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

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