Comparative Omics Analysis of <i>Brassica napus</i> Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles

The early and specific diagnosis of a macronutrient deficiency is challenging when seeking to better manage fertilizer inputs in the context of sustainable agriculture. Consequently, this study explored the potential for transcriptomic and metabolomic analysis of <i>Brassica napus</i> ro...

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Autores principales:	Galatéa Courbet, Aurélien D’Oria, Anne Maillard, Lun Jing, Sylvain Pluchon, Mustapha Arkoun, Stéphanie Pateyron, Christine Paysant Le Roux, Sylvain Diquélou, Alain Ourry, Jacques Trouverie, Philippe Etienne
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	macronutrient deprivations metabolic pathways metabolomic molecular indicators regulations of nutrient metabolism transcriptomic Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/36a86bcfca73411a8d90170009995fa4
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spelling	oai:doaj.org-article:36a86bcfca73411a8d90170009995fa42021-11-11T17:08:36ZComparative Omics Analysis of <i>Brassica napus</i> Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles10.3390/ijms2221116791422-00671661-6596https://doaj.org/article/36a86bcfca73411a8d90170009995fa42021-10-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/21/11679https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067The early and specific diagnosis of a macronutrient deficiency is challenging when seeking to better manage fertilizer inputs in the context of sustainable agriculture. Consequently, this study explored the potential for transcriptomic and metabolomic analysis of <i>Brassica napus</i> roots to characterize the effects of six individual macronutrient deprivations (N, Mg, P, S, K, and Ca). Our results showed that before any visual phenotypic response, all macronutrient deprivations led to a large modulation of the transcriptome and metabolome involved in various metabolic pathways, and some were common to all macronutrient deprivations. Significantly, comparative transcriptomic analysis allowed the definition of a subset of 3282, 2011, 6325, 1384, 439, and 5157 differentially expressed genes (DEGs) specific to N, Mg, P, S, K, and Ca deprivations, respectively. Surprisingly, gene ontology term enrichment analysis performed on this subset of specific DEGs highlighted biological processes that are common to a number of these macronutrient deprivations, illustrating the complexity of nutrient interactions. In addition, a set of 38 biochemical compounds that discriminated the macronutrient deprivations was identified using a metabolic approach. The opportunity to use these specific DEGs and/or biochemical compounds as potential molecular indicators to diagnose macronutrient deficiency is discussed.Galatéa CourbetAurélien D’OriaAnne MaillardLun JingSylvain PluchonMustapha ArkounStéphanie PateyronChristine Paysant Le RouxSylvain DiquélouAlain OurryJacques TrouveriePhilippe EtienneMDPI AGarticlemacronutrient deprivationsmetabolic pathwaysmetabolomicmolecular indicatorsregulations of nutrient metabolismtranscriptomicBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 11679, p 11679 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	macronutrient deprivations metabolic pathways metabolomic molecular indicators regulations of nutrient metabolism transcriptomic Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	macronutrient deprivations metabolic pathways metabolomic molecular indicators regulations of nutrient metabolism transcriptomic Biology (General) QH301-705.5 Chemistry QD1-999 Galatéa Courbet Aurélien D’Oria Anne Maillard Lun Jing Sylvain Pluchon Mustapha Arkoun Stéphanie Pateyron Christine Paysant Le Roux Sylvain Diquélou Alain Ourry Jacques Trouverie Philippe Etienne Comparative Omics Analysis of <i>Brassica napus</i> Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles
description	The early and specific diagnosis of a macronutrient deficiency is challenging when seeking to better manage fertilizer inputs in the context of sustainable agriculture. Consequently, this study explored the potential for transcriptomic and metabolomic analysis of <i>Brassica napus</i> roots to characterize the effects of six individual macronutrient deprivations (N, Mg, P, S, K, and Ca). Our results showed that before any visual phenotypic response, all macronutrient deprivations led to a large modulation of the transcriptome and metabolome involved in various metabolic pathways, and some were common to all macronutrient deprivations. Significantly, comparative transcriptomic analysis allowed the definition of a subset of 3282, 2011, 6325, 1384, 439, and 5157 differentially expressed genes (DEGs) specific to N, Mg, P, S, K, and Ca deprivations, respectively. Surprisingly, gene ontology term enrichment analysis performed on this subset of specific DEGs highlighted biological processes that are common to a number of these macronutrient deprivations, illustrating the complexity of nutrient interactions. In addition, a set of 38 biochemical compounds that discriminated the macronutrient deprivations was identified using a metabolic approach. The opportunity to use these specific DEGs and/or biochemical compounds as potential molecular indicators to diagnose macronutrient deficiency is discussed.
format	article
author	Galatéa Courbet Aurélien D’Oria Anne Maillard Lun Jing Sylvain Pluchon Mustapha Arkoun Stéphanie Pateyron Christine Paysant Le Roux Sylvain Diquélou Alain Ourry Jacques Trouverie Philippe Etienne
author_facet	Galatéa Courbet Aurélien D’Oria Anne Maillard Lun Jing Sylvain Pluchon Mustapha Arkoun Stéphanie Pateyron Christine Paysant Le Roux Sylvain Diquélou Alain Ourry Jacques Trouverie Philippe Etienne
author_sort	Galatéa Courbet
title	Comparative Omics Analysis of <i>Brassica napus</i> Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles
title_short	Comparative Omics Analysis of <i>Brassica napus</i> Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles
title_full	Comparative Omics Analysis of <i>Brassica napus</i> Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles
title_fullStr	Comparative Omics Analysis of <i>Brassica napus</i> Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles
title_full_unstemmed	Comparative Omics Analysis of <i>Brassica napus</i> Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles
title_sort	comparative omics analysis of <i>brassica napus</i> roots subjected to six individual macronutrient deprivations reveals deficiency-specific genes and metabolomic profiles
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/36a86bcfca73411a8d90170009995fa4
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Comparative Omics Analysis of <i>Brassica napus</i> Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles

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