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Physiological characteristics and miRNA sequencing of two root zones with contrasting ammonium assimilation patterns in Populus

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Abstract

Background

The net ammonium fluxes differ among the different root zones of Populus, but the physiological and microRNA regulatory mechanisms are unclear.

Objective

To elucidate the physiological and miRNA regulatory mechanisms, we investigated the two root zones displaying significant differences in net NH4+ effluxes of P. × canescens.

Methods

Populus plantlets were cultivated with 500 μM NH4Cl for 10 days. Six plants were randomly selected to determine the net NH4+ fluxes using a noninvasive microtest technique. High-throughput sequencing were used to determine the dynamic expression profile of miRNA among the different root zones of Populus.

Results

Net NH4+ efflux in zone I (from 0 to 40 mm from the root apex) was − 19.64 pmol cm−2 s−1 and in zone II (from 40 to 80 mm) it was − 43.96 pmol cm−2 s−1. The expression of eleven miRNAs was significantly upregulated, whereas fifteen miRNAs were downregulated. Moreover, eighty-eight target genes of the significantly differentially expressed miRNAs were identified in root zone II compared with zone I. Particularly, ptc-miR171a/b/e and their target, SCL6, were found to be important for the difference in net NH4+ effluxes in the two root zones. Moreover, the expression of the target of ptc-miR169d, NFYA3 was upregulated in root zone II compared with root zone I, contributing to increased NH4+ efflux and decreased NH4+ assimilation in root zone II.

Conclusion

These results indicate that miRNAs regulate the expression levels of their target genes and thus play key roles in net NH4+ fluxes and NH4+ assimilation in different poplar root zones.

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Availability of data

Sequence data in this article have been deposited with the NCBI GenBank Data Library under the accession codes listed in materials and methods.

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Acknowledgements

We thank Prof. Xiaohua Su and Dr. Weixi Zhang from the Research Institute of Forestry, Chinese Academy of Forestry for providing the NMT system to analyze net NH4+ fluxes.

Funding

This work was supported by the National Natural Science Foundation of China (Grant no. 31500507) and the Fundamental Research Funds for the Central Non-profit Research Institution of CAF (Grant no. CAFYBB2016QB005).

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  1. State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China

    Jing Zhou & Jiang ting Wu

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  1. Jing Zhou
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Correspondence to Jing Zhou.

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Zhou, J., Wu, J.t. Physiological characteristics and miRNA sequencing of two root zones with contrasting ammonium assimilation patterns in Populus. Genes Genom 44, 39–51 (2022). https://doi.org/10.1007/s13258-021-01156-2

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