Development of Biomarker Metabolites for Use in Crop Physiology.

As a plant grows and develops, the balance among metabolic pathways shifts in response to developmental stage, tissue, environment and genetics. Advances in functional genomics and systems biology are providing ways to thoroughly characterize these shifts for small numbers of samples. In crop physiology, however, we often wish to characterize the response of plants to environment. This typically entails the analysis of many samples varying in developmental stage, tissue, genotype, and exposure to specific environmental factors. Although the plant response to environment is both chemical and physical in nature, our ability to characterize the shifts among metabolic pathways as part of the response is limited by the moderate throughput provided by traditional and metabolomic methods. A set of biomarkers was developed for use in following changes in the metabolome. The selected biomarkers capture most of the variance of comprehensive metabolomic data, and are also amenable to high throughput screening needed for characterizing large numbers of plant samples. The use of biomarker metabolites to characterize the shifts in metabolic pathways in large numbers of plant samples provides a new level in defining plant chemical involvement in, and response to, differences in genetics, tissue, developmental stage, and environmental factors, including those imposed in crop management. The biomarker metabolite results can further target studies for comprehensive integrated functional genomic analyses, in which transcriptomics is combined with metabolomics or proteomics for very powerful gene discovery.