Comparative genomics of Standardbred horses reveals candidate regions under selection for harness racing performance.

Overview

• This study used whole-genome sequencing to compare the genomes of Standardbred horses to other breeds in order to identify specific genetic regions that have been influenced by selective breeding for harness racing performance.

Background and Objective

• Harness racing performance in horses is influenced by many factors including genetics, training, environment, and breeding history.
• The trait is polygenic, meaning many genes contribute to it rather than a single gene.
• Understanding how long-term artificial selection shapes horse genomes can help identify the genetic basis of performance traits and breed-specific differences.
• The main goal of this study was to characterize genetic differences, population structure, and candidate genomic regions that show signs of historical selection in Standardbred horses compared to a range of other horse breeds.

Methods

• Whole-genome sequencing data of 86 horses representing 16 different breeds were obtained from public data repositories.
• A standardized bioinformatics pipeline was applied to process the sequencing data and ensure quality control.
• Multiple population genetics analyses were performed, including:
  • Principal Component Analysis (PCA) to visualize patterns of genomic variation and clustering among breeds.
  • ADMIXTURE analysis to identify the best number of genetic clusters that explain data structure, revealing shared ancestry and admixture.
  • Neighbor-Joining phylogenetic trees to illustrate genetic relationships among the breeds.
  • ChromoPainter-based haplotype sharing analysis to analyze fine-scale genetic relationships based on shared DNA segments.
• Genomic diversity within breeds was evaluated using:
  • Runs of Homozygosity (ROH), which identify long stretches of identical DNA that indicate inbreeding or selection.
  • Nucleotide diversity (π), a measure of overall genetic variation within a breed population.
• Genetic differentiation between breeds was assessed with the fixation index (F_ST), focusing on identifying genomic regions highly differentiated in Standardbreds.
• Functional annotation of differentiated regions was performed to identify candidate genes potentially related to racing performance.

Results

• After processing, over 18 million high-quality autosomal single nucleotide polymorphisms (SNPs) were retained for analyses.
• Standardbred horses consistently grouped as a genetically distinct cluster across multiple analyses:
  • PCA showed that the first two principal components explained a moderate amount of variation (5.00% and 3.66%), clearly separating Standardbreds from other breeds.
  • ADMIXTURE analysis supported two main genetic clusters (K=2) with the lowest cross-validation error, confirming a distinct genetic makeup for Standardbreds.
• ROH analyses revealed breed-specific differences in genome-wide homozygosity, indicating varying degrees of inbreeding or selection pressures.
• Areas of the genome with high differentiation (F_ST) and differences in nucleotide diversity between Standardbreds and other breeds contained genes linked to traits relevant for harness racing, including:
  • Growth and skeletal development (e.g., LCORL, NCAPG)
  • Muscle function and signaling pathways (e.g., PDE1A, CDH13)
  • Nervous system function, which could affect behavior or coordination (e.g., HTR1A)

Conclusions and Implications

• This study successfully identified candidate genomic regions under historical selection in Standardbred horses connected to harness racing performance.
• The findings provide a better understanding of how selective breeding has shaped the Standardbred genome relative to other horse breeds.
• Candidate genes identified may be involved in physiological and neurological traits important for racing ability.
• These insights have potential applications in horse breeding programs aiming to improve or maintain performance traits through genetic selection.
• Overall, the study contributes to the broader knowledge of breed-specific genetic differentiation and functional specialization in horses.