Genome-wide identification of auxin-responsive microRNAs in the poplar stem

Abstract Background Wood (secondary xylem) of forests is widely used used in construction, paper making, furniture, and as a feedstock for biofuels. Wood development is strictly regulated by the phytohormone auxin and MicroRNAs (miRNAs). Currently, the regulatory mechanisms of auxin-induced miRNAs during wood formation in tree species remain unclear.Methods and results Here, we investigated the effect of auxin application on wood development in poplar and identified miRNAs in the stems treated with different concentrations (0 mg/L, CK; 5 mg/L, Low; 10 mg/L, High) of indol-3-butyric acid (IBA). High-throughput sequencing showed that the 24-nt sRNAs were the most abundant classes in three types of small RNA libraries. A total of 118 known miRNAs and 134 novel miRNAs were obtained. Sixty-nine unique developmental-related miRNAs exhibited specific expression patterns in response to auxin, which was consistent with the influence of auxin on wood development. 269 target genes of 69 auxin-responsive miRNAs were predicted. Of them, three novel miRNAs had the most number (≥9) of target genes, which correspondingly belong to SPL, GRF and ARF families. The evolutionary relationships and tissue expression patterns of these target genes were further analyzed. The relative expression levels of four representative miRNAs and their partial target genes were confirmed by using RT-qPCR.Conclusions The present study provides new insights into auxin-responsive miRNAs during wood development in trees.