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

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.