Expression of CoQ biosynthesis genes in <i>MSTN</i> genotype (CC/II, CT/IN, TT/NN) horses.

<p><i>COQ4</i> (A) and <i>ADCK3</i> (B) gene expression was determined for CC/II: n = 36, CT/IN: n = 34 and TT/NN: n = 11, performed in at least duplicate. Gene expression was normalised to <i>HPRT</i> using the ΔΔCt method. Results presented with mean ± SEM, p-values where shown indicate significance as measured by a one-way ANOVA with a Bonferroni multiple comparison post-test, * = p ≤ 0.05, ** = p ≤ 0.01, *** = p ≤ 0.001.</p

Skeletal muscle mitochondrial bioenergetics and associations with <i>myostatin</i> genotypes in the Thoroughbred horse

<div><p>Variation in the <i>myostatin</i> (<i>MSTN</i>) gene has been reported to be associated with race distance, body composition and skeletal muscle fibre composition in the horse. The aim of the present study was to test the hypothesis that <i>MSTN</i> variation influences mitochondrial phenotypes in equine skeletal muscle. Mitochondrial abundance and skeletal muscle fibre types were measured in whole muscle biopsies from the <i>gluteus medius</i> of n = 82 untrained (21 ± 3 months) Thoroughbred horses. Skeletal muscle fibre type proportions were significantly (p < 0.01) different among the three <i>MSTN</i> genotypes and mitochondrial content was significantly (p < 0.01) lower in the combined presence of the C-allele of SNP g.66493737C>T (C) and the SINE insertion 227 bp polymorphism (I). Evaluation of mitochondrial complex activities indicated higher combined mitochondrial complex I+III and II+III activities in the presence of the C-allele / I allele (p ≤ 0.05). The restoration of complex I+III and complex II+III activities following addition of exogenous coenzyme Q₁ (ubiquinone₁) (CoQ₁) <i>in vitro</i> in the TT/NN (homozygous T allele/homozygous no insertion) cohort indicated decreased coenzyme Q in these animals. In addition, decreased gene expression in two coenzyme Q (CoQ) biosynthesis pathway genes (<i>COQ4</i>, p ≤ 0.05; <i>ADCK3</i>, p ≤ 0.01) in the TT/NN horses was observed. This study has identified several mitochondrial phenotypes associated with <i>MSTN</i> genotype in untrained Thoroughbred horses and in addition, our findings suggest that nutritional supplementation with CoQ may aid to restore coenzyme Q activity in TT/NN horses.</p></div

Individual electron transport chain complex enzyme activities among <i>MSTN</i> genotype (CC/II, CT/IN, TT/NN) horses.

<p>NADH-ubiquinone oxidoreductase (Complex I), Succinate dehydrogenase (Complex II), Decylubiquinol cytochrome c oxidoreductase (Complex III) and Cytochrome c oxidase (Complex IV) (A-D, respectively) activities were measured spectrophotometrically in whole skeletal muscle homogenates (CC/II: n = 20, CT/IN: n = 15 and TT/NN: n = 8), performed in at least duplicate. Results presented with mean ± SEM, p-values where shown indicate significance as measured by a one-way ANOVA with a Bonferroni multiple comparison post-test.</p

Skeletal muscle fibre type proportions among <i>MSTN</i> genotype (CC/II, CT/IN, TT/NN) horses.

<p>qPCR was used to measure gene expression levels of three genes: <i>MYH7</i> (A), <i>MYH2</i> (B) and <i>MYH1</i> (C) inferring MHC isoforms and interpreted as Type I, Type IIA and Type IIX fibres, respectively among CC/II: n = 36, CT/IN: n = 34 and TT/NN: n = 11, performed in at least duplicate. Gene expression was normalised to <i>HPRT</i> using the ΔΔCt method and expressed as a percentage of total MHC gene expression. Results presented with mean ± SEM, p-values where shown indicate significance as measured by a one-way ANOVA with a Bonferroni multiple comparison post-test, * = p ≤ 0.05, ** = p ≤ 0.01, *** = p ≤ 0.001.</p

Skeletal muscle mitochondrial content of <i>MSTN</i> genotype (CC/II, CT/IN, TT/NN) horses.

<p>Mitochondrial abundance determined by the activity of citrate synthase (CS) measured spectrophotometrically, expressed (A) as nmol/min/mg of muscle protein and (B) as nmol/min/g of skeletal muscle (wet weight), CC/II: n = 37, CT/IN: n = 32 and TT/NN: n = 11, performed in at least duplicate; and (C) mtDNA:nDNA ratio measured by qPCR, CC/II: n = 19, CT/IN: n = 17 and TT/NN: n = 8, performed in at least triplicate. Results presented with mean ± SEM, p-values where shown indicate significance as measured by a one-way ANOVA with a Bonferroni multiple comparison post-test, * = p ≤ 0.05, ** = p ≤ 0.01, *** = p ≤ 0.001.</p

Phylogenetic tree of domestic horse breeds and Przewalski's Horse.

<p>Parsimony analysis across 46,244 autosomal loci in the Domestic and Przewalski's Horse. The tree is rooted with the domestic ass.</p

Phylogenetic tree of extant Hippomorpha.

<p>Unrooted cladogram constructed via parsimony analysis, considering only the Hippomorpha, using 40,697 autosomal markers. Bootstrap support >50% calculated from 1000 replicates is shown.</p

Multidimensional scaling with 14 domestic horse breeds.

<p>Metric multidimensional scaling analysis of pair-wise genetic distance was used as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002451#s4" target="_blank">Materials and Methods</a> to identify relationships between the 14 domestic horse breeds.</p

Distribution of pair-wise genetic distances.

<p>a), within and between domestic horse breeds; b), between domestic horse breeds and between domestic horse breeds and Przewalski's Horse. Genetic distance (D) between pair-wise combinations of individuals was calculated as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002451#s4" target="_blank">Materials and Methods</a>.</p

Allele association analysis for three known equine coat color loci.

<p>a), mapping of the chestnut locus across breeds, based on inferred coat color phenotype; b), mapping of the black (agouti) locus across breeds, based on inferred black coat color; c), mapping of the gray locus across breeds. Phenotypes were inferred from the genotypes at 9 known coat color loci and known inheritance models as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002451#s4" target="_blank">Materials and Methods</a>. Unstructured case control association analyses using chi-square tests for allelic association were then performed on a pruned SNP set also as described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002451#s4" target="_blank">Materials and Methods</a>. SNPs on each chromosome are labeled with a different color on the X axis as indicated.</p