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New Phytol. 2016 Jun;210(4):1466-78. doi: 10.1111/nph.13861. Epub 2016 Feb 8.

Identifying developmental phases in the Arabidopsis thaliana rosette using integrative segmentation models.

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INRA, UMR LEPSE, 34060, Montpellier, France.
CIRAD, UMR AGAP and Inria, Virtual Plants, 34095, Montpellier, France.


The change in leaf size and shape during ontogeny associated with heteroblastic development is a composite trait for which extensive spatiotemporal data can be acquired using phenotyping platforms. However, only part of the information contained in such data is exploited, and developmental phases are usually defined using a selected organ trait. We here introduce new methods for identifying developmental phases in the Arabidopsis rosette using various traits and minimum a priori assumptions. A pipeline of analysis was developed combining image analysis and statistical models to integrate morphological, shape, dimensional and expansion dynamics traits for the successive leaves of the Arabidopsis rosette. Dedicated segmentation models called semi-Markov switching models were built for selected genotypes in order to identify rosette developmental phases. Four successive developmental phases referred to as seedling, juvenile, transition and adult were identified for the different genotypes. We show that the degree of covering of the leaf abaxial surface with trichomes is insufficient to define these developmental phases. Using our pipeline of analysis, we were able to identify the supplementary seedling phase and to uncover the structuring role of various leaf traits. This enabled us to compare on a more objective basis the vegetative development of Arabidopsis mutants.


Arabidopsis thaliana; heteroblasty; multiscale analysis; segmentation model; semi-Markov switching model; shoot development

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