A total of 37 CsTCP genes were identified and divided into two classes, class I (PCF, group 1) and class II (CIN CYC/TB1, groups 2, and 3). TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors TEOSINTE BRANCHED1/CYCLOIDEA/PCF have been suggested to control the cell growth and proliferation in meristems and lateral organs. The findings will contribute to the comprehensive understanding of miRNA-mediated regulatory mechanism governing floral bud break and dormancy cycling in wood perennials. In general, our study revealed the miRNA-mediated networks in modulating floral bud break in P. Finally, we integrated weighted gene co-expression analysis and constructed miRNA-mRNA regulatory networks mediating floral bud flushing competency. We further validated the regulatory relationship between differentially expressed miRNAs and their target genes combining computational prediction, degradome sequencing, and expression pattern analysis. Additionally, we identified 48 known miRNAs and 53 novel miRNAs targeting genes enriched in biological processes such as floral organ morphogenesis and hormone signaling transudation. In total, we characterized 1,553 DEGs associated with endodormancy release and 2,084 DEGs associated with bud flush. Through expression profiling, we identified a few candidate genes and miRNAs during different developmental stage transitions. In this study, we applied transcriptome and small RNA sequencing together to systematically explore the transcriptional and post-transcriptional regulation of floral bud break in P. Though miRNAs and their target genes have been widely studied in many plant species, their functional roles in floral bud break and dormancy release in woody perennials is still unclear. MicroRNAs is one class of small non-coding RNAs that play important roles in plant growth and development. All the results serve as a valuable resource for the plant community. Finally, we generated an extended PPI network that predicts new players in gynoecium development. Furthermore, we analysed the network by combining PPI data, expression, and genetic data, which helped us to dissect it into several dynamic spatio-temporal subnetworks related to gynoecium development processes. Additionally, we observed a close relationship between TFs involved in auxin and cytokinin signalling pathways and other TFs. Topological analyses suggest hidden functions and novel roles for many TFs. We analysed almost 4,500 combinations and detected more than 250 protein-protein interactions (PPIs), resulting in a process-specific interaction map. This work used a systems biology approach to understand the formation of a complex reproductive unit - as the gynoecium - by mapping binary interactions between well-characterised TFs. However, broad knowledge about the interactions among these TFs and their participation during development remains scarce. TFs have been described as regulators of gynoecium development, and some interactions and complexes have been identified. After the establishment of carpel identity, many tissues arise to form a mature gynoecium. The gynoecium is the flower’s female reproductive part, crucial for fruit and seed production and, hence, for reproductive success. The interactions between MADS-box TFs and protein complex formation have been schematized in the floral quartet model of flower development. Scale bars = 1 cm (A, B), 100 μm (inset to B, F, H, I), 50 μm (D), 1 mm (E) and 0.5 mm (G).įlowers are composed of organs whose identity is defined by the combinatorial activity of transcription factors (TFs). Right: GUS staining of a Cyc1At::GUS pTCP 14:TCP14:SRDX flower receptacle (arrowheads indicate tissue outgrowth). (I) Scanning electron micrographs of WT (top left) and pTCP14:TCP14:SRDX (bottom left) flower receptacles. (H) Close-up of the carpel/replum boundary tissue outgrowth: micrograph (left) (arrowheads indicate stigmatic papillae) GUS staining in a Cyc1At::GUS pTCP14:TCP14:SRDX line (right). (G) Gynecium micrographs (carpel valve view) of dissected mature flowers from WT, and pTCP14:TCP14:SRDX in WT and tcp14-4 tcp15-3 backgrounds (arrowheads show tissue outgrowth). (F) Scanning electron micrographs of sepal adaxial epidermis of wild-type and pTCP14:TCP14:SRDX flowers. (E) Mature wild-type flower (top), pTCP15:TCP15:SRDX flower (middle) and pTCP14:TCP14:SRDX flower (bottom). (D) Trichomes from WT and pTCP14:TCP14:SRDX leaves. (C) Density of adaxial epidermal cells of mature leaves from WT (black bar) and pTCP14:TCP14:SRDX (white bar). The inset panels show scanning electron micrographs of the adaxial epidermis of mature leaves of WT and pTCP14:TCP14:SRDX. (B) Leaves from WT and pTCP14:TCP14:SRDX plants at young (right) and mature (left) stages of development. Phenotype of TCP14 EAR repression domain fusion lines (pTCP14:TCP14:SRDX).
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