Genome-wide identification, characterization and expression analysis of novel long non-coding RNAs that mediate IBA-induced adventitious root formation in apple rootstocks

Adventitious roots (ARs) induced are essential for apple rootstock vegetative propagation, however, a transcriptomic analysis of long non-coding RNAs (lncRNAs) that mediate AR formation under exogenous indole-3-butyric acid (IBA) treated in the apple dwarf rootstock ‘M26’ (Malus pumila Mill.) rarely been explored. To explore this, we examined ‘M26’ stem cuttings treated with IBA (1 mg L−1) and control (without IBA treatment), where anatomical analysis showed IBA-treated stems began to develop AR primordia within third day and ARs occurred after 16 days, while the control had no ARs developed. An assessment of hormone content levels in basal stem cuttings showed that, after IBA treatment, indole-3-acetic acid, zeatin riboside, and jasmonic acid were increased at third day but subsequently decreased later, however gibberellin-3 was decreased at third day. The control and IBA-treated third day basal stem cuttings were sent for whole-genome, high-throughput RNA sequencing. The results showed a total of 855 reliable lncRNAs were identified as novel lncRNAs and 63 novel lncRNAs were defined as IBA-responsive lncRNAs. Fifteen IBA-responsive lncRNAs were predicted to be putative targets for 94 miRNAs and three IBA-responsive lncRNA (CUFF.16781, CUFF.2143 and CUFF.41325) was predicted to be the target mimic of mdm-miR156 and mdm-miR396. Functional annotations of these potential target genes suggest that they are involved in many different biological processes, including plant hormone and sucrose signaling, which suggests that IBA-responsive lncRNAs may participate in AR formation in apple rootstocks. This study sheds light on IBA-mediated AR formation in apple rootstock cuttings and provides a foundation for further research.