Global transcriptome and weighted gene co-expression network analyses reveal hybrid-specific modules and candidate genes related to plant height development in maize.

key messageWeighted gene co-expression network analysis was explored to find key hub genes involved in plant height regulation. Plant height, an important trait for maize breeding because of its close relatedness to lodging resistance and yield, has been reported to be determined by multiple qualitative and quantitative genes. However, few genes related to plant height have been characterized in maize. Herein, three different maize hybrids, with extremely distinct plant height, which were further classified into low (L), middle (M) and high (H) group, were selected for RNA sequencing at three key developmental stages, namely, jointing stage (I), big flare period (II) and tasseling stage (III). Intriguingly, transcriptome profiles for hybrids ranging from low to high group exhibited significantly similarity in both jointing stage and big flare period. However, remarkably larger differentially expressed genes could be detected between hybrid from low to either middle or high group in tasseling stage. These results were repeatedly observed in both phenotyping and gene ontology enrichment analysis, indicating that transition from big flare period to tasseling stage plays a critical role in determination of plant height. Furthermore, weighted gene co-expression network analysis was explored to find key hub genes involved in plant height regulation. Hundreds of candidate genes, encoding various transcription factors, and regulators involved in internode cell regulation and cell wall synthesis were identified in our network. More importantly, great majority of candidates were correlated to either metabolism or signaling pathway of several plant phytohormones. Particularly, numerous functionally characterized genes in gibberellic acid as well as brassinosteroids signaling transduction pathways were also discovered, suggesting their critical roles in plant height regulation. The present study could provide a modestly comprehensive insight into networks for regulation of plant height in maize.