3D Grapevine Inflorescence Architecture: X-ray Imaging & Morphometrics

Original video: https://youtu.be/RJx2TCgyGxM

Inflorescence architecture provides the scaffold on which flowers and fruits develop, and consequently is a primary trait under investigation in many crop systems. Yet the challenge remains to analyse these complex 3D branching structures with appropriate tools. High information content datasets are required to represent the actual structure and facilitate full analysis of both the geometric and the topological features relevant to phenotypic variation in order to clarify evolutionary and developmental inflorescence patterns. We combined advanced imaging (X-ray tomography) and computational approaches (topological and geometric data analysis and structural simulations) to comprehensively characterize grapevine inflorescence architecture (the rachis and all branches without berries) among 10 wild Vitis species. Clustering and correlation analyses revealed unexpected relationships, for example pedicel branch angles were largely independent of other traits. We identified multivariate traits that typified species, which allowed us to classify species with 78.3% accuracy, versus 10% by chance. Twelve traits had strong signals across phylogenetic clades, providing insight into the evolution of inflorescence architecture. We provide an advanced framework to quantify 3D inflorescence and other branched plant structures that can be used to tease apart subtle, heritable features for a better understanding of genetic and environmental effects on plant phenotypes.

An emerging mathematical approach to interpret topological models is persistent homology (PH). PH extracts morphological features from two- or three-dimensional representations and can be used to compare very different shapes. PH has been applied to explain a wide range of features including atomic structures, urban and forested areas, cancers, cell shapes, and jaw shape, among others (Edelsbrunner & Morozov, 2013). In plants, PH has been used to estimate shapes that are otherwise difficult to measure including leaves, leaflet serration, spikelet shape, stomatal patterning, and root architecture (Haus et al., 2018; Li et al., 2018a,b; Migicovsky et al. 2017; McAllister et al., 2019). Previous work showed that PH could capture more quantitative variation than traditional plant morphological measures (described above) resulting in the identification of otherwise latent quantitative trait loci (Li et al., 2018b). PH is especially well-suited for quantifying branching topology as it can quantitatively summarize complex variation with a single measure (Li et al., 2017; Delory et al., 2018). Rachis, pedicel, and branches include inherently topological features that can be especially well-analysed with PH-based methods.

Keywords: 3D architecture, inflorescence, morphology, persistent homology, phylogenetic analysis, topological data analysis, Vitis spp, X-ray tomography

Citation:

Pascal Hunziker, Barbara Ann Halkier, Alexander Schulz, Arabidopsis glucosinolate storage cells transform into phloem fibres at late stages of development, Journal of Experimental Botany, Volume 70, Issue 16, 15 August 2019, Pages 4305–4317, https://doi.org/10.1093/jxb/erz176

Published on: 12 April 2019

Attribution 4.0 International — CC BY 4.0 - Creative Commons