A Journey Through a Leaf: Phenomics Analysis of Leaf Growth inArabidopsis thaliana

Abstract

In Arabidopsis, leaves contribute to the largest part of the aboveground biomass. In these organs, light is captured and converted into chemical energy, which plants use to grow and complete their life cycle. Leaves emerge as a small pool of cells at the vegetative shoot apical meristem and develop into planar, complex organs through different interconnected cellular events. Over the last decade, numerous phenotyping techniques have been developed to visualize and quantify leaf size and growth, leading to the identification of numerous genes that contribute to the final size of leaves. In this review, we will start at the Arabidopsis rosette level and gradually zoom in from a macroscopic view on leaf growth to a microscopic and molecular view. Along this journey, we describe different techniques that have been key to identify important events during leaf development and discuss approaches that will further help unraveling the complex cellular and molecular mechanisms that underlie leaf growth.

PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics

“…The fully automatic segmentation of individual cells by PaCeQuant is a major advance because currently all measurements of PCs require manual segmentation. Manual segmentation is very time consuming and prone to bias introduced by the subjectivity of sample choice and contour labeling (Vanhaeren et al, 2015;Wu et al, 2016). PaCeQuant efficiently detects cell outlines in confocal input images using a combination of contrast and boundary enhancement, analysis of skeletons in binary images and watershed-based gap closing (Fig.…”

“…Variance can be generated by manual segmentation due to bias caused by different persons and even by a single person between segmentations generated at different time points (Vanhaeren et al, 2015). The accuracy of manual segmentation further depends on the sampling density, i.e.…”

“…First, it is very time consuming and laborious and prevents high-throughput analysis of PC shape. Second, unless segmentation is carried out in blind studies, it is prone to bias by the experimenter (Vanhaeren et al, 2015). Hence, for objective quantification of PC shape characteristics, robust and fully automatic techniques for the segmentation of cell regions, as well as meaningful and clearly defined shape descriptors are required.…”

“…For example, shapes were quantified by use of Fourier-based descriptors (McLellan and Endler, 1998), moments, geometric codes, and margin statistics (Kalyoncu and Toygar, 2015), and leaf serration was quantified using hierarchy analyses (Biot et al, 2016). With improving imaging techniques, several studies addressed the dynamics and changes of PC shape during leaf development and expansion (Iwata and Ukai, 2002;Andriankaja et al, 2012;Elsner et al, 2012;Barbier de Reuille et al, 2015;Vanhaeren et al, 2015). Key regulators of PC interdigitation were identified by mutant phenotyping (Xu et al, 2010;Lin et al, 2012;Li et al, 2013;Guo et al, 2015).…”

“…Genetic and phenotypic analyses, mostly in the model species Arabidopsis (Arabidopsis thaliana), provide insights into the dynamics of cellular events that underlie the development from primordia to the final flat and polar organ (Tsukaya, 2010(Tsukaya, , 2013Vanhaeren et al, 2015). Growth and development are controlled by complex molecular networks that integrate internal and external signals (Cho et al, 2007;Wolters and Jürgens, 2009).…”