Computational method to analyze linear developmental gradients reveals specific metabolite enrichment patterns in stress-tolerant maize.

Abstract

Metabolic processes are essential for regulating and maintaining developmental transitions. However, the distinct metabolite-driven mechanisms that are crucial for development remain poorly characterized due to inherent challenges in measuring their localization and function in situ. We applied desorption electrospray ionization mass spectrometry imaging (DESI-MSI) to generate near single-cell resolution (50-80 µm) images of metabolites in the maize root tip, which has a well-characterized longitudinal developmental gradient. We developed a new computational tool, called Developmental Imaging Mass Spectrometry Pipeline for Linear Evaluation (DIMPLE), which processes mass signatures along linear gradients and clusters metabolites based on their developmental enrichment patterns. We employed this method to compare developmental enrichment of metabolites in Oaxacan Green, a salt-resilient maize variety, to B73, which is salt sensitive. DIMPLE uncovers specific differences in individual mass signatures and overall enrichment patterns between these varieties. Further characterization of these differences revealed meristem enrichment of D-erythrose, a metabolite that can improve stress tolerance in maize. Overall, DIMPLE enables comprehensive and rapid analysis of metabolite patterns along a linear gradient, informing biological hypotheses related to plant growth and stress response.

Plant phenotyping relevance

植物根端の発達勾配に沿った代謝物分布を画像化・解析する計算ツールを開発しており、植物の発達状態やストレス応答に関わる表現型抽出が研究の中心である。

Code and data availability

The paper's authors publicly deposited the DIMPLE analysis code and raw DESI-MSI data on the Dickinson Lab GitHub and Zenodo, as stated in the Technical aspects and Data availability sections.