Simple SummaryThe heritability of a trait is the proportion of phenotypic variance explained via genetic variance. Prior to the advent of genomics, heritability was estimated using extensive pedigree analyses. With the availability of genome-wide genotyping arrays, an alternative method became available to estimate heritability using genomic relationship matrices derived from genotype data. We used approaches that consider patterns of linkage disequilibrium and relatedness to estimate heritability of osteochondrosis dissecans in Hanoverian Warmblood horses based on genotype data from SNP arrays and imputed genotype data. Taking into account linkage disequilibrium patterns and relatedness in the data, heritability estimates on the linear scale for fetlock-, hock- and stifle-OCD were 0.41–0.43, 0.62–0.63, and 0.23–0.25, respectively, with standard errors of 0.11–0.14. In summary, SNP-based approaches are able to capture a greater proportion of additive genetic variance than previous estimates based on pedigree data.AbstractBefore 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.