Breed-specific SNP and genomic regions associated with equine recurrent exertional rhabdomyolysis susceptibility overlapping withup- and down-regulatory histone modifications

Recurrent exertional rhabdomyolysis (RER) is a myopathy characterised by episodes of exercise-induced myofibre necrosis, muscle stiffness and fasciculations, with extreme cases resulting in kidney failure or death. There is a genetic component attributed to RER1-3, but specific causative genes and mutations have not been identified. Due to the disease’s metabolic nature, we hypothesised that regulatory regions of the genome may be implicated4. We aimed to identify genetic markers for RER in Thoroughbreds (TB), Warmbloods (WB) and Connemara ponies (CP). Since many of these were located in non-coding regions we compared their location with peaks in the publicly-available equine ChIP-seq data obtained from the FAANG portal5.33 CP (17 cases, 16 controls) and 94 WB (50 cases, 44 controls) were genotyped using a 670k genotyping array. GWAS, regional heritability mapping (RHM) and FST analyses were thenrun both across and within breeds. Various window sizes around significant and suggestive markers from these analyses, and 26 previously-identified US TB RER markers2 re-mapped to EquCab3.0, were compared to locations of histone markers identified in longissimus dorsi samples from two horses in the FAANG data using bedtools. No ChIP-seq peaks directly overlapped TB QTLs, but 6 in CPs and 2 in WBs overlapped with significant and suggestive significant SNPs for RER susceptibility. Within 10 kb of TB QTLs there were significantly fewer H3K27me3 and more H3K4me3 peaks than expected, whilst WB RHM regions contained significantly more H3K27me3 peaks and fewer H3K4me1 peaks than expected. No Bonferroni-corrected significant differences were identified in CP alone. <br/

Characterisation of phenotypic patterns in equine exercise-associated myopathies

Background: Equine exercise-associated myopathies are prevalent, clinically heterogeneous, generally idiopathic disorders characterised by episodes of myofibre damage that occur in association with exercise. Episodes are intermittent and vary within and between affected horses and across breeds. The aetiopathogenesis is often unclear; there might be multiple causes. Poor phenotypic characterisation hinders genetic and other disease analyses. Objectives: The aim of this study was to characterise phenotypic patterns across exercise-associated myopathies in horses. Study design: Historical cross-sectional study, with subsequent masked case–control validation study. Methods: Historical clinical and histological features from muscle samples (n = 109) were used for k-means clustering and validated using principal components analysis and hierarchical clustering. For further validation, a blinded histological study (69 horses) was conducted comparing two phenotypic groups with selected controls and horses with histopathological features characterised by myofibrillar disruption. Results: We identified two distinct broad phenotypes: a non-classic exercise-associated myopathy syndrome (EAMS) subtype was associated with practitioner-described signs of apparent muscle pain (p &lt; 0.001), reluctance to move (10.85, p = 0.001), abnormal gait (p &lt; 0.001), ataxia (p = 0.001) and paresis (p = 0.001); while a non-specific classic RER subtype was not uniquely associated with any particular variables. No histological differences were identified between subtypes in the validation study, and no identifying histopathological features for other equine myopathies identified in either subtype. Main limitations: Lack of an independent validation population; small sample size of smaller identified subtypes; lack of positive control myofibrillar myopathy cases; case descriptions derived from multiple independent and unblinded practitioners. Conclusions: This is the first study using computational clustering methods to identify phenotypic patterns in equine exercise-associated myopathies, and suggests that differences in patterns of presenting clinical signs support multiple disease subtypes, with EAMS a novel subtype not previously described. Routine muscle histopathology was not helpful in sub-categorising the phenotypes in our population.</p

Variants in the 3'UTR of the ovine Acetyl-Coenzyme A Acyltransferase 2 gene are associated with dairy traits and exhibit differential allelic expression

The acetyl-CoA acyltransferase 2 (ACAA2) gene encodes an enzyme of the thiolase family that is involved in mitochondrial fatty acid elongation and degradation by catalyzing the last step of the respective β-oxidation pathway. The increased energy needs for gluconeogenesis and triglyceride synthesis during lactation are met primarily by increased fatty acid oxidation. Therefore, the ACAA2 enzyme plays an important role in the supply of energy and carbon substrates for lactation and may thus affect milk production traits. This study investigated the association of the ACAA2 gene with important sheep traits and the putative functional involvement of this gene in dairy traits. A single nucleotide substitution, a T to C transition located in the 3′ untranslated region of the ACAA2 gene, was used in mixed model association analysis with milk yield, milk protein yield and percentage, milk fat yield and percentage, and litter size at birth. The single nucleotide polymorphism was significantly associated with total lactation production and milk protein percentage, with respective additive effects of 6.81 ± 2.95 kg and −0.05 ± 0.02%. Additionally, a significant dominance effect of 0.46 ± 0.21 kg was detected for milk fat yield. Homozygous TT and heterozygous CT animals exhibited higher milk yield compared with homozygous CC animals, whereas the latter exhibited increased milk protein percentage. Expression analysis from age-, lactation-, and parity-matched female sheep showed that mRNA expression of the ACAA2 gene from TT animals was 2.8- and 11.8-fold higher in liver and mammary gland, respectively. In addition, by developing an allelic expression imbalance assay, it was estimated that the T allele was expressed at an average of 18% more compared with the C allele in the udder of randomly selected ewes. We demonstrated for the first time that the variants in the 3′ untranslated region of the ovine ACAA2 gene are differentially expressed in homozygous ewes of each allele and exhibit allelic expression imbalance within heterozygotes in a tissue-specific manner, supporting the existence of cis-regulatory DNA variation in the ovine ACAA2 gene. This is the first study reporting differential allelic imbalance expression of a candidate gene associated with milk production traits in dairy sheep

A prospective cohort study examining the association of claw anatomy and sole temperature with the development of claw horn disruption lesions in dairy cattle

Foot characteristics have been linked to the development of sole lesions (sole hemorrhage and sole ulcers) and white line lesions, also known as claw horn disruption lesions (CHDL). The objective of this study was to examine the association of claw anatomy and sole temperature, with the development of CHDL. A cohort of 2,352 cows was prospectively enrolled from 4 UK farms and assessed at 3 time points; before calving (T1-Precalving), immediately post-calving (T2-Calving), and in early lactation. At each time point body condition score was recorded, a thermography image of each foot was taken for sole temperature measurement, the presence of CHDL was assessed by veterinary surgeons, and an ultrasound image was taken to retrospectively measure the digital cushion and sole horn thickness. Additionally, at the post-calving time point, foot angle and heel depth were recorded. Four multivariable logistic regression models were fit to separately examine the relationship of pre-calving and post-calving explanatory variables with the development of either white line lesions or sole lesions. Explanatory variables tested included digital cushion thickness, sole horn thickness, sole temperature, foot angle, and heel depth. Farm, parity, body condition score, and the presence of a lesion at the time of measurement were also included in the models. A thicker digital cushion shortly after calving was associated with decreased odds of cows developing sole lesions during early lactation (OR: 0.74, 95% CI: 0.65 – 0.84). No association was found between digital cushion thickness and the development of white line lesions. Sole temperature post-calving was associated with increased odds of the development of sole lesions (OR: 1.03, 95% CI: 1.02 – 1.05), and sole temperature before and post-calving was associated with the development of white line lesions (T1-Precalving; OR: 1.04, 95% CI: 1.01 – 1.07, T2-Calving; OR: 0.96 95% CI: 0.93 – 0.99). Neither foot angle nor heel depth was associated with the development of either lesion type. However, an increased sole horn thickness after calving reduced the odds of cows developing sole lesions during early lactation (OR: 0.88, 95% CI: 0.83 – 0.93), highlighting the importance of maintaining adequate sole horn when foot trimming. Before calving, animals with a lesion at the time of measurement and a thicker sole were more likely to develop a sole lesion (OR: 1.23, 95% CI: 1.09 – 1.40), compared with those without a sole lesion. The results presented here suggest that white line and sole lesions may have differing etiopathogenesis. Results also confirm the association between the thickness of the digital cushion and the development of sole lesions, highlight the association between sole horn thickness and sole lesions, and challenge the potential importance of foot angle and heel depth in the development of CHDL