Genetic diversity and genomic inbreeding trends in the Japanese Thoroughbred population

Thoroughbreds are maintained under a closed studbook and have undergone intense selection for racing performance, potentially reducing genetic diversity and increasing inbreeding. As inbreeding can adversely affect fitness, monitoring inbreeding levels and conserving genetic diversity are essential. In this study, we assessed the temporal changes in genomic diversity and genomic inbreeding in Japanese Thoroughbreds using high-density single nucleotide polymorphism (SNP) genotyping. We genotyped 96 foals born in each of the years 2000, 2018, and 2022 using a 670 K Axiom Equine Genotyping Array, excluding two samples due to insufficient genotypic information. After quality control, we retained 363,301 autosomal SNPs for downstream analysis. Per-locus expected heterozygosity (mean ± standard deviation [SD]) revealed only a slight decline across the cohorts: 0.309 ± 0.156, 0.305 ± 0.158, and 0.304 ± 0.159 for 2000, 2018, and 2022, respectively, with a statistically significant but negligible effect size (η²=0.00019). Runs of homozygosity (ROH) covered approximately 27.5%, 28.5%, and 29.0% of the autosomal genome in the three cohorts. Genomic inbreeding, estimated from the mean ROH-based inbreeding, increased from 0.276 ± 0.021 in 2000 to 0.286 ± 0.023 and 0.290 ± 0.024 in 2018 and 2022, respectively. The per-generation increase (assuming an 11-year generation interval) was higher in 2018-2022 (1.10 percentage points/generation) than in 2000-2018 (0.611 percentage points/generation), driven mainly by increased long ROH (≥5 Mb) length. Our results indicate a modest reduction in genome-wide diversity and recently accelerated genomic inbreeding in the Japanese Thoroughbred population, supporting the need for continued SNP genotyping-based monitoring.