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

Scientific Reports
Parul GoelAnil Kumar Singh

Abstract

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 KNO3), medium (2 mM KNO3) and high (4 mM KNO3) nitrate treatments, respectively, as compared to control (0 mM KNO3). 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 transc...Continue Reading

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Citations

May 23, 2019·Molecular Biology Reports·Shilpa GuptaSurinder Singh Banga
Jan 26, 2020·Scientific Reports·Jagesh Kumar TiwariSwarup Kumar Chakrabarti
Jul 27, 2021·Frontiers in Plant Science·Alexandre Hild AonoAnete Pereira de Souza

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Datasets Mentioned

BETA
PRJNA383771

Methods Mentioned

BETA
RNA-Seq
chip

Software Mentioned

BLASTX
R statistical package
DistTOM
DisTOM
Weighted Gene Co - Expression Network Analysis ( WGCNA ) library
- CAP3
trans
SOAPdenovo assembler
Bowtie
SOAPdenovo

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