RNA-seq and sRNA-seq analysis in lateral buds and leaves of juvenile and adult roses

Abstract The timing of juvenile-to-adult phase changes are crucial for woody plants, but the molecular mechanisms involved in these changes are still unclear. In this study, 6-month-old F1 seedlings of Rosa chinensis var. chinensis ‘Zhaiye Tengben Yuejihua’ × ‘Old Blush’ were used to compare the transcriptome and sRNAome profiles of lateral buds and leaves in adult and juvenile rose seedlings and to detect the molecular mechanism responsible for the extremely short juvenile phase of roses. The results showed that there were 4316 and 4230 differentially expressed genes (DEGs) identified in lateral buds between adult and juvenile roses and in leaves, respectively. There were 79 differentially expressed miRNAs in the lateral buds and leaves of adult and juvenile roses, including 24 known miRNAs and 55 new miRNAs. Gene Ontology (GO) analysis showed that transcription factor activity and catalytic activity were representative of the molecular function (MF) of DEGs in lateral buds and leaves of adult and juvenile roses, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis, starch and sucrose metabolism, and carbon fixation were the most dominant groups in the DEGs of lateral buds and leaves between adult and juvenile roses. Further analysis revealed that some significant differences existed in carbon and nitrogen metabolism, age pathway (miR172-AP2s), and other miRNAs (miRNA164-NAC100/NAC021, miRNA396-GRFs, and miRNA394a-NAC086/MYB23) between adult and juvenile roses. Finally, WGCNA analysis revealed that the hub transcription factors between adult and juvenile roses involved in photoperiod pathway (NFYC4, GATA1, WRKY3, TGA21, COL5, and COL13), IAA signal transduction pathway (NAC086, IAA13), GA signal transduction pathway (SCL32), autonomous pathway (TCP9), histone methylation pathway (ATX3), and flowering pathway integrators (AGL42-like). The results provide a reference for further research of the molecular mechanism of rose flowering time and the juvenile-to-adult phase change of woody plants.