Comparison of ventilatory and oxygen consumption measurements of yearling Thoroughbred colts and fillies exercising unridden on an all-weather track

Sex effects on ventilatory and oxygen consumption (V̇O2) measurements during exercise have been identified in humans. This study's aim was to evaluate the hypothesis that there are sex effects on ventilatory and V̇O2 measurements in exercising, untrained yearling Thoroughbreds (Tb). Forty-one Tbs (16 colts, 25 fillies; 19.8 ± 1.4 months old) were recruited. Physiological, ventilatory and exercise data were gathered from horses exercising unridden at high intensity on an all-weather track from a global positioning-heart rate unit and a portable ergospirometry system. Data were analysed with an unpaired Student's t-test and the Benjamini-Hochberg correction for multiple testing (P ≤ 0.05 significant). Mean bodyweight (BW, P = 0.002) and wither height (P = 0.04) were greater for colts than fillies. There were no differences in physiological and exercise data and absolute peak V̇O2 between groups. However, fillies had a higher mass specific peak V̇O2 (P = 0.03) than colts (121.5 ± 21.6 mL/kg.min vs. 111.9 ± 27.4 mL/kg.min). The peak breathing frequency was greater for fillies (P < 0.001) while the peak inspiratory (P < 0.001) and expiratory air flow (P < 0.001), peak expiratory tidal volume (VTE; P < 0.001) and peak minute ventilation (V̇E; P = 0.01) were greater for colts; there were no differences for peak VTE and V̇E when adjusted for BW. Differences in BW explain the differences in mass specific peak V̇O2 between groups. Given their morphological differences, it is likely that lung volumes and airway diameters are smaller for fillies, resulting in greater resistance and lower air flows and volumes. Further research is required to investigate the ventilatory differences and how they may change with maturation and impact performance.

Inbreeding depression and durability in the North American Thoroughbred horse

The proportion of the genome containing runs of homozygosity (ROH) affects production traits in livestock populations. In European and Australasian Thoroughbreds inbreeding, quantified using ROH (F_ROH ), is associated with the probability of ever racing. Here, we measured F_ROH using 333 K SNP genotypes from 768 Thoroughbred horses born in North America to evaluate the effect of inbreeding on racing traits in that region. Among North American horses, F_ROH was not associated (p = 0.518) with the probability of ever racing but was significantly associated with the number of race starts (p = 0.002). Among raced horses, those with a 10% higher F_ROH than the mean inbreeding coefficient were predicted to have 3.5 fewer race starts compared to horses with a mean inbreeding coefficient. Considering the trend of increasing inbreeding and a decline in the average number of race starts per runner in North America, mitigating inbreeding in the population could positively influence racing durability.

Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health

BACKGROUND

Thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations. Consequently, genomic signatures of selection can provide insights into the human-mediated selection history of specific traits and evolutionary adaptation to diverse environments. Here, we used genome-wide SNPs from five distinct Chinese Mongolian horse populations to identify genomic regions under selection for the population-specific traits, gait, black coat colour, and hoof quality. Other global breeds were used to identify regional-specific signatures of selection.

RESULTS

We first identified the most significant selection peak for the Wushen horse in the region on ECA23 harbouring DMRT3, the major gene for gait. We detected selection signatures encompassing several genes in the Baicha Iron Hoof horse that represent good biological candidates for hoof health, including the CSPG4, PEAK1, EXPH5, WWP2 and HAS3 genes. In addition, an analysis of regional subgroups (Asian compared to European) identified a single locus on ECA3 containing the ZFPM1 gene that is a marker of selection for the major domestication event leading to the DOM2 horse clade.

CONCLUSIONS

Genomic variation at these loci in the Baicha Iron Hoof may be leveraged in other horse populations to identify animals with superior hoof health or those at risk of hoof-related pathologies. The overlap between the selection signature in Asian horses with the DOM2 selection peak raises questions about the nature of horse domestication events, which may have involved a prehistoric clade other than DOM2 that has not yet been identified.

Variation in salivary cortisol responses in yearling Thoroughbred racehorses during their first year of training

Thoroughbred horses are bred for competitive racing and undergo intense training regimes. The maintenance of physical soundness and desirable behavioural characteristics are critical to the longevity of a racing career. Horses intended for Flat racing generally enter training as yearlings and undergo introductory training prior to exercise conditioning for racing. This period requires rapid adjustment to a novel environment. As a prey animal, a horse's 'fight-or-flight' response is highly adapted, in which a well-understood component of this response, the hypothalamic-pituitary-axis, is activated in response to a stress stimulus, releasing cortisol. In the Thoroughbred, a significant difference in salivary cortisol concentrations between pre- and post-first time ridden (i.e., first backing) by a jockey have previously been identified. Here, to test the hypothesis that salivary cortisol concentrations may be used to objectively detect individual variations in the acute physiological stress response we investigate individual variation in cortisol response to training milestones. Saliva samples were collected from a cohort of n = 96 yearling Flat racehorses, at the same training yard, across three timepoints at rest: before entering the training yard (n = 66), within three days of entry to the training yard (n = 67) and following 2-3 weeks in the training yard (n = 50). Salivary cortisol concentration was measured using an ELISA. There was no significant difference in cortisol concentration (ANOVA, P > 0.05) across the samples collected at timepoints at rest. Samples were also collected before and 30 minutes after exposure to three novel training events: first time long-reined (n = 6), first time backed by a jockey (n = 34), and first time ridden on the gallops (n = 10). Mean salivary cortisol concentration after all three novel training events was significantly higher than prior to the training event (Paired t-test, P <0.005). The ranges of post-event salivary cortisol concentration across all timepoints suggest individual variation in the measured stress response, reflecting individual differences in stress response to the early training environment. This measure may be used as an objective assessment of the stress response of Thoroughbred racehorses during training.

Common protein-coding variants influence the racing phenotype in galloping racehorse breeds

Selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.

Inbreeding depression and the probability of racing in the Thoroughbred horse

Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs of homozygosity (ROH) using 297 K SNP genotypes from 6128 horses born in Europe and Australia, of which 13.2% were unraced. We show that a 10% increase in inbreeding (F_ROH) is associated with a 7% lower probability of ever racing. Moreover, a ROH-based genome-wide association study identified a haplotype on ECA14 which, in its homozygous state, is linked to a 32.1% lower predicted probability of ever racing, independent of F_ROH. The haplotype overlaps a candidate gene, EFNA5, that is highly expressed in cartilage tissue, which when damaged is one of the most common causes of catastrophic musculoskeletal injury in racehorses. Genomics-informed breeding aiming to reduce inbreeding depression and avoid damaging haplotype carrier matings will improve population health and racehorse welfare.

Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations

The Mongolian horse is one of the oldest extant horse populations and although domesticated, most animals are free-ranging and experience minimal human intervention. As an ancient population originating in one of the key domestication centers, the Mongolian horse may play a key role in understanding the origins and recent evolutionary history of horses. Here we describe an analysis of high-density genome-wide single-nucleotide polymorphism (SNP) data in 40 globally dispersed horse populations (n = 895). In particular, we have focused on new results from Chinese Mongolian horses (n = 100) that represent 5 distinct populations. These animals were genotyped for 670K SNPs and the data were analyzed in conjunction with 35K SNP data for 35 distinct breeds. Analyses of these integrated SNP data sets demonstrated that the Chinese Mongolian populations were genetically distinct from other modern horse populations. In addition, compared to other domestic horse breeds, the Chinese Mongolian horse populations exhibited relatively high genomic diversity. These results suggest that, in genetic terms, extant Chinese Mongolian horses may be the most similar modern populations to the animals originally domesticated in this region of Asia. Chinese Mongolian horse populations may therefore retain ancestral genetic variants from the earliest domesticates. Further genomic characterization of these populations in conjunction with archaeogenetic sequence data should be prioritized for understanding recent horse evolution and the domestication process that has led to the wealth of diversity observed in modern global horse breeds.

Inspiratory muscle training in young, race-fit Thoroughbred racehorses during a period of detraining

Although inspiratory muscle training (IMT) is reported to improve inspiratory muscle strength in humans little has been reported for horses. We tested the hypothesis that IMT would maintain and/or improve inspiratory muscle strength variables measured in Thoroughbreds during detraining. Thoroughbreds from one training yard were placed into a control (Con, n = 3 males n = 7 females; median age 2.2±0.4 years) or treatment group (Tr, n = 5 males, n = 5 females; median age 2.1±0.3 years) as they entered a detraining period at the end of the racing/training season. The Tr group underwent eight weeks of IMT twice a day, five days per week using custom-made training masks with resistance valves and an incremental threshold of breath-loading protocol. An inspiratory muscle strength test to fatigue using an incremental threshold of breath-loading was performed in duplicate before (T₀) and after four (T₁) and eight weeks (T₂) of IMT/no IMT using a custom-made testing mask and a commercial testing device. Inspiratory measurements included the total number of breaths achieved during the test, average load, peak power, peak volume, peak flow, energy and the mean peak inspiratory muscle strength index (IMSi). Data were analysed using a linear mixed effects model, P≤0.05 significant. There were no differences for inspiratory measurements between groups at T₀. Compared to T₀, the total number of breaths achieved (P = 0.02), load (P = 0.003) and IMSi (P = 0.01) at T₂ had decreased for the Con group while the total number of breaths achieved (P<0.001), load (P = 0.03), volume (P = 0.004), flow (P = 0.006), energy (P = 0.01) and IMSi (P = 0.002) had increased for the Tr group. At T₂ the total number of breaths achieved (P<0.0001), load (P<0.0001), volume (P = 0.02), energy (P = 0.03) and IMSi (P<0.0001) were greater for the Tr than Con group. In conclusion, our results support that IMT can maintain and/or increase aspects of inspiratory muscle strength for horses in a detraining programme.

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (FIS R2 = 0.942, P = 2.19 × 10-13; FROH R2 = 0.88, P = 1.81 × 10-10) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend.

Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome

While over ten thousand genetic loci have been associated with phenotypic traits and inherited diseases in genome-wide association studies, in most cases only a relatively small proportion of the trait heritability is explained and biological mechanisms underpinning these traits have not been clearly identified. Expression quantitative trait loci (eQTL) are subsets of genomic loci shown experimentally to influence gene expression. Since gene expression is one of the primary determinants of phenotype, the identification of eQTL may reveal biologically relevant loci and provide functional links between genomic variants, gene expression and ultimately phenotype. Skeletal muscle (gluteus medius) gene expression was quantified by RNA-seq for 111 Thoroughbreds (47 male, 64 female) in race training at a single training establishment sampled at two time-points: at rest (n = 92) and four hours after high-intensity exercise (n = 77); n = 60 were sampled at both time points. Genotypes were generated from the Illumina Equine SNP70 BeadChip. Applying a False Discovery Rate (FDR) corrected P-value threshold (P_FDR < 0.05), association tests identified 3,583 cis-eQTL associated with expression of 1,456 genes at rest; 4,992 cis-eQTL associated with the expression of 1,922 genes post-exercise; 1,703 trans-eQTL associated with 563 genes at rest; and 1,219 trans-eQTL associated with 425 genes post-exercise. The gene with the highest cis-eQTL association at both time-points was the endosome-associated-trafficking regulator 1 gene (ENTR1; Rest: P_FDR = 3.81 × 10^-27, Post-exercise: P_FDR = 1.66 × 10^-24), which has a potential role in the transcriptional regulation of the solute carrier family 2 member 1 glucose transporter protein (SLC2A1). Functional analysis of genes with significant eQTL revealed significant enrichment for cofactor metabolic processes. These results suggest heritable variation in genomic elements such as regulatory sequences (e.g. gene promoters, enhancers, silencers), microRNA and transcription factor genes, which are associated with metabolic function and may have roles in determining end-point muscle and athletic performance phenotypes in Thoroughbred horses. The incorporation of the eQTL identified with genome and transcriptome-wide association may reveal useful biological links between genetic variants and their impact on traits of interest, such as elite racing performance and adaptation to training.

A candidate-SNP retrospective cohort study for fracture risk in Japanese Thoroughbred racehorses

Fractures are medical conditions that compromise the athletic potential of horses and/or the safety of jockeys. Therefore, the reduction of fracture risk is an important horse and human welfare issue. The present study used molecular genetic approaches to determine the effect of genetic risk for fracture at four candidate SNPs spanning the myostatin (MSTN) gene on horse chromosome 18. Among the 3706 Japanese Thoroughbred racehorses, 1089 (29.4%) had experienced fractures in their athletic life, indicating the common occurrence of this injury in Thoroughbreds. In the case/control association study, fractures of the carpus (carpal bones and distal radius) were statistically associated with g.65809482T/C (P = 1.17 x 10^-8 ), g.65868604G/T (P = 2.66 x 10^-9 ), and g.66493737C/T (P = 6.41 x 10^-8 ). In the retrospective cohort study using 1710 racehorses born in 2000, the relative risk (RR) was highest for male horses at g.65868604G/T, based on the dominant allele risk model (RR = 2.251, 95% confidence interval 1.407-3.604, P = 0.00041), and for female horses at g.65868604G/T, based on the recessive allele risk model (RR = 2.313, 95% confidence interval 1.380-3.877, P = 0.00163). Considering the association of these SNPs with racing performance traits such as speed, these genotypes may affect the occurrence of carpus fractures in Japanese Thoroughbred racehorses as a consequence of the non-genetic influence of the genotype on the distance and/or intensity of racing and training. The genetic information presented here may contribute to the development of strategic training programs and racing plans for racehorses that improve their health and welfare.

Analysis of genetic variation contributing to measured speed in Thoroughbreds identifies genomic regions involved in the transcriptional response to exercise

Despite strong selection for athletic traits in Thoroughbred horses, there is marked variation in speed and aptitude for racing performance within the breed. Using global positioning system monitoring during exercise training, we measured speed variables and temporal changes in speed with age to derive phenotypes for GWAS. The aim of the study was to test the hypothesis that genetic variation contributes to variation in end-point physiological traits, in this case galloping speed measured during field exercise tests. Standardisation of field-measured phenotypes was attempted by assessing horses exercised on the same gallop track and managed under similar conditions by a single trainer. PCA of six key speed indices captured 73.9% of the variation with principal component 1 (PC1). Verifying the utility of the phenotype, we observed that PC1 (median) in 2-year-old horses was significantly different among elite, non-elite and unraced horses (P < 0.001) and the temporal change with age in PC1 varied among horses with different myostatin (MSTN) g.66493737C>T SNP genotypes. A GWAS for PC1 in 2-year-old horses (n = 122) identified four SNPs reaching the suggestive threshold for association (P < 4.80 × 10^-5 ), defining a 1.09 Mb candidate region on ECA8 containing the myosin XVIIIB (MYO18B) gene. In a GWAS for temporal change in PC1 with age (n = 168), five SNPs reached the suggestive threshold for association and defined candidate regions on ECA2 and ECA11. Both regions contained genes that are significantly differentially expressed in equine skeletal muscle in response to acute exercise and training stimuli, including MYO18A. As MYO18A plays a regulatory role in the skeletal muscle response to exercise, the identified genomic variation proximal to the myosin family genes may be important for the regulation of the response to exercise and training.

A genomic prediction model for racecourse starts in the Thoroughbred horse

Durability traits in Thoroughbred horses are heritable, economically valuable and may affect horse welfare. The aims of this study were to test the hypotheses that (i) durability traits are heritable and (ii) genetic data may be used to predict a horse's potential to have a racecourse start. Heritability for the phenotype 'number of 2- and 3-year-old starts' was estimated to be h m 2  = 0.11 ± 0.02 (n = 4499). A genome-wide association study identified SNP contributions to the trait. The neurotrimin (NTM), opioid-binding protein/cell adhesion molecule like (OPCML) and prolylcarboxypeptidase (PRCP) genes were identified as candidate genes associated with the trait. NTM functions in brain development and has been shown to have been selected during the domestication of the horse. PRCP is an established expression quantitative trait locus involved in the interaction between voluntary exercise and body composition in mice. We hypothesise that variation at these loci contributes to the motivation of the horse to exercise, which may influence its response to the demands of the training and racing environment. A random forest with mixed effects (RFME) model identified a set of SNPs that contributed to 24.7% of the heritable variation in the trait. In an independent validation set (n = 528 horses), the cohort with high genetic potential for a racecourse start had significantly fewer unraced horses (16% unraced) than did low (27% unraced) potential horses and had more favourable race outcomes among those that raced. Therefore, the information from SNPs included in the model may be used to predict horses with a greater chance of a racecourse start.

Chinese Mongolian horses may retain early domestic male genetic lineages yet to be discovered

The Mongolian horse represents one of the most ancient extant horse populations. In this study we determined the male-specific region of the Y chromosome (MSY) haplotype distribution in 60 Chinese Mongolian horses representing five distinct populations. Cosmopolitan male lineages were predominant in horses from one improved (Sanhe), one Chinese Mongolian subtype (Baicha Iron Hoof) and one indigenous (Abaga Black) population. In contrast, autochthonous Y chromosome diversity was evident among the two landrace populations (Wushen and Wuzhumuqin), as the majority of their MSY haplotypes were situated at root nodes in a network. Our results also suggest gene flow between Chinese Mongolian and Arabian horses, as an appreciable number of Wuzhumuqin horses carried haplotypes that are typically observed in Arabian horses. Although most horses carried modern haplotypes as a direct result of recent breed improvement, authentic Chinese Mongolian horses retain an ancient signature of paternal lineages that has not previously been described in extant horse populations. Therefore, further characterization of MSY variation in these populations will be important for the discovery of lost diversity in modern domestic horses and also for understanding the evolutionary history of equine paternal lineages.

The contribution of myostatin (MSTN) and additional modifying genetic loci to race distance aptitude in Thoroughbred horses racing in different geographic regions

BACKGROUND

Race distance aptitude in Thoroughbred horses is highly heritable and is influenced largely by variation at the myostatin gene (MSTN).

OBJECTIVES

In addition to MSTN, we hypothesised that other modifying loci contribute to best race distance.

STUDY DESIGN

Using 3006 Thoroughbreds, including 835 'elite' horses, which were >3 years old, had race records and were sampled from Europe/Middle-East, Australia/New Zealand, North America and South Africa, we performed genome-wide association (GWA) tests and separately developed a genomic prediction algorithm to comprehensively catalogue additive genetic variation contributing to best race distance.

METHODS

48,896 single-nucleotide polymorphism (SNP) genotypes were generated from high-density SNP genotyping arrays. Heritability estimates, tests of GWA and genomic prediction models were derived for the phenotypes: average race distance, best race distance for elite, nonelite and all winning horses.

RESULTS

Heritability estimates were high ( h m 2  = 0.51, best race distance - elite; h m 2  = 0.42, best race distance - nonelite; h m 2  = 0.40, best race distance - all) and most of the variation was attributed to the MSTN gene. MSTN locus SNPs were the most strongly associated with the trait and included BIEC2-438999 (ECA18:66913090; P = 4.51 × 10^-110 , average race distance; P = 2.33 × 10^-42 , best race distance - elite). The genomic prediction algorithm enabled the inclusion of variation from all SNPs in a model that partitioned horses into short and long cohorts following assignment of MSTN genotype. Additional genes with minor contributions to best race distance were identified.

MAIN LIMITATIONS

The nongenetic influence of owner/trainer decisions on placement of horses in suitable races could not be controlled.

CONCLUSIONS

MSTN is the single most important genetic contributor to best race distance in the Thoroughbred. Employment of genetic prediction models will lead to more accurate placing of horses in races that are best suited to their inherited genetic potential for distance aptitude.

Impact of pharyngeal endoscopic tip placement and water flushing interval on upper respiratory tract disorders in horses undergoing overground endoscopy

BACKGROUND

Endoscopic tip placement in the pharynx and water flushing interval (FI) may affect exercising upper respiratory tract (URT) endoscopic results.

OBJECTIVES

To determine associations between the endoscopic tip position in the pharynx and automated FI with overground endoscopic (OGE) results.

STUDY DESIGN

Randomised balanced 2X5 factorial design.

METHODS

A total of n = 200 horses undergoing OGE were randomly assigned into 10 groups (n = 20/group) of different automated endoscopic FIs (no flushing, 60, 120, 180, 240 s) with the endoscope tip positioned either rostrally (position A) or caudally (position B) in the pharynx. Endoscopic videos were analysed and all URT abnormalities graded using published scales. Disorders with ≤10% prevalence were excluded from the final analysis with only arytenoid asymmetry at exercise (AAex), vocal fold collapse (VFC), palatal dysfunction (PD) and medial deviation of the aryepiglottic folds (MDAF) included. The association of endoscope position and FI with URT disorders was assessed using ordinal regression models with P≤0.05 significant.

RESULTS

Endoscope tip positioning was significantly associated with PD grading (P = 0.002), with 63/100 horses diagnosed with PD in position A and 45/100 in position B. No other significant direct associations between URT disease and endoscope tip position were identified, although interactions between exercise velocity and endoscope position affected MDAF grade. FI was not directly associated with alterations in disorder grading, although interactions between exercise velocity and FI appeared to affect MDAF grade.

MAIN LIMITATIONS

The same horse was not evaluated under each test condition potentially resulting in sample bias. Interactions between disorders were not evaluated. The sample size was insufficient to conclusively explore relationships between all factors and disorder grading.

CONCLUSIONS

Position of the endoscope tip within the pharynx appears to affect grading of PD during OGE examination. Exercise velocity may affect MDAF grade through interactions with endoscope position and FI.

Genetic contributions to precocity traits in racing Thoroughbreds

Adaptation to early training and racing (i.e. precocity), which is highly variable in racing Thoroughbreds, has implications for the selection and training of horses. We hypothesised that precocity in Thoroughbred racehorses is heritable. Age at first sprint training session (work day), age at first race and age at best race were used as phenotypes to quantify precocity. Using high-density SNP array data, additive SNP heritability (hSNP2) was estimated to be 0.17, 0.14 and 0.17 for the three traits respectively. In genome-wide association studies (GWAS) for age at first race and age at best race, a 1.98-Mb region on equine chromosome 18 (ECA18) was identified. The most significant association was with the myostatin (MSTN) g.66493737C>T SNP (P = 5.46 × 10^-12 and P = 1.89 × 10^-14 respectively). In addition, two SNPs on ECA1 (g.37770220G>A and g.37770305T>C) within the first intron of the serotonin receptor gene HTR7 were significantly associated with age at first race and age at best race. Although no significant associations were identified for age at first work day, the MSTN:g.66493737C>T SNP was among the top 20 SNPs in the GWAS (P = 3.98 × 10^-5 ). Here we have identified variants with potential roles in early adaptation to training. Although there was an overlap in genes associated with precocity and distance aptitude (i.e. MSTN), the HTR7 variants were more strongly associated with precocity than with distance. Because HTR7 is closely related to the HTR1A gene, previously implicated in tractability in young Thoroughbreds, this suggests that behavioural traits may influence precocity.

Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components

BACKGROUND

A single bout of exercise induces changes in gene expression in skeletal muscle. Regular exercise results in an adaptive response involving changes in muscle architecture and biochemistry, and is an effective way to manage and prevent common human diseases such as obesity, cardiovascular disorders and type II diabetes. However, the biomolecular mechanisms underlying such responses still need to be fully elucidated. Here we performed a transcriptome-wide analysis of skeletal muscle tissue in a large cohort of untrained Thoroughbred horses (n = 51) before and after a bout of high-intensity exercise and again after an extended period of training. We hypothesized that regular high-intensity exercise training primes the transcriptome for the demands of high-intensity exercise.

RESULTS

An extensive set of genes was observed to be significantly differentially regulated in response to a single bout of high-intensity exercise in the untrained cohort (3241 genes) and following multiple bouts of high-intensity exercise training over a six-month period (3405 genes). Approximately one-third of these genes (1025) and several biological processes related to energy metabolism were common to both the exercise and training responses. We then developed a novel network-based computational analysis pipeline to test the hypothesis that these transcriptional changes also influence the contextual molecular interactome and its dynamics in response to exercise and training. The contextual network analysis identified several important hub genes, including the autophagosomal-related gene GABARAPL1, and dynamic functional modules, including those enriched for mitochondrial respiratory chain complexes I and V, that were differentially regulated and had their putative interactions 're-wired' in the exercise and/or training responses.

CONCLUSION

Here we have generated for the first time, a comprehensive set of genes that are differentially expressed in Thoroughbred skeletal muscle in response to both exercise and training. These data indicate that consecutive bouts of high-intensity exercise result in a priming of the skeletal muscle transcriptome for the demands of the next exercise bout. Furthermore, this may also lead to an extensive 're-wiring' of the molecular interactome in both exercise and training and include key genes and functional modules related to autophagy and the mitochondrion.

Functional biocompatibility testing of silicone breast implants and a novel classification system based on surface roughness

PURPOSE

Increasing numbers of women undergo breast implantation for cosmetic and reconstructive purposes. Contracture of the fibrous capsule, which encases the implant leads to significant pain and reoperation. Texture, wettability and the cellular reaction to implant surfaces are poorly understood determinants of implant biocompatibility. The aim of this study was to evaluate the in-vitro characteristics of a range of commercial available implants using a macrophage based assay of implant biocompatibility and a quantitative assessment of wettability and texture.

METHODS

Thirteen commercially available surfaces were subjected to wettability and texture characterisation using scanning and laser confocal microscopy. THP-1 macrophages were cultured on their surfaces and assessed using Integrin αV immunocytochemistry, SEM and RT-PCR for the expression of TNF-Alpha, IL-6, IL-10 and a cytokine array for the production of TNF-alpha, IL-10, IL-1RA and IL1β; important indicators of inflammation and macrophage polarization.

RESULTS

Textured surfaces can be accurately sub-categorized dependent upon roughness and re-entrant features into four main types (macro, micro, meso and nano-textured surfaces). Significant (P < 0.0001) differences in implant hydrophobicity and texture exist. Certain surfaces promoted poor macrophage polarization and an innate potential to foster a proinflammatory response. A subgroup analysis showed that texture had a variable effect on markers of inflammation in these surfaces.

CONCLUSIONS

We propose a classification of implant surfaces based on roughness and present a macrophage based assay of breast implant biocompatibility with a quantitative assessment of implant wettability and texture. The breast implant surface-cell interaction is variable and sufficient to alter healing response and capsular contracture fate in-vivo.

Education as an Economic Development Resource

The relationship between labor-market conditions which are expected to exist in the United States in the year 2000 and current primary and secondary public education policy is examined in this paper. The role of educational attainment in the development of the economy is outlined and a policy model of the functions of publicly supported primary and secondary education is presented. The educational policy implications for the future structure of the US labor market are examined in the context of this model.

Skeletal muscle adaptations and muscle genomics of performance horses

Skeletal muscles in horses are characterised by specific adaptations, which are the result of the natural evolution of the horse as a grazing animal, centuries of selective breeding and the adaptability of this tissue in response to training. These adaptations include an increased muscle mass relative to body weight, a great locomotor efficiency based upon an admirable muscle-tendon architectural design and an adaptable fibre-type composition with intrinsic shortening velocities greater than would be predicted from an animal of comparable body size. Furthermore, equine skeletal muscles have a high mitochondrial volume that permits a higher whole animal aerobic capacity, as well as large intramuscular stores of energy substrates (glycogen in particular). Finally, high buffer and lactate transport capacities preserve muscles against fatigue during anaerobic exercise. Many of these adaptations can improve with training. The publication of the equine genome sequence in 2009 has provided a major advance towards an improved understanding of equine muscle physiology. Equine muscle genomics studies have revealed a number of genes associated with elite physical performance and have also identified changes in structural and metabolic genes following exercise and training. Genes involved in muscle growth, muscle contraction and specific metabolic pathways have been found to be functionally relevant for the early performance evaluation of elite athletic horses. The candidate genes discussed in this review are important for a healthy individual to improve performance. However, muscle performance limiting conditions are widespread in horses and many of these conditions are also genetically influenced.

Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance

Athletic performance is influenced by a complex interplay among the environment and a suite of genes, which contributes to system-wide structure and function. In a panel of elite and non-elite Thoroughbred horses (n=148), we genotyped 68 SNPs in 17 putative exercise-relevant genes chosen from a genome scan for selection. We performed a series of case-control and quantitative association tests for relationships with racecourse performance. Thirteen SNPs in nine genes were significantly (P<0.05) associated with a performance phenotype. We selected five SNPs in four genes (ACSS1, ACN9, COX4I1, PDK4) for validation in an independent sample set of elite and non-elite Thoroughbreds (n=130). Two SNPs in the PDK4 gene were validated (P<0.01) for associations with elite racing performance. When all samples were considered together (n=278), the PDK4_ 38973231 SNP was strongly associated (P<0.0005) with elite racing performance. Individuals with the A:A and A:G genotypes had a 16.2-16.6 lb advantage over G:G individuals in terms of handicap rating. Re-sequencing of the PDK4 gene and further genotyping will be required to identify the causative variant that is likely influencing exercise-induced variation in expression of the gene. Notwithstanding, this information may be employed as a marker for the selection of racehorses with the genetic potential for superior racing ability.

Horses for courses: a DNA-based test for race distance aptitude in thoroughbred racehorses

Variation at the myostatin (MSTN) gene locus has been shown to influence racing phenotypes in Thoroughbred horses, and in particular, early skeletal muscle development and the aptitude for racing at short distances. Specifically, a single nucleotide polymorphism (SNP) in the first intron of MSTN (g.66493737C/T) is highly predictive of best race distance among Flat racing Thoroughbreds: homozygous C/C horses are best suited to short distance races, heterozygous C/T horses are best suited to middle distance races, and homozygous T/T horses are best suited to longer distance races. Patent applications for this gene marker association, and other linked markers, have been filed. The information contained within the patent applications is exclusively licensed to the commercial biotechnology company Equinome Ltd, which provides a DNA-based test to the international Thoroughbred horse racing and breeding industry. The application of this information in the industry enables informed decision making in breeding and racing and can be used to assist selection to accelerate the rate of change of genetic types among distinct populations (Case Study 1) and within individual breeding operations (Case Study 2).

Genetic diversity in the modern horse illustrated from genome-wide SNP data

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 distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Genome-wide analysis reveals selection for important traits in domestic horse breeds

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 biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.

Thoroughbred racehorse mitochondrial DNA demonstrates closer than expected links between maternal genetic history and pedigree records

The potential future earnings and therefore value of Thoroughbred foals untested in the racing arena are calculated based on the performance of their forebears. Thus, lineage is of key importance. However, previous research indicates that maternally inherited mitochondrial DNA (mtDNA) does not correspond to maternal lineage according to recorded pedigree, casting doubt on the voracity of historic pedigrees. We analysed mtDNA of 296 Thoroughbred horses from 33 maternal lineages and identified an interesting trend. Subsequent to the founding of the Thoroughbred breed in the 16th century, well-populated maternal lineages were divided into sub-lineages. Only six in 10 of the Thoroughbreds sampled shared mitochondrial haplotype with other members of their maternal lineage, despite having a common maternal ancestor according to pedigree records. However, nine in 10 Thoroughbreds from the 103 sub-lineages sampled shared mtDNA with horses of their maternal pedigree sub-lineage. Thus, Thoroughbred maternal sub-lineage pedigree represents a more accurate breeding record than previously thought. Errors in pedigrees must have occurred largely, though, not exclusively, at sub-lineage foundation events, probably due to incomplete understanding of modes of inheritance in the past, where maternal sub-lineages were founded from individuals, related, but not by female descent.

MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance

Myostatin, encoded by the MSTN gene, is a member of the TGF-β superfamily that regulates skeletal muscle development. A MSTN SNP significantly associated with Thoroughbred horse racing phenotypes has recently been identified as well as significant reductions in Thoroughbred skeletal muscle gene expression for three transcripts 400-1500 base pairs downstream of the MSTN gene following a period of training. Together, these findings indicate that MSTN genotypes may influence MSTN gene expression. To investigate this, MSTN mRNA expression was measured in biopsies from the middle gluteal muscle from 60 untrained yearling Thoroughbreds (C/C, n = 15; C/T, n = 28; T/T, n = 17) using two independent real-time qRT-PCR assays. MSTN gene expression was also evaluated in a subset (N = 33) of these animals using samples collected after a ten-month period of training. A significant association was observed between genotype and mRNA abundance for the untrained horses (assay I, P = 0.0237; assay II, P = 0.003559), with the C/C cohort having the highest MSTN mRNA levels, the T/T group the lowest levels and the C/T group intermediate levels. Following training, there was a significant decrease in MSTN mRNA (-3.35-fold; P = 6.9 × 10(-7) ), which was most apparent for the C/C cohort (-5.88-fold, P = 0.001). These data demonstrate the tight relationship between phenotype, genotype and gene expression at the MSTN gene in Thoroughbred racehorses.

A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies

An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50-100 kb and reached background levels within 1-2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.

MSTN genotype (g.66493737C/T) association with speed indices in Thoroughbred racehorses

Sequence variation at the equine myostatin gene (MSTN) locus has previously been shown to have a singular genomic influence on optimum race distance in Thoroughbred racehorses. Myostatin, encoded by the MSTN gene, is a member of the TGF-β superfamily that regulates skeletal muscle development in a range of mammalian species including the horse. In the Thoroughbred, the C-allele at the g.66493737C/T SNP has been found at significantly higher frequency in subgroups of the population that are suited to fast, short distance, sprint races and also influences body composition phenotypes. We investigated the influence of the g.66493737C/T SNP on speed indexes measured in a cohort of n = 85 Thoroughbred horses-in-training. We found significant associations between genotypes at the g.66493737C/T SNP and all measured speed variables: Dist(6) [distance travelled during 6 s before and after maximal velocity (V(max)); P = 0.0040], V(maxt) (duration at V(max); P = 0.0249), V(max) (P = 0.0265), Dist(6b) (distance travelled during 6 s before V(max); P = 0.0032), and Dist(6a)(distance travelled during 6 s after V(max); P = 0.0317). For each measure, horses with the C/C and C/T genotypes outperformed T/T horses, indicating the requirement for at least one C-allele to improve speed. For the most significantly associated variables (Dist(6) and Dist(6b)) the C/C cohort performed better than the T/T cohort with the heterozygotes intermediate, indicating a dose-dependent manifestation. These findings clearly indicate that variation at the MSTN gene influences speed in Thoroughbred horses.

Moderate and high intensity sprint exercise induce differential responses in COX4I2 and PDK4 gene expression in Thoroughbred horse skeletal muscle

REASONS FOR PERFORMING STUDY

The role of molecular signalling pathways in the phenotypic adaptation of skeletal muscle to different exercise stimuli in the Thoroughbred horse has not been reported previously.

OBJECTIVE

To examine CKM, COX4I1, COX4I2 and PDK4 gene expression following high intensity sprint and moderate intensity treadmill exercise stimuli in skeletal muscle of Thoroughbred horses.

MATERIALS AND METHODS

Two groups of trained 3-year-old Thoroughbred horses participated. Group A (n = 6 females, n = 3 males) participated in an incremental step test (moderate intensity) to fatigue or HR(max) on a Sato high speed treadmill (distance = 5418.67 m ± 343.21). Group B (n = 8 females) participated in routine 'work' (sprint) on an all-weather gallop (distance = 812.83 m ± 12.53). Biopsy samples were obtained from the gluteus medius pre-exercise (T(0)), immediately post exercise (T(1)) and 4 h post exercise (T(2)). For physiological relevance venous blood samples were collected to measure plasma lactate and creatine kinase concentrations. Changes in mRNA expression were determined by quantitative real-time RT-PCR for creatine kinase muscle (CKM), cytochrome c oxidase subunit IV isoform 1 (COX4I1), cytochrome c oxidase subunit IV isoform 2 (COX4I2) and pyruvate dehydrogenase kinase, isozyme 4 (PDK4) genes. Statistical significance (α < 0.05) was determined using Student's t tests.

RESULTS

COX4I2 mRNA expression decreased significantly in Group A and remained unchanged in Group B between T(0) vs. T(2) (-1.7-fold, P = 0.017; -1.0-fold, P = 0.859). PDK4 mRNA expression increased significantly in Group B but not in Group A between T(0) vs. T(1) (3.8-fold, P = 0.039; 1.4-fold, P = 0.591). There were no significant changes in the expression in CKM or COX4I1 mRNA abundance in either group.

CONCLUSIONS

Different exercise protocols elicit variable transcriptional responses in key exercise relevant genes in equine skeletal muscle due to variation in metabolic demand.

The association of various speed indices to training responses in Thoroughbred flat racehorses measured with a global positioning and heart rate monitoring system

REASONS FOR PERFORMING STUDY

Fitness assessment can be challenging. The use of global positioning systems (GPS) with heart rate (HR) monitors has been promising; however, evaluation of speed parameters during training has not been reported.

OBJECTIVES

To evaluate speed indices during training in Thoroughbreds using a GPS-HR monitor.

METHODS

Thoroughbreds (n = 102) were assessed during training with data collected each work day (WD; sprinting). Speed indices evaluated included maximal velocity (V(max)), duration at V(max) (V(maxt)), acceleration rate (m/s(2)) from 800 m to V(max) (Acc800-V(max)), the distance (m) 6 (V(maxD6)) and 12 (V(maxD12)) s before (acceleration [a]) and after (deceleration [d]) V(max) and the deceleration rate from V(max) to the finish (V(maxDFd)). Blood for plasma lactate ([LA]) and creatine kinase ([CK]) measurements were taken before (T(0)), 5 mins (T(1)) and 6 h after exercise (T(2)). WD accumulation, jockey, gallop condition, horse gender, age, total distance covered (DistT), maximum HR (HR(max)), velocity at 200 beats/min (V(200)) and velocity at maximum HR (VHR(max)) for each WD were evaluated for associations with [LA], [CK], speed indices and racing performance. Data were analysed by repeated measures ANOVA with P < 0.05 significant.

RESULTS

No speed parameter clearly changed with training. Gallop condition affected V(max), V(maxt) and all distances covered with V(max) and distances increasing and V(maxt) decreasing as gallop surface became firmer. Jockey influenced V(max), V(maxD6a) and all decelerations, while DistT was inversely associated with Acc800-V(max), HR(max) and V(200) and positively associated with V(max), all accelerations and decelerations. [LA] at T(1) was positively associated with DistT and V(maxDFd).

CONCLUSIONS

Speed parameters did not change with training but were affected by jockey, gallop condition and exercise distance. This information may help to modify training to maximise fitness, minimise injury and choose distances best suited for individuals.

The cosmopolitan maternal heritage of the Thoroughbred racehorse breed shows a significant contribution from British and Irish native mares

The paternal origins of Thoroughbred racehorses trace back to a handful of Middle Eastern stallions, imported to the British Isles during the seventeenth century. Yet, few details of the foundation mares were recorded, in many cases not even their names (several different maternal lineages trace back to ‘A Royal Mare’). This has fuelled intense speculation over their origins. We examined mitochondrial DNA from 1929 horses to determine the origin of Thoroughbred foundation mares. There is no evidence to support exclusive Arab maternal origins as some historical records have suggested, or a significant importation of Oriental mares (the term used in historic records to refer to Middle East and western Asian breeds including Arab, Akhal-Teke, Barb and Caspian). Instead, we show that Thoroughbred foundation mares had a cosmopolitan European heritage with a far greater contribution from British and Irish Native mares than previously recognized.

Circadian regulation of locomotor activity and skeletal muscle gene expression in the horse

Circadian rhythms are innate 24-h cycles in behavioral and biochemical processes that permit physiological anticipation of daily environmental changes. Elucidating the relationship between activity rhythms and circadian patterns of gene expression may contribute to improved human and equine athletic performance. Six healthy, untrained mares were studied to determine whether locomotor activity behavior and skeletal muscle gene expression reflect endogenous circadian regulation. Activity was recorded for three consecutive 48-h periods: as a group at pasture (P), and individually stabled under a light-dark (LD) cycle and in constant darkness (DD). Halter-mounted Actiwatch-L data-loggers recorded light exposure and motor activity. Analysis of mean activity (average counts/min, activity bouts/day, average bout length) and cosinor parameters (acrophase, amplitude, mesor, goodness of fit) revealed a predominantly ultradian (8.9 ± 0.7 bouts/24 h) and weakly circadian pattern of activity in all three conditions (P, LD, DD). A more robust circadian pattern was observed during LD and DD. Muscle biopsies were obtained from the middle gluteal muscles every 4 h for 24 h under DD. One-way qRT-PCR results confirmed the circadian expression (P < 0.05) of six core clock genes (Arntl, Per1, Per2, Nr1d1, Nr1d2, Dbp) and the muscle-specific transcript, Myf6. Additional genes, Ucp3, Nrip1, and Vegfa, demonstrated P values approaching significance. These findings demonstrate circadian regulation of muscle function and imply that human management regimes may strengthen, or unmask, equine circadian behavioral outputs. As exercise synchronizes circadian rhythms, our findings provide a basis for future work determining peak times for training and competing horses, to reduce injury and to achieve optimal performance.

Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training

Background

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: T₁ - untrained, (9 ± 0.5 months old) and T₂ - trained (20 ± 0.7 months old).

Results

The most abundant mRNA transcripts in the muscle transcriptome were those involved in muscle contraction, aerobic respiration and mitochondrial function. A previously unreported over-representation of genes related to RNA processing, the stress response and proteolysis was observed. Following training 92 tags were differentially expressed of which 74 were annotated. Sixteen genes showed increased expression, including the mitochondrial genes ACADVL, MRPS21 and SLC25A29 encoded by the nuclear genome. Among the 58 genes with decreased expression, MSTN, a negative regulator of muscle growth, had the greatest decrease.

Functional analysis of all expressed genes using FatiScan revealed an asymmetric distribution of 482 Gene Ontology (GO) groups and 18 KEGG pathways. Functional groups displaying highly significant (P < 0.0001) increased expression included mitochondrion, oxidative phosphorylation and fatty acid metabolism while functional groups with decreased expression were mainly associated with structural genes and included the sarcoplasm, laminin complex and cytoskeleton.

Conclusion

Exercise training in Thoroughbred racehorses results in coordinate changes in the gene expression of functional groups of genes related to metabolism, oxidative phosphorylation and muscle structure.

Clinical skills required of ophthalmic nurse practitioners in tertiary level public hospitals in the Western Cape Province

BACKGROUND

South Africa has a 32-year history of training ophthalmic nurse practitioners (ONPs). The role and required skills and competencies of ONPs are not well documented in the international literature and are also absent from South African publications, including South African Nursing Council publications.

AIM

This study aims to inform curriculum development and human resource planning by reporting on the clinical skills expected of ONPs by members of multidisciplinary ophthalmology teams.

METHOD

A limited survey was undertaken in the ophthalmology wards and outpatient departments of three tertiary level hospitals in the Western Cape Province. A researcher-designed structured self-completion questionnaire was distributed to 30 ophthalmology practitioners: doctors, nurses and technicians. Respondents were asked to indicate the expected clinical skills of ONPs.

FINDINGS

All questionnaires were completed. All respondents favoured ONPs taking histories and performing emergency eye irrigations. There was less support for more complex procedures, such as B-scans. One-third of respondents did not expect ONPs to have skills in eight key areas, including examination of the anterior chamber angle for glaucoma. No statistically significant differences were found between responses of doctors and nurses, with one exception: more nurses (15/18) than doctors (4/10) had confidence in the ONP undertaking basic eye examinations for ocular motility (Fisher's exact test, P = 0.035).

CONCLUSION

In the study settings, ONPs are not using their specialist skills to the full. Not all practitioners were receptive to ONPs using the skills that they had acquired during their postgraduate diploma, threatening the educational effectiveness of this initiative.

Transcriptional adaptations following exercise in thoroughbred horse skeletal muscle highlights molecular mechanisms that lead to muscle hypertrophy

Background

Selection for exercise-adapted phenotypes in the Thoroughbred racehorse has provided a valuable model system to understand molecular responses to exercise in skeletal muscle. Exercise stimulates immediate early molecular responses as well as delayed responses during recovery, resulting in a return to homeostasis and enabling long term adaptation. Global mRNA expression during the immediate-response period has not previously been reported in skeletal muscle following exercise in any species. Also, global gene expression changes in equine skeletal muscle following exercise have not been reported. Therefore, to identify novel genes and key regulatory pathways responsible for exercise adaptation we have used equine-specific cDNA microarrays to examine global mRNA expression in skeletal muscle from a cohort of Thoroughbred horses (n = 8) at three time points (before exercise, immediately post-exercise, and four hours post-exercise) following a single bout of treadmill exercise.

Results

Skeletal muscle biopsies were taken from the gluteus medius before (T₀), immediately after (T₁) and four hours after (T₂) exercise. Statistically significant differences in mRNA abundance between time points (T₀ vs T₁ and T₀ vs T₂) were determined using the empirical Bayes moderated t-test in the Bioconductor package Linear Models for Microarray Data (LIMMA) and the expression of a select panel of genes was validated using real time quantitative reverse transcription PCR (qRT-PCR). While only two genes had increased expression at T₁ (P < 0.05), by T₂ 932 genes had increased (P < 0.05) and 562 genes had decreased expression (P < 0.05). Functional analysis of genes differentially expressed during the recovery phase (T₂) revealed an over-representation of genes localized to the actin cytoskeleton and with functions in the MAPK signalling, focal adhesion, insulin signalling, mTOR signaling, p53 signaling and Type II diabetes mellitus pathways. At T₁, using a less stringent statistical approach, we observed an over-representation of genes involved in the stress response, metabolism and intracellular signaling. These findings suggest that protein synthesis, mechanosensation and muscle remodeling contribute to skeletal muscle adaptation towards improved integrity and hypertrophy.

Conclusions

This is the first study to characterize global mRNA expression profiles in equine skeletal muscle using an equine-specific microarray platform. Here we reveal novel genes and mechanisms that are temporally expressed following exercise providing new knowledge about the early and late molecular responses to exercise in the equine skeletal muscle transcriptome.

Genome sequence, comparative analysis, and population genetics of the domestic horse

We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

Divergent antimicrobial peptide (AMP) and acute phase protein (APP) responses to Trypanosoma congolense infection in trypanotolerant and trypanosusceptible cattle

African animal trypanosomiasis (AAT) is endemic across Sub-Saharan African and is a major constraint to livestock production. The ability of certain cattle breeds to remain productive despite infection is known as trypanotolerance; however, the underlying immune mechanisms contributing to this trait remain poorly understood. Antimicrobial peptides (AMPs) and acute phase proteins (APPs) are evolutionarily conserved effector molecules of the innate immune system that have important roles in the resolution of infection and activation of the adaptive immune response. Expression levels of AMP genes (TAP, LAP, BNBD4, DEFB1, DEFB5 and LEAP2) and APP genes (HP, CP, AGP, LBP, SAA3 and CRP) were investigated using real time quantitative reverse transcription PCR (qRT-PCR) in peripheral blood mononuclear cells (PBMC) isolated from two breeds of African cattle (trypanotolerant N'Dama and trypanosusceptible Boran), experimentally infected with Trypanosoma congolense. Haptoglobin and serum amyloid A (SAA) were also measured in plasma using quantitative protein assays. Results demonstrated that tracheal antimicrobial peptide (TAP) gene expression increased by 32-fold in Boran, compared to only 3-fold in N'Dama, by 14 days post-infection (dpi) and rising to 136-fold at 29 dpi in Boran, compared to 47-fold in N'Dama (P<0.05). Protein expression levels of SAA are elevated in N'Dama, rising to 163 microg/ml at 14 dpi compared with 72 microg/ml in Boran. The SAA expression profile mirrors the wave of parasitaemia detected in N'Dama. Seven single nucleotide polymorphisms (SNPs) were identified in the promoter regions of the SAA3 and SAA4 genes, which are predicted to affect transcription factor binding and thereby contributing to the differential patterns of expression detected between the breeds. Whereas elevated TAP expression is a conserved component of the innate immune response to infection in both breeds, higher SAA expression levels may contribute toward trypanotolerance in N'Dama.

Alterations in oxidative gene expression in equine skeletal muscle following exercise and training

Intense selection for elite racing performance in the Thoroughbred horse (Equus caballus) has resulted in a number of adaptive physiological phenotypes relevant to exercise; however, the underlying molecular mechanisms responsible for these characteristics are not well understood. Adaptive changes in mRNA expression in equine skeletal muscle were investigated by real-time qRT-PCR for a panel of candidate exercise-response genes following a standardized incremental-step treadmill exercise test in eight untrained Thoroughbred horses. Biopsy samples were obtained from the gluteus medius before, immediately after, and 4 h after exercise. Significant (P < 0.05) differences in gene expression were detected for six genes (CKM, COX4I1, COX4I2, PDK4, PPARGC1A, and SLC2A4) 4 h after exercise. Investigation of relationships between mRNA and velocity at maximum heart rate (VHR(max)) and peak postexercise plasma lactate concentration ([La]T(1)) revealed significant (P < 0.05) associations with postexercise COX4I1 and PPARCG1A expression and between [La]T(1) and basal COX4I1 expression. Gene expression changes were investigated in a second cohort of horses after a 10 mo period of training. In resting samples, COX4I1 gene expression had significantly increased following training, and, after exercise, significant differences were identified for COX4I2, PDK4, and PPARGC1A. Significant relationships with VHR(max) and [La]T(1) were detected for PPARGC1A and COX4I1. These data highlight the roles of genes responsible for the regulation of oxygen-dependent metabolism, glucose metabolism, and fatty acid utilization in equine skeletal muscle adaptation to exercise.

A genome scan for positive selection in thoroughbred horses

Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selected loci in the extreme tail-ends of the empirical distributions for (1) deviations from expected heterozygosity (Ewens-Watterson test) in Thoroughbred (n = 112) and (2) global differentiation among four geographically diverse horse populations (F(ST)). We found positively selected genomic regions in Thoroughbred enriched for phosphoinositide-mediated signalling (3.2-fold enrichment; P<0.01), insulin receptor signalling (5.0-fold enrichment; P<0.01) and lipid transport (2.2-fold enrichment; P<0.05) genes. We found a significant overrepresentation of sarcoglycan complex (11.1-fold enrichment; P<0.05) and focal adhesion pathway (1.9-fold enrichment; P<0.01) genes highlighting the role for muscle strength and integrity in the Thoroughbred athletic phenotype. We report for the first time candidate athletic-performance genes within regions targeted by selection in Thoroughbred horses that are principally responsible for fatty acid oxidation, increased insulin sensitivity and muscle strength: ACSS1 (acyl-CoA synthetase short-chain family member 1), ACTA1 (actin, alpha 1, skeletal muscle), ACTN2 (actinin, alpha 2), ADHFE1 (alcohol dehydrogenase, iron containing, 1), MTFR1 (mitochondrial fission regulator 1), PDK4 (pyruvate dehydrogenase kinase, isozyme 4) and TNC (tenascin C). Understanding the genetic basis for exercise adaptation will be crucial for the identification of genes within the complex molecular networks underlying obesity and its consequential pathologies, such as type 2 diabetes. Therefore, we propose Thoroughbred as a novel in vivo large animal model for understanding molecular protection against metabolic disease.

Effect of a high-kappa environment on charge carrier mobility in graphene

It is widely assumed that the dominant source of scattering in graphene is charged impurities in a substrate. We have tested this conjecture by studying graphene placed on various substrates and in high-kappa media. Unexpectedly, we have found no significant changes in carrier mobility either for different substrates or by using glycerol, ethanol, and water as a top dielectric layer. This suggests that Coulomb impurities are not the scattering mechanism that limits the mean free path attainable for graphene on a substrate.

Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility

Background

African animal trypanosomiasis (AAT) caused by tsetse fly-transmitted protozoa of the genus Trypanosoma is a major constraint on livestock and agricultural production in Africa and is among the top ten global cattle diseases impacting on the poor. Here we show that a functional genomics approach can be used to identify temporal changes in host peripheral blood mononuclear cell (PBMC) gene expression due to disease progression. We also show that major gene expression differences exist between cattle from trypanotolerant and trypanosusceptible breeds. Using bovine long oligonucleotide microarrays and real time quantitative reverse transcription PCR (qRT-PCR) validation we analysed PBMC gene expression in naïve trypanotolerant and trypanosusceptible cattle experimentally challenged with Trypanosoma congolense across a 34-day infection time course.

Results

Trypanotolerant N'Dama cattle displayed a rapid and distinct transcriptional response to infection, with a ten-fold higher number of genes differentially expressed at day 14 post-infection compared to trypanosusceptible Boran cattle. These analyses identified coordinated temporal gene expression changes for both breeds in response to trypanosome infection. In addition, a panel of genes were identified that showed pronounced differences in gene expression between the two breeds, which may underlie the phenomena of trypanotolerance and trypanosusceptibility. Gene ontology (GO) analysis demonstrate that the products of these genes may contribute to increased mitochondrial mRNA translational efficiency, a more pronounced B cell response, an elevated activation status and a heightened response to stress in trypanotolerant cattle.

Conclusion

This study has revealed an extensive and diverse range of cellular processes that are altered temporally in response to trypanosome infection in African cattle. Results indicate that the trypanotolerant N'Dama cattle respond more rapidly and with a greater magnitude to infection compared to the trypanosusceptible Boran cattle. Specifically, a subset of the genes analyzed by real time qRT-PCR, which display significant breed differences, could collectively contribute to the trypanotolerance trait in N'Dama.

Detection of individual gas molecules adsorbed on graphene

The ultimate aim of any detection method is to achieve such a level of sensitivity that individual quanta of a measured entity can be resolved. In the case of chemical sensors, the quantum is one atom or molecule. Such resolution has so far been beyond the reach of any detection technique, including solid-state gas sensors hailed for their exceptional sensitivity. The fundamental reason limiting the resolution of such sensors is fluctuations due to thermal motion of charges and defects, which lead to intrinsic noise exceeding the sought-after signal from individual molecules, usually by many orders of magnitude. Here, we show that micrometre-size sensors made from graphene are capable of detecting individual events when a gas molecule attaches to or detaches from graphene's surface. The adsorbed molecules change the local carrier concentration in graphene one by one electron, which leads to step-like changes in resistance. The achieved sensitivity is due to the fact that graphene is an exceptionally low-noise material electronically, which makes it a promising candidate not only for chemical detectors but also for other applications where local probes sensitive to external charge, magnetic field or mechanical strain are required.

Mitochondrial DNA sequence diversity in extant Irish horse populations and in ancient horses

Equine mitochondrial DNA sequence variation was investigated in three indigenous Irish horse populations (Irish Draught Horse, Kerry Bog Pony and Connemara Pony) and, for context, in 69 other horse populations. There was no evidence of Irish Draught Horse or Connemara Pony sequence clustering, although the majority of Irish Draught Horse sequences (47%) were assigned to haplogroup D. Conversely, 31% of the Kerry Bog Pony sequences were assigned to the rare haplogroup E. In addition to the extant population analyses, ancient DNA sequences were generated from three out of four Irish archaeological specimens, all of which were assigned to haplogroup A.

Evidence for biogeographic patterning of mitochondrial DNA sequences in Eastern horse populations

Equine mitochondrial DNA (mtDNA) phylogeny reconstruction reveals a complex pattern of variation unlike that seen in other large domesticates. It is likely that this pattern reflects a process of multiple and repeated, although not necessarily independent, domestication events. Until now, no clear geographic affiliation of clades has been apparent. In this study, amova analyses have revealed a significant non-random distribution of the diversity among equine populations when seven newly sequenced Eurasian populations were examined in the context of previously published sequences. The association of Eastern mtDNA types in haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00000). For the first time, clear biogeographic partitioning has been detected in equine mtDNA sequence.

Cytokine mRNA profiling of peripheral blood mononuclear cells from trypanotolerant and trypanosusceptible cattle infected with Trypanosoma congolense

To examine differences in cytokine profiles that may confer tolerance/susceptibility to bovine African trypanosomiasis, N'Dama (trypanotolerant, n = 8) and Boran (trypanosusceptible, n = 8) cattle were experimentally challenged with Trypanosoma congolense. Blood samples were collected over a 34-day period, and RNA was extracted from peripheral blood mononuclear cells. The expression levels of a panel of 14 cytokines were profiled over the time course of infection and between breeds. Messenger RNA (mRNA) transcript levels for the IL2, IL8, and IL1RN genes were significantly downregulated across the time course of infection in both breeds. There was an early increase in transcripts for genes encoding proinflammatory mediators (IFNG, IL1A, TNF, and IL12) in N'Dama by 14 days postinfection (dpi) compared with preinfection levels that was not detected in the susceptible Boran breed. By the time of peak parasitemia, a type 2 helper T cells (T(H)2)-like cytokine environment was prevalent that was particularly evident in the Boran. Increases in transcripts for the IL6 (29 and 34 dpi) and IL10 (21, 25, and 29 dpi) genes were detected that were higher in the Boran compared with N'Dama. These findings highlight the implications for using murine models to study the bovine immune response to trypanosomiasis, where in some cases cytokine expression patterns differ. Overall, these data suggest that the trypanotolerant N'Dama are more capable of responding very early in infection with proinflammatory and T(H)1 type cytokines than the trypanosusceptible Boran and may explain why N'Dama control parasitemia more efficiently than Boran during the early stages of infection.