KymoRod: a method for automated kinematic analysis of rod‐shaped plant organs

Abstract

A major challenge in plant systems biology is the development of robust, predictive multiscale models for organ growth. In this context it is important to bridge the gap between the, rather well-documented molecular scale and the organ scale by providing quantitative methods to study within-organ growth patterns. Here, we describe a simple method for the analysis of the evolution of growth patterns within rod-shaped organs that does not require adding markers at the organ surface. The method allows for the simultaneous analysis of root and hypocotyl growth, provides spatio-temporal information on curvature, growth anisotropy and relative elemental growth rate and can cope with complex organ movements. We demonstrate the performance of the method by documenting previously unsuspected complex growth patterns within the growing hypocotyl of the model species Arabidopsis thaliana during normal growth, after treatment with a growth-inhibiting drug or in a mechano-sensing mutant. The method is freely available as an intuitive and user-friendly Matlab application called KymoRod.

Gradients in Wall Mechanics and Polysaccharides along Growing Inflorescence Stems

“…At early stages (less than 4 cm), the entire stem elongated; later, the basal region ceased elongation. This evolution in elongation pattern resembles that of Arabidopsis hypocotyls, where elongation is spatially delocalized at early times and later becomes localized to the apical region (Bastien et al, 2016). For inflorescence stems 5 to 6 cm long, elongation was slightly faster in the light compared with the dark (mean of 1.13 versus 0.94 mm h 21 , SE = 0.04; n = 20-23); consequently, our measurements and sample collections were made during the light period.…”

“…This dynamic process is properly quantified by growth kinematics, a conceptual framework based on fluid dynamics and continuum mechanics (Silk, 1984;Bastien et al, 2016). The process has been likened to a fountain: a fluid structure that is stable despite a continuous flow of materials through the growth zone.…”

On hormonal regulation of the dynamic apical hook development

“…For instance, twisting of the hypocotyl during hook formation has been proposed to be involved in the exaggeration of hook curvature by ethylene (Raz & Ecker, ; Raz & Koornneef, ). The employment of recently developed automated suborgan image quantification algorithms, such as KymoRod , will facilitate the detection and assessment of the contribution of such within‐organ geometry changes in diverse hook‐promoting conditions (Bastien et al ., ).…”

“…For instance, twisting of the hypocotyl during hook formation has been proposed to be involved in the exaggeration of hook curvature by ethylene (Raz & Ecker, 1999;Raz & Koornneef, 2001). The employment of recently developed automated suborgan image quantification algorithms, such as KYMOROD, will facilitate the detection and assessment of the contribution of such within-organ geometry changes in diverse hook-promoting conditions (Bastien et al, 2016). Given the central role of asymmetric auxin distribution-driven differential growth during apical hook formation (Beziat & Kleine-Vehn, 2018), it is reasonable to speculate that the peak of auxin or the location of the auxin maxima may also travel and, principally, would precede, or at least be concurrent with, the traveling of hook curvature (Fig.…”

Non-invasive Protocol for Kinematic Monitoring of Root Growth under Infrared Light

“…In the 90s, new digital cameras and informatics tools enabled the development of automatic tracking algorithms used for particle image velocimetry. RootFlowRT (Van der Weele et al, 2003), Kineroot (Basu et al, 2007), RootTrace (French et al, 2009), GrowthTracer (Iwamoto et al, 2013) and Kymorod (Bastien et al, 2016) are among many recent examples of software dedicated to the monitoring of root growth. However, all particle image velocimetry methods rely on the use of identifiable image texture patterns in each successive picture.…”