Post-transcriptional gene regulation by microRNAs during barley malting

Background: Barley malting is an agro-industrial process that produces malt, an essential ingredient for the brewing and distilling industries. Previous messenger RNA (mRNA) profiling has revealed a myriad of transcriptional changes during malting, but less is known about what regulates these changes. In this study, the spring 2-row malting barley variety ‘Conrad’ was malted and sampled at five stages of the process. Using small RNA (sRNA)-sequencing and degradome-sequencing data from these malting stages, we performed de novo discovery of micro RNA loci (MIR) and mature micro RNA (miRNA) as well as identified mRNAs targeted for slicing by the observed miRNAs. Discovery and annotation of miRNAs is challenging in part because the abundance of genuine miRNAs is far lower than other smallRNA classes. Here we used ShortStack v4.1.0 to map sRNA-sequencing reads to the Hordeum vulgare Morex V3 genome and to perform MIR loci prediction. Results: In total, 33 expressed MIR were identified, six of which may be novel. miRNA-5p and miRNA-3p sequences corresponding to these loci belong to 15 miRNA families. Using the degradome-sequencing data from the same malting stages, CleaveLand4 v4.5 was used to predict 64 sliced H. vulgare mRNA targets of these miRNAs. Target genes were predominantly transcription factors associated with root development. Novel miRNAs were targeting genes involved in organellar metabolism. Eight miRNA families regulated by five different phytohormones were identified. Conclusions: This study provides an insight into the miRNA-mRNA targets during malting, as well as interactions between miRNAs and miRNAs-phytohormones.