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Application of Metabolomics in Plant Research

Application of Metabolomics in Plant Research

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Plant metabolites are a reflection of the physiological state of the plant organism at the metabolic level. Any perturbation of the plant body by internal or external factors such as growth and development and environmental factors can cause changes in plant metabolite concentrations or metabolic flow. In most cases such changes are not manifested as changes in one or a few metabolites, but rather changes in multiple metabolites or even multiple metabolic pathways. Metabolomics can detect changes in metabolites in a holistic manner and is therefore increasingly used in research in plant biology and related fields.

Schematic illustrations portraying metabolomics workflow and various applications of metabolomics in plant scienceSchematic illustrations portraying metabolomics workflow and various applications of metabolomics in plant science (Panda et al., 2018).

Gene function analysis

Gene function analysis is currently a hot topic of research in molecular biology, and is the basis for revealing the genetic background and developmental patterns of organisms. In the traditional gene function analysis, changes in gene expression levels are often determined by phenotypic changes. In contrast, it is difficult to judge the changes in expression level by external observation for those without obvious changes in phenotype. Metabolic components are the final expression products of gene expression, and extremely small changes in gene expression levels can lead to changes in metabolite types and levels. Metabolomics is now often used in combination with transcriptomic and proteomic approaches to mine biological information and to resolve gene function.

Metabolic pathways and metabolic network regulation mechanism research

A metabolic pathway typically consists of a series of metabolites and is jointly controlled by several enzymes. In a complex metabolic network, multiple metabolic pathways intersect with each other. The metabolic network of plants is probably one of the most complex natural network structures in nature. The metabolic pathways in plants are divided into primary metabolism and secondary metabolism.

The traditional approach to study metabolism is to validate hypothetical pathways by isotopic tracing or localized detection of several predetermined metabolites, combined with kinetic characteristics and subcellular localization of key enzymes. This approach yields little information, is highly subjective, and cannot quantitatively regulate the size of metabolic flow in metabolic pathways and construct new metabolic pathways. Metabolomics technology makes it possible to detect and analyze hundreds or even thousands of metabolites simultaneously for global understanding and regulation of metabolism, and to rapidly characterize and quantify the precursors, derivatives and degradation products associated with a metabolic pathway. It is even possible to detect dynamic changes among only a few related metabolites to identify metabolic pathways and metabolic networks.

Study of plant biotic and abiotic adversity interactions

When changes occur in the plant growth environment (high temperature, high humidity, drought, pests and diseases, etc.), plants themselves will self-regulate through a series of phenotypic, molecular, physiological and biochemical changes to adapt to these adversities. In the process of self-regulation to adapt to the environment, plants produce a large number of metabolites in a series of processes occurring in themselves, which mainly contain primary and secondary metabolites such as organic acids, amino acids, signaling-related factors, and growth factors.

Plants that are infected by pathogenic bacteria develop an autoimmune response, and metabolites play a very important role in this immune response. After recognition of the pathogen by the plant, the cells undergo a series of mobilization activities that activate their own anti-disease response to resist the invasion of the pathogen. This disease resistance response requires a large amount of energy, reducing power and carbon skeleton from primary metabolic pathways for energy replenishment and scheduling. Also, when plants are infiltrated by pathogenic bacteria, the normal metabolic activities in plants are disrupted to meet the energy required for the disease resistance response, etc. The use of metabolomic approaches can help analyze the metabolism in biotic and abiotic adversity plants in vivo.


  1. Panda, A., Parida, A. K., & Rangani, J. (2018). Advancement of metabolomics techniques and their applications in plant science: Current scenario and future prospective. In Plant Metabolites and Regulation Under Environmental Stress (pp. 1-36). Academic Press.
For Research Use Only. Not for use in diagnostic procedures.

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