Patch Track Software for Measuring Kinematic Phenotypes of Arabidopsis Roots Demonstrated on Auxin Transport Mutants.

Abstract

Plant roots elongate when cells produced in the apical meristem enter a transient period of rapid expansion. To measure the dynamic process of root cell expansion in the elongation zone, we captured digital images of growing Arabidopsis roots with horizontal microscopes and analyzed them with a custom image analysis program (PatchTrack) designed to track the growth-driven displacement of many closely spaced image patches. Fitting a flexible logistics equation to patch velocities plotted versus position along the root axis produced the length of the elongation zone (mm), peak relative elemental growth rate (% h -1 ), the axial position of the peak (mm from the tip), and average root elongation rate (mm h -1 ). For a wild-type root, the average values of these kinematic traits were 0.52 mm, 23.7% h -1 , 0.35 mm, and 0.1 mm h -1 , respectively. We used the platform to determine the kinematic phenotypes of auxin transport mutants. The results support a model in which the PIN2 auxin transporter creates an area of expansion-suppressing, supraoptimal auxin concentration that ends 0.1 mm from the quiescent center (QC), and that ABCB4 and ABCB19 auxin transporters maintain expansion-limiting suboptimal auxin levels beginning approximately 0.5 mm from the QC. This study shows that PatchTrack can quantify dynamic root phenotypes in kinematic terms.

Plant phenotyping relevance

PatchTrackによる画像解析で根の動的な伸長・細胞伸長形質を抽出する手法とプラットフォームを開発・実証しており、表現型取得が研究の中心です。

Code and data availability

The paper's Data Availability Statement explicitly deposits the authors' PatchTrack image-analysis code (used to produce the kinematic phenotyping measurements) on a public GitHub repository. No phenotype dataset or image deposit is stated.