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/

Pharmacological inhibition of acetylcholinesterase improves the locomotion defective phenotype of a SCA3 C. elegans model.

Inhibition of acetylcholinesterase (AChE) is a common used treatment option for Alzheimer’s disease. However, there has been limited research on the potential use of AChE inhibitors for the treatment of Machado-Joseph disease (MJD)/Spinocerebellar Ataxia 3 (SCA3), in spite of the positive results using AChE inhibitors in patients with other inherited ataxias. MJD/SCA3, the most common form of dominant Spinocerebellar Ataxia worldwide, is caused by an expansion of the polyglutamine tract within the ataxin-3 protein, and is characterized by motor impairments. Our study shows that administration of the AChE inhibitor neostigmine is beneficial in treating the locomotion defective phenotype of a SCA3/MJD model of C. elegans and highlights the potential contribution of AChE enzymes to mutant ataxin-3-mediated toxicity

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

Does inbreeding contribute to pregnancy loss in Thoroughbred horses?

Background: Excessive inbreeding increases the probability of uncovering homozygous recessive genotypes and has been associated with an increased risk of retained placenta and lower semen quality. No genomic analysis has investigated the association between inbreeding levels and pregnancy loss. Objectives: This study compared genetic inbreeding coefficients (F) of naturally occurring Thoroughbred Early Pregnancy Loss (EPLs), Mid and Late term Pregnancy Loss (MLPL), and Controls. The F value was hypothesised to be higher in cases of pregnancy loss (EPLs and MLPLs) than Controls. Study design: Observational case-control study. Methods: Allantochorion and fetal DNA from EPL (n=37, gestation age 14-65 days), MLPL (n=94, gestational age 70 days–24 hours post parturition) and Controls (n=58) were genotyped on the Axiom Equine 670K SNP Genotyping Array. Inbreeding coefficients using Runs Of Homozygosity (FROH) were calculated using PLINK software. ROHs were split into size categories to investigate the recency of inbreeding. Results: MLPLs had significantly higher median number of ROH (188 interquartile range (IQR), 180.8-197.3), length of ROH (3.10, IQR 2.93-3.33), and total number of ROH (590.8, IQR 537.3-632.3), and FROH (0.26, IQR 0.24-0.28) when compared with the Controls and the EPLs (p&lt;0.05). There was no significant difference in any of the inbreeding indices between the EPLs and Controls. The MLPLs had a significantly higher proportion of long (&gt;10 Mb) ROH (2.5%, IQR 1.6-3.6) than the Controls (1.7%, IQR 0.6-2.5), p=0.001. No unique ROHs were found in the EPL or MLPL populations. Limitations: SNP-array data does not allow analysis of every base in the sequence. Conclusions: This first study of the effect of genomic inbreeding levels on pregnancy loss showed that inbreeding is a contributor to MLPL, but not EPL in the UK Thoroughbred population. Mating choices remain critical, because inbreeding may predispose to MLPL by increasing the risk of homozygosity for specific lethal allele(s)

Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach

Abstract Background The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds. Results The k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (FST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (Neb) to effective population size (Ne). Conclusions Distinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of Neb to Ne was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB