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The evaluation of conformation traits is an important part of selection for breeding stallions and mares. Some of these judged conformation traits involve joint angles that are associated with performance, health, and longevity. To improve our understanding of the genetic background of joint angles in horses, we have objectively measured the angles of the poll, elbow, carpal, fetlock (front and hind), hip, stifle, and hock joints based on one photograph of each of the 300 Franches-Montagnes (FM) and 224 Lipizzan (LIP) horses. After quality control, genome-wide association studies (GWASs) for these traits were performed on 495 horses, using 374,070 genome-wide single nucleotide polymorphisms (SNPs) in a mixed-effect model. We identified two significant quantitative trait loci (QTL) for the poll angle on ECA28 ( p = 1.36 × 10 -7 ), 50 kb downstream of the ALX1 gene, involved in cranial morphology, and for the elbow joint on ECA29 ( p = 1.69 × 10 -7 ), 49 kb downstream of the RSU1 gene, and 75 kb upstream of the PTER gene. Both genes are associated with bone mineral density in humans. Furthermore, we identified other suggestive QTL associated with the stifle joint on ECA8 ( p = 3.10 × 10 -7 ); the poll on ECA1 ( p = 6.83 × 10 -7 ); the fetlock joint of the hind limb on ECA27 ( p = 5.42 × 10 -7 ); and the carpal joint angle on ECA3 ( p = 6.24 × 10 -7 ), ECA4 ( p = 6.07 × 10 -7 ), and ECA7 ( p = 8.83 × 10 -7 ). The application of angular measurements in genetic studies may increase our understanding of the underlying genetic effects of important traits in equine breeding.

Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses