Genetic and genomic insights into morphological knee defects in Pura Raza Española horses

Conformation is a key selection criterion in horse breeding, influencing performance, health and appearance. Knee defects are a common morphological limb defect in horses, and their poorly understood genetics pose a major challenge to breeders. This study aimed to estimate genetic parameters and identify genomic regions associated with knee defects in Pura Raza Español (PRE) horses. Two evaluation approaches were used: continuous variables scored from −4 to 4 for side and front view knee angles (SVKA and FVKA); and multinomial variables on a 5–class scale assessing: buck and calf knee; bench and knock knee. 0 indicated no defect. Genetic analysis and genome-wide association study (GWAS) were performed using weighted single-step genomic BLUP methodology, assessing the knee angle of a total of 58,922 horses, with genotypes available for 4,057 individuals using the Axiom EQUIGENE array. The most prevalent severe defect for the population was knock knee (5.22%), while buck knee and bench knee were the least common (0.12%). Heritability estimates for continuous traits ranged from 0.19 (SVKA) to 0.20 (FVKA), and from 0.13 (bench knee) to 0.38 (knock knee) for independently evaluated traits. GWAS identified 17 genomic regions across seven chromosomes associated with knee defects. Additionally, candidate genes related to musculoskeletal diseases, bone malformations, joint disorders, and cartilage defects were identified. These findings enhance understanding of the genetic basis of knee defects and represent a first step towards genomic selection strategies in PRE horses. Further research is needed to deepen knowledge of conformation-related issues in equine breeding. Analysis of the PRE horse genome has allowed us to locate regions associated with conformation and knee defects. The estimated heritability values indicated a moderate to high genetic influence on the morphological defect of the knee. Seventeen genomic regions were associated with knee conformational defects in horses. Genes related to chondrocytes, synovial joints, bone and cartilage formation, and joint disorders have been found within these regions. This research supports the development of genomic selection strategies to reduce knee defects in PRE horses.