Considerable progress has been made in plant genome-scale metabolic reconstruction and modeling in recent years. Such reconstructions made it possible to explore metabolic phenotypes through appropriate model formulation and optimization methods. As a result, plant genome-scale modeling has increasingly attracted interest from the plant research community. In this chapter, the first generation of plant genome- scale metabolic reconstructions is presented, along with the important concepts behind model and con- straint formulation. A brief protocol describing the use of constraint-based reconstruction and analysis (COBRA) Toolbox in flux simulation and model modification is provided. This is followed by a presenta- tion of metabolic constraints required to generate fluxes in AraGEM using COBRA that describe photo- synthesis, photorespiration, and respiration, respectively. Overall, plant genome-scale modeling is a powerful approach that is accessible and readily adopted.
CITATION STYLE
Dal’Molin, C. G. O., Quek, L.-E., Palfreyman, R. W., & Nielsen, L. K. (2014). Plant Metabolic Flux Analysis. Plant Metabolic Networks: Methods and Protocols, 1090(1), 317–332. https://doi.org/10.1007/978-1-62703-688-7
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