Digital and genetic tools to improve bones of laying hens

Bone damage is widespread in laying hens. This thesis explores the potential use of X-ray imaging and genetic tools to improve bone health. In a cohort of purebred hens, we investigated the genomics of bone composition and strength. An inverse relationship was found between bone lipids and strength, identifying genetic markers linked to lipid levels that could guide practical interventions to enhance bone strength. Since purebreds are typically selected to improve crossbred performance, we studied the bones of crossbreds and the potential use of crossbred data to inform purebred selection for various crossbred environments. The genetics, including SNP effects, of bones from crossbred hens in cage and cage-free housing were predicted with an accuracy of 0.42–0.65, potentially aiding purebred selection. In another experiment, crossbred hens were repeatedly X-rayed on-farm, and both keel and tibia bones were measured on the X-ray images. X-ray measurements of keel and tibia density, as well as keel geometry, were tested for associations with post-mortem findings of keel damage and pelvic capacity. Larger pelvic capacity was associated with increased keel damage. A higher ratio of keel length to mid-depth at 42, 55, and 68 weeks of age was associated with greater deviations observed in dissected keels. A higher tibia radiographic density at 55 weeks of age was associated with fewer deviations and fractures. Automating X-ray analysis is crucial for efficiently phenotyping thousands of birds. Using deep learning and computer vision, we developed algorithms to segment the keel bone from whole-body X-ray images (with 0.88–0.90 accuracy) and compute keel geometry and density metrics. These metrics showed weak to moderate heritability and moderate to strong genetic correlations with keel deviations and fractures, enabling quick phenotyping once birds are Xrayed. Breeding companies can use the new methods to select for reduced keel damage and optimize housing and nutrition strategies for better keel health.