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

BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.