A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule

Abstract

A fundamental question in biology is how morphogenesis integrates the multitude of processes that act at different scales, ranging from the molecular control of gene expression to cellular coordination in a tissue. Using machine-learning-based digital image analysis, we generated a three-dimensional atlas of ovule development in Arabidopsis thaliana , enabling the quantitative spatio-temporal analysis of cellular and gene expression patterns with cell and tissue resolution. We discovered novel morphological manifestations of ovule polarity, a new mode of cell layer formation, and previously unrecognized subepidermal cell populations that initiate ovule curvature. The data suggest an irregular cellular build-up of WUSCHEL expression in the primordium and new functions for INNER NO OUTER in restricting nucellar cell proliferation and the organization of the interior chalaza. Our work demonstrates the analytical power of a three-dimensional digital representation when studying the morphogenesis of an organ of complex architecture that eventually consists of 1900 cells.

Plant phenotyping relevance

機械学習による3Dデジタル画像解析と細胞・組織レベルの定量的アトラス構築が研究の中心であり、胚珠の形態・成長パターンを抽出する植物フェノタイピング手法に該当する。

Code and data availability

The paper's 3D digital ovule datasets (raw images, PlantSeg predictions, segmented cells, annotated 3D cell meshes, and csv attribute files) are publicly deposited in EMBL-EBI BioStudies under accessions S-BSST475, S-BSST498, S-BSST497, and S-BSST513. Additionally, the PlantSeg 'generic_confocal_3D_unet' model was re/​