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Transcriptomics, proteomics, and metabolomics to reveal mechanisms underlying plant secondary metabolism

Plant secondary metabolites play an important role in the fields of food, medicine, agriculture, and biofuels. Secondary metabolites are an important focus of crop breeding and metabolic engineering research. However, our understanding of secondary metabolism is far from complete, particularly in nonmodel plants. Functional genomics, which includes transcriptomics, proteomics, and metabolomics, opens a new avenue for deciphering secondary metabolism. Here we review the applications of functional genomics in secondary metabolism, including the discovery of novel genes, the identification of gene function, and the detection of novel pathways of the metabolic network. Results from these studies will accelerate our understanding of elicitation mechanism of secondary metabolism and how plants interact with their environment, ultimately improving the production of secondary metabolites by means of metabolic engineering.