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

Harness racing performance in horses is a complex polygenic trait influenced by genetic background, breeding history, training, and environment. Understanding genomic patterns shaped by long-term artificial selection provides insights into performance-related traits and breed-specific genomic variation. This study aimed to characterize genomic differentiation, population structure, and candidate genomic regions potentially influenced by historical selection in Standardbred horses using comparative whole-genome sequencing involving diverse horse breeds. Whole-genome sequencing data from 86 horses representing 16 breeds were retrieved from public repositories and processed using a standardized bioinformatics pipeline. Population structure was investigated using principal component analysis (PCA), ADMIXTURE, Neighbor-Joining phylogeny, and ChromoPainter-based haplotype sharing. Genomic diversity was evaluated using runs of homozygosity (ROH) and nucleotide diversity (π), whereas genetic differentiation was assessed using fixation index (FST) analyses with functional annotation. After quality control, 18,384,176 autosomal SNPs were retained. Standardbred horses consistently formed a distinct genomic group, with principal components 1 and 2 explaining 5.00% and 3.66% of genomic variation, respectively. ADMIXTURE supported K = 2 as the best-supported clustering solution (cross-validation error = 0.523). ROH analyses revealed variation in genome-wide homozygosity among breeds, while FST and nucleotide diversity analyses identified differentiated genomic regions containing candidate genes associated with growth, skeletal development, muscle function, signaling, metabolism, and nervous system function, including LCORL, NCAPG, PDE1A, CDH13, and HTR1A. This comparative whole-genome analysis identified candidate genomic regions potentially shaped by historical selection in Standardbred horses and contributes to understanding genomic differentiation associated with breed history and functional specialization.