High-Resolution Kinematic Analysis of Root Gravitropic Bending Using RootPlot

Aditi Bhat, Cody L. DePew, Gabriele B. Monshausen

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Root gravitropic bending is a complex growth process resulting from differential expansion of cells on the upper and lower sides of a gravistimulated root. In order to genetically dissect the molecular machinery underlying root bending, a thorough understanding of the kinetics and spatial distribution of the growth process is required. We have developed an experimental workflow that enables us to image growing roots at high spatiotemporal resolution and then convert XY-coordinates of root cellular markers into 3D representations of root growth profiles. Here, we present a detailed description of the setup for monitoring vertically oriented roots before and after gravistimulation. We also introduce our newly developed custom R-based program RootPlot, which calculates root velocity profiles from root XY-coordinate data obtained using a previously published image processing software. The raw velocity and derived relative elemental growth rate (REGR) curves are then fitted via LOWESS regression for assumption-free data analysis. The resulting smoothed growth profiles are plotted as heatmaps to visualize how different regions of the root contribute to the growth response over time. Additionally, RootPlot provides analysis of overall growth and bending rates based on root XY-coordinates.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages95-109
Number of pages15
DOIs
StatePublished - 2022

Publication series

NameMethods in Molecular Biology
Volume2368
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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