La Trobe

Developmental normalization of phenomics data generated by high throughput plant phenotyping systems

journal contribution
posted on 2025-01-17, 04:56 authored by Diego Lozano Claros, Xiangxiang Meng, Edhem Custovic, Guang DengGuang Deng, Oliver BerkowitzOliver Berkowitz, James WhelanJames Whelan, Mathew LewseyMathew Lewsey
Background: Sowing time is commonly used as the temporal reference for Arabidopsis thaliana (Arabidopsis) experiments in high throughput plant phenotyping (HTPP) systems. This relies on the assumption that germination and seedling establishment are uniform across the population. However, individual seeds have different development trajectories even under uniform environmental conditions. This leads to increased variance in quantitative phenotyping approaches. We developed the Digital Adjustment of Plant Development (DAPD) normalization method. It normalizes time-series HTPP measurements by reference to an early developmental stage and in an automated manner. The timeline of each measurement series is shifted to a reference time. The normalization is determined by cross-correlation at multiple time points of the time-series measurements, which may include rosette area, leaf size, and number. Results: The DAPD method improved the accuracy of phenotyping measurements by decreasing the statistical dispersion of quantitative traits across a time-series. We applied DAPD to evaluate the relative growth rate in Arabidopsis plants and demonstrated that it improves uniformity in measurements, permitting a more informative comparison between individuals. Application of DAPD decreased variance of phenotyping measurements by up to 2.5 times compared to sowing-time normalization. The DAPD method also identified more outliers than any other central tendency technique applied to the non-normalized dataset. Conclusions: DAPD is an effective method to control for temporal differences in development within plant phenotyping datasets. In principle, it can be applied to HTPP data from any species/trait combination for which a relevant developmental scale can be defined.

Funding

Work in the Lewsey and Whelan labs was funded by the Australian Research Council Industrial Transformation Hub in Medicinal Agriculture (IH180100006). Work in the Whelan Lab was funded by the Australian Research Council Centre of Excellence in Plant Energy Biology (CE140100008). DL was the recipient of scholarships from La Trobe University Graduate Research School. Construction of our HTPP system was funded by a La Trobe University Research Infrastructure Grant.

History

Publication Date

2020-08-12

Journal

Plant Methods

Volume

16

Article Number

111

Pagination

11p.

Publisher

Springer Nature

ISSN

1746-4811

Rights Statement

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