Large-scale RNAseq analysis provide a new insight into the critical genes and regulatory networks of tiller development mediated by gibberellin in sugarcane

Abstract

Tillering plays a key role in sugarcane growth, development, and cane yield. Gibberellin (GA) and its biosynthesis inhibitor, paclobutrazol, have been used to manipulate the tiller production in sugarcane planting. However, the key genes and regulatory networks of sugarcane tiller development remain unclear. In this study, we applied GA3 and paclobutrazol to soak the sugarcane seeds for generating samples with varying tiller numbers. A total of 54 samples from multiple tissues of three tillering stages were employed for transcriptome sequencing using two full-length transcript isoform sequences datasets as reference. We observed significant downregulation of two genes within the GA metabolism pathway in response to the GA synthesis inhibitor. Additionally, we noted a substantial enrichment of genes associated with photosynthesis following treatment with GA3 or paclobutrazol. Using all the differentially expressed genes (DEGs) between each sample group, 41 gene modules were generated in the coexpression network. The associations between modules and traits were performed. The Gene Ontology (GO) enrichment, KEGG pathway enrichment, and hub genes analysis were implemented in the modules correlated with traits, especially, the modules correlated with GA3 content and tiller number were emphasized. Notably, the pathway of ubiquitin-mediated proteolysis were enriched in both the GA3 content positive correlated module and the tiller number negative correlated module, while an E3 ubiquitin ligase gene, RZFP34, was the top hub gene in these two modules, indicating the vital role of ubiquitin-mediated proteasomal degradation system in tillering regulation in sugarcane. Our study provides a comprehensive insight into regulatory networks involved in GA-mediated regulation of tiller development in sugarcane, which would lay the foundation of hormone regulation to promote sugarcane production.