Mitogenomics of thoroughbred horses

Thoroughbred is a horse breed developed mainly for racing. Because racing performance of horses is mainly dependent upon aerobic energy metabolism, it is hypothesized that elite performance might be associated with unique genotypes in mitochondrial DNA. Although the full sequence of mitochondrial DNA has already been obtained for horses, there is a lack of information about the relationship between the genotype of Thoroughbred mitochondrial DNA and phenotype in racing performance and/or energy metabolism, either within or between species. The aim of this study was to investigate the variations of mitochondrial genomes in Thoroughbred horses and compare these with available non-thoroubred horses mitochondrial gene sequences. We have determined 80 complete mitochondrial genomes of non-related Thoroughbred race horses, with the sizes range from 16,654 to 16,664 base pairs, and an average length of 16,656 base pairs. There were three hundred thirteen (313) polymorphic sites identified and spanning over the functional regions. The haplogroups classified by alleles at several polymorphic sites and the variations in the coding regions of the mitochondrial genome were determined. Five phylogenetic haplogroups were identified by neighbor joining method and could be separated into two monophyletic clades. Results of principal component analysis based on mitochondrial cytochrome b (CYTB) gene sequences also agreed with that these horses could be clustered into two subgroups. Lower number of haplotypes (14 vs. 62) and similar lower number of non-synonymous changes (3 vs. 14) in Thoroughbred compared to the non-Thoroughbred horses upon CYTB gene were also observed. The results suggest that at least two founder events have occurred in the Thoroughbred horse populations, which support the notion of multiple origins of Thoroughbred horses. Future research should examine the potential correlations between these variations in mitogenomics and racing performance.