Transcriptome and small RNA analysis unveils novel insights into the C gene regulation in sugarcane.

This study reveals miRNA indirect regulation of C genes in sugarcane through transcription factors, highlighting potential key regulators like SsHAM3a. C photosynthesis is crucial for the high productivity and biomass of sugarcane, however, the miRNA regulation of C genes in sugarcane remains elusive. We have identified 384 miRNAs along the leaf gradients, including 293 known miRNAs and 91 novel miRNAs. Among these, 86 unique miRNAs exhibited differential expression patterns, and we identified 3511 potential expressed targets of these differentially expressed miRNAs (DEmiRNAs). Analyses using Pearson correlation coefficient (PCC) and Gene Ontology (GO) enrichment revealed that targets of miRNAs with positive correlations are integral to chlorophyll-related photosynthetic processes. In contrast, negatively correlated pairs are primarily associated with metabolic functions. It is worth noting that no C genes were predicted as targets of DEmiRNAs. Our application of weighted gene co-expression network analysis (WGCNA) led to a gene regulatory network (GRN) suggesting miRNAs might indirectly regulate C genes via transcription factors (TFs). The GRAS TF SsHAM3a emerged as a potential regulator of C genes, targeted by miR171y and miR171am, and exhibiting a negative correlation with miRNA expression along the leaf gradient. This study sheds light on the complex involvement of miRNAs in regulating C genes, offering a foundation for future research into enhancing sugarcane's photosynthetic efficiency.