Identification of Gene Regulatory Network for Nitrogen-Promoted Tiller Regrowth in Perennial Rice

Perennial rice, which has shortened rhizomes derived from Oryza longistaminata, regenerates tillers from shoot basal regions after harvest, enabling multi-year perenniality. This crop represents an innovative approach to enhance global food security and promote sustainable agricultural development. However, the mechanisms regulating tiller regrowth in perennial rice remain poorly understood. Our study demonstrates that nitrogen (N) fertilizer application more effectively promotes tiller bud regrowth in perennial rice compared to annual rice. RNA-seq analysis identified 1038 differentially expressed genes (DEGs) in the shoot basal regions between perennial and annual rice after N application. Weighted Gene Co-expression Network Analysis (WGCNA) hierarchically clustered these DEGs into seven modules. The yellow module exhibited a significant positive correlation with tiller bud growth. Five core genes, OsCCA1, OsRDD1, OsRDD2 and OsMTG3 from the yellow module and OsGSNOR from the brown module involved in N or magnesium (Mg) utilization, exhibited significantly increased expression in perennial rice. Knockout of OsCCA1 inhibited N-promoted tiller bud growth in perennial rice. OsCCA1 may regulate tiller bud growth by regulating hundreds of downstream genes based on the integration of RNA-seq data and the reported DAP-seq data. Additionally, perennial rice showed reduced indole-3-acetic acid (IAA) level and downregulated expression of auxin signaling response genes in shoot basal regions. Furthermore, IAA negatively regulated the expression of the five core genes and inhibited tiller growth in perennial rice. Our findings suggest that perennial rice efficiently utilizes N to promote tiller regrowth, potentially through regulating genes associated with IAA metabolism, auxin signaling, nutrient utilization, and plant growth.