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

Abstract

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.

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

“…While ADAMTS16 has been identified among selection signals for high altitude adaptation in pigs 47 , IRX1 is associated with bone mineral density in humans 46 and influences chondrocyte differentiation and may therefore contribute to joint www.nature.com/scientificreports www.nature.com/scientificreports/ flexibility 48 . In horses, genes with functions in bone mineral density have been associated with measurements of joint angles 49 . Since the angle of the pelvis is a major determinant of physical conformation in Thoroughbreds and is associated with injury and performance 50 , we hypothesise that the selection signature on ECA21 reflects the evolution of the Thoroughbred conformation phenotype.…”

Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes

“…In Arabian horses, a deletion of 2.7 Kb near to HOXD3 is related to occipitoatlantoaxial malformation as craniocervical junction abnormality [43]. This phenotype is closely related to poll angle and neck posture [44]. The attachments of the head and neck play pivotal roles in athletic ability, movement, flexion, and balance of horses [45].…”

Genomic inbreeding trends in the global Thoroughbred horse population driven by influential sire lines and selection for exercise trait-related genes

“…While ADAMTS16 has been identified among selection signals for high altitude adaptation in pigs [44], IRX1 is associated with bone mineral density in humans [43] and influences chondrocyte differentiation and may therefore contribute to joint flexibility [72]. In horses, genes with functions in bone mineral density have been associated with measurements of joint angles [42]. Since the angle of the pelvis is a major determinant of physical conformation in Thoroughbreds and is associated with injury and performance [73], we hypothesise that the selection signature on ECA21 reflects the evolution of the Thoroughbred conformation phenotype.…”