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Agronomy
Volume 15
Issue 11
10.3390/agronomy15112564
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

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

by
Na Ma
1,2,
Ziwen Xiao
1,2,
Liqing Lu
1,2,
Haiqi Zhang
1,2,
Chunyan Liu
1,2,
Yiliu Xu
1,2,
Yongjie Qi
1,2,* and
Zhenghui Gao
1,2,3,*
1
Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-Construction by Ministry and Province), Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031, China
2
Key Laboratory of Genetic Improvement and Eco-Physiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031, China
3
College of Horticulture, China Agricultural University, Beijing 100000, China
*
Authors to whom correspondence should be addressed.
Agronomy 2025, 15(11), 2564; https://doi.org/10.3390/agronomy15112564
Submission received: 15 October 2025 / Revised: 2 November 2025 / Accepted: 5 November 2025 / Published: 6 November 2025
(This article belongs to the Special Issue Fruit Tree Germplasm Innovation Driven by Molecular Breeding and Genomics)
Versions Notes

Abstract

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.
Keywords: pear; lenticel spots/fruit dots; lignin and cellulose synthesis; transcriptome; metabolomics; co-expression analysis pear; lenticel spots/fruit dots; lignin and cellulose synthesis; transcriptome; metabolomics; co-expression analysis

Share and Cite

MDPI and ACS Style

Ma, N.; Xiao, Z.; Lu, L.; Zhang, H.; Liu, C.; Xu, Y.; Qi, Y.; Gao, Z. Multi-Omics Dissection of Gene–Metabolite Networks Underlying Lenticel Spot Formation via Cell-Wall Deposition in Pear Peel. Agronomy 2025, 15, 2564. https://doi.org/10.3390/agronomy15112564

AMA Style

Ma N, Xiao Z, Lu L, Zhang H, Liu C, Xu Y, Qi Y, Gao Z. Multi-Omics Dissection of Gene–Metabolite Networks Underlying Lenticel Spot Formation via Cell-Wall Deposition in Pear Peel. Agronomy. 2025; 15(11):2564. https://doi.org/10.3390/agronomy15112564

Chicago/Turabian Style

Ma, Na, Ziwen Xiao, Liqing Lu, Haiqi Zhang, Chunyan Liu, Yiliu Xu, Yongjie Qi, and Zhenghui Gao. 2025. "Multi-Omics Dissection of Gene–Metabolite Networks Underlying Lenticel Spot Formation via Cell-Wall Deposition in Pear Peel" Agronomy 15, no. 11: 2564. https://doi.org/10.3390/agronomy15112564

APA Style

Ma, N., Xiao, Z., Lu, L., Zhang, H., Liu, C., Xu, Y., Qi, Y., & Gao, Z. (2025). Multi-Omics Dissection of Gene–Metabolite Networks Underlying Lenticel Spot Formation via Cell-Wall Deposition in Pear Peel. Agronomy, 15(11), 2564. https://doi.org/10.3390/agronomy15112564

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