Using the identification of several morphological criteria and considering the plant as a whole, from germination to death, architectural analysis is essentially a detailed, multilevel, comprehensive and dynamic approach to plant development. Despite their recent origin, architectural concepts and analysis methods provide a powerful tool for studying plant form and ontogeny. Completed by precise morphological observations and appropriated quantitative methods of analysis, recent researches in this field have greatly increased our understanding of plant structure and development and have led to the establishment of a real conceptual and methodological framework for plant form and structure analysis and representation. This paper is a summarized update of current knowledge on plant architecture and morphology; its implication and possible role in various aspects of modern plant biology is also discussed.

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Exceptional climatic events from 2003 to 2005 (scorching heat and drought) affected the whole of the vegetation in the French Mediterranean region and in particular the Scots pine (Pinus sylvestris L.), one of the most important forest tree species in this area. To understand its response to these extreme conditions, we investigated its radial growth, branch length growth, architectural development and reproduction for the period 1995-2005, and linked these variables to climatic parameters. We used four plots situated in southeastern France and presenting different levels of site quality and potential forest productivity. The results show that: (1) the climatic episode 2003-2005 was highly detrimental to the growth (bole and branches), crown development, and cone production but favored the production of male flowers; (2) these variables depend on climatic factors of both the current and previous years; (3) the 2003 scorching heat impact was strong but was mainly apparent from 2004; it was part of a 6-year-long unfavorable cycle beginning in 2000, characterized by high minimum and maximum temperatures and very dry springs; (4) in spite of a significant effect of site quality, the Scots pine's response to extreme climatic conditions was homogeneous in the French Mediterranean area; and (5) the stress induced by poor site conditions generally resulted in the same consequences for tree growth, architecture, and reproduction as in unfavorable climatic conditions.

In the last decades, architectural analysis has been used to understand and to model plant development. These studies have lead us to reconsider the problem of measuring plants while taking into account their topological structure at several scales of detail. A computational platform, called AMAPmod, was created to work on such plant representations. This paper outlines the general methodology used in AMAPmod to represent plant topological structures and to explore these special types of databases. Plant structures are first encoded in order to build corresponding formal representations. Then, a dedicated language, AML, enables the user to extract various types of information from the plant databases and provides appropriate analyzing tools.

Polycyclism, the ability for a plant to produce several flushes in the same growing season, is a key process of plant development. Polycyclism frequency is likely to change with the anticipated climate trend, expected to impact plant growth over the next century. However, polycyclism processes are not well described in the literature, and an important lack of knowledge prevents any possible prediction for the twenty-first century. Aleppo pine is a good model to study polycyclism: it is known to produce up to four annual flushes in one growing season. In this study, we used architectural analysis to describe and reconstruct polycyclism processes, periodicity and frequency on Aleppo pine in a Mediterranean site for the last 15 years. We also assessed relationships between polycyclism frequency and climate. Since 1995, climate was far hotter and drier than normal in South-eastern France: polycyclism was significantly reduced, particularly after 2003 heat-wave, which delayed effect remains till 2008, exacerbated by repeated droughts. Morphologically, polycyclism is primarily influenced by twig vigour, status (principal/secondary and strong axes) and position (low, middle or top crown). Climatically, it depends on summer temperatures of the current and preceding year, rainfall of the first half of preceding year and winter rainfall. Previous year abundant rainfall combined with colder temperatures and high rainfall in spring or at the end of summer of the current year increase tricyclism frequency. Polycyclism is likely to decrease significantly in the twenty-first century due to a hotter and drier climate.

Summary• Plant architecture is the result of repetitions that occur through growth and branching processes. During plant ontogeny, changes in the morphological characteristics of plant entities are interpreted as the indirect translation of different physiological states of the meristems. Thus connected entities can exhibit either similar or very contrasted characteristics.• We propose a statistical model to reveal and characterize homogeneous zones and transitions between zones within tree-structured data: the hidden Markov tree (HMT) model. This model leads to a clustering of the entities into classes sharing the same 'hidden state'.• The application of the HMT model to two plant sets (apple trees and bush willows), measured at annual shoot scale, highlights ordered states defined by different morphological characteristics. The model provides a synthetic overview of state locations, pointing out homogeneous zones or ruptures. It also illustrates where within branching structures, and when during plant ontogeny, morphological changes occur.• However, the labelling exhibits some patterns that cannot be described by the model parameters. Some of these limitations are addressed by two alternative HMT families.

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