OUP accepted manuscript

Plant roots acquire nitrogen predominantly as two inorganic forms, nitrate (NO3-) and ammonium (NH4+), to which plants respond differentially. Rapeseed (Brassica napus L.) is an important oil-crop species with very low nitrogen-use efficiency (NUE), the regulatory mechanism of which was elusive due to the vastness and complexity of the rapeseed genome. In this study, a comparative transcriptomic analysis was performed to investigate the differential signatures of nitrogen-starved rapeseed in responses to NO3- and NH4+ treatments and to identify the key genes regulating rapeseed NUE. The two nitrogen sources differentially affected the shoot and root transcriptome profiles, including those of genome-wide nitrogen transporter and transcription factor (TF)-related genes. Differential expression profiling showed that BnaA6.NRT2;1 and BnaA7.AMT1;3 might be the core transporters responsible for efficient NO3- and NH4+ uptake, respectively; the TF genes responsive to inorganic nitrogen, specifically responding to NO3-, and specifically responsive to NH4+ were also identified. The genes which were commonly and most significantly affected by both NO3- and NH4+ treatments were related to glutamine metabolism. Among the glutamine synthetase (GS) family genes, we found BnaA2.Gln1;4, significantly responsive to low-nitrogen conditions and showed higher transcription abundance and GS activity in the leaf veins, flower sepals, root cortex and stele, silique petiole and stem tissues. These characters were significantly different from those of AtGln1;4. The heterologous overexpression of BnaA2.Gln1;4 in Arabidopsis increased plant biomass, NUE, GS activity and total amino acid concentrations under both sufficient- and low-nitrogen conditions. Overall, this study provided novel information about the genes involved in the adaptation to different nitrogen regimes and identified some promising candidate genes for enhancing NUE in rapeseed.