MiRNAs play important roles in aroma formation during room temperature storage of 'Binzi' apple (<i>Malus domestica</i>)

MicroRNAs are non-coding RNAs that play a crucial regulatory role in plant growth, development, and environmental stress response. 'Binzi' is an ancient apple cultivar renowned for its unique aroma, however, the mechanisms of miRNAs underlying aroma formation remain largely unknown. In this study, we performed small RNA sequencing to investigate the role of miRNAs during post-harvest storage of 'Binzi' apple. Peel samples from 'Binzi' fruit (namely BZP01 and BZP02) at two storage stages (20 ± 1 °C) were sequenced. A total of 29 DEMs (15 miRNAs uniquely detected at specific storage periods and 14 miRNAs differentially expressed in different storage periods) were predicted to regulate aroma compound biosynthesis in 'Binzi' apple peels. A total of 604 genes were predicted to be targeted by 29 miRNAs. GO enrichment analysis was performed on the target genes, with 'cellular process', 'metabolic process', 'single-organism process', and 'catalytic activity' being the over-enriched biological processes. KEGG analysis showed that three pathways related to aroma synthesis ('fatty acid metabolism', 'biosynthesis of unsaturated fatty acid biosynthesis', and 'carotenoid biosynthesis') were enriched in the top 20 of the KEGG enrichment. We verified the regulatory relationship between miRNAs and their target genes by qRT-PCR. mdm-miR408c was negatively correlated with three target genes (two <italic>MdfabDs</italic> and one <italic>MdfabG</italic>) and was involved in the regulation of fatty acids biosynthesis. Furthermore, novel_Chr17_18081 was negatively correlated with <italic>MdMFP2</italic> and was involved in the regulation of the fatty acid degradation. Our research indicated that mdm-miR408c, novel_Chr17_18081, and their target genes (<italic>MdfabDs</italic>, <italic>MdfabG</italic>, and <italic>MdMFP2</italic>) were collectively involved in 'Binzi' aroma production.