Transcriptome analysis of rice (Oryza sativa L.) in response to ammonium resupply reveals the involvement of phytohormone signaling and the transcription factor OsJAZ9 in reprogramming of nitrogen uptake and metabolism.

NH₄⁺ is not only the primary nitrogen for rice, a well-known NH₄⁺ specialist, but is also the chief limiting factor for its production. Limiting NH₄⁺ triggers a series of physiological and biochemical responses that help rice optimise its nitrogen acquisition. However, the dynamic nature and spatial distribution of the adjustments at the whole plant level during this response are still unknown. Here, nitrogen-starved rice seedlings were treated with 0.1 mM (NH₄)₂SO₄ for 4 or 12 h, and then the shoots and roots were harvested for RNA-Seq analysis. We identified 138 and 815 differentially expressed genes (DEGs) in shoots, and 597 and 1074 in roots following 4 and 12 h treatment, respectively. Up-regulated DEGs mainly participated in phenylpropanoid, sugar, and amino acid metabolism, which was confirmed by chemical content analysis. The transcription factor OsJAZ9 was the most pronouncedly induced component under low NH₄⁺ in roots, and a significant increase in root growth, NH₄⁺ absorption, amino acid, and sugar metabolism in response to resupplied NH₄⁺ following nitrogen starvation was identified in JAZ9ox (OsJAZ9-overexpressed) and coi1 (OsCOI1-RNAi). Our data provide comprehensive insight into the whole-plant transcriptomic response in terms of metabolic processes and signaling transduction to a low-NH₄⁺ signal, and identify the transcription factor OsJAZ9 and its involvement in the regulation of carbon/nitrogen metabolism as central to the response to low NH₄⁺.