Analysis of the plant architecture via tree-structured statistical models: the hidden Markov tree models

Authors

  • J.-B. Durand,

    Corresponding author
    1. Institut National Polytechnique de Grenoble, Laboratoire de Modélisation et Calcul/IMAG, BP 53, 38041 Grenoble cedex 9, France;
    Search for more papers by this author
  • Y. Guédon,

    1. Unité Mixte de Recherche CIRAD/CNRS/INRA/IRD/Université de Montpellier II, Botanique et Bioinformatique de l’Architecture des Plantes TA40/PS2, 34398 Montpellier cedex 5, France;
    Search for more papers by this author
  • Y. Caraglio,

    1. Unité Mixte de Recherche CIRAD/CNRS/INRA/IRD/Université de Montpellier II, Botanique et Bioinformatique de l’Architecture des Plantes TA40/PS2, 34398 Montpellier cedex 5, France;
    Search for more papers by this author
  • E. Costes

    1. Unité Mixte de Recherche INRA/Agro.M/CIRAD/IRD BDPPC, Equipe ‘Architecture et Fonctionnement des Espèces Fruitières’, 2 place Pierre Viala, 34060 Montpellier cedex 1, France
    Search for more papers by this author

Author for correspondence: Jean-Baptiste Durand Tel: +33 4 76 63 57 09 Fax: +33 4 76 63 12 63 Email: Jean-Baptiste.Durand@imag.fr

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.

Ancillary