Integrated metabolomic and transcriptomic analysis to uncover the developmental mechanism of Zanthoxylum armatum prickles

Zanthoxylum armatum is a commercially valuable plant species widely cultivated in China; however, its dense coverage of sharp prickles is a serious challenge for the agricultural production and fruit harvesting of Z. armatum . To elucidate the molecular and physiological mechanisms underlying the prickle development of Z. armatum , this study employed an integrated approach of metabonomic and transcriptomic analysis to uncover the developmental mechanism of Z. armatum prickles. Microscopic examination showed prickles of Z. armatum are epidermal-derived structures lacking vascular bundles, featuring a specialized cellular transition region termed the “resembling abscission zone” that enables easy detachment. Metabonomic analysis revealed stage-specific fluctuations in multiple hormonal pathways, with auxin (IAA), cytokinin (CTK), abscisic acid (ABA), gibberellin (GA), and ethylene (ETH) exhibiting distinct temporal patterns that correlate with critical phases of prickle morphogenesis. Transcriptomic sequencing analysis identified 26,053 differentially expressed genes (DEGs) between prickly (TJ) and prickleless (CJ2) cultivars, with significant enrichment in phenylpropanoid biosynthesis and plant hormone signaling pathways. We identified 22 hub genes strongly associated with prickle development using WGCNA analysis, including key regulators of JAR4 , MYC2 , and Tify6B . Furthermore, comparative transcriptome analysis revealed differential expression of numerous transcription factor families, particularly AP2/ERF , MYB , WRKY , and NAC members, between the two cultivars. The expression patterns of candidate genes were rigorously validated by RT-qPCR verification, demonstrating consistently higher transcript levels in the prickleless CJ2 cultivar. These findings provide novel insights into the complex regulatory networks governing prickle formation in Z. armatum , establishing a crucial foundation for molecular breeding programs aimed at developing improved cultivars with reduced or eliminated prickles. • Prickles lack vasculature, derive from dense epidermal cells, and feature an abscission-like zone. • IAA, CTK, ABA, GA, ETH dynamically regulate prickle initiation and lignification across development. • Nine hub genes (e.g., JAR4, MYC2, BRI1, PP2C) strongly associated with hormone metabolism and prickle development. • Candidate gene expression validated by RT-qPCR provides genetic targets for breeding low-prickle Z. armatum varieties.