Introduction - Two decades ago, a mathematical formalism was introduced to represent the complexity of plant branching structures at different scales with a unified approach. Using Multiscale Tree Graph (MTG), it was possible to capture the topology and the geometry of a multitude of plant species at different scales in a precise manner. However, the use of this formalism was initially dedicated to quantitative acquisition and analysis of plant branching systems. Its use in mechanistic models of plant growth has progressively emerged in various works to support multiscale modeling. In this paper, we review how the MTG formalism has been applied to models of plant development and extend it to comply fully with the requirements of Functional-Structural Plant Models (FSPM) at different scales. Methods - Formalizing plant structure representation – To represent branching, different mathematical formalisms have been proposed such as Axial Tree (Prusinkiewicz et Lindenmeyer, 90), MTG (Godin and Caraglio, 1998), which define plant multiscale topological structures as a serie of nested tree graph, and more recently a structure-ofscales (Ong and Kurth, 2012) that, inspired from MTGs, models the scales as a partially ordered sets and allows to manage an extensive range of scales. Here we review how MTGs can be embedded in the context of FSPMs. This includes the possibility to grow MTG using developmental rules expressed for instance in the formalism of L-systems, and to encode the dynamic structure at different developmental stages as a time-series. We also discuss new extensions such as the possibility to manipulate continuous representations of plant properties at different scales. Generic algorithms - Various algorithms have been designed to manipulate MTGs in a generic manner. We defined multiscale traversal (basipetal or acropetal) and user-defined visitors to model flows through plant structure at different scales, interaction with the environment as well as 3D visualiz