Integrated transcriptomic and metabolomic analysis reveals the regulatory role of lignin biosynthesis in raspberry (Rubus niveus) prickle development

Prickles on raspberry (Rubus niveus) stems severely impede harvesting efficiency. To elucidate their formation mechanism, this study employed the thorny R. niveus and the thornless cultivar Qianberry 1 (a Guizhou-originated variety) as contrasting materials. We innovatively adopted a hierarchical strategy analyzing primary, secondary, and tertiary lateral branches combined with transcriptomic and metabolomic profiling. Prickles on primary branches of R. niveus exhibited significantly higher lignin content than secondary/tertiary branches, with safranin staining confirming lignin-specific deposition, while PAL enzyme activity peaked in secondary branches. We generated 18 RNA-seq libraries from primary, secondary, and tertiary branches of two cultivars (with three biological replicates per tissue). Transcriptome analysis identified 39 lignin-related DEGs, including key upregulated genes (PAL, CCR, POX) in R. niveus promoting G/H-lignin deposition. Metabolomic screening revealed 6,083 differentially accumulated metabolites enriched in secondary metabolite biosynthesis pathways that positively correlated with hierarchical prickle hardness. WGCNA further delineated a core regulatory hub within the magenta module where 12 structural genes (CCoAOMT, LAC) and 25 transcription factors (MYB/NAC) with strong node connectivity (GS > 0.8, MM > 0.8) co-regulated eight lignin precursors. Critically, suppression of this pathway underlies the thornless phenotype in the Qianberry 1 cultivar. This study first reveals the hierarchical spatiotemporal accumulation of lignin and its coordination with transcriptional-metabolic networks. The molecular basis of Qianberry 1’s thornlessness identifies candidate targets for future breeding prickle-free Rosaceae crops, laying a theoretical foundation to reduce harvesting costs. These findings enhance the economic viability of raspberry production, particularly for Guizhou’s specialty berry industry, and highlight promising avenues for further research.