Multi-Omics Dissection of Gene–Metabolite Networks Underlying Lenticel Spot Formation via Cell-Wall Deposition in Pear Peel

Lenticel spots (fruit dots) on pear peel strongly influence consumer preference and market price, yet the regulatory networks underlying their lignin/cellulose deposition remain elusive. Here, we integrated electron microscopy, metabolomics, and RNA-seq across three developmental stages (30, 40, and 60 d after full bloom, DAFB) in the pear cultivar ‘Dangshansuli’ (SL) and its bud-sport ‘Dangshanxisu’ (XS). XS exhibited fewer lenticel spots and lower lignin, cellulose, and hemicellulose contents than SL, with the critical onset of lignin and cellulose accumulation detected between 40 and 60 DAFB. Metabolome-wide analysis detected five differentially accumulated lignin monomers, while transcriptome profiling revealed 79 differentially expressed genes (padj ≤ 0.05, |log2FC| ≥ 1) enriched in phenylpropanoid and cellulose-synthase pathways. Weighted gene co-expression network analysis (WGCNA) uncovered two modules (|r| > 0.8, p < 0.05) positively correlated with lignin and cellulose content, harboring 11 structural genes (4CL, F5H, CCR, COMT, PRX/POD and CESA isoforms) and five transcription-factor families (MYB, NAC, AP2/ERF, WRKY, bHLH). RT-qPCR validated the coordinated down-regulation of these genes in XS relative to SL. Our results decipher the gene–metabolite circuitry driving lenticel lignification in pear, providing molecular targets for breeding peel-perfect cultivars and for cultural practices that minimize superficial blemishes.