Genome Wide Association Study of Hoof Health Traits in Canadian Holsteins

Hoof lesions in dairy herds represent a welfare problem for cows, and pose a financial loss for farmers, due to the costs associated with treating lesions, as well as to decreased cow performance. The objective of this study was to identify chromosome regions associated with hoof lesions in Canadian Holsteins. Hoof lesions were recorded by hoof trimmers serving herds located in Alberta, British Columbia, Ontario and Quebec, between 2009 and 2012. The final data set consisted of 104,446 hoof-trimming records from 70,394 cows in 365 herds. Digital dermatitis, interdigital hyperplasia, and sole ulcer were analyzed as binary traits, as the presence or the absence of the lesions, using a linear animal model, and their heritabilities (SE) were 0.053 (0.005), 0.025 (0.004) and 0.031 (0.004), respectively. Only estimated breeding values of sires with genotypes were considered (n = 5,064) for further analyses. Sires were genotyped with either low density or 50k SNP panels and their genotypes were imputed to HD (777k) using FImpute software. A genome wide association study was carried out using a single SNP regression method, which included a polygenic effect. Significant peaks were detected on chromosomes 1, 5, 8, 14 and 26 for digital dermatitis, and on chromosomes 4, 7, 10, 18, and 26 for sole ulcer, suggesting the presence of candidate genes in these regions. For interdigital hyperplasia significant peaks were detected only on chromosomes 5 and 22.