Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

Area of Science:

• Plant molecular biology
• Genomics
• Bioinformatics

Background:

• Gene expression regulation is crucial for biological processes.
• Gene regulatory networks (GRNs) map transcription factors (TFs) to target genes.
• Understanding GRNs in maize (Zea mays) is vital for crop improvement.

Purpose of the Study:

• To construct multiple coexpression-based GRNs for maize using extensive transcriptome data.
• To investigate TF-target gene associations and their relationship with gene expression variation.
• To identify TFs regulating key metabolic pathways and provide targets for breeding.

Main Methods:

• Analysis of >6000 public maize RNA sequencing samples.
• Generation of 45 coexpression-based GRNs.
• Prediction of TF-target relationships and integration with eQTL data.

Main Results:

• Multiple maize GRNs revealed distinct TF-target associations and biological processes.
• Presence/absence of TF genes, not expression levels, better predicts target gene expression changes.
• 68 TFs were linked to 74 trans-eQTL hotspots in various metabolic pathways.

Conclusions:

• Developing multiple GRNs is effective for discovering gene regulators in maize.
• Identified TFs offer potential targets for maize breeding and biotechnological applications.
• This study enhances understanding of gene regulation in a major crop species.