Topic:Cluster Analysis
Cluster analysis is a statistical method used to group objects, such as horses, into clusters based on similarities in their characteristics or behaviors. In equine research, cluster analysis can help identify patterns and relationships within large datasets, such as genetic information, performance metrics, or health parameters. This technique is valuable for categorizing horses into distinct groups for further analysis, such as distinguishing between different breeds, identifying common traits in performance horses, or assessing health risks. This page aggregates peer-reviewed research studies and scholarly articles that explore the application, methodologies, and findings of cluster analysis in various aspects of equine science.
Application of Genomic Estimation Methods of Inbreeding and Population Structure in an Arabian Horse Herd. Horse breeders rely heavily on pedigrees for identification of ancestry in breeding stock. Inaccurate pedigrees may erroneously assign individuals to false lineages or breed memberships resulting in wrong estimates of inbreeding and coancestry. Moreover, discrepancies in pedigree records can lead breeders seeking to limit inbreeding into making misguided breeding decisions. Genome-wide SNPs provide a quantitative tool to aid in the resolution of lineage assignments and the calculation of genomic measures of relatedness. The aim of this project was to pilot a comparison between pedigree and gen...
LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells. Lipopolysaccharide (endotoxin, LPS) is a strong inducer of the innate immune response. It is widespread in our environment, e.g. in house dust and contributes to asthma. Compared to humans, horses are even more sensitive to LPS. However, data on LPS effects on the equine transcriptome are very limited. Using RNA-seq we analysed LPS-induced differences in the gene expression in equine peripheral blood mononuclear cells at the gene and gene-network level in two half-sib families and one group of unrelated horses. 24 h-LPS challenge of equine immune cells resulted in substantial changes in the t...
Genetic diversity of the Yonaguni horse based on polymorphisms in microsatellites and mitochondrial DNA. Thirty-two microsatellites and a mitochondrial DNA haplotypes of endangered Yonaguni horses were analyzed to establish a pedigree registration system and to understand their genetic diversity for planning effective conservation. Blood samples were collected from 78 of the 130 horses in existence, and DNA was extracted and genotyped. There were two major findings. One is that it is possible to use microsatellites for Yonaguni horse pedigree registration in the future because the power of exclusion of parentage testing is reliable at 0.999998. The second is the clarification of the current genet...
Profiling of exercise-induced transcripts in the peripheral blood cells of Thoroughbred horses. Transcriptome analyses based on DNA microarray technology have been used to investigate gene expression profiles in horses. In this study, we aimed to identify exercise-induced changes in the expression profiles of genes in the peripheral blood of Thoroughbred horses using DNA microarray technology (15,429 genes on 43,603 probes). Blood samples from the jugular vein were collected from six horses before and 1 min, 4 hr, and 24 hr after all-out running on a treadmill. After the normalization of microarray data, a total of 26,830 probes were clustered into four groups and 11 subgroups showing si...
Vertical transmission of hepatitis C virus-like non-primate hepacivirus in horses. Non-primate hepacivirus (NPHV), a recently discovered hepatotropic virus infecting horses, is phylogenetically the closest known homologue of hepatitis C virus (HCV). The main route for acquiring HCV infection in childhood is vertical transmission. However, nothing is known about the natural mode of transmission for NPHV. To investigate the possibility of vertically transmitted NPHV infection in horses, 20 Thoroughbred broodmares and their foals were monitored during foaling season 2015 until 6 months post-partum. Prepartal serum was taken from the mares, and during foaling umbilical cord bloo...
Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material. There are many choices for methods of extracting bacterial DNA for Next Generation Sequencing (NGS) from fecal samples. Here, we compare our modifications of a phenol/chloroform extraction method plus an inhibitor removal solution (C3) (ph/Chl+C3) to the PowerFecal® DNA Isolation Kit (MoBio-K). DNA quality and quantity coupled to NGS results were used to assess differences in relative abundance, Shannon diversity index, unique species, and principle coordinate analysis (PCoA) between biological replicates. Six replicate samples, taken from a single ball of horse feces manually collected from ...
Classification of Horse Gaits Using FCM-Based Neuro-Fuzzy Classifier from the Transformed Data Information of Inertial Sensor. In this study, we classify four horse gaits (walk, sitting trot, rising trot, canter) of three breeds of horse (Jeju, Warmblood, and Thoroughbred) using a neuro-fuzzy classifier (NFC) of the Takagi-Sugeno-Kang (TSK) type from data information transformed by a wavelet packet (WP). The design of the NFC is accomplished by using a fuzzy c-means (FCM) clustering algorithm that can solve the problem of dimensionality increase due to the flexible scatter partitioning. For this purpose, we use the rider's hip motion from the sensor information collected by inertial sensors as feature data for the cla...
The prevalence, abundance and distribution of cyathostomins (small stongyles) in horses from Western Romania. Forty seven working horses from Romania were post-mortem examined for small strongyles (Cyathostominae) infections. All horses were found infected. The overall cyathostomins intensity ranged from 390 to 13,010 and horses were infected by 8-24 species. The intensity was higher in ventral colon (1531) and dorsal colon (824), the lowest in the caecum (524). Twenty four species were identified. Cyathostomum catinatum, Cylicocyclus insigne, and C. Nassatus had 100% of prevalence. Over 50% of horses were infected by Coronocyclus coronatus, Cylicostephanus calicatus, C. goldi, and C. longibursatus. O...
The Equine Embryo Influences Immune-Related Gene Expression in the Oviduct. Although the equine oviduct clearly affects early embryo development and the selective transport of equine embryos through the oviduct indicates a reciprocal interaction, the influence of the embryo on gene expression in the oviduct remains to be determined in the horse. The aim of this study was to examine this by means of RNA sequencing. Four days after ovulation, epithelial cells ipsilateral and contralateral to the ovulation side from five cyclic and five pregnant mares were collected from the oviduct. RNA was extracted, samples were sequenced, and data analysis was performed to determine ...
The complete mitochondrial genome of Hequ horse. The complete mitochondrial genome of Hequ horse was determined in this study. The mitogenome is 16 656 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a D-loop region. The overall base composition of the H-strand is 32.20% for A, 28.55% for C, 13.38% for G and 25.86% for T. Tree constructed using MEGA 6 with Maximum-likelihood (ML) methods demonstrated that Hequ horse was clustered in subfamily Equidae.
Equine grass sickness in Scotland: A case-control study of environmental geochemical risk factors. We hypothesised that the apparent geographical distribution of equine grass sickness (EGS) is partly attributable to suboptimal levels of soil macro- and trace elements in fields where EGS occurs. If proven, altering levels of particular elements could be used to reduce the risk of EGS. Objective: To determine whether the geographical distribution of EGS cases in eastern Scotland is associated with the presence or absence of particular environmental chemical elements. Methods: Retrospective time-matched case-control study. Methods: This study used data for 455 geo-referenced EGS cases and 910 ...
Immune gene expression profiling of PBMC isolated from horses vaccinated with attenuated African horsesickness virus serotype 4. Development of African horsesickness (AHS) subunit vaccines will have to include a rational approach that uses knowledge of how the virus interacts with the host immune system. The global in vivo immune response induced by attenuated AHSV serotype 4 in horses was characterised using transcriptome sequencing. PBMC were collected with 24h intervals for four days after inoculation and four days after a second boost, 21 days later. Transcriptome data were normalised to the day 0 naïve transcriptome and up- or down-regulated immune genes identified using the CLC workbench. Peak expression was obse...
Could it be colic? Horse-owner decision making and practices in response to equine colic. Little is known about lay understanding and decision making in response to colic. Horse-owners/carers are key to identifying colic and initiating veterinary intervention. Understanding how owners think and act in relation to colic could assist veterinary surgeons in tailoring information about colic with the aim of improving colic outcomes. Methods: A mixed methods approach was employed including qualitative in-depth interviews and a cross-sectional questionnaire. Qualitative data were analysed using Grounded theory to conceptualise processes involved in horse-owner management of colic. Follow...
Impact of race training on volumetric bone mineral density and its spatial distribution in the distal epiphysis of the third metatarsal bone of 2-year-old horses. The aim of the study was to use spatial and multiple correspondence analysis (MCA) to describe and compare the regional proportion and spatial pattern of volumetric bone mineral density (BMDv) values within loaded regions of the plantar metatarsal epiphysis of young horses in race training. A single 2 mm transverse peripheral quantitative computed tomography 'slice', 10 mm proximal from the distal limit of the sagittal ridge of the distal metatarsal epiphysis was obtained from 14 2-year-old Thoroughbred fillies (7 exercised and 7 controls). Six regions of interest were generated and examin...
Evaluation of a mouse model for the West Nile virus group for the purpose of determining viral pathotypes. West Nile virus (WNV; family Flaviviridae; genus Flavivirus) group members are an important cause of viral meningoencephalitis in some areas of the world. They exhibit marked variation in pathogenicity, with some viral lineages (such as those from North America) causing high prevalence of severe neurological disease, whilst others (such as Australian Kunjin virus) rarely cause disease. The aim of this study was to characterize WNV disease in a mouse model and to elucidate the pathogenetic features that distinguish disease variation. Tenfold dilutions of five WNV strains (New York 1999, MRM16 a...
RNA-seq transcriptome profiling of equine inner cell mass and trophectoderm. Formation of the inner cell mass (ICM) and trophectoderm (TE) marks the first differentiation event in mammalian development. These two cell types have completely divergent fates for the remainder of the developmental process. The molecular mechanisms that regulate ICM and TE formation are poorly characterized in horses. The objective of this study was to establish the transcriptome profiles of ICM and TE cells from horse blastocysts using RNA sequencing (RNA-seq). A total of 12 270 genes were found to be expressed in either lineage. Global analysis of the transcriptome profiles by unsupervi...
Untangling the complex inter-relationships between horse managers’ perceptions of effectiveness of biosecurity practices using Bayesian graphical modelling. On-farm biosecurity practices have been promoted in many animal industries to protect animal populations from infections. Current approaches based on regression modelling techniques for assessing biosecurity perceptions and practices are limited for analysis of the interrelationships between multivariate data. A suitable approach, which does not require background knowledge of relationships, is provided by Bayesian network modelling. Here we apply such an approach to explore the complex interrelationships between the variables representing horse managers' perceptions of effectiveness of on-far...
Macrolide- and rifampin-resistant Rhodococcus equi on a horse breeding farm, Kentucky, USA. Macrolide and rifampin resistance developed on a horse breeding farm after widespread use was instituted for treatment of subclinical pulmonary lesions in foals. Resistance occurred in 6 (24%) of 25 pretreatment and 8 (62%) of 13 (62%) posttreatment isolates from affected foals. Drug-resistant isolates formed 2 distinct genotypic clusters.
Exploration of global gene expression changes during the estrous cycle in equine endometrium. 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:...
Epidemiology and genetic characterization of equine infectious anaemia virus strains isolated in Belgium in 2010. In January 2010, the United Kingdom notified cases of equine infectious anaemia (EIA) in two horses introduced from Belgium. The animals came from one assembly centre in Romania and had transited through Belgium with 16 other horses. Nine of them, bought by a Belgian horse breeder, were investigated in Belgium and revealed one additional EIA-positive animal. Afterwards, the Belgian Federal Agency for the Safety of the Food Chain (FASFC) organized a serological EIA survey of the horses introduced into Belgium from Romania between 2007 and 2009. Among the 95 horses identified, six additional ser...
Spatial epidemiology of eastern equine encephalitis in Florida. Eastern Equine Encephalitis virus (EEEV) is an alphavirus with high pathogenicity in both humans and horses. Florida continues to have the highest occurrence of human cases in the USA, with four fatalities recorded in 2010. Unlike other states, Florida supports year-round EEEV transmission. This research uses GIS to examine spatial patterns of documented horse cases during 2005-2010 in order to understand the relationships between habitat and transmission intensity of EEEV in Florida. Methods: Cumulative incidence rates of EEE in horses were calculated for each county. Two cluster analyses wer...
Explaining spatial heterogeneity in population dynamics and genetics from spatial variation in resources for a large herbivore. Fine-scale spatial variation in genetic relatedness and inbreeding occur across continuous distributions of several populations of vertebrates; however, the basis of observed variation is often left untested. Here we test the hypothesis that prior observations of spatial patterns in genetics for an island population of feral horses (Sable Island, Canada) were the result of spatial variation in population dynamics, itself based in spatial heterogeneity in underlying habitat quality. In order to assess how genetic and population structuring related to habitat, we used hierarchical cluster analys...
Reproductive performance of Thoroughbred mares in the Waikato region of New Zealand: 2. Multivariable analyses and sources of variation at the mare, stallion and stud farm level. The objective of this study was to utilise multivariable statistical methods appropriate for clustered data to identify mare-related explanatory variables that significantly affected the reproductive performance of Thoroughbred mares in the Waikato region of New Zealand. In addition, we aimed to determine the relative contribution of the mare, stallion and stud farm to reproductive performance. Methods: A prospective cohort study was performed involving five stud farms in the Waikato region of New Zealand during three consecutive breeding seasons (2006-2008). A total of 1,482 individual mares ...
Genetic diversity and population structure of Chinese pony breeds using microsatellite markers. China is one of the principal origins of ponies in the world. We made a comprehensive analysis of genetic diversity and population structure of Chinese ponies based on 174 animals of five indigenous Chinese pony breeds from five provinces using 13 microsatellite markers. One hundred and forty-four alleles were detected; the mean number of effective alleles among the pony breeds ranged from 5.38 (Guizhou) to 6.78 (Sichuan); the expected heterozygosity ranged from 0.82 (Guizhou) to 0.85 (Debao, Sichuan). Although abundant genetic variation was found, the genetic differentiation was low between t...
[Strongylids (Nematoda: Strongylidae) of domestic horses in Ukraine: modern state of Fauna and structure of the parasite community]. Species composition and structure of the strongylid community was studies on helminthological material collected from 162 domestic horses from 11 regions of Ukraine by the in vivo method. Animals were treated with anthelmintic drug "Univerm" (0.2% aversectin C, Russia). Faecal samples (200 g each) were collected from every horse at 24, 36, 48 and 60 hours after treatment; all nematodes expelled (90.851 specimens) were collected and identified. Thirty-three strongylid species from 12 genera (8 species of subfamily Strongylinae and 25--of Cyathostominae) were found in domestic horses in Ukraine....
Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations. As part of the requirements of the Convention on Biological Diversity, Canada has been investigating the genetic diversity of its native equine and pony populations. Along with examining four indigenous Canadian equine populations (Canadian horse, Lac La Croix pony, Newfoundland pony and Sable Island population), another 10 Mountain and Moorland, three Nordic, four horse and two feral equine populations (thought to have influenced some pony breeds) were also investigated. In total, 821 individuals were genotyped at 38 microsatellite loci. Results of the analysis of molecular variance indicated...
Equine stomachs harbor an abundant and diverse mucosal microbiota. Little is known about the gastric mucosal microbiota in healthy horses, and its role in gastric disease has not been critically examined. The present study used a combination of 16S rRNA bacterial tag-encoded pyrosequencing (bTEFAP) and fluorescence in situ hybridization (FISH) to characterize the composition and spatial distribution of selected gastric mucosal microbiota of healthy horses. Biopsy specimens of the squamous, glandular, antral, and any ulcerated mucosa were obtained from 6 healthy horses by gastroscopy and from 3 horses immediately postmortem. Pyrosequencing was performed on bio...
Genetic structure and differentiation of the Italian catria horse. Catria is 1 of the 22 native Italian horse breeds that now survive from a larger number. Thirty individuals, representative of the Catria horse, were analyzed for 11 microsatellites and compared with data of 10 breeds reared in Italy. Three different approaches, genetic distances, correspondence analysis, and clustering methods, were considered to study genetic relationships among Catria and the other horse populations. Genetic differentiation among breeds was highly significant (P < 0.01) for all loci. Average F(ST) values indicate that around 10% of the total genetic variation was explain...
Complex dynamic upper airway collapse: associations between abnormalities in 99 harness racehorses with one or more dynamic disorders. Many horses demonstrate dynamic collapse of more than one upper respiratory tract (URT) structure during high-speed treadmill videoendoscopy (HSTV). Objective: To report the frequency of complex dynamic URT collapse in harness racehorses and determine if an association exists between occurrence of certain disorders. Methods: Retrospective study of 99 Standardbreds and Coldblooded trotters that had one or more dynamic URT disorders identified during HSTV between 1998 and 2006. The horses underwent HSTV using a protocol that included periods of free head carriage and poll flexion until fully fat...
Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons. The diversity of the equine fecal bacterial community was evaluated using pyrosequencing of 16S rRNA gene amplicons. Fecal samples were obtained from horses fed cool-season grass hay. Fecal bacteria were characterized by amplifying the V4 region of bacterial 16S rRNA gene. Of 5898 mean unique sequences, a mean of 1510 operational taxonomic units were identified in the four fecal samples. Equine fecal bacterial richness was higher than that reported in humans, but lower than that reported in either cattle feces or soil. Bacterial classified sequences were assigned to 16 phyla, of which 10 were ...