Multiomics Profiling Unveils Key Genes and MetabolitesInvolved in the Salt Tolerance of Gossypium hirsutum

Weng, Zheng; Wang, Fan; Wei, Xin; Zhao, Lianjia; Wang, Wei; Lei, Jianfeng

doi:10.3390/genes17010022

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Multiomics Profiling Unveils Key Genes and MetabolitesInvolved in the Salt Tolerance of Gossypium hirsutum

by

Zheng Weng

^1,†,

Fan Wang

^2,†,

Xin Wei

³,

Lianjia Zhao

²,

Wei Wang

^2,* and

Jianfeng Lei

^1,*

¹

College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China

²

Institute of Crop Research, Xinjiang Uyghur Autonomous Region Academy of Agricultural Sciences, 403 Nanchang Road, Urumqi 830091, China

³

Institute of Cotton Research, Xinjiang Uyghur Autonomous Region Academy of Agricultural Sciences, 403 Nanchang Road, Urumqi 830091, China

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Genes 2026, 17(1), 22; https://doi.org/10.3390/genes17010022 (registering DOI)

Submission received: 4 December 2025 / Revised: 23 December 2025 / Accepted: 25 December 2025 / Published: 26 December 2025

(This article belongs to the Special Issue Genetic Regulation of Plant Metabolism in Environmental Adaptation)

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Abstract

Background: Salt stress is a primary abiotic constraint on cotton growth, significantly impairing yield and fiber quality. Methods: To elucidate the regulatory mechanisms underlying salt stress responses in Gossypium hirsutum, we performed transcriptomic and metabolomic profiling at multiple time points following salt treatment. Results: We identified 33,975 differentially expressed genes (DEGs), with significant enrichment in pathways related to plant hormone signal transduction, amino acid metabolism, and starch and sucrose metabolism. K-means clustering grouped the DEGs into six expression modules corresponding to distinct response stages. Additionally, UPLC‒MS analysis identified 6292 metabolites—spanning lipids, carbohydrates, and amino acids—and revealed substantial metabolic reprogramming with increasing stress duration. An integrated multiomics analysis highlighted the ABC transporter and starch and sucrose metabolism pathways as key regulatory modules for salt tolerance and identified critical genes within them. Conclusions: Collectively, these findings provide a comprehensive view of the transcriptional and metabolic dynamics of G. hirsutum under salt stress, offering valuable insights for understanding the molecular mechanisms of salt tolerance.

Keywords: G. hirsutum; salt stress; ABC transporter pathway; starch and sucrose metabolism

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MDPI and ACS Style

Weng, Z.; Wang, F.; Wei, X.; Zhao, L.; Wang, W.; Lei, J. Multiomics Profiling Unveils Key Genes and MetabolitesInvolved in the Salt Tolerance of Gossypium hirsutum. Genes 2026, 17, 22. https://doi.org/10.3390/genes17010022

AMA Style

Weng Z, Wang F, Wei X, Zhao L, Wang W, Lei J. Multiomics Profiling Unveils Key Genes and MetabolitesInvolved in the Salt Tolerance of Gossypium hirsutum. Genes. 2026; 17(1):22. https://doi.org/10.3390/genes17010022

Chicago/Turabian Style

Weng, Zheng, Fan Wang, Xin Wei, Lianjia Zhao, Wei Wang, and Jianfeng Lei. 2026. "Multiomics Profiling Unveils Key Genes and MetabolitesInvolved in the Salt Tolerance of Gossypium hirsutum" Genes 17, no. 1: 22. https://doi.org/10.3390/genes17010022

APA Style

Weng, Z., Wang, F., Wei, X., Zhao, L., Wang, W., & Lei, J. (2026). Multiomics Profiling Unveils Key Genes and MetabolitesInvolved in the Salt Tolerance of Gossypium hirsutum. Genes, 17(1), 22. https://doi.org/10.3390/genes17010022

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Multiomics Profiling Unveils Key Genes and MetabolitesInvolved in the Salt Tolerance of Gossypium hirsutum

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