Quinoa (Chenopodium quinoa) is an Andean allotetraploid pseudocereal crop with higher protein content and balanced amino acid composition in the seeds. Ammonium (NH₄⁺), a direct source of organic nitrogen assimilation, mainly transported by specific transmembrane ammonium transporters (AMTs), plays important roles in the development, yield, and quality of crops. Many AMTs and their functions have been identified in major crops; however, no systematic analyses of AMTs and their regulatory networks, which is important to increase the yield and protein accumulation in the seeds of quinoa, have been performed to date. In this study, the CqAMTs were identified, followed by the quantification of the gene expression, while the regulatory networks were predicted based on weighted gene co-expression network analysis (WGCNA), with the putative transcriptional factors (TFs) having binding sites on the promoters of CqAMTs, nitrate transporters (CqNRTs), and glutamine-synthases (CqGSs), as well as the putative TF expression being correlated with the phenotypes and activities of GSs, glutamate synthase (GOGAT), nitrite reductase (NiR), and nitrate reductase (NR) of quinoa roots. The results showed a total of 12 members of the CqAMT family with varying expressions in different organs and in the same organs at different developmental stages. Complementation expression analyses in the triple mep1/2/3 mutant of yeast showed that except for CqAMT2.2b, 11/12 CqAMTs restored the uptake of NH₄⁺ in the host yeast. CqAMT1.2a was found to mainly locate on the cell membrane, while TFs (e.g., CqNLPs, CqG2Ls, B3 TFs, CqbHLHs, CqZFs, CqMYBs, CqNF-YA/YB/YC, CqNACs, and CqWRKY) were predicted to be predominantly involved in the regulation, transportation, and assimilation of nitrogen. These results provide the functions of CqAMTs and their possible regulatory networks, which will lead to improved nitrogen use efficiency (NUE) in quinoa as well as other major crops.

Nitrogen application rate and topping are two key agronomic factors affecting tobacco leaf quality, but the synergistic regulatory mechanisms remain unclear. This study aimed to elucidate the physiological and molecular mechanisms by which nitrogen application rate and topping synergistically regulate tobacco leaf quality, and to identify key candidate genes involved in nicotine biosynthesis. Using the tobacco cultivar K326, three nitrogen application levels were established: low (0 kg/ha), medium (120 kg/ha), and high (210 kg/ha). Agronomic traits and rhizosphere soil physicochemical properties were monitored, carbon and nitrogen metabolism enzyme activities were measured before and after topping, and mature leaf chemical composition was determined, integrated with transcriptomic and metabolomic analyses. The results showed that medium nitrogen achieved high yield while enhancing organic matter turnover efficiency, reducing rhizosphere water-soluble chloride content, and alleviating soil acidification and ammonium–potassium ion uptake competition caused by excessive fertilization. Combined with topping, it significantly enhanced carbon and nitrogen metabolism, promoted starch-to-soluble-sugar conversion, and increased nicotine accumulation, thereby optimizing leaf chemical composition. Integrated transcriptomic and metabolomic analyses revealed that medium nitrogen combined with topping exerted the most pronounced effects on gene expression and metabolite accumulation. Weighted gene co-expression network analysis (WGCNAs) identified a module highly correlated with nicotine biosynthesis, with hub genes mainly annotated as cytochrome P450 and terpene synthase family members. In conclusion, this study elucidated the molecular mechanisms by which the combination of medium nitrogen application and topping, as an integrated agronomic practice, improves tobacco leaf quality through coordinating carbon-nitrogen metabolism and optimizing chemical composition, and identified key candidate genes potentially regulating nicotine biosynthesis, providing a theoretical basis for nitrogen fertilizer management and high-quality cultivation of tobacco.