Transcriptomic Characterization of Adventitious Root Formation in Cunninghamia lanceolata (Lamb.) Hook. During Cutting Propagation

Background: Cunninghamia lanceolata (Lamb.) Hook. (C. lanceolata) is an important timber tree species in southern China. However, the molecular regulatory mechanisms underlying adventitious root formation during cutting propagation remain largely unclear. The lack of genetic resources has hindered molecular breeding efforts in this species. Methods: In this study, transcriptome analysis was performed on the root systems of scions from elite C. lanceolata clones at 7, 30, and 60 d after cutting. Results: Approximately 69.30 Gb of clean data were obtained. De novo assembly and gene prediction yielded 43,433 protein-coding genes, of which 32,886 (75.7%) were functionally annotated. Temporal clustering and comparative functional enrichment analyses revealed a distinct temporal functional shift during adventitious root development in C. lanceolata. Early stages were dominated by metabolic processes such as pyrimidine metabolism and carbohydrate biosynthesis, whereas later stages were governed by phytohormone signal transduction. Key components of the auxin pathway, including AUX1, AFB, IAA, and SAUR, exhibited dynamic and differential expression, which may be associated with adventitious root growth. Based on the transcriptome data, we identified nine members of the PIN gene family. Both transcriptomic expression profiles and qRT-PCR validation demonstrated that these PIN genes showed divergent expression trends across developmental stages, suggesting that they may participate in rooting by regulating polar auxin transport. Conclusions: This study systematically elucidates the molecular network underlying adventitious root formation in C. lanceolata cuttings. It enriches the omics resources for conifers and provides a theoretical foundation and omics basis for molecular breeding and efficient propagation of elite C. lanceolata clones.