Gene Regulatory Network of Secondary Cell Wall Biosynthesis during VND7 Induced de novo Xylem Formation

Accumulation of -omics data allows us to analyze the coordination and cooperation of multiple genes involved in different biological processes. Gene regulatory networks (GRNs) are used to characterize the regulatory relationships between transcription factors and downstream genes involved in different biological processes. The secondary cell wall (SCW) formation is involved with many important biological processes in plants, such as stress defense, mechanical reinforcement, and the transportation of water and nutrients. We construct GRNs based on the time-series data of VND7-induced de novo SCW formation using multiple algorithms, and then evaluate each GRN model based on the MYB46 experimental validated regulation data. From the optimal GRN model, we not only identify 8 TFs that have been previously demonstrated as the master regulators of SCW formation, but also show 6 novel SCW regulators which include EGL3, DREB19, TCP14, BZIP61, RGA2, and a zinc-finger type TF. From further in silico annotation of the downstream genes that are regulated by these TFs, we find the shared transcriptional program between the SCW formation and the processes of photosynthesis and drought response. Overall, our work suggests a pipeline for reconstructing and analyzing GRN to pinpoint gene functions in biological processes.