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

Abstract

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.

Use of Omics Data in Fracture Prediction; a Scoping and Systematic Review in Horses and Humans

“…Overall, 10 studies were assessed using the JBI critical appraisal tool for quasi-experimental studies ( Supplementary Table S13 ). Five studies [ 50 , 51 , 52 , 53 ] met all 10 criteria, six studies [ 54 , 55 , 56 , 57 , 58 , 59 ] met 8/9 criteria, with the exception of criterion 4 (control). For primary outcome 1c, there were six case-control studies [ 60 , 61 , 62 , 63 , 64 , 65 ] that met 9 out of 10 criteria.…”

“…A review of miRNAs and their targets in response to exercise and mechanical loading in horses and humans identified 11 publications including 5 horse miRNA profiling studies [ 50 , 53 , 55 , 56 , 57 ], 1 human miRNA profiling study [ 49 ], 2 human miRNA candidate studies [ 52 , 54 ], 2 horse mRNA profiling studies [ 51 , 59 ] and 1 horse mRNA candidate study [ 58 ] ( Supplementary Table S14 ). Overall 10 of the 11 studies were quasi-experimental studies, e.g., before and after the intervention (exercise), where miRNAs were measured at two points in time.…”

Selection of a reference gene for studies on lipid‐related aquatic adaptations of toothed whales (Grampus griseus)

“…The convergent and divergent evolution of mammalian genes has been discussed in a comparison of pigs and humans (Wei et al, 2018). Thus, RT-qPCR based gene expression analysis is valuable for future research on the evolution of genes in quantitative or complex traits in organisms (e.g., genetic variance and heritability; Farries et al, 2019). Consequently, reference genes are also crucial for toothed whales' quantitative and population genetics.…”

“…Assessing quantitative genetic parameters of wild marine vertebrates has also attracted immense interest (DiBattista et al, 2009). RT‐qPCR and transcriptomics are reliable approaches for the genetic analysis of quantitative or complex traits in organisms (e.g., genetic variance and heritability; Farries et al, 2019). Consequently, reference genes are also crucial for toothed whales’ quantitative and population genetics.…”

Survey of Risk Factors and Genetic Characterization of Ewe Neck in a World Population of Pura Raza Español Horses

“…Some studies estimate the heritability of musculoskeletal defects or diseases as osteochondrosis dissecans in Maremmano horses [ 22 ], Hanoverian warmblood horses [ 23 ], and Swiss Warmblood horses [ 24 ]; suspensory ligament injury and tendon injury in Thoroughbred racehorses [ 17 ]; osteoarthrosis in distal and proximal interphalangeal joints, fetlock, hock, and stifle joints in Hanoverian warmblood [ 25 ]; tarsocrural osteochondrosis and palmar first phalanx osteochondral fragments in Standardbred trotters [ 26 ]; the deformity of the dorsal edge of the neck (Cresty Neck) in PRE horses [ 27 ]; and Club Foot in Arabian Pureblood horses [ 28 ]. Further characterization of the equine genome and identification of mutations in genes associated with muscular disorders, has led to important advances in the field of inherited skeletal muscle disease research [ 29 ].…”