Comparative Transcriptome Analysis in Oilseed Rape (Brassica napus) Reveals Distinct Gene Expression Details between Nitrate and Ammonium Nutrition

Nitrate (NO(3)(−)) and ammonium (NH(4)(+)) 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 NH(4)(+) nutrition, though both cultivars grew normally under NO(3)(−) 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), NO(3)(−) (NT), and NH(4)(+) (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.