The robustness and resilience of our livestock describes the ability to react to changes in the environment in such a way that well-being, health and performance are maintained. The processes of genotype-phenotype mapping, i.e. the pathways of information on the DNA for the expression of appearance in a specific environment, allow the molecular basis of robustness and resilience and the interactions of performance traits with animal welfare and health to be clarified. Our studies within the FUGATOplus project GeneDialog and the AgroCluster PHAENOMICS on pigs differing in muscle approach, stress and immune response and coping behavior have shown that stimuli such as vaccination and psychosocial stress are associated with the regulation of many signaling and metabolic pathways at the molecular level, which partly explains the observed trait correlations. Our studies also indicate that animals with active behavioral patterns, compared to passive animals, activate molecular pathways that promote effective defense and regeneration more strongly.