Significance Mice manipulated by targeted deletion of a specific brain gene show diverse pathological phenotypes, apparent, for example, in behavioral experiments. To explain observed findings, connectome genetics attempts to uncover how brain functional connectivity is affected by genetics. However the causal impact of a single gene on whole-brain networks is still unclear. Here the sole targeted deletion of the mu opioid receptor gene ( Oprm 1), the main target for morphine, induced widespread remodeling of brain functional connectome in mice. The strongest perturbations occurred within the so-called reward/aversion-circuitry, predominantly influencing the negative affect centers. We present a hypothesis-free analysis of combined structural and functional connectivity data obtained via MRI of the living mouse brain, and identify a specific Oprm 1 gene-to-network signature.