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Different root zones have distinct capacities for nitrate (NO 3  − ) uptake in  Populus  species, but the underlying physiological and microRNA (miRNA) regulatory mechanisms remain largely unknown. To address this question, two root zones of  Populus × canescens  (Ait.) Smith. with contrasting capacities for NO 3  −  uptake were investigated. The region of 0–40 mm (root zone I) to the root apex displayed net influxes, whereas the region of 40–80 mm (root zone II) exhibited net effluxes. Concentrations of NO 3  −  and ammonium (NH 4  + ) as well as nitrate reductase activity were lower in zone II than in zone I. Forty one upregulated and twenty three downregulated miRNAs, and 576 targets of these miRNAs were identified in zone II in comparison with zone I. Particularly,  growth-regulating factor 4 (GRF4) , a target of upregulated ptc-miR396g-5p and ptc-miR396f_L + 1R-1, was downregulated in zone II in comparison with zone I, probably contributing to lower NO 3  −  uptake rates and assimilation in zone II. Furthermore, several miRNAs and their targets, members of  C2H2  zinc finger family and  APETALA2 /ethylene-responsive element binding protein family, were found in root zones, which probably play important roles in regulating NO 3  −  uptake. These results indicate that differentially expressed miRNA–target pairs play key roles in regulation of distinct NO 3  −  uptake rates and assimilation in different root zones of poplars.

Physiological characteristics and RNA sequencing in two root zones with contrasting nitrate assimilation of Populus × canescens