Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives

Abstract

Plants are natural experts in organic synthesis being able to generate large numbers of specific metabolites with widely varying structures in order to adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics and biochemical expertise. Its ongoing development provides solutions for the systematic understanding of quantitative changes in the levels of these metabolites and is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics with metabolomics, although at an earlier developmental stage than genomics, transcriptomics and proteomics, offering the distinct advantage of studying the cellular entities which have the greatest influence on end-phenotype. Here we summarize the state-of-the-art of metabolite detection and identification, also illustrating this with case study applications including (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal changes in metabolism during plant development, (iii) mining characteristic metabolites in different ecological environments and upon exposure to various stresses, and (iv) the performance of metabolomics on panels of natural genetic variance as a means of functional gene identification, metabolic pathway elucidation and metabolomics-assisted breeding. We additionally highlight the prominent contributions of joint analysis of metabolomics with other-omics including genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes and ion-omics. Finally, we provide an outlook for further directions and challenges of metabolomics in enhancing our understanding of plant metabolic diversity.