Genome-wide SNP analysis of Japanese Thoroughbred racehorses.
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ABSTRACT:
SUBMITTER: Fawcett JA
PROVIDER: S-EPMC6655603 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThoroughbred racehorses are subject to non-traumatic distal limb bone fractures that occur during racing and exercise. Susceptibility to fracture may be due to underlying disturbances in bone metabolism which have a genetic cause. Fracture risk has been shown to be heritable in several species but this study is the first genetic analysis of fracture risk in the horse.ResultsFracture cases (n = 269) were horses that sustained catastrophic distal limb fractures while racing on UK racecourses, necessitating euthanasia. Control horses (n = 253) were over 4 years of age, were racing during the same time period as the cases, and had no history of fracture at the time the study was carried out. The horses sampled were bred for both flat and National Hunt (NH) jump racing. 43,417 SNPs were employed to perform a genome-wide association analysis and to estimate the proportion of genetic variance attributable to the SNPs on each chromosome using restricted maximum likelihood (REML). Significant genetic variation associated with fracture risk was found on chromosomes 9, 18, 22 and 31. Three SNPs on chromosome 18 (62.05 Mb - 62.15 Mb) and one SNP on chromosome 1 (14.17 Mb) reached genome-wide significance (p < 0.05) in a genome-wide association study (GWAS). Two of the SNPs on ECA 18 were located in a haplotype block containing the gene zinc finger protein 804A (ZNF804A). One haplotype within this block has a protective effect (controls at 1.95 times less risk of fracture than cases, p = 1 × 10(-4)), while a second haplotype increases fracture risk (cases at 3.39 times higher risk of fracture than controls, p = 0.042).ConclusionsFracture risk in the Thoroughbred horse is a complex condition with an underlying genetic basis. Multiple genomic regions contribute to susceptibility to fracture risk. This suggests there is the potential to develop SNP-based estimators for genetic risk of fracture in the Thoroughbred racehorse, using methods pioneered in livestock genetics such as genomic selection. This information would be useful to racehorse breeders and owners, enabling them to reduce the risk of injury in their horses.
| S-EPMC4008154 | biostudies-literature
Project description:Thoroughbreds are some of the most famous racehorses worldwide and are currently animals of high economic value. To understand genomic variability in Thoroughbreds, we identified genome-wide insertions and deletions (INDELs) and obtained their allele frequencies in this study. INDELs were obtained from whole-genome sequencing data of 101 Thoroughbred racehorses by mapping sequence reads to the horse reference genome. By integrating individual data, 1,453,349 and 113,047 INDELs were identified in the autosomal (1-31) and X chromosomes, respectively, while 18 INDELs were identified on the mitochondrial genome, totaling 1,566,414 INDELs. Of those, 779,457 loci (49.8%) were novel INDELs, while 786,957 loci (50.2%) were already registered in Ensembl. The sizes of diallelic INDELs ranged from -286 to +476, and the majority, 717,736 (52.14%) and 220,672 (16.03%), were 1-bp and 2-bp variants, respectively. Numerous INDELs were found to have lower frequencies of alternative (Alt) alleles. Many rare variants with low Alt allele frequencies (<0.5%) were also detected. In addition, 5955 loci were genotyped as having a minor allele frequency of 0.5 and being heterogeneous genotypes in all the horses. While short-read sequencing and its mapping to reference genome is a simple way of detecting variants, fake variants may be detected. Therefore, our data help to identify true variants in Thoroughbred horses. The INDEL database we constructed will provide useful information for genetic studies and industrial applications in Thoroughbred horses, including a gene-editing test for gene-doping control and a parentage test using INDELs for horse registration and identification.
| S-EPMC10048024 | biostudies-literature
Project description:The Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) revealed 11,570,312 and 602,756 SNVs in autosomal (1-31) and X chromosomes, respectively, yielding a total of 12,173,068 SNVs. About 6.9% of identified SNVs were rare variants observed only in one allele in 101 horses. The number of SNVs detected in individual horses ranged from 4.8 to 5.3 million. Individual horses had a maximum of 25,554 rare variants; several of these were functional variants, such as non-synonymous substitutions, start-gained, start-lost, stop-gained, and stop-lost variants. Therefore, these rare variants may affect differences in traits and phenotypes among individuals. When observing the distribution of rare variants among horses, one breeding stallion had a smaller number of rare variants compared to other horses, suggesting that the frequency of rare variants in the Japanese Thoroughbred population increases through breeding. In addition, our variant database may provide useful basic information for industrial applications, such as the detection of genetically modified racehorses in gene-doping control and pedigree-registration of racehorses using SNVs as markers.
| S-EPMC8346562 | biostudies-literature
Project description:Training has a great impact on the physiology of an athlete and, like all stressful stimuli, can trigger an innate immune response and inflammation, which is part of a wider coping strategy of the host to restore homeostasis. The Thoroughbred racehorse is a valid animal model to investigate these changes thanks to its homogeneous training and highly selected genetic background. The aim of this study was to investigate modifications of the innate immune response and inflammation in young untrained Thoroughbred racehorses during the first training season through haematological and molecular investigations. Twenty-nine Thoroughbred racehorses were followed during their incremental 3-month sprint exercise schedule. Blood collection was performed at time 0 (T0; before starting the intense training period), 30 days after T0 (T30), and 90 days after T0 (T90). Haematological parameters (red and white blood cells, haemoglobin, and platelets) were evaluated and haematocrit (HCT), mean corpuscular haemoglobin concentration (MCHC), and red cells width distribution + standard deviation (RDW-SD) were calculated. Moreover, via RT-qPCR, we investigated the expression of, Interleukin 1? (IL-1?), Interleukin 4 (IL-4) Interleukin 6 (IL-6), Interleukin 2 (IL-2), Interleukin 3 (IL-3), Interleukin 5 (IL-5) Interleukin 8 (IL-8), Trasformig Growth Factor ? and ? (TGF-?), Tumor necrosis factor ? (TNF-?), and Interferon ? (IFN-?)genes. Main corpuscular volume (MCV) showed a significant (p = 0.008) increase at T90. Main corpuscular haemoglobin (MCH) and haemoglobin concentration (MCHC) values were significantly augmented at both T30 (p < 0.001) and T90 (p < 0.001). Basophils were significant increased at T30 (p = 0.02) and eosinophils were significantly increased at T90 (p = 0.03). Significant differences in gene expression were found for all the genes under study, with the exception of IFN-? and TNF-?. In particular, IL-2 (T30, p = 0.011; T90, p = 0.015), IL-4 (T30, p = 0.009; T90, p < 0.001), and IL-8 (T30, p < 0.001; T90, p < 0.001) genes were significantly upregulated at both T30 and T90 with respect to T0, TGF-? was intensely downregulated at T30 (p < 0.001), IL-5 gene expression was significantly decreased at T90 (p = 0.001), while IL-1? (p = 0.005) and IL-3 (p = 0.001) expression was strongly augmented at the same time. This study highlighted long-term adjustments of O2 transport capability that can be reasonably traced back to exercise adaptation. Moreover, the observed changes of granulocyte numbers and functions and inflammatory cytokine gene expression confirm a major role of the innate immune system in the response to the complex of stressful stimuli experienced during the training period.
| S-EPMC7600081 | biostudies-literature
Project description:BACKGROUND:The important property of the quantitative traits of model organisms is time-dependent. However, the methodology for investigating the genetic interaction network over time is still lacking. Our study aims to provide insights into the mechanistic basis of epistatic interactions affecting the phenotypes of model organisms. RESULTS:We performed an exhaustive genome-wide search for significant SNP-SNP interactions associated with male birds' body weight (BW) (n = 475) at multiple time points (day of hatch (BW0) and 1, 3, 5, and 7 weeks (BW1, BW3, BW5, and BW7)). Statistical analysis detected 67, four, and two significant SNP pairs associated with BW0, BW1, and BW3, respectively, with a significance threshold at 8.67 × 10- 12 (Bonferroni-adjusted: 1%). Meanwhile, no significant SNP pairs associated with BW5 and BW7 were found. The SNP-SNP interaction networks of BW0, BW1, and BW3 were built and annotated. CONCLUSIONS:With strong annotated information and a strict significant threshold, SNP-SNP interactions underpinned the gene-gene interactions that might occur between chromosomes or within the same chromosome. Comparing and combing the networks, the results indicated that the genetic network for chicken body weight was dynamic and time-dependent.
| S-EPMC6813082 | biostudies-other
Project description:BackgroundThoroughbred horses have been selected for traits contributing to speed and stamina for centuries. It is widely recognized that inherited variation in physical and physiological characteristics is responsible for variation in individual aptitude for race distance, and that muscle phenotypes in particular are important.ResultsA genome-wide SNP-association study for optimum racing distance was performed using the EquineSNP50 Bead Chip genotyping array in a cohort of n = 118 elite Thoroughbred racehorses divergent for race distance aptitude. In a cohort-based association test we evaluated genotypic variation at 40,977 SNPs between horses suited to short distance (? 8 f) and middle-long distance (> 8 f) races. The most significant SNP was located on chromosome 18: BIEC2-417495 ~690 kb from the gene encoding myostatin (MSTN) [P(unadj.) = 6.96 x 10??]. Considering best race distance as a quantitative phenotype, a peak of association on chromosome 18 (chr18:65809482-67545806) comprising eight SNPs encompassing a 1.7 Mb region was observed. Again, similar to the cohort-based analysis, the most significant SNP was BIEC2-417495 (P(unadj.) = 1.61 x 10??; P(Bonf.) = 6.58 x 10??). In a candidate gene study we have previously reported a SNP (g.66493737C>T) in MSTN associated with best race distance in Thoroughbreds; however, its functional and genome-wide relevance were uncertain. Additional re-sequencing in the flanking regions of the MSTN gene revealed four novel 3' UTR SNPs and a 227 bp SINE insertion polymorphism in the 5' UTR promoter sequence. Linkage disequilibrium was highest between g.66493737C>T and BIEC2-417495 (r² = 0.86).ConclusionsComparative association tests consistently demonstrated the g.66493737C>T SNP as the superior variant in the prediction of distance aptitude in racehorses (g.66493737C>T, P = 1.02 x 10?¹?; BIEC2-417495, P(unadj.) = 1.61 x 10??). Functional investigations will be required to determine whether this polymorphism affects putative transcription-factor binding and gives rise to variation in gene and protein expression. Nonetheless, this study demonstrates that the g.66493737C>T SNP provides the most powerful genetic marker for prediction of race distance aptitude in Thoroughbreds.
| S-EPMC3091701 | biostudies-literature
Project description:Laterality can be observed as side biases in locomotory behaviour which, in the horse, manifest inter alia as forelimb preferences, most notably in the gallop. The current study investigated possible leading-leg preferences at the population and individual level in Thoroughbred racehorses (n = 2095) making halt-to-gallop transitions. Videos of flat races in the UK (n = 350) were studied to record, for each horse, the lead-leg preference of the initial stride into gallop from the starting stalls. Races from clockwise (C) and anti-clockwise (AC) tracks were chosen alternately at random to ensure equal representation. Course direction, horse age and sex, position relative to the inside rail and finishing position were also noted. On C courses, the left/right ratio was 1.15, which represents a significant bias to the left (z = -2.29, p = 0.022), while on AC courses it was 0.92 (z = 0.51, p = 0.610). In both course directions, there was no significant difference between winning horses that led with the left leading leg versus the right (C courses, z = -1.32, p = 0.19 and AC courses, z = -0.74, p = 0.46). Of the 2,095 horses studied 51.26% led with their L fore and 48.74% with their R, with no statistically significant difference (z = -1.16, p = 0.25). Therefore, there was no evidence of a population level motor laterality. Additionally, 22 male and 22 female horses were randomly chosen for repeated measures of leading leg preference. A laterality index was calculated for each of the 44 horses studied using the repeated measures: 22 exhibited right laterality (of which two were statistically significant) and 21 exhibited left laterality (eight being statistically significant); one horse was ambilateral. Using these data, left lateralized horses were more strongly lateralized on an individual level than the right lateralized horses (t = 2.28, p = 0.03, DF = 34) and mares were more left lateralized than males (t = 2.4, p = 0.03, DF = 19).
| S-EPMC5993273 | biostudies-literature
Project description:Equine influenza (EI) outbreaks occurred on 19 premises in Ireland during 2014. Disease affected thoroughbred (TB) and non-TB horses/ponies on a variety of premises including four racing yards. Initial clinical signs presented on 16 premises within a two-month period. Extensive field investigations were undertaken, and the diagnostic effectiveness of a TaqMan RT-PCR assay was demonstrated in regularly-vaccinated and sub-clinically-affected horses. Epidemiological data and repeat clinical samples were collected from 305 horses, of which 40% were reported as clinically affected, 39% were identified as confirmed cases and 11% were sub-clinically affected. Multivariable analysis demonstrated a significant association between clinical signs and age, vaccination status and number of vaccine doses received. Vaccine breakdown was identified in 31% of horses with up to date vaccination records. This included 27 horses in four different racing yards. Genetic and antigenic analysis identified causal viruses as belonging to Clade 2 of the Florida sublineage (FCL2). At the time of this study, no commercially available EI vaccine in Ireland had been updated in line with World Organisation for Animal Health (OIE) recommendations to include a FCL2 virus. The findings of this study highlight the potential ease with which EI can spread among partially immune equine populations.
| S-EPMC6027538 | biostudies-literature
Project description:Ontario's Alcohol and Gaming Commission records equine racing fatalities through its Equine Health Program. The present study examined all Thoroughbred fatalities from 2003 to 2015, inclusive, to identify associations. Official records and details of fatalities were combined in multivariable logistic regression modelling of 236,386 race work-events (433 fatalities), and 459,013 workout work-events (252 fatalities). Fatality rates were 2.94/1000 race starts (all fatalities) and 1.96/1000 (breakdowns only) with an overall rate of 2.61% or 26.1 fatalities/1000 horses. Comparison with published reports reveals rates to be high. Musculoskeletal injury was the predominant complaint and there was a high incidence of horses dying suddenly. Liability was high for young horses early in the season with a differential according to sex and whether a male horse was gelded. Horses undertaking repeated workouts had a higher liability and liability was higher in workouts for horses switching from dirt/synthetic to turf racing and for young horses in sprints. Race distance was not significant but high fatality rates in some large field, distance races combined with effects of age and workload identified groups at particular risk. As field size increased, fatality liability increased for early-finishing horses. Findings suggest jockey strategy could be an important factor influencing fatalities. Probability of fatality declined over the study period. Findings indicate that rapid accumulation of workload in animals early in their preparation is likely to be damaging. Fatality fell toward the end of a season and for horses with a long career history of successful performance; however, horses not exhibiting this robustness and staying power represent the population of greatest concern. Associations may be characterised as representing sources of stress, current or cumulative, and identifying at-risk animals on this basis may be as productive as targeting specific, discrete mechanisms suspected to contribute to individual fatalities.
| S-EPMC8532649 | biostudies-literature
Project description:The Thoroughbred horse breed was developed primarily for racing, and has a significant contribution to the qualitative improvement of many other horse breeds. Despite the importance of Thoroughbred racehorses in historical, cultural, and economical viewpoints, there was no temporal and spatial dynamics of them using the mitogenome sequences. To explore this topic, the complete mitochondrial genome sequences of 14 Thoroughbreds and two Przewalski's horses were determined. These sequences were analyzed together along with 151 previously published horse mitochondrial genomes from a range of breeds across the globe using a Bayesian coalescent approach as well as Bayesian inference and maximum likelihood methods. The racing horses were revealed to have multiple maternal origins and to be closely related to horses from one Asian, two Middle Eastern, and five European breeds. Thoroughbred horse breed was not directly related to the Przewalski's horse which has been regarded as the closest taxon to the all domestic horses and the only true wild horse species left in the world. Our phylogenomic analyses also supported that there was no apparent correlation between geographic origin or breed and the evolution of global horses. The most recent common ancestor of the Thoroughbreds lived approximately 8,100-111,500 years ago, which was significantly younger than the most recent common ancestor of modern horses (0.7286 My). Bayesian skyline plot revealed that the population expansion of modern horses, including Thoroughbreds, occurred approximately 5,500-11,000 years ago, which coincide with the start of domestication. This is the first phylogenomic study on the Thoroughbred racehorse in association with its spatio-temporal dynamics. The database and genetic history information of Thoroughbred mitogenomes obtained from the present study provide useful information for future horse improvement projects, as well as for the study of horse genomics, conservation, and in association with its geographical distribution.
| S-EPMC6138400 | biostudies-literature