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A network of genes associated with poplar root development in response to low nitrogen.

ABSTRACT: Deployment of the root system is highly sensitive to the levels and spatial distribution of nutrients like nitrogen. However, the genetic determinants of these sensing and deployment mechanisms are still poorly understood. Previously, using system approaches based on temporal changes in root transcriptome in relation to low nitrogen (LN), we have been able to identify a module that activates root production in poplar in response to LN conditions. Here, using comparative, gene ontology and expression analyses, we provide further evidence that the genes in this module are indeed involved in regulation of root development under LN. Better understanding of these modules will enable approaches for breeding for better nitrogen use efficiency through development of a more sensitive and plastic root system.

SUBMITTER: Dash M

PROVIDER: S-EPMC5022414 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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A network of genes associated with poplar root development in response to low nitrogen.

Dash Madhumita M Yordanov Yordan S YS Georgieva Tatyana T Kumari Sapna S Wei Hairong H Busov Victor V

Plant signaling & behavior 20160801 8

Deployment of the root system is highly sensitive to the levels and spatial distribution of nutrients like nitrogen. However, the genetic determinants of these sensing and deployment mechanisms are still poorly understood. Previously, using system approaches based on temporal changes in root transcriptome in relation to low nitrogen (LN), we have been able to identify a module that activates root production in poplar in response to LN conditions. Here, using comparative, gene ontology and expres ...[more]

PMID: 27449227

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Project description:Secondary development is a key biological characteristic of woody plants and the basis of wood formation. Exogenous nitrogen can affect the secondary growth of poplar, and some regulatory mechanisms have been found in the secondary xylem. However, the effect of nitrogen on cambium has not been reported. Herein, we investigated the effects of different nitrogen concentrations on cambium development using combined transcriptome and metabolome analysis. The results show that, compared with 1 mM NH4NO3 (M), the layers of hybrid poplar cambium cells decreased under the 0.15 mM NH4NO3 (L) and 0.3 mM NH4NO3 (LM) treatments. However, there was no difference in the layers of hybrid poplar cambium cells under the 3 mM NH4NO3 (HM) and 5 mM NH4NO3 (H) treatments. Totals of 2365, 824, 649 and 398 DEGs were identified in the M versus (vs.) L, M vs. LM, M vs. HM and M vs. H groups, respectively. Expression profile analysis of the DEGs showed that exogenous nitrogen affected the gene expression involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the starch and sucrose metabolism pathway and the ubiquitin-mediated proteolysis pathway. In M vs. L, M vs. LM, M vs. HM and M vs. H, differential metabolites were enriched in flavonoids, lignans, coumarins and saccharides. The combined analysis of the transcriptome and metabolome showed that some genes and metabolites in plant hormone signal transduction, phenylpropanoid biosynthesis and starch and sucrose metabolism pathways may be involved in nitrogen regulation in cambium development, whose functions need to be verified. In this study, from the point of view that nitrogen influences cambium development to regulate wood formation, the network analysis of the transcriptome and metabolomics of cambium under different nitrogen supply levels was studied for the first time, revealing the potential regulatory and metabolic mechanisms involved in this process and providing new insights into the effects of nitrogen on wood development.

Project description:BackgroundPlant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but also environmental problems, we lack a comprehensive understanding of how crops under elevated nutrient input shape root-associated microbial communities, especially through adjusting the quantities and compositions of root metabolites and exudates.MethodsThe compositions of bacterial and fungal communities from the roots and rhizosphere of wheat (Triticum aestivum L.) under four levels of long-term inorganic nitrogen (N) fertilization were characterized at the tillering, jointing and ripening stages. The root-released organic carbon (ROC), organic acids in the root exudates and soil organic carbon (SOC) and soil active carbon (SAC) in the rhizosphere were quantified.ResultsROC levels varied dramatically across wheat growth stages and correlated more with the bacterial community than with the fungal community. Rhizosphere SOC and SAC levels were elevated by long-term N fertilization but varied only slightly across growth stages. Variation in the microbial community structure across plant growth stages showed a decreasing trend with N fertilization level in the rhizosphere. In addition, more bacterial and fungal genera were significantly correlated in the jointing and ripening stages than in the tillering stage in the root samples. A number of bacterial genera that shifted in response to N fertilization, including Arthrobacter, Bacillus and Devosia, correlated significantly with acetic acid, oxalic acid, succinic acid and tartaric acid levels.ConclusionsOur results indicate that both plant growth status and N input drive changes in the microbial community structure in the root zone of wheat. Plant growth stage demostrated a stronger influence on bacterial than on fungal community composition. A number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded positively to N fertilization, and their abundance correlated significantly with the organic acid level, suggesting that the secretion of organic acids may be a strategy developed by plants to recruit beneficial microbes in the root zone to cope with high N input. These results provide novel insight into the associations among increased N input, altered carbon availability, and shifts in microbial communities in the plant roots and rhizosphere of intensive agricultural ecosystems.

Dataset Information

A network of genes associated with poplar root development in response to low nitrogen.

Publications

A network of genes associated with poplar root development in response to low nitrogen.

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