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Agriculture
Volume 15
Issue 23
10.3390/agriculture15232475
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Article

Integrated Morphological, Physicochemical, Metabolomic, and Transcriptomic Analyses Elucidate the Mechanism Underlying Melon (Cucumis melo L.) Peel Cracking

by
Yanping Hu
1,2,3,
Yuxin Li
2,
Tingting Zhang
2,4,
Chongchong Wang
1,3,
Baibi Zhu
1,
Libo Tian
2,5,
Min Wang
1,3,* and
Yang Zhou
2,*
1
Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou 571199, China
2
Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou 570228, China
3
Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572025, China
4
Xiangyang Academy of Agricultural Sciences, Xiangyang 441057, China
5
Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China
*
Authors to whom correspondence should be addressed.
Agriculture 2025, 15(23), 2475; https://doi.org/10.3390/agriculture15232475 (registering DOI)
Submission received: 29 September 2025 / Revised: 26 November 2025 / Accepted: 26 November 2025 / Published: 28 November 2025
(This article belongs to the Section Crop Production)
Versions Notes

Abstract

Fruit peel cracking significantly reduces the commercial value of melons (Cucumis melo). To elucidate the underlying mechanisms of peel cracking, we conducted integrated investigations including morphological, physiological, metabolomic and transcriptomic analyses of cracked and non-cracked peels from the crack-resistant ‘Xizhoumi 17’ and crack-susceptible ‘Xizhoumi 25’ cultivars. The parenchyma cells in ‘Xizhoumi 17’ exhibited a compact and well-organized arrangement, whereas those in ‘Xizhoumi 25’ displayed a loosely packed and disordered structure. Notably, cracked peels exhibited significantly higher levels of water-soluble pectin and lignin, along with increased cellulase, polygalacturonase, catalase, superoxide dismutase, and peroxidase activities. In contrast, protopectin, cellulose, and hemicellulose contents, as well as polyphenol oxidase activity, were markedly reduced compared to non-cracked peels. Metabolomic analysis revealed that the phenylpropanoid biosynthesis pathway is positively correlated with the progression of peel cracking. RNA-seq analysis revealed 119 and 82 differentially expressed genes associated with cell wall metabolism and lignin biosynthesis pathways, respectively. Collectively, these findings underscore the involvement of genes related to cell wall synthesis and degradation, as well as lignin synthesis, in modulating peel cracking through alterations in cell wall composition and structural stability, thereby offering practical implications for reducing melon peel cracking incidence via targeted molecular breeding of key genes regulating cell wall composition and the phenylpropanoid pathway.
Keywords: Cucumis melo; fruit cracking; pericarp structure; transcriptome sequencing; metabolome; lignin synthesis Cucumis melo; fruit cracking; pericarp structure; transcriptome sequencing; metabolome; lignin synthesis

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MDPI and ACS Style

Hu, Y.; Li, Y.; Zhang, T.; Wang, C.; Zhu, B.; Tian, L.; Wang, M.; Zhou, Y. Integrated Morphological, Physicochemical, Metabolomic, and Transcriptomic Analyses Elucidate the Mechanism Underlying Melon (Cucumis melo L.) Peel Cracking. Agriculture 2025, 15, 2475. https://doi.org/10.3390/agriculture15232475

AMA Style

Hu Y, Li Y, Zhang T, Wang C, Zhu B, Tian L, Wang M, Zhou Y. Integrated Morphological, Physicochemical, Metabolomic, and Transcriptomic Analyses Elucidate the Mechanism Underlying Melon (Cucumis melo L.) Peel Cracking. Agriculture. 2025; 15(23):2475. https://doi.org/10.3390/agriculture15232475

Chicago/Turabian Style

Hu, Yanping, Yuxin Li, Tingting Zhang, Chongchong Wang, Baibi Zhu, Libo Tian, Min Wang, and Yang Zhou. 2025. "Integrated Morphological, Physicochemical, Metabolomic, and Transcriptomic Analyses Elucidate the Mechanism Underlying Melon (Cucumis melo L.) Peel Cracking" Agriculture 15, no. 23: 2475. https://doi.org/10.3390/agriculture15232475

APA Style

Hu, Y., Li, Y., Zhang, T., Wang, C., Zhu, B., Tian, L., Wang, M., & Zhou, Y. (2025). Integrated Morphological, Physicochemical, Metabolomic, and Transcriptomic Analyses Elucidate the Mechanism Underlying Melon (Cucumis melo L.) Peel Cracking. Agriculture, 15(23), 2475. https://doi.org/10.3390/agriculture15232475

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