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

Abstract Different root zones have distinct capacities for nitrate (NO3−) 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 NO3− 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 NO3− and ammonium (NH4+) 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 NO3− 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 NO3− uptake. These results indicate that differentially expressed miRNA–target pairs play key roles in regulation of distinct NO3− uptake rates and assimilation in different root zones of poplars.