An incoherent feed-forward loop coordinates nitrate uptake and tillering in wheat

Nitrogen fertilization has increased wheat yields since the Green Revolution, but these gains have plateaued. Excessive nitrogen application reduces nitrogen use efficiency by promoting nonproductive tillers, and balancing nitrogen uptake with tillering in wheat remains a challenge. Here, we demonstrate that TaNLP3 is a master regulator of nitrate signaling that, together with the SWI/SNF complex, regulates chromatin accessibility to fine-tune nitrate uptake and tiller formation through a temporal transcriptional cascade. In short-term nitrate signaling, TaNLP3 activates the expression of primary nitrate response genes, including TaNRT2.1, to promote nitrate uptake. In long-term nitrate signaling, TaLBD38 is induced by TaNLP3 and represses TaNRT2.1, limiting nitrate uptake and promoting tillering by inhibiting TaCKX4/5, negative modulators of tillering. Furthermore, we identified elite haplotypes of TaNLP3-3B, TaLBD38-4A, and TaNRT2.1-6B4 that enable higher yields under equivalent nitrogen supply. Taken together, our findings reveal the dynamic coordination between nitrate uptake and tillering under fluctuating nitrogen conditions, offering valuable resources for breeding wheat varieties with improved nitrogen use efficiency and productivity.