Transcriptome sequencing analysis of maize roots reveals the effects of substrate and root hair formation in a spatial context

Abstract Background Plant roots sense and respond to changes in their soil environment, but conversely contribute rhizosphere organization through chemical, mechanical biotic interactions. Transcriptomic profiling of plant can be used assess how the adjusts its gene expression relation genotype processes; thus enabling us achieve a better understanding root-soil Methods We standardized column experimental platform investigate impact texture (loam, sand) root hair formation (wildtype, defective rth3 mutant) spatial context (three sampling depths) assessed maize transcriptomic profiles using next-generation RNA sequencing. Results Substrate induced largest patterns, affecting functions related immunity, stress, growth water uptake. Genes with depth-related levels were associated defense. The influence hairs mainly manifested differential epidermal cell differentiation wall organization, defense response-related genes. type strongly modified patterns depth elongation, highlighting strong texture. Conclusions Our results demonstrate that substrate, interactively affect expression, suggest feedback processes between plant, microbiome. obtained form foundational basis for integration interpretation future experiments utilizing same platform.