Magnetic skyrmions are prime candidates as information carriers for spintronic devices due to their topological nature and nanometric size. However, unavoidable inhomogeneities inherent to any material leads to pinning or repulsion of skyrmions that, in analogy to biology concepts, define the phenotype of the skyrmion-defect interaction, generating complexity in their motion and challenging their application as future bits of information. Here, we demonstrate that atomby-atom manufacturing of multi-atomic defects, being antiferromagnetic or ferromagnetic, permits the breeding of their energy profiles, for which we build schematically a Punnet-square. As established from first-principles for skyrmions generated in PdFe bilayer on Ir(111) surface, the resulting interaction phenotype is rich. it can be opposite to the original one and eventually be of dual pinning-repulsive nature yielding energy landscapes hosting multi-domains. this is dictated by the stacking site, geometry, size and chemical nature of the adsorbed defects, which control the involved magnetic interactions. this work provides new insights towards the development of disruptive device architectures incorporating defects into their design aiming to control and guide skyrmions. Magnetic skyrmions 1,2 , i.e. non-collinear spin textures with particle-like properties, are promising future magnetic bits for future data storage technologies based on topological concepts 3-11. Of great technological relevance are skyrmions in thin films and magnetic multilayers 12-22 , which can be stabilized as a result of the competition among the Heisenberg exchange interaction (HEI), Dzyaloshinskii-Moriya interaction (DMI) 23,24 and the perpendicular magnetic anisotropy. The low spin polarized current thresholds required to manipulate skyrmions compared to typical ferromagnetic domain walls 3,25 along with their high mobility, high stability and small sizes make them ideal for achieving efficient and functional devices. However, defects that are ineluctable in any device and materials are often seen as inhibitors for applications. The dynamical behavior of the skyrmion motion as function of applied currents hinges on the presence of defects, which define the three motion regimes: pinning, creep-and steady-flow-motion as demonstrated experimentally in ultrathin heavy metal/ferromagnetic bilayers and multilayers 15,26,27. Considerable effort has been performed to explore the dynamics pertaining to current-induced skyrmion motion 3,4,15,28-32 , with a particular attention to the role of defects 33-36. In particular, simulations using realistic parameters extracted from ab-initio showed that by controlling the mutual distance of the pinning defects, one may engineer a double track to guide the skyrmion motion and enhance its velocity 36. Atomic-scale imaging based on scanning tunneling microscopy demonstrated that skyrmions in PdFe bilayer on Ir(111) are inert to the presence of a single Co adatom, in accordance to recent ab-initio simulations 34 , but react to the presence...