Systems biology is a recently developed research area. The main feature of systems biology is the integration of multiple high-throughput omics data such as genomics, transcriptomics, protein-protein interaction network, reactome and phenomics with computational tools. Rice, one of the most important food crops for humans, is the first crop plant to have its genome sequenced. Resources for systems biology in rice mentioned above have recently been generated and discovering the function of the estimated 41,000 rice genes with systems biology is now within reach. Crop biotech institute in our university retains the world-largest gene indexed mutant population for systems genetics approaches. This resource will facilitate the functional genomics study in rice coupled with exponential increasing information of rice gene function based on multi-omics data. Using systems biology, our group has tried to quickly identify and characterize functions of rice genes associated with important agronomic traits such as water stress tolerance, root development and increase of phosphate use efficiency.