Dynamic transcriptome analysis indicates extensive and discrepant transcriptomic reprogramming of two rapeseed genotypes with contrasting NUE in response to nitrogen deficiency

Aims Oilseed rape (Brassica napusL.) has high nitrogen (N) requirement for its optimal growth and yield. However, little is known about the transcriptomic reprogramming of rapeseed in response to N deficiency. Methods Two rapeseed genotypes with contrasting N use efficiency (NUE) were used to perform whole-transcriptome sequencing on the shoots and roots supplied with or without N in a time-course experiment. Results A total of 24,435 differentially expressed genes (DEGs) were identified. Among them, 8811 genes were differentially expressed between two N treatments and between the two genotypes. Coexpression networks reveal central N-deficiency-response modules with diverse expression patterns between the two genotypes. Major expression hubs involved in phytohormone signaling were identified and showed strong association with DEGs in each module. Genes involved in N uptake and assimilation, carbohydrate catabolism, amino acid metabolism, and fatty acid biosynthesis were enriched between the two genotypes under N deprivation. In addition, photosynthesis and carbon assimilation declined under prolonged N stress, but starch biosynthesis was enhanced by N deprivation. Conclusions Our results revealed N-responsive genes and gene networks and expanded the knowledge of regulatory hubs in N-deprived rapeseed. The detailed gene information might assist the genetic improvement of NUE inB. napus.