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

Abstract

Since the Green Revolution, nitrogen fertilizer has boosted wheat yields, but gains have plateaued. Excessive nitrogen reduces nitrogen use efficiency (NUE) by promoting nonproductive tillers, and balancing nitrogen uptake with tillering remains a challenge in wheat. Here, we identified TaNLP3 as a master regulator of nitrate signaling that, with the SWI/SNF complex, regulates chromatin accessibility to fine-tune nitrate uptake and tiller formation via a temporal transcriptional cascade. In short-term nitrate signaling, TaNLP3 activates the expression of primary nitrate response (PNR) genes, including TaNRT2.1, to promote nitrate uptake. In long-term nitrate signaling, TaLBD38 induced by TaNLP3 represses TaNRT2.1, limiting nitrate uptake, while promoting tillering by inhibiting TaCKX4/5, negative modulators of tillering. We further identified elite haplotypes of TaNLP3-3B, TaLBD38-4A, and TaNRT2.1-6B4 that enable higher yield under equivalent nitrogen supply, offering valuable resources for breeding wheat varieties with improved NUE. Together, our findings reveal the dynamic coordination between nitrate uptake and tillering under fluctuating nitrogen conditions, offering insights for the sustainable improvement of wheat productivity.