Systems-based approach to the analyses of plant functions: Conceptual understanding, implementation, and analysis

Systems biology is a systemic approach for the study of biological systems through the constructive alignment of biological interests (genetics, physiology, or biochemical), monitoring of molecular determinants (gene, protein, and metabolite), information processing and responses (metabolic and signaling pathway behavior), data integration, and ultimately formulation of mathematical models for the elucidation of structure and function of the system and system perturbations. Therefore, integration of computational and experimental research is a fundamental requirement of systems biology. The recent advancements in computational resources and high-throughput techniques (DNA microarrays, next-generation sequencing, proteomics, and metabolomics) for the processing of a large number of biological samples have increased the pace of systems biology research in plant science. Systems biology approaches have been employed on the cell, tissue, organ, and whole-plant level in various studies for the understanding of plant structure and function and reported the discovery of new genes, transcription factors, regulators, gene regulation networks, promoter sites, and pathways and their functional characterization in varying physiological and environmental conditions. These cutting-edge researches have allowed us to address the complexity of biological systems for plant structure and functions. This chapter discusses how to predict plant function in different homeostasis utilizing systems biology-based approaches.