title: Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement.
abstract: Crop productivity is severely limited by various biotic and abiotic stresses. Thus, it is highly needed to understand the underlying mechanisms of environmental stress response and tolerance in plants, which could be addressed by systems biology approach. To this end, high-throughput omics profiling andin silicomodeling can be considered to explore the environmental effects on phenotypic states and metabolic behaviors of rice crops at the systems level. Especially, the advent of constraint-based metabolic reconstruction and analysis paves a way to characterize the plant cellular physiology under various stresses by combining the mathematical network models with multi-omics data. Rice metabolic networks have been reconstructed since 2013 and currently six such networks are available, where five are at genome-scale. Since their publication, these models have been utilized to systematically elucidate the rice abiotic stress responses and identify agronomic traits for crop improvement. In this review, we summarize the current status of the existing rice metabolic networks and models with their applications. Furthermore, we also highlight future directions of rice modeling studies, particularly stressing how these models can be used to contextualize the aﬄuent multi-omics data that are readily available in the public domain. Overall, we envisage a number of studies in the future, exploiting the available metabolic models to enhance the yield and quality of rice and other food crops.
authors.affiliation: Bioprocessing Technology Institute, Agency for Science, Technology and Research Singapore, Singapore.
authors.forename: Meiyappan
authors.initials: M
authors.lastname: Lakshmanan
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore Singapore, Singapore.
authors.forename: C Y Maurice
authors.initials: CY
authors.lastname: Cheung
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore Singapore, Singapore.
authors.forename: Bijayalaxmi
authors.initials: B
authors.lastname: Mohanty
authors.affiliation: Bioprocessing Technology Institute, Agency for Science, Technology and ResearchSingapore, Singapore; Department of Chemical and Biomolecular Engineering, National University of SingaporeSingapore, Singapore; Synthetic Biology for Clinical and Technological Innovation, Life Sciences Institute, National University of SingaporeSingapore, Singapore.
authors.forename: Dong-Yup
authors.initials: DY
authors.lastname: Lee
keywords: -omics data; flux-balance analysis; genome-scale metabolic networks and models; metabolism; rice; systems biology