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Understanding the role of nitrate in driving cambial growth in hybrid aspen stem using single cell RNA sequencing

ABSTRACT: We utilized scRNA-seq method from 10x Genomics to sequence the developing xylem cells of hybrid aspen stem after two hours of nitrate treatment. Using correlation with public datasets, marker genes and reporter lines, different cell types of xylem tissue were annotated. From a differential gene expression analysis across the scRNA-seq datasets, we found an upregulation of early nitrate-responsive genes in nearly all the cell types. The results suggested that although all the xylem cells could sense the presence of nitrate, but they respond to a unique and variable extent.

ORGANISM(S): Populus tremula x Populus tremuloides

PROVIDER: GSE304804 | GEO | 2026/09/08

REPOSITORIES: GEO

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Project description:Background Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth. Results Treatment of the aspen roots with 500 µM Al induced a strong inhibition of root growth within 6 h of exposure time. The root growth subsequently recovered, reaching growth rates comparable to that of control plants. Changes in gene expression were determined after 6 h, 2 d, and 10 d of Al exposure. Replicated transcriptome analyses using the Affymetrix poplar genome array revealed a total of 175 significantly up-regulated and 69 down-regulated genes, of which 70% could be annotated based on Arabidopsis genome resources. Between 6 h and 2 d, the number of responsive genes strongly decreased from 202 to 26, and then the number of changes remained low. The responses after 6 h were characterized by genes involved in cell wall modification, ion transport, and oxidative stress. Two genes with prolonged induction were closely related to the Arabidopsis Al tolerance genes ALS3 (for Al sensitive 3) and MATE (for multidrug and toxin efflux protein, mediating citrate efflux). Patterns of expression in different plant organs and in response to Al indicated that the two aspen genes are homologs of the Arabidopsis ALS3 and MATE. Conclusion Exposure of aspen roots to Al results in a rapid inhibition of root growth and a large change in root gene expression. The subsequent root growth recovery and the concomitant reduction in the number of responsive genes presumably reflect the success of the roots in activating Al tolerance mechanisms. The aspen genes ALS3 and MATE may be important components of these mechanisms.

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Understanding the role of nitrate in driving cambial growth in hybrid aspen stem using single cell RNA sequencing

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