A deep dive into plant metabolomics: Milestones, technologies, and translational impact

Metabolomics has emerged as an essential pillar of plant functional genomics, filling the gap between genotype and phenotype with direct biochemical readout of plant physiology. This update review highlights the contribution of metabolomics as a field toward our current knowledge of plant biology, starting from targeted analysis to the present high-throughput untargeted era of metabolomics. We elaborate on how metabolomics revolutionized the study of plant stress response, unveiling roles of specialized metabolites in defense, adaptation, and ecological interactions, and, in extension, its contribution toward functional genomics leading to the improvement of plants with desired traits. We identified and summarized over 500 open-source computational tools for analyzing metabolomics datasets, encompassing processes from mass feature extraction to metabolite annotation. We discuss its use in the elucidation of biosynthetic pathways, especially specialized metabolites in medicinal plants, and the discovery of candidates through comparative transcriptome-metabolome profiling. This review further covers the emergence of metabolome-wide association study and metabolite QTL analysis, which exploit genetic diversity to localize biosynthetic genes and regulatory sites. Emerging technology such as imaging MS, single-cell metabolomics, AI-powered metabolite identification and annotation, and global data repositories promise to scale metabolomics to precision crop improvement and synthetic biology. In covering all areas with completeness and vision, we intend that this review acts as the go-to guide for plant metabolism decoders, teachers, and practitioners working to unlock plant metabolism for sustainable agriculture, medicine, and biotechnology.