## 5 Conclusions  
In the present study, the biomass, N accumulation and root architecture of two oilseed rape cultivars with different N efficiencies were significantly and analogously influenced by NO3- and NH4+ nutrition. To reveal the molecular mechanisms responsible for the differences in the two cultivars in response to CK, NO3-, and NH4+ conditions, RNA-Seq of root samples collected at 48 h after exposure to different N treatments was performed to analyze gene expression patterns related to N metabolism and other crucial metabolic pathways in plants. NH4+ directly decreased the biomass, N accumulation, and root architecture of the two oilseed rape cultivars and affected the overall metabolism of shoots and roots; this result was related to downregulated expression of NO3-/NH4+ transporters or channels and crucial metabolic pathways (including carbohydrate, lipid, and protein metabolism) in the two oilseed rape. The root expression levels of _CESA_ genes encoding cellulose synthase decreased under NH4+ nutrition, inhibiting root growth. These results provide insight into the regulatory mechanisms of some candidate genes, which will reveal the molecular mechanisms of decreased oilseed rape growth in response to a high concentration of NH4+ as the sole N source.  
**Supplementary Materials:** The following are available online at [[http://www.mdpi.com/2073-4425/10/5/391/s1](http://www.mdpi.com/2073-4425/10/5/391/s1)]([http://www.mdpi.com/2073-4425/10/5/391/s1](http://www.mdpi.com/2073-4425/10/5/391/s1)), Figure S1: Enriched Gene Ontology terms in comparison group CKvsNT (15 and 814). Figure S2: Enriched Gene Ontology terms in comparison group CKvsNT (15 and 814). Figure S3: Top fifteen enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in CKvsNT (15 and 814). Figure S4: Top fifteen enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in CKvsAT (15 and 814). Figure S5: Numbers of up- and downregulated DEG and fold change were analyzed in 15 vs814 (NT). Figure S6: Enriched Gene Ontology (GO) terms in 15 vs814 (NT). Figure S7: Top fifteen enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in 15 vs814 (NT). Table S1: List of primer sequences used for qRT-PCR analysis. Table S2: Summary of transcriptomic data. Table S3: Information for the 14,355 significantly differentially expressed genes (DEGs) detected in the six cDNA libraries. Table S4: Pearson correlation of gene expression levels between different comparison groups. Table S5: Information on the differentially expressed genes (DEGs) involved in starch and sucrose metabolism, fatty acid biosynthesis, ribosome and plant-type primary cell wall biogenesis in the six comparison groups. Table S6: Numbers of up- and downregulated genes in each pathway involved in carbohydrate metabolism, lipid metabolism and translation in the six comparison groups. Table S7: Genes encoding NO3-/NH4+ protein transporters and assimilation enzymes differing in expression between genotypes in response to different nitrogen treatments. Table S8: Numbers of up- and downregulated DEGs related to cell wall in 15 vs814(NT). Table S9: Important DEGs related to N uptake, transport and assimilation in 15 vs814(NT).  
**Author Contributions:** [PERSON], [PERSON], and [PERSON] conceived and designed the experiments. [PERSON], [PERSON], and [PERSON] prepared the experimental materials. The bioinformatics analysis was carried out by [PERSON] and [PERSON]. [PERSON] wrote the manuscript. [PERSON], [PERSON], and [PERSON] provided intellectual input and revised the manuscript. All authors read and approved the final manuscript.  
Funding: This work was supported by the Earmarked Fund for China Agriculture Research System (CARS-13), the National Science and Technology Support Project of China (2014 BAD11B03) and the Oil Crop Innovation Team in Yunnan Province, China (2017 HC021).