Demographic change and selection patterns in thoroughbred racing horses over the 20th century.

The Thoroughbred horse is a legacy of centuries of selective breeding for speed, emerging from the admixture of British mares and imported Oriental stallions. While previous work explored its genetic diversity, inbreeding, and selection signatures, the breed demographic and selection dynamics during the 20th-century remain poorly understood. Here, we sequenced the genome of Phar Lap, a late-1920s/early-1930s racing champion, and analyzed the largest time-series of Thoroughbred whole-genome sequences, within a global panel of 850 horse genomes. Demographic modeling reveals a marked decline in genetic diversity since 1932, driven by a reduced effective population size, particularly until 1960. This aligns with a modest yet significant increase in long runs-of-homozygosity (ROH), suggesting that breeding practices only partially mitigated ROH accumulation and inbreeding depression. Temporal shifts in genetic variation identify candidate loci linked to racing performance, offering insights into past and ongoing selection, and new loci of major potential for the global racing industry.