Legumes can utilize atmospheric nitrogen via symbiotic nitrogen fixation, but this process is inhibited by high soil inorganic nitrogen. So far, how high nitrogen inhibits N₂ fixation in mature nodules is still poorly understood. Here we construct a co-expression network in soybean nodule and find that a dynamic and reversible transcriptional network underlies the high N inhibition of N₂ fixation. Intriguingly, several NAC transcription factors (TFs), designated as Soybean Nitrogen Associated NAPs (SNAPs), are amongst the most connected hub TFs. The nodules of snap1/2/3/4 quadruple mutants show less sensitivity to the high nitrogen inhibition of nitrogenase activity and acceleration of senescence. Integrative analysis shows that these SNAP TFs largely influence the high nitrogen transcriptional response through direct regulation of a subnetwork of senescence-associated genes and transcriptional regulators. We propose that the SNAP-mediated transcriptional network may trigger nodule senescence in response to high nitrogen.

Soybean serves as a primary global source of high-quality protein and oil, and improving its yield and quality is critical for global food security. Despite advances in gene editing and molecular breeding, the regulatory mechanisms underlying leaf senescence remain poorly understood, limiting yield gains in soybean. Building on our previous identification of SNAP1/2/3/4—a cluster of NAC transcription factors regulating nodule senescence—we reported their pivotal role in modulating aboveground agronomic traits. The knockout mutants of SNAP1/2/3/4 exhibited delayed leaf senescence and prolonged maturation period. These changes led to concurrent improvements in grain yield, seed size, and oil content. Our study reveals a dual regulatory function of SNAP1/2/3/4 in both nodule and leaf senescence and uncovers a molecular target to coordinately enhance soybean yield and quality by fine-tuning of developmental timing.