Genetic Diversity and Divergence Among Six Performance Groups of the American Quarter Horse

The American Quarter Horse (QH) is the most popular breed of horse in the US, and with over five million individuals, represents the largest registry in the world.  Originally bred to excel at sprinting ¼ mile and for ranch work, the QH is also a popular show horse in classes such as western pleasure, which evaluates the horses’ movement at a leisurely pace, and in halter, where horses are judged based upon their conformation, balance, and muscling.  This study utilized genome-wide SNP data from 20-24 top performers in each of six performance groups of QH (halter, western pleasure, racing, reining, cutting, and working cow), to examine genetic diversity within the breed.  In addition, analyses were conducted considering breeds that continue to admix with the QH (Paint, Appaloosa, and Thoroughbred).  With the exception of the working cow and cutting horses, pairwise F_ST values show significant population structure among the six performance groups with the highest divergence observed between the cutting and racing QH.  Racing QHs were more divergent from each of the other performance groups than they were from the Thoroughbred, Paint, and Appaloosa.  Principal component and cluster analyses suggest a close relationship among cutting, working cow, and reining horses, likely due to similarity among the skills required for those competitions.  With the QH breed registry established in 1940, these results suggest that strong selective pressure for performance type has resulted in significant population structure within the breed.  These data will be useful for future monitoring of breed diversity and management.