Integrating Orthology and Cross-Species Transcriptomics to Unravel Root Drought Responses in Faba Bean and Maize

Abstract

During soil drying, roots in upper and deeper soil layers experience different hydraulic environments, yet the molecular programs that accompany and potentially drive depth-specific changes in root water uptake capacity remain poorly understood. Here, we address this gap by coupling depth-resolved RNA-seq with previously measured hydraulic uptake profiles in pot-grown faba bean (Vicia faba) and maize (Zea mays), two crop species with contrasting root architecture, sampled from upper (drying) and lower (comparatively wet) root zones at the onset and after four days of soil drying. Differential expression analysis revealed strongly top-region of the roots dominated transcriptional responses in both species, consistent with the steeper hydraulic challenge in drying upper layers. Maize displayed a TIP- and dehydrin-dominated drought response, whereas faba bean induced NIP-like aquaporins and a broader LEA repertoire, suggesting divergent strategies for root water and cellular stress protection. To compare transcriptome responses across these distally related species, we grouped orthologous genes across 26 species using OrthoFinder. With this approach, we identified 905 drought-responsive orthogroups, of which only 17% were shared between species despite broadly convergent gene onthology (GO) enrichment profiles. Phylogenetic tracing showed that 95.7% of faba bean-specific and 90.3% of maize-specific drought-responsive orthogroups are conserved across monocot and dicot lineages, indicating that species-specific drought transcriptomes arise primarily through differential recruitment of ancestral gene families rather than lineage-specific innovation. These findings define a molecular framework linking root hydraulic architecture to gene regulation under drought and identify conserved transcriptional regulatory hubs as targets for broad-spectrum abiotic stress improvement in both faba bean and maize.