Cell type identity determines transcriptomic immune responses in Arabidopsis thaliana roots

Root pathogens are a major thread in global crop production and protection strategies are required to sustainably enhance the efficiency of root immunity. Our understanding of root immunity is still limited in comparison to the knowledge gained for the regulation of immune response in leaves. In an effort to reveal the organisation of root immunity in roots, we undertook a cell type-specific transcriptome analysis to identify gene networks in epidermis, cortex and pericycle cells of Arabidopsis roots upon treatment with two immunity elicitors, bacterial microbe-associated molecular pattern flagellin and the endogenous damage-associated molecular pattern Pep1. Our analyses revealed that both elicitors induced cell type-specific immunity gene networks. Interestingly, both elicitors did not alter cell identity determining gene networks. Using sophisticated paired motif promoter analyses, we identified key transcription factor pairs involved in the regulation of cell type-specific immunity networks. In addition, our data show that cell identity networks are liaised with cell immunity networks to activate cell type-specific immune response according to the functional capabilities of each cell type. The response of epidermis, cortex and pericycle cells, isolated using Fluorescence Activated Cell Sorting (FACS) was analysed 2 hours after treatment with 1uM flg22 or 1uM Pep1 or H2O in Arabidopsis thaliana Col0 roots; genotypes carried GFP reporters marking either epidermis, cortex or pericycle root cells. Gene expression was analysed using RNAseq, aligned to the TAIR10 genome.