In silico analysis of miR156-mediated post-transcriptional regulation of SPL genes involved in cell wall formation and cellulose biosynthesis in Oryza sativa

BELKOZHAYEV AYAZ MARATOVICH, Bekzhan D. Kossalbayev, Nargiz N. Gizatullina, Gaukhar Toleutay

2026

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DOI 10.31489/2026feb2/91-104
Data confidence 85 high
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Abstract

Plant cell wall formation and cellulose biosynthesis are central processes determining plant growth, mechanical strength, and biomass quality. Rice (Oryza sativa), the second most important crop worldwide after maize, represents a well-established model system due to its fully sequenced and well-annotated genome. In this study, an in silico approach was applied to investigate microRNA (miRNA) mediated post-transcriptional regulation of genes involved in cell wall formation and cellulose biosynthesis in Oryza sativa (O. sativa). Using publicly available databases, including miRBase, TarDB, and NCBI, we systematically predicted miRNA — target gene interactions and reconstructed regulatory networks associated with structural, enzymatic, and signaling components of the plant cell wall. A total of 20 high-confidence miRNA — target gene pairs were identified, involving transcription factors (SPL, NAC, GRAS, AP2, TCP and HD-ZIP III), cell wall-related enzymes (laccases, redox- and copper-dependent proteins), and hormone-responsive regulators. The miR156 — SPL regulatory module emerged as a central and evolutionarily conserved node controlling secondary cell wall formation and cellulose microfibril organization. Additional regulatory layers included miR164 — NAC, miR397 laccase, and miR408/miR528-mediated redox pathways, as well as auxin-related miRNA networks. The results demonstrate that cellulose biosynthesis and cell wall formation in rice are governed by complex, multilevel miRNA-mediated regulatory systems. These findings provide a theoretical framework for future experimental validation and for biotechnological strategies aimed at improving agricultural biomass utilization and cellulose-based sustainable materials.