Résumé
Plants are modular organisms that develop by the repetition of elementary botanical entities or constructional units through the three main and fundamental morphogenetic processes of growth, branching and reiteration (Barthélémy and Caraglio, 2007). Repetition of these entities induces gradual or abrupt changes in their characteristics. These characteristics are quantified through several variables, called the entity attributes. On the one hand, differences between entities reflect different stages of differentiation in the meristems (Nicolini and Chanson, 1999), which are ordered in time and correspond to the notion of physiological age of meristems (Barthélémy and Caraglio, 2007). The changes of one attribute through the plant structure are referred to as morphogenetic gradient. On the other hand, part of the entity differences can be imputed to environmental factors. Based on this botanical model of plant functioning, our approach jointly relies on categories of entities with similar characteristics, a description of those within-category characteristics and the category topological organisation within the plant. This constitutes a useful summary of the plant architecture, which is the basis for 1) highlighting hidden regularities in plant structures, for a better understanding of the gradients and organisation rules; 2) proposing and validating ecophysiological hypotheses, and new sampling protocols; 3) adopting a powerful paradigm for modelling plant development. In this work, the entity categories are identified using a hidden Markov tree (HMT) model, in which local dependencies only ( i.e. interactions between connected entities) are accounted for. This is not sufficient to accurately describe the topological distribution of the entities within the plant, and the changes of the plant topology. This is why various complementary methods and models (among which edit distance algorithms and sequence analysis using Markovian models), performed at different scales, are used in our approach to provide a more detailed description of the architecture, and to assess how various controlled factors affect architecture plasticity.