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

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

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...

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Autores principales: Parul Goel, Nitesh Kumar Sharma, Monika Bhuria, Vishal Sharma, Rohit Chauhan, Shivalika Pathania, Mohit Kumar Swarnkar, Vandna Chawla, Vishal Acharya, Ravi Shankar, Anil Kumar Singh
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Publicado: Nature Portfolio 2018
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Acceso en línea:https://doaj.org/article/549a1697b4724d8fb40e873943dc3fe6
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spelling oai:doaj.org-article:549a1697b4724d8fb40e873943dc3fe62021-12-02T15:07:59ZTranscriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.10.1038/s41598-018-25826-62045-2322https://doaj.org/article/549a1697b4724d8fb40e873943dc3fe62018-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-25826-6https://doaj.org/toc/2045-2322Abstract 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 transcription factors like mTERF, FHA, Orphan, bZip and FAR1, which may be the key regulators of nitrate-mediated response in B. juncea.Parul GoelNitesh Kumar SharmaMonika BhuriaVishal SharmaRohit ChauhanShivalika PathaniaMohit Kumar SwarnkarVandna ChawlaVishal AcharyaRavi ShankarAnil Kumar SinghNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-18 (2018)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Parul Goel
Nitesh Kumar Sharma
Monika Bhuria
Vishal Sharma
Rohit Chauhan
Shivalika Pathania
Mohit Kumar Swarnkar
Vandna Chawla
Vishal Acharya
Ravi Shankar
Anil Kumar Singh
Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
description 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 transcription factors like mTERF, FHA, Orphan, bZip and FAR1, which may be the key regulators of nitrate-mediated response in B. juncea.
format article
author Parul Goel
Nitesh Kumar Sharma
Monika Bhuria
Vishal Sharma
Rohit Chauhan
Shivalika Pathania
Mohit Kumar Swarnkar
Vandna Chawla
Vishal Acharya
Ravi Shankar
Anil Kumar Singh
author_facet Parul Goel
Nitesh Kumar Sharma
Monika Bhuria
Vishal Sharma
Rohit Chauhan
Shivalika Pathania
Mohit Kumar Swarnkar
Vandna Chawla
Vishal Acharya
Ravi Shankar
Anil Kumar Singh
author_sort Parul Goel
title Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
title_short Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
title_full Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
title_fullStr Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
title_full_unstemmed Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
title_sort transcriptome and co-expression network analyses identify key genes regulating nitrogen use efficiency in brassica juncea l.
publisher Nature Portfolio
publishDate 2018
url https://doaj.org/article/549a1697b4724d8fb40e873943dc3fe6
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