Polymorphisms in selected genes and analysis of their relationship with osteochondrosis in Polish sport horse breeds

SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses

Before the genomics era, heritability estimates were performed using pedigree data. Data collection for pedigree analysis is time consuming and holds the risk of incorrect or incomplete data. With the availability of SNP-based arrays, heritability can now be estimated based on genotyping data. We used SNP array and 1.6 million imputed genotype data with different minor allele frequency restrictions to estimate heritabilities for osteochondrosis dissecans in the fetlock, hock and stifle joints of 446 Hanoverian warmblood horses. SNP-based heritabilities were estimated using a genomic restricted maximum likelihood (GREML) method and accounting for patterns of regional linkage disequilibrium in the equine genome. In addition, we employed GREML for family data to account for different degrees of relatedness in the study population. Our results indicate that we were able to capture a larger proportion of additive genetic variance compared to pedigree-based estimates in the same population of Hanoverian horses. Heritability estimates on the linear scale for fetlock-, hock- and stifle-osteochondrosis dissecans were 0.41-0.43, 0.62-0.63, and 0.23-0.25, respectively, with standard errors of 0.11-0.14. Accounting for linkage disequilibrium patterns had an upward effect on the imputed data and a downward impact on the SNP array genotype data. GREML for family data resulted in higher heritability estimates for fetlock-osteochondrosis dissecans and slightly higher estimates for hock-osteochondrosis dissecans, but had no effect on stifle-osteochondrosis dissecans. The largest and most consistent heritability estimates were obtained when we employed GREML for family data with genomic relationship matrices weighted through patterns of regional linkage disequilibrium. Estimation of SNP-based heritability should be recommended for traits that can only be phenotyped in smaller samples or are cost-effective.

Genetics of Equine Orthopedic Disease

Orthopedic diseases are a common cause for limited exercise capacity in the horse. They often underlie genetic risk factors, which can affect bone, articular cartilage, tendons, ligaments, and adnexal structures among others. The genetic effects can directly interfere with tissue development and skeletal growth or can trigger degenerative or inflammatory processes. Many of these diseases of the locomotor system like osteochondrosis are complex and can be affected by multifactorial influences. For this reason, it is important for those performing diagnostic procedures to have a comprehensive knowledge of orthopedic diseases, their prevalence within breeds, and genetic background.