Main Conclusion

This study reveals miRNA indirect regulation of C₄ genes in sugarcane through transcription factors, highlighting potential key regulators like SsHAM3a.

Abstract

C₄ photosynthesis is crucial for the high productivity and biomass of sugarcane, however, the miRNA regulation of C₄ 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 C₄ 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 C₄ genes via transcription factors (TFs). The GRAS TF SsHAM3a emerged as a potential regulator of C₄ 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 C₄ genes, offering a foundation for future research into enhancing sugarcane's photosynthetic efficiency.

中文翻译：

---

转录组和小RNA分析揭示了甘蔗C4基因调控的新见解

主要结论

这项研究揭示了 miRNA通过转录因子对甘蔗中C ₄基因的间接调节，突出了SsHAM3a等潜在的关键调节因子。

抽象的

C ₄光合作用对于甘蔗的高产和生物量至关重要，然而，甘蔗中C ₄基因的miRNA调控仍然难以捉摸。我们沿着叶子梯度鉴定了 384 个 miRNA，其中包括 293 个已知的 miRNA 和 91 个新的 miRNA。其中，86 个独特的 miRNA 表现出差异表达模式，我们鉴定了这些差异表达 miRNA (DEmiRNA) 的 3511 个潜在表达靶标。使用 Pearson 相关系数 (PCC) 和基因本体 (GO) 富集进行的分析表明，具有正相关性的 miRNA 靶标是叶绿素相关光合作用过程中不可或缺的一部分。相反，负相关对主要与代谢功能相关。值得注意的是，没有 C ₄基因被预测为 DEmiRNA 的靶标。我们应用加权基因共表达网络分析 (WGCNA) 得出了基因调控网络 (GRN)，表明 miRNA 可能通过转录因子 (TF)间接调控 C ₄基因。 GRAS TF SsHAM3a成为 C ₄基因的潜在调节因子，受到 miR171y 和 miR171am 的靶向，并与叶片梯度上的 miRNA 表达呈负相关。这项研究揭示了 miRNA 在调节 C ₄基因中的复杂参与，为未来提高甘蔗光合效率的研究奠定了基础。