###### Abstract  
Nitrate (NO3-) and ammonium (NH4+) are the main inorganic nitrogen (N) sources absorbed by oilseed rape, a plant that exhibits genotypic differences in N efficiency. In our previous study, the biomass, N accumulation, and root architecture of two oilseed rape cultivars, Xiangyou 15 (high N efficiency, denoted \"15\") and 814 (low N efficiency, denoted \"814\"), were inhibited under NH4+ nutrition, though both cultivars grew normally under NO3- nutrition. To gain insight into the underlying molecular mechanisms, transcriptomic changes were investigated in the roots of 15 and 814 plants subjected to nitrogen-free (control, CK), NO3- (NT), and NH4+ (AT) treatments at the seedling stage. A total of 14,355 differentially expressed genes (DEGs) were identified. Among the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway categories of these DEGs, carbohydrate metabolism, lipid metabolism, protein metabolism, and cell wall biogenesis were inhibited by AT treatment. Interestingly, DEGs such as N transporters, genes involved in N assimilation and _CESA_ genes related to cellulose synthase were also mostly downregulated in the AT treatment group. This downregulation of genes related to crucial metabolic pathways resulted in inhibition of oilseed rape growth after AT treatment. o 1 391 391 391 391 391 391 391 391 391 391 391 391 391 391 391 391 391 391 391 391 391 392 392 393 393 394 395 396 397 398 399 397 398 399 399 399 390 391  
prefer NH4\({}^{+}\) and grow better under NH4\({}^{+}\) nutrition [2; 3; 4], whereas others such as wheat, watermelon, and _Arabidopsis thaliana_ prefer NO3\({}^{-}\)[5; 6; 7]. Oilseed rape is a crucial source of plant oil worldwide, with a large demand for N fertilizer, and judicious application of N fertilizer can significantly improve the yield of oilseed rape [8]. Furthermore, a certain amount of N can increase oilseed rape biomass and yield, though excessive N decreases the oil content of oilseed rape [9]. Moreover, different oilseed rape genotypes exhibit distinct differences in their absorption and utilization of N fertilizers [10]. In most dryland soils, NO3\({}^{-}\) is the primary form of inorganic N; however, in natural environments, the N form may be highly variable, with NH4\({}^{+}\) often predominant in acidic and/or water-logged soils [11; 12]. Dryland and acidic soils are both suitable for planting oilseed rape. To date, NO3\({}^{-}\) accumulation and utilization have been a major emphasis of studies on N use in oilseed rape. In contrast, less is known about the growth performance and gene expression of these plants under NH4\({}^{+}\) nutrition and whether oilseed rape cultivars with different N efficiencies have the same or different reactions to NO3\({}^{-}\) and NH4\({}^{+}\) nutrition. Hence, we evaluated the effects of NO3\({}^{-}\) and NH4\({}^{+}\) on the growth and physiology of two oilseed rape cultivars with different N efficiencies. The results demonstrated that NH4\({}^{+}\) greatly inhibited the growth and root architecture of both cultivars but that they grew and developed normally under NO3\({}^{-}\) nutrition [13]. Although NO3\({}^{-}\) and NH4\({}^{+}\) clearly have distinct effects on the growth of the two cultivars, studies of oilseed rape under NO3\({}^{-}\) and NH4\({}^{+}\) nutrition at the molecular level are rare. Oilseed rape is closely related to _Arabidopsis_. Differences in gene expression in _Arabidopsis_ under NO3\({}^{-}\) and NH4\({}^{+}\) nutrition have been explored using microarray analysis, and the results suggest that the underlying bases of nitrate- and ammonium-specific patterns of gene expression differ [14]. In general, comparative high-throughput RNA sequencing (RNA-Seq) analyses of different cultivars and treatments can provide a deep understanding of the actual metabolic pathways involved, and a rice transcriptomic encyclopedia has recently been used to explore a large number of ammonium-responsive genes [2]. Moreover, [PERSON] et al.