Nitrate/ammonium-responsive microRNA-mRNA regulatory networks affect root system architecture in Populus × canescens.

BACKGROUND: Nitrate (NO3-) and ammonium (NH4+) are the primary forms of inorganic nitrogen (N) taken up by plant roots, and a lack of these N sources commonly limits plant growth. To better understand how NO3- and NH4+ differentially affect root system architecture, we analyzed the expression profiles of microRNAs and their targets in poplar roots treated with three forms of nitrogen S1 (NO3-), S2 (NH4NO3, normal), and S3 (NH4+) via RNA sequencing. RESULTS: The results revealed a total of 709 miRNAs. Among them, 57 significantly differentially expressed miRNAs and 28 differentially expressed miRNA-target pairs showed correlated expression profiles in S1 vs. S2. Thirty-six significantly differentially expressed miRNAs and 12 differentially expressed miRNA-target pairs showed correlated expression profiles in S3 vs. S2. In particular, NFYA3, a target of upregulated ptc-miR169i and ptc-miR169b, was downregulated in S1 vs. S2, while NFYA1, a target of upregulated ptc-miR169b, was downregulated in S3 vs. S2 and probably played an important role in the changes in root morphology observed when the poplar plants were treated with different N forms. Furthermore, the miRNA-target pairs ptc-miR169i/b-D6PKL2, ptc-miR393a-5p-AFB2, ptc-miR6445a-NAC14, ptc-miR172d-AP2, csi-miR396a-5p_R + 1_1ss21GA-EBP1, ath-miR396b-5p_R + 1-TPR4, and ptc-miR166a/b/c-ATHB-8 probably contributed to the changes in root morphology observed when poplar plants were treated with different N forms. CONCLUSIONS: These results demonstrate that differentially expressed miRNAs and their targets play an important role in the regulation of the poplar root system architecture by different N forms.

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

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.