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

• Published in: Molecular plant Vol. 16; no. 1; pp. 43 - 63
• Main Authors: Shen, Shuangqian, Zhan, Chuansong, Yang, Chenkun, Fernie, Alisdair R., Luo, Jie
• Format: Journal Article
• Language: English
• Published: England Elsevier Inc 02.01.2023
• Subjects: analytical chemistry; bioactive markers; biochemical pathways; case studies; data collection; epigenetics; genes; genomics; Genomics - methods; high-throughput; metabolic profiling; metabolites; metabolomics; Metabolomics - methods; microbiome; multi-omics; multiomics; phenomics; phenotype; Plant Breeding; plant development; Plants - metabolism; proteomics; Proteomics - methods; species; statistics; transcriptomics; multi-omics; bioactive markers; metabolic profiling; metabolomics; high-throughput
• ISSN: 1674-2052; 1752-9867; 1752-9867
• DOI: 10.1016/j.molp.2022.09.007

Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics 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, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity. This review summarizes the state of the art of methods and techniques in plant metabolomics research and presents different metabolic profiling scenarios in plant sciences. In addition, the latest studies combining metabolomics and other omics approaches to understand the metabolic regulatory network are discussed. Finally, the authors propose key challenges and future directions in the use of metabolomics for enhancing our understanding of plant metabolic diversity.