Comparative in silico analysis of miRNA targeting of NAC and MYB transcription factors associated with secondary cell wall regulation in rice and maize

Abstract

Cellulose biosynthesis and secondary cell wall formation are regulated by hierarchical networks involving NAC and MYB transcription factors and their post-transcriptional regulation by miRNAs. Here, we performed a cross-species in silico analysis of the complete annotated NAC and MYB transcription factor gene sets of O. sativa subsp. japonica and Z. mays using MirTarget, with selected high-priority interactions independently assessed by psRNATarget. Predicted miRNA-binding sites (BSs) were identified in 138 of 170 rice NAC genes (81.2%), 110 of 130 rice MYB genes (84.6%), 87 of 189 maize NAC genes (46.0%), and 117 of 203 maize MYB genes (57.6%), corresponding to 591, 480, 331, and 487 predicted sites, respectively. Members of the miR164 family predominated among NAC candidates in both species, whereas MYB transcripts showed greater miRNA diversity. The analysis recovered the established miR164–NAC and miR159–MYB modules as positive benchmarks. In contrast, miR5075-3p–LOC_Os04g38740.1 emerged as a leading novel transcript-specific candidate, with concordant computational support from MirTarget and psRNATarget. These findings define comparative patterns of predicted miRNA targeting rather than experimentally validated regulatory interactions and provide prioritized hypotheses for direct functional testing.