Using STR Data to Investigate the Impact of the Studbook Cap on Genetic Diversity in the American Standardbred Horse from 1998 to 2021

<b>Background/Objectives:</b> Standardbreds, a breed of horses used in harness racing at either the trot or the pace, established a closed studbook in 1973. Concerns about genetic diversity within the breed led the United States Trotting Association (USTA) to establish a limit of mares bred per stallion (i.e., a studbook cap) in 2009. Here, we aimed to evaluate the impact of the breeding restrictions on genetic diversity between and among subpopulations. <b>Methods</b>: Sixteen short tandem repeats (STRs) were analyzed across a dataset of 176,424 Standardbreds foaled in the United States between 1998 and 2021. We examined allelic richness (<i>Na</i>), number of effective alleles (<i>Ne</i>), expected heterozygosity (<i>H_E</i>), observed heterozygosity (<i>H_O</i>), inbreeding coefficient (<i>F_IS</i>), and fixation index (<i>F_ST</i>) across 24 years, differentiating by gate type, and comparing pre-(1998-2009) and post-(2010-2021) studbook cap periods using regression analysis. <b>Results</b>: Our results support decreased genetic diversity for both trotters and pacers over time. However, pacing Standardbreds exhibited significantly slower rates of decrease in genetic diversity after the 2009 studbook cap, as evidenced by <i>Ne</i>, <i>H_E</i>, and <i>F_IS</i> (<i>P_Bonferroni</i> < 0.01). Additionally, moderate levels of genetic differentiation were found between trotters and pacers (0.05 < <i>F_ST</i> < 0.09), which increased over time. <b>Conclusions</b>: Given that the rate of loss of diversity does not appear to differ pre and post studbook cap in trotters and that there is an increase in genetic differentiation between the groups over time, developing additional breeding tools and strategies is necessary to help the subpopulation mitigate further decline.