Indole-3-acetic acid has long-term effects on long non-coding RNA gene methylation and growth in Populus tomentosa

DNA methylation and long non-coding RNAs (lncRNAs) regulate plant growth and development, but their relationship and effect on responses to the auxin phytohormone indole-3-acetic acid (IAA) remain largely unknown, particularly in woody plants such as poplar (Populus tomentosa). Following treatment of 1-year-old clonal plants with 100 µM IAA, key poplar lncRNA genes showed changes in methylation, but whole-genome methylation levels showed no significant change. Moreover, 100 µM IAA inhibited growth of the 1-year-old poplar clones, possibly through the suppression of photosynthesis. This inhibition had a long-term effect, persisting at 1 month after removal of the exogenous IAA. Transcriptome analysis identified two candidate lncRNA genes that show changes in expression following IAA treatment, TCONS_00003480 and TCONS_00004832. TCONS_00003480 contains the same microRNA target sites of ptc-miR6464 as the 4-coumarate: CoA ligase 2 transcript, which encodes a lignin biosynthesis enzyme. And TCONS_00004832 shares the same target sites of ptc-miR6437a with the Photosystem II reaction center protein D and Cytochrome C Oxidase 17 transcripts, which are related to photosynthesis. The two lncRNAs as the mimics to corresponding target genes of miRNAs to prevent them from degrading. Examination of lncRNA gene expression and methylation revealed a negative relationship (r = - 0.29, P < 0.05); moreover, hypermethylation of the two candidate lncRNA genes remained 1 month after IAA treatment, suggesting that changes in methylation might be involved in the long-term effects of plant hormones. Therefore, our study reveals a long-term effect of IAA on the growth of P. tomentosa, possibly via methylation-mediated epigenetic changes in lncRNA gene expression and the interaction with corresponding miRNAs, leading to regulation of genes related to photosynthesis and growth.