One of the long-standing goals in plant biology has been to link genotypic variation to natural variation in plant development and adaptive traits. From recent studies it has become clear that a complex interacting network is underlying phenotypic diversity. A major role in this regulatory mechanism is assigned to the metabolism since plants are extremely rich and variable in metabolic content profiles. Technological advances in detecting and quantifying biochemical content as well as novel experimental approaches have accelerated data generation and increased our understanding of regulatory mechanisms in plant biology. It is now clear that modern plant sciences can benefit enormously from integrated multidisciplinary approaches.