Degenerative suspensory ligament (SL) desmitis (DSLD) is a progressive idiopathic condition that leads to scarring and rupture of SL fibers in multiple limbs in horses. Prevalence of DSLD is breed-related. Risk is high in the Peruvian Horse (PH), whereas pony and draft breeds have low breed risk. DSLD occurs in families of PHs, but its genetic architecture has not been definitively determined. We investigated contrasts between breeds with differing risk of DSLD and identified associated risk variants and candidate genes. We analyzed 670K single nucleotide polymorphisms (SNPs) from ten breeds, each of which was assigned one of four breed DSLD risk categories: Control (Belgian, Icelandic Horse, Shetland Pony, and Welsh Pony), Low Risk (Lusitano, Arabian), Medium Risk (Standardbred, Thoroughbred, Quarter Horse), and High Risk (Peruvian Horse). SNPs were used for genome-wide association and selection signature analysis using breed assigned risk levels. We found that the PH is a population with low effective population size and our breed contrasts suggest that DSLD is a polygenic disease. Variant frequency exhibited signatures of positive selection across DSLD breed risk groups on chromosomes 7, 18, and 23. Our results suggest DSLD breed risk is associated with disturbances to SL homeostasis where matrix responses to mechanical loading are perturbed through disturbances to aging in tendon (PIN1), mechanotransduction (KANK1, KANK2, JUNB, SEMA7A), collagen synthesis (COL4A1, COL5A2, COL5A3, COL6A5), matrix responses to hypoxia (PRDX2), lipid metabolism (LDLR, VLDLR), and BMP signaling (GREM2). Our results do not suggest that SL proteoglycan turnover is a primary factor in disease pathogenesis.