The domestication of the horse approximately 5,000 years ago marked the beginning of a long history of selective breeding, primarily for agriculture, transportation, and warfare. Over the last 400 years, the establishment of formal breed registries and continuous specialization has increasingly focused on preserving and enhancing aesthetic and performance traits. This has resulted in most modern horse breeds being genetically closed populations with high uniformity within, yet significant variation among breeds. Advanced whole-genome SNP arrays now offer a powerful tool to leverage this population structure, enabling the identification of genomic regions targeted by selective breeding and the underlying genetic variants responsible for desired phenotypes.
Identifying Genetic Signatures of Selection
This study utilized a population-based approach, analyzing 744 individuals from 33 distinct horse breeds genotyped with the Equine SNP50 Beadchip. By calculating the FST-based statistic, di, in 500-kb windows across the genome, researchers identified regions exhibiting significant divergence between breeds, indicating potential targets of selection. Windows falling within the 99th percentile of the empirical distribution were considered putative signatures of selection.
Muscle Characteristics and Racing Aptitude
A striking signature of selection was observed on Equine Chromosome 18 (ECA18) in both the Paint and Quarter Horse breeds. This region, spanning approximately 5.5 Mb and centered on the myostatin (MSTN) gene, showed the highest di values in these breeds. Further analysis revealed a shared 780.7 kb haplotype composed of 21 SNPs present in nearly all Quarter Horses and Paints, and also in a significant proportion of Thoroughbreds. Sequencing of the MSTN gene identified a promoter variant (SINE insertion) and an intronic SNP (g.66493737C/T) within this haplotype. Histological examination of gluteal muscle biopsies from Quarter Horses demonstrated that the presence of the SINE insertion or the “C” allele of the intron 1 SNP was significantly associated with a higher proportion of Type 2B muscle fibers and a lower proportion of Type 1 fibers. This finding provides functional evidence that selection at the MSTN locus has influenced muscle fiber composition, likely contributing to the sprinting ability favored in racing breeds.
Gait Determination
On ECA23, a distinct signature of selection was identified across all gaited breeds sampled, including the Icelandic, Peruvian Paso, Standardbred, and Tennessee Walking Horse. This region contained a shared 186-kb haplotype including two doublesex and mab-3 related transcription factor genes, DMRT2 and DMRT3. Subsequent research, concurrent with this study, identified a mutation in DMRT3 within this haplotype that appears crucial for the ability to perform alternative gaits. This finding strongly supports the hypothesis that selection has targeted this locus to facilitate the development of specialized gaits in certain horse breeds.
Size Determination
In the context of size, a conserved haplotype on ECA11 was identified in all draft breeds and the Miniature horse, suggesting its involvement in the determination of size. This region, containing the Miniature haplotype and overlapping with the draft breed haplotype, includes genes hypothesized to influence size. Additionally, analysis of candidate genes for size, such as IGF1, NCAPG, and HMGA2, revealed evidence of selection in specific breeds. Notably, a conserved haplotype near NCAPG was found across draft breeds, and a distinct haplotype near HMGA2 was identified in Clydesdale horses, further implicating these regions in the genetic control of size variation.
Conclusion
This genome-wide analysis has successfully identified several genomic regions under significant selective pressure in domestic horse breeds. The findings highlight the importance of MSTN in racing breeds, providing functional evidence for its role in muscle fiber type and performance. Furthermore, strong evidence supports selection on ECA23 for gait determination, with the DMRT3 gene emerging as a key player. The study also provides insights into the genetic basis of size variation, with identified loci on ECA11 and near candidate genes like NCAPG and HMGA2. This research underscores the utility of population-based genomic approaches for uncovering the genetic underpinnings of important equine phenotypes and offers a foundation for future investigations into novel functional mutations and their impact on horse diversity and performance.
