Construction of a Hierarchical Gene Regulatory Network to Reveal the Drought Tolerance Mechanism of Shanxin Poplar

Abstract

Drought stress is a common adverse environment that plants encounter, and many drought-tolerant genes have been characterized. The gene regulatory network (GRN) is important in revealing the drought tolerance mechanism. Here, to investigate the regulatory mechanism of Shanxin poplar (Populus davidiana × P. bolleana) responding to drought stress, a three-layered GRN was built, and the regulatory relationship between genes in the GRN were predicted from expression correlation using a partial correlation coefficient-based algorithm. The GRN contains 1869 regulatory relationships, and includes 11 and 19 transcription factors (TFs) in the first and second layers, respectively, and 158 structural genes in the bottom layers involved in eight enriched biological processes. ChIP-PCR and qRT-PCR based on transient transformation were performed to validate the reliability of the GRN. About 88.0% of predicted interactions between the first and second layers, and 82.0% of predicted interactions between the second and third layers were correct, suggesting that the GRN is reliable. Six TFs were randomly selected from the top layer for characterizing their function in drought, and all of these TFs can confer drought tolerance. The important biological processes related to drought tolerance were identified, including “response to jasmonic acid”, “response to oxidative stress”, and “response to osmotic stress”. In this GRN, PdbERF3 is predicted to play an important role in drought tolerance. Our data revealed the key regulators, TF-DNA interactions, and the main biological processes involved in adaption of drought stress in Shanxin poplar.

Keywords

• gene regulatory network (GRN)
• drought stress
• Shanxin poplar (<i>Populus davidiana</i> × <i>P. bolleana</i>)
• transcription factor
• TF-DNA interactions
• PdbERF3