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.

Genome‐wide association study and network analysis of in vitro transformation in Populus trichocarpa support key roles of diverse phytohormone pathways and cross talk

“…Key regulators of auxin‐related epigenetic reprogramming are in the GRF family (Szczygieł‐Sommer & Gaj, 2019), members of which appear to be involved in recruitment of SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complex (Debernardi et al ., 2014) and include our candidate Potri.002G115100 (homolog of GRF1 ). This poplar homolog is a likely target of a stem‐expressed microRNA transcriptionally regulated downstream of auxin (Yang et al ., 2023). In addition to acting both upstream (Szczygieł‐Sommer & Gaj, 2019) and downstream (Beltramino et al ., 2021; Yang et al ., 2023) of auxin, the GRF family has been implicated downstream of gibberellin signaling (van der Knaap et al ., 2000) and upstream of cytokinin, JA and SA, among other phytohormone pathways (Piya et al ., 2020).…”

“…This poplar homolog is a likely target of a stem‐expressed microRNA transcriptionally regulated downstream of auxin (Yang et al ., 2023). In addition to acting both upstream (Szczygieł‐Sommer & Gaj, 2019) and downstream (Beltramino et al ., 2021; Yang et al ., 2023) of auxin, the GRF family has been implicated downstream of gibberellin signaling (van der Knaap et al ., 2000) and upstream of cytokinin, JA and SA, among other phytohormone pathways (Piya et al ., 2020). A key role of GRF1 as a regeneration regulatory hub is supported by our epistasis results, showing significant interactions with 18 other candidates.…”