The present invention relates to improved methods for increasing containment and traceability of transgenic seeds, both prior to harvest and post harvest. Disclosed are methods to produce and select a desirable plant cultivar for molecular farming characterized by being easily amenable for transformation and regeneration and with visual characteristic feature such as in particular characteristic pigmentation of the seed coat or other parts of the seed that can be traced and are easily distinguished in the field or during and/or after harvesting from non-transgenic seeds of the same species that have not the visual characteristic feature.