Prediction of miRNA target genes in poplar and the expression analysis under low nitrogen stress

ObjectiveThe target genes of miRNAs under low nitrogen stress were identified, and the differential expression of target genes after nitrogen stress was analyzed and their functions were annotated. This investigation provides a reference for the revealing of the functions of miRNAs under low nitrogen stress. It also provides important candidate genes for the molecular improvement of low nitrogen nutrition utilization efficiency in trees.

MethodBased on the conservation of miRNAs and the perfect complementary pairing between miRNAs and target genes, this investigation uses the target gene prediction software psRNATarget to compare the gene sequence of Populus tomentosa transcriptome to identify target genes with the miRNAs of poplar as a probe. Further analysis and functional annotation of target genes in P. tomentosa under low nitrogen stress were carried out.

Result3 024 target genes corresponding to 242 miRNA members of 131 miRNA families were obtained, which were involved in pathways such as plant hormone signal transduction, biosynthesis of secondary metabolites, amino acid anabolism, carbon metabolism and RNA transport. 57 target genes changed significantly in P. tomentosa treated with low nitrogen stress, and the number of genes induced (29) and inhibited (28) was almost the same. There were also significant differential expression changes in the 11 target genes corresponding to 14 low-nitrogen-responsive miRNAs, among which, the opposite expression change was found between 8 miRNAs and the corresponding target genes.This investigation found that target genes involved in plant hormone signaling (2) or involved in metabolic pathways (6) were differentially expressed. The target gene of miR162 encodes the ABC transporter, miR393 acts on the target gene KAT2, which could regulate the dynamic balance of Na⁺ and K⁺. The target gene PIF3 of miR399 encodes the phytochrome interaction factor PIFs protein. These miRNAs and target genes might play important roles in the response of poplar to low nitrogen stress.

ConclusionIn this investigation, we identified some low-nitrogen-stress-responsive miRNA target genes in P. tomentosa, which should regulate the response of poplar to nitrogen stress signals. The identification of these miRNAs and target genes should provide useful research clues for the further elucidation of the regulatory functions of miRNAs and targets involved in low nitrogen stress response and could be important candidate genes for the improvement of low nitrogen utilization efficiency in trees.