Transcriptional regulation of photosynthesis under heat stress in poplar

Background Photosynthesis has been recognized as a complicated process that is modulated through the intricate regulating network at transcriptional level. However, its underlying mechanism at molecular level under heat stress remains to be understood. Analysis of the adaptive response and regulatory networks of trees to heat stress will expand our understanding of thermostability in perennial plants. In this study, we used a multi-gene network to investigate the regulatory pathway under heat stress, as constructed by a multifaceted approach of combining time-course RNA-seq, regulatory motif enrichment, and expression-trait association analysis. Results By analyzing changes in the transcriptome under heat stress, we identified 77 key photosynthetic genes, of which 97.4% (75 genes) were down-regulated, and these results conformed to the decreased photosynthesis measured values. According to analysis of regulating motif enrichment, these 77 differentially expressed genes (DEGs) had common vital light-responsive elements involved in photosynthesis. When integrating all the differential expressed genes, 5 co-expressed gene modules (1,548 genes) were identified to be significantly correlated with 4 photosynthesis-related traits. Thus, based on this, a three-layered gene regulatory network (GRN) was established, which had included 77 photosynthetic genes (in the bottom layer), 40 TFs/miRNAs (in the second layer), as well as 20 TFs/miRNAs (in the top layer), using a backward elimination random forest (BWERF) algorithm. Importantly, 6 miRNAs and 4 TFs were found to be key regulators in this regulatory pathway, emphasizing the significant roles of TFs/miRNAs in affecting photosynthetic traits. The results imply a functional role for these key genes in mediating photosynthesis under heat stress, demonstrating the potential of combining time-course transcriptome-based regulatory pathway construction, cis-elements enrichment analysis, and expression-trait association approaches to dissect complex genetic networks. Conclusions The heat-responsive pathway in regulating photosynthesis is a multi-layered complex network which is co-controlled by TFs and miRNAs. Our work not only imply a functional role for these key genes in mediating photosynthesis responding to abiotic stress in poplar, but demonstrate time-course transcriptome-based regulatory network construction will facilitate further the genetic network and key nodes examining in plants.