Analysis of Genetic Diversity in the American Standardbred Horse Utilizing Short Tandem Repeats and Single Nucleotide Polymorphisms

American Standardbreds were developed as a harness racing horse breed. The United States Trotting Association closed the studbook in 1973 and implemented a book size cap in 2009. This study aimed to investigate genetic diversity in the American Standardbred after the studbook cap was introduced using short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs). Sixteen STRs from horses foaled from 2010 to 2015 and their sires and dams (n = 50 621) were utilized to examine allelic richness (A(r)), expected heterozygosity (H(E)), observed heterozygosity (H(O)), unbiased heterozygosity (H(U)), inbreeding coefficient (F(IS)), and fixation index (F(ST)). These analyses found that trotting and pacing sires were less genetically diverse than dams (H(E)P(Bonferroni) = 0.029 and 6.3 × 10(−5), respectively) and their offspring (A(r)P(Bonferroni) = 0.034 and 6.9 × 10(-6), respectively), and pacing offspring were significantly less diverse than their dams (H(E)P(Bonferroni) = 2 × 10(-3)). Inbreeding coefficients for trotters (F(IS) = −0.014) and pacers (F(IS) = −0.012) suggest that breeding practices have maintained diversity. Moderate levels of genetic differentiation (0.066 < F(ST) < 0.11) were found between pacing and trotting groups. Additionally, 10 of the most prolific trotting sires and their male offspring (n = 84) were genotyped on the 670K Axiom Equine HD Array. H(O) values higher than H(E) (P < 0.001), low inbreeding coefficients (mean F = −0.064), and mean F(ROH) = 21% indicate relatively high levels of diversity in this cohort, further supporting the STR data. However, in contrast, H(O) values were higher for trotting sires (0.41) than their offspring (0.36). This observation warrants further monitoring of diversity over time. These data provide an updated foundation of diversity indices for further, long-term analysis in the breed.