Development and applications of metabolic models in plant multi-omics research

Plant growth and development are characterized by systematic and continuous processes, each involving intricate metabolic coordination mechanisms. Mathematical models are essential tools for investigating plant growth and development, metabolic regulation networks, and growth patterns across different stages. These models offer insights into secondary metabolism patterns in plants and the roles of metabolites. The proliferation of data related to plant genomics, transcriptomics, proteomics, and metabolomics in the last decade has underscored the growing importance of mathematical modeling in this field. This review aims to elucidate the principles and types of metabolic models employed in studying plant secondary metabolism, their strengths, and limitations. Furthermore, the application of mathematical models in various plant systems biology subfields will be discussed. Lastly, the review will outline how mathematical models can be harnessed to address research questions in this context.