Historical Thoroughbred Genome
The Thoroughbred horse stands as a living legacy to centuries of closed selective breeding for speed. This breed emerged with the official opening of the studbook in 1791, through the crossing of native British mares and a handful of imported Oriental stallions. Primarily bred for excellence in short distance sprinting, the breed engendered extraordinary champions, known around the world for their outstanding athletic performance. While previous genome-scale studies have explored global genetic diversity, inbreeding, and selection signatures, the demographic trajectory and the selection dynamics of the breed over the 20th century remain largely unknown. In this study, we sequenced the genome of an elite Thoroughbred horse, Phar Lap, from the early 1930s and integrated the largest time-series of whole-genome sequences for Thoroughbreds to date, analyzing these with a global comparative panel of 850 horse genomes. Demographic modelling indicates a marked decline in genetic diversity since 1932, resulting from a dramatic reduction of population effective size, particularly until 1960. This demographic pattern aligns with the genome fraction covered by long Runs-Of-Homozygosity (ROH>5Mb) showing a modest but statistically significant increase over time. The overall magnitude of this increase remains limited, suggesting that breeding practices have effectively limited the accumulation of long ROH, thereby mitigating the risk of inbreeding depression. By examining temporal patterns of genetic variation, we identify candidate loci associated with racing performance and athletic traits, highlighting past and ongoing selection targets. Our work not only illuminates the genetic history of Thoroughbreds but also uncover loci of potential major importance for the global racing industry.
The Thoroughbred horse stands as a living legacy to centuries of closed selective breeding for speed. This breed emerged with the official opening of the studbook in 1791, through the crossing of native British mares and a handful of imported Oriental stallions. Primarily bred for excellence in short distance sprinting, the breed engendered extraordinary champions, known around the world for their outstanding athletic performance. While previous genome-scale studies have explored global genetic diversity, inbreeding, and selection signatures, the demographic trajectory and the selection dynamics of the breed over the 20th century remain largely unknown. In this study, we sequenced the genome of an elite Thoroughbred horse, Phar Lap, from the early 1930s and integrated the largest time-series of whole-genome sequences for Thoroughbreds to date, analyzing these with a global comparative panel of 850 horse genomes. Demographic modelling indicates a marked decline in genetic diversity since 1932, resulting from a dramatic reduction of population effective size, particularly until 1960. This demographic pattern aligns with the genome fraction covered by long Runs-Of-Homozygosity (ROH>5Mb) showing a modest but statistically significant increase over time. The overall magnitude of this increase remains limited, suggesting that breeding practices have effectively limited the accumulation of long ROH, thereby mitigating the risk of inbreeding depression. By examining temporal patterns of genetic variation, we identify candidate loci associated with racing performance and athletic traits, highlighting past and ongoing selection targets. Our work not only illuminates the genetic history of Thoroughbreds but also uncover loci of potential major importance for the global racing industry.
CNRS UMR 5288