Post-transcriptional Gene Regulation by MicroRNAs During Barley Malting

Authors: Whitcomb, Sarah; Vinje, Marcus; Mahalingam, Ramamurthy

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/5/2026
Publication Date: 6/9/2026
Citation: Whitcomb, S.J., Vinje, M.A., Mahalingam, R. 2026. Post-transcriptional Gene Regulation by MicroRNAs During Barley Malting. Genes. https://doi.org/10.3390/genes17060676.
DOI: https://doi.org/10.3390/genes17060676

Interpretive Summary: Malt produced from barely seeds is a key ingredient of the brewing industry. Malting is a three stage process involving steeping, germination and kilning. On an industrial scale these processes consume significant amount of water and energy. Improvements to the barley seed physiology could greatly reduce the water and/energy consumption during malting. In this study we investigated the changes in a type of small RNA molecules called microRNAs that regulate the levels of transcribed genes during different stages of malting. Not surprisingly, we identified many miRNAs that were identified during germination since malting is essentially controlled germination. We also identified some novel miRNAs that may be unique to the malting process. Understanding the molecular mechanisms that occur during malting will provide tools for improving the efficiency of the process that can help reduce the production costs.

Technical Abstract: Malting is an agro-industrial process that produces an essential ingredient for the brewing and distilling industries, malt. Previous mRNA profiling has revealed a myriad of dynamic transcripts 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 5 stages of the process. Using smallRNA-seq and degradome-seq data from these malting stages, we performed de novo discovery of miRNA loci and mature miRNA as well as identified mRNAs targeted for slicing by the observed miRNA. Discovery and annotation of genuine 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 malting smallRNA-seq reads to the Hordeum vulgare Morex v3 genome and to perform miRNA loci prediction. In total, 33 expressed miRNA loci 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-seq data from the same malting stages, CleaveLand4 v4.5 was used to predict 64 sliced Hordeum vulgare mRNA targets of the miRNAs identified. Target mRNAs were predominantly transcription factors in the Growth Regulating Factor, Squamosa promoter binding protein, and Auxin Response Factor families. Novel miRNAs targeting genes involved in organellar development were identified that may be unque to the malting process. This study reveals the complexity of the post-transcriptional regulation invovling developmental transitions during malting. This includes interactions between miRNA-mRNA targets, miRNAs from different families, miRNA-target mRNAs and phytohormones.