There is a worldwide consensus that the production of food, biomolecules and bioenergy should be sustainably intensified within the next decades. To achieve these goals will depend on the intensification of current practices in agricultural systems fused with a wider understanding and acceptance of genomics, metabolomics, synthetic biology and metabolic engineering. However, genetically modified-derived crops, including commodities and non-commodities, may contribute to establishing a new parameter in the agricultural, pharmaceutical and industrial sectors. Seeds will also play an important role in allowing large-scale production of innovative molecules prospected from biodiversity.