance (7 furlongs and under compared to 8-10 furlongs) identified a locus on ECA18 that was statistically significant (-log 10 EMP2=1.63) at the genome-wide level following permutation analysis (10,000 permutations). Bioinformatic analysis revealed that the two ECA18 SNPs with the highest statistical significance spanned the MSTN (myostatin) lo...
van der Geize R, Grommen AW, Hessels GI, Jacobs AA, Dijkhuizen L.Rhodococcus equi causes fatal pyogranulomatous pneumonia in foals and immunocompromised animals and humans. Despite its importance, there is currently no effective vaccine against the disease. The actinobacteria R. equi and the human pathogen Mycobacterium tuberculosis are related, and both cause pulmonary diseases. Recently, we have shown that essential steps in the cholesterol catabolic pathway are involved in the pathogenicity of M. tuberculosis. Bioinformatic analysis revealed the presence of a similar cholesterol catabolic gene cluster in R. equi. Orthologs of predicted M. tuberculosis vi...
