Gene expression changes in tomato hairy root cultures with pertubations in exodermis-enriched transcription factors.

This study provides the overall changes in gene expression in tomato hairy root cultures with CRISPR knockouts (ko) or 35Spro-driven overexpression (OX) of exodermis enriched transcription factors. The transcription factors investigated in this study are: SlMYB41 (Solyc02g079280.3.1), SlMYB92 (Solyc05g051550.2.1) and SlWRKY71 (Solyc02g071130.3.1). In this study, RNA was extracted and sequenced from 1cm root tips of tomato (Solanum lycopersicum) cultivar M82 hairy-root cultures to investigate the transcriptome impact of transcription factor genes, specifically SlMYB41, SlMYB92, and SlWRKY71. Hairy-root cultures were transformed with different constructs to generate three experimental groups: (1) control lines transformed with an empty vector, (2) knock-out (KO) lines transformed with CRISPR/Cas9 constructs carrying guide RNAs to specifically knock out SlMYB41, SlMYB92, and SlWRKY71, and (3) overexpression (OE) lines transformed with constructs expressing SlMYB41-3xFLAG, SlMYB92-3xFLAG, and SlWRKY71-3xFLAG under the control of the constitutive CaMV 35S promoter. For each group, mRNA was isolated from the hairy-root cultures, and RNA sequencing was performed to profile global gene expression changes associated with the knockout or overexpression of the target transcription factors.