Integrated transcriptomic analysis identifies coordinated responses to nitrogen and phosphate deficiency in rice

Nitrogen (N) and phosphorus (P) are two primary components of fertilizers for crop production. Coordinated acquisition and utilization of N and P are crucial for plants to achieve nutrient balance and optimal growth in a changing rhizospheric nutrient environment. However, little is known about how N and P signaling pathways are integrated. We performed transcriptomic analyses and physiological experiments to explore gene expression profiles and physiological homeostasis in the response of rice (Oryza sativa) to N and P deficiency. We revealed that N and P shortage inhibit rice growth and uptake of other nutrients. Gene Ontology (GO) analysis of differentially expressed genes (DEGs) suggested that N and Pi deficiency stimulate specific different physiological reactions and also some same physiological processes in rice. We established the transcriptional regulatory network between N and P signaling pathways based on all DEGs. We determined that the transcript levels of 763 core genes changed under both N or P starvation conditions. Among these core genes, we focused on the transcription factor gene NITRATE-INDUCIBLE, GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1) and show that its encoded protein is a positive regulator of P homeostasis and a negative regulator of N acquisition in rice. NIGT1 promoted Pi uptake but inhibited N absorption, induced the expression of Pi responsive genes PT2 and SPX1 and repressed the N responsive genes NLP1 and NRT2.1. These results provide new clues about the mechanisms underlying the interaction between plant N and P starvation responses.

Automated summary

Nitrogen (N) and phosphorus (P) are essential components of fertilizers for crop production. However, the integration of N and P signaling pathways in plants remains poorly understood. In this study, we investigated the gene expression profiles and physiological responses of rice (Oryza sativa) to N and P deficiency. We found that N and P shortage significantly inhibited rice growth and nutrient uptake. Through the analysis of differentially expressed genes (DEGs), we identified specific physiological reactions and processes induced by N and Pi deficiency. We also discovered a transcriptional regulatory network between N and P signaling pathways, with a focus on the transcription factor gene NITRATE-INDUCIBLE, GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1), which plays a role in P homeostasis and N acquisition in rice.