Ancestral DOF27 and GDH1 haplotypes drive rice adaptation to ammonium habitats

Plant adaptation to environmental nitrogen fluctuation involves intricate regulatory mechanisms. Ammonium (NH₄⁺) serves as the primary nitrogen (N) source for rice in paddy fields. However, excessive NH₄⁺ inhibits plant growth and reduces yield. Wild rice (Oryza rufipogon Griff.) thrives in nutrient-poor marginal wetlands characterized by low-nitrogen conditions and harbors elite genetic alleles that confer ammonium-use efficiency. It remains largely elusive how plants develop the sophisticated mechanisms to sense and adapt to dynamic conditions such as nutrition availability. Here, we identify a superior allele of glutamate dehydrogenase 1 (GDH1), termed GDH1^OR, from wild-rice species Oryza rufipogon. A 5-bp insertion in the GDH1⁹³¹¹ promoter disrupts the conserved binding activity and transactivation by the N-responsive transcription factor DOF27. Notably, an R-loop structure in the promoter of DOF27 triggers low-ammonium-induced epigenetic regulation through the DOF27-GDH1 module. Targeted editing of the DOF27 promoter increases the abundance of the R-loop, thereby enhancing nitrogen-use efficiency and yield, particularly under low-nitrogen conditions. Strikingly, the elite allele GDH1^OR has been lost in modern cultivated rice during historical rice breeding. We found that GDH1^OR enhances ammonium-use efficiency and stabilizes yield by promoting NH₄⁺ uptake and assimilation under low-nitrogen conditions. Our findings reveal a novel ammonium-induced epigenetic regulatory mechanism and provide a promising strategy for enhancing ammonium-use efficiency by leveraging the ancestral alleles from wild rice in breeding programs.