This second edition volume expands on the previous edition with an update on the latest techniques used to study plant systems biology on three specific scales: the molecular level, the tissue level, and the whole plant. Chapters cover topics such as gene regulatory network inference and dynamic modeling using ordinary differential equations or Boolean formalisms; protocols for at-will induction of plant aerial or root organs, or quantification of tissue mechanical properties; mathematical modeling of plant tissue using SimuPlant or VirtualLeaf; and simulating crop root systems using OpenSimRoot or R-SWMS. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols or software tutorials, and tips on troubleshooting and avoiding known pitfalls.