The invention provides methods of preventing flooding of a cavity within a shoot restraint of a manufactured seed by lowering the water potential of the nutritive media relative to the water potential of a plant embryo disposed within the cavity. A exemplary method may comprise the steps of: (a) assembling a manufactured seed comprising a seed coat and a shoot restraint, wherein the shoot restraint comprises a cavity; (b) lowering the water potential of nutritive media to be used in the manufactured seed, wherein the water potential of the nutritive media relative to the water potential of a plant embryo disposed in the cavity of the shoot restraint is such that an excessive amount of water does not flow out of the nutritive media and accumulate within the cavity, thereby preventing flooding of the cavity; and (c) adding the nutritive media prepared in step (b) to the manufactured seed.