Nitrate/ammonium-responsive microRNA-mRNA regulatory networks affect root system architecture in Populus × canescens
Jing Zhou, Jiangting Wu
Abstract
Abstract Background Nitrate (NO 3 − ) and ammonium (NH 4 + ) 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 NO 3 − and NH 4 + 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 (NO 3 − ), S2 (NH 4 NO 3 , normal), and S3 (NH 4 + ) 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.