Leveraging joint-specific phenotypes for genome-wide association studies and SNP heritability estimation of equine osteochondrosis and fetlock osteochondral fragments

Abstract

Equine osteochondrosis (OC) and fetlock osteochondral fragments are prevalent developmental joint disorders caused by failure of the growing skeleton, often leading to intra-articular fragments that require arthroscopic surgery and impose substantial economic and animal welfare burdens. To reduce prevalence, phenotype-based selection has been performed but with limited success, prompting interest in genomic approaches. Progress in genetic research has been hindered by difficulties in assembling sufficiently large study populations and by inconsistent phenotype definitions. In addition, false-negative classifications may occur because of the age dependent lesion dynamics and undocumented previous surgical removal of osteochondral fragments that leave little or no radiographic evidence after removal. This study aimed to perform joint-specific case–control genome‐wide association studies (GWAS) and estimate single nucleotide polymorphism (SNP) based heritabilities for OC and fetlock osteochondral fragments in horses. Seven base phenotypes with two to four levels of specificity were defined using a novel semi-quantitative scoring system, and paired with high-density genotypes. After quality control, the final study population comprised 716 horses, including 442 males and 274 females. Warmblood horses accounted for 99.9% of the study population, and 84% were registered with one of three Belgian warmblood studbooks. Mean age at radiographic screening was 36 months. At the least stringent specificity level, the numbers of eligible cases/controls were 307/325 for total OC, 187/478 for hock OC, 165/504 for distal intermediate ridge of the tibia (DIRT) OC, 110/588 for stifle OC, 51/536 for fetlock OC, 76/619 for palmaro-/plantaroproximal osteochondral fragments of the proximal phalanx (POF) and 100/590 for dorsoproximal fragments of the proximal phalanx (DOF). Across 23 GWAS, 214 suggestive SNPs were identified, including 50 that reached genome-wide significance. Based on predefined criteria, eight genomic regions of interest were identified, revealing 11 novel candidate genes: LDB2 for total OC; SCUBE3 , MAPK13 and MAPK14 for hock OC; and FGF6 , FGF23 , IL17A , IL17F , TRAM2 , BMP5 , and PPP2R5C for POF. No candidate genes were detected for DIRT OC. For stifle OC, fetlock OC, and DOF, suggestive SNPs did not define genomic regions of interest. SNP-based heritability estimates ranged from 26.2 to 27.1% for total OC, 53.9–61.0% for hock OC, 49.4–61.2% for DIRT OC, 1.5–14.2% for stifle OC, 0.0-13.7% for fetlock OC, 10.0-54.8% for POF, and 5.7–39.6% for DOF. This study presents results from the first DOF-specific GWAS in horses and identifies novel candidate genes involved in angiogenesis and bone development for total OC, hock OC and POF. The results demonstrate the importance of stringent, joint-specific phenotype definitions, as even minor differences in phenotype definition substantially affected SNP-based heritability estimates and the detection of genomic associations and candidate genes. The high heritability estimates of hock and DIRT OC indicates considerable potential for genetic improvement. The lower heritability estimates obtained for total OC, fetlock OC, and stifle OC may reflect either incomplete capture of the underlying genetic variation by the genotyped SNPs, leading to an underestimation of the genetic contribution to phenotypic variance, or a genuinely greater contribution of non-genetic factors. Future studies should prioritize standardized joint-specific phenotyping, large multi-population datasets, and validation of identified loci, candidate genes, and SNP-based heritability estimates to support breeding strategies that improve osteoarticular health while preserving genetic diversity.