TRiP: Tracking Rhythms in Plants, an automated leaf movement analysis program for circadian period estimation

Kathleen Greenham,Hany Farid,Ping Lou,C Robertson Mcclung,Sara E Remsen

doi:10.1186/s13007-015-0075-5

Abstract

BackgroundA well characterized output of the circadian clock in plants is the daily rhythmic movement of leaves. This process has been used extensively in Arabidopsis to estimate circadian period in natural accessions as well as mutants with known defects in circadian clock function. Current methods for estimating circadian period by leaf movement involve manual steps throughout the analysis and are often limited to analyzing one leaf or cotyledon at a time.ResultsIn this study, we describe the development of TRiP (Tracking Rhythms in Plants), a new method for estimating circadian period using a motion estimation algorithm that can be applied to whole plant images. To validate this new method, we apply TRiP to a Recombinant Inbred Line (RIL) population in Arabidopsis using our high-throughput imaging platform. We begin imaging at the cotyledon stage and image through the emergence of true leaves. TRiP successfully tracks the movement of cotyledons and leaves without the need to select individual leaves to be analyzed.ConclusionsTRiP is a program for analyzing leaf movement by motion estimation that enables high-throughput analysis of large populations of plants. TRiP is also able to analyze plant species with diverse leaf morphologies. We have used TRiP to estimate period for 150 Arabidopsis RILs as well as 5 diverse plant species, highlighting the broad applicability of this new method.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-015-0075-5) contains supplementary material, which is available to authorized users.

Highlights

A well characterized output of the circadian clock in plants is the daily rhythmic movement of leaves
We have developed a motion estimation algorithm [12] called Tracking Rhythms in Plants (TRiP) that tracks leaf movement of cotyledons and true leaves simultaneously
We introduced 3 different amplitude trends and 3 noise levels that approximate the traces generated from leaf movement data (Figure 2A; Table 1)

Summary

Introduction

A well characterized output of the circadian clock in plants is the daily rhythmic movement of leaves. With the decreasing cost of Generation Sequencing (NGS) technology the use of highthroughput experimentation on large plant populations is possible. This shift towards expanded genetic and phenotypic analysis has led to generation mapping populations which include Nested Association Mapping (NAM) populations [1] and Multiparent Advanced Generation Inter-Cross (MAGIC) lines [2] for enhanced gene mapping and trait discovery. To determine the timing of leaf movement, time-lapse photography is used to image every 10-20 min over a window of 5-10 days under constant light conditions

Methods

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Conclusion