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Nitrate is the main source of inorganic nitrogen for plants, which also act as signaling molecule. Present study was aimed to understand nitrate regulatory mechanism in  Brassica juncea  cultivars, with contrasting nitrogen-use-efficiency (NUE)  viz . Pusa Bold (PB, high-NUE) and Pusa Jai Kisan (PJK, low-NUE), employing RNA-seq approach. A total of 4031, 3874 and 3667 genes in PB and 2982, 2481 and 2843 genes in PJK were differentially expressed in response to early, low (0.25 mM KNO 3 ), medium (2 mM KNO 3 ) and high (4 mM KNO 3 ) nitrate treatments, respectively, as compared to control (0 mM KNO 3 ). Genes of N-uptake ( NRT1 . 1 ,  NRT1 . 8 , and  NRT2 . 1 ), assimilation ( NR1 ,  NR2 ,  NiR ,  GS1 . 3 , and  Fd-GOGAT ) and remobilization ( GDH2 ,  ASN2–3  and  ALaT ) were highly-upregulated in PB than in PJK in response to early nitrate treatments. We have also identified transcription factors and protein kinases that were rapidly induced in response to nitrate, suggesting their involvement in nitrate-mediated signaling. Co-expression network analysis revealed four nitrate specific modules in PB, enriched with GO terms like, “Phenylpropanoid pathway”, “Nitrogen compound metabolic process” and “Carbohydrate metabolism”. The network analysis also identified HUB transcription factors like mTERF, FHA, Orphan, bZip and FAR1, which may be the key regulators of nitrate-mediated response in  B .  juncea .

Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.