Unraveling Nitrogen Uptake and Metabolism: Gene Families, Expression Dynamics, and Functional Insights in Aspen (Populus tremula). Zhang, Y., Choudhary, S., Renström, A., Luomaranta, M., Chantreau, M., Fleig, V., Gaboreanu, I., Grones, C., Nilsson, O., Robinson, K. M, & Tuominen, H. Tree Physiology, August, 2025. ![Unraveling Nitrogen Uptake and Metabolism: Gene Families, Expression Dynamics, and Functional Insights in Aspen (Populus tremula) [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex The influence of nitrogen on wood formation is well established. To gain insight into the underlying molecular mechanism, we first identified genes in fourteen gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. This study provides insight into the genetic basis of nitrogen uptake and assimilation and its connection to wood formation, providing interesting targets for improving nitrogen use efficiency and growth of aspen trees.
@article{zhang_unraveling_2025,
title = {Unraveling {Nitrogen} {Uptake} and {Metabolism}: {Gene} {Families}, {Expression} {Dynamics}, and {Functional} {Insights} in {Aspen} ({Populus} tremula)},
issn = {1758-4469},
shorttitle = {Unraveling {Nitrogen} {Uptake} and {Metabolism}},
url = {https://doi.org/10.1093/treephys/tpaf099},
doi = {10.1093/treephys/tpaf099},
abstract = {The influence of nitrogen on wood formation is well established. To gain insight into the underlying molecular mechanism, we first identified genes in fourteen gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. This study provides insight into the genetic basis of nitrogen uptake and assimilation and its connection to wood formation, providing interesting targets for improving nitrogen use efficiency and growth of aspen trees.},
urldate = {2025-08-15},
journal = {Tree Physiology},
author = {Zhang, Yupeng and Choudhary, Shruti and Renström, Anna and Luomaranta, Mikko and Chantreau, Maxime and Fleig, Verena and Gaboreanu, Ioana and Grones, Carolin and Nilsson, Ove and Robinson, Kathryn M and Tuominen, Hannele},
month = aug,
year = {2025},
pages = {tpaf099},
}
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To gain insight into the underlying molecular mechanism, we first identified genes in fourteen gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. 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To gain insight into the underlying molecular mechanism, we first identified genes in fourteen gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. 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