The CUP-SHAPED COTYLEDON 2 (CUC2) gene, which is negatively regulated by microRNA164 (miR164), has been specifically linked to the regulation of leaf margin serration and the maintenance of phyllotaxy in model plants. However, few studies have investigated these effects in woody plants. In this study, we integrated genomic, transcriptomic, and physiology approaches to explore the function of BpCUC2 gene in Betula pendula growth and development. Our results showed that Betula pendula plants overexpressing BpCUC2, which is targeted by BpmiR164, exhibit shortened internodes and abnormal leaf shapes. Subsequent analysis indicated that the short internodes of BpCUC2 overexpressed transgenic lines and were due to decreased epidermal cell size. Moreover, transcriptome analysis, yeast one-hybrid assays, and ChIP-PCR suggested that BpCUC2 directly binds to the LTRECOREATCOR15 (CCGAC), CAREOSREP1 (CAACTC), and BIHD1OS (TGTCA) motifs of a series of IAA-related and cyclin-related genes to regulate expression. These results may be useful to our understanding of the functional role and genetic regulation of BpCUC2.

To investigate the molecular mechanism of the mutation of a multiple-branches birch mutant (br), we explored genes that were genome-wide differentially expressed in the main and lateral branches’ apical buds of br. The plant architecture not only has effects on the process of plant growth and development, but also affects the agronomic characters. In woody plants, branches determine the application value of timber. Therefore, analyzing genes that were differentially expressed in br apical buds will bring new insights to understand the molecular basis of plant architecture alteration. Wild type (WT) birch, Cinnamoyl-CoA reductase 1 (CCR1)-overexpressed transgenic birch (OE2) and the mutant br were used as materials to observe phenotype differences between br and the control lines (WT and OE2). The transcriptome sequencing of the main and lateral branches’ apical buds of br and controls were further performed to explore genes that were genome-wide differentially expressed in br. Compared to the control lines, br exhibited a multiple-branches and dwarf phenotype. In addition, biomass, rooting number, leaf area, internal diameter, and external diameter of stomata, and the size of terminal buds of br were less than that of WT and OE2. Transcriptome analysis results indicated that gene expression profiles of br were different from the control lines. The genes that were differentially expressed in br apical buds were involved in multiple pathways, including organogenesis, fertility regulation, cell division and differentiation, plant hormone biosynthesis, and signal transduction. The multiple-branches, dwarf, and small leaves and buds of br might be due to the differentially expressed genes (DEGs) involved in organogenesis, cell division and differentiation, plant hormone biosynthesis and signal transduction.