## 4 Discussion
### Expression Levels of Genes Involved in Cell Wall Biogenesis Decreased with AT treatment  
In this work, the root length, root surface area and root volume in the NT treatment group were significantly greater than those in the AT treatment group, which demonstrated that AT inhibited root development. All plant cells are surrounded by an extensible primary cell wall, which contains cellulose, pectin and noncellulosic polysaccharides [50]. Additions and rearrangements of cell wall components are required throughout growth and development, such as for cell elongation and cell proliferation in developing roots [51]. The _AtCESA_ gene superfamily, which encodes the catalytic subunits of cellulose synthase, has been identified in hundreds of seed plant species and well characterized in _Arabidopsis_[52]. Plants have evolved complex regulatory mechanisms, including expression of _CESA_ genes and modification of _CESA_ proteins, to control cellulose biosynthesis and assembly in cell  
Figure 8: A proposed model for N metabolism and other primary metabolism in oilseed rape roots in NT and AT treatment groups. The colored rectangles indicate the following: red, N transporters, enzymes or physiological processes that increased; and green, N transporters, enzymes or physiological processes that decreased. Red or green solid arrows represent the strengthening or weakening of physiological processes, and black solid arrows represent physiological processes that did not significantly change. Compared with AT treatment, NT treatment led to upregulation of the _NRT/AMT_ genes in roots and facilitated NO3– uptake. Simultaneously, _NR_ and _NIR_ activities increased, and _BnNRT1.5_ gene expression was upregulated, which facilitated more NO3– transport into shoots from roots for assimilation under NT treatment. This enhanced transport was beneficial for oilseed rape growth because NO3– assimilation efficiency is known to be higher in shoots than in roots due to the utilization of solar energy by oilseed rape shoots. Furthermore, carbohydrate metabolism (CAR), lipid metabolism (LIP), protein metabolism (PRO), and CWB were promoted by NT treatment, which facilitated oilseed rape root growth and development. Thus, NT treatment was more beneficial to oilseed rape growth than was AT treatment.  
walls [53]. In this work, genes related to primary CWB (GO: 0009833) (Figure 8) were differentially expressed under the different N treatments, including _BnCESA1_, _BnCESA2_, _BnCESA3_, and _BnCESA6_, which encode cellulose synthase family proteins (Table S4). In _A. thaliana_, _AtCESA1_ (_A. thaliana_ cellulose synthase _1_), _AtCESA3_, and _AtCESA6_ are preferentially expressed in expanding tissues [54], but _AtCESA2_ is poorly understood. The NT treatment greatly increased the transcript levels of _BnCESA1_, _BnCESA2_, _BnCESA3_, and _BnCESA6_, whereas the AT treatment had no distinct effects (Table S5, Figure 8). This difference might constitute one line of evidence explaining why AT treatment inhibited root development in oilseed rape in this study.  
In summary, there were significant differences between NO3- and NH4+ nutrition with regard to biomass, N accumulation and root architecture in oilseed rape cultivars. The potential molecular mechanisms may be explained by most of the downregulated genes being related to N metabolism, cell wall biosynthesis, and carbohydrate, lipid, and protein metabolism in oilseed rape exposed to a high concentration of NH4+. To the best of our knowledge, this is the first comprehensive transcriptomic analysis of oilseed rape grown under NO3- and NH4+ conditions, and the findings provide valuable resources for better understanding the responses of oilseed rape to NO3- and NH4+ and subsequent improvement of N utilization efficiency.