ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Abiotic Stress
This article is part of the Research TopicPlant Responses to Abiotic Stress: Unraveling Complex Mechanisms through Genomics and PhysiologyView all 9 articles
Transcriptomics and Non-Targeted Metabolomics Reveal the Mechanisms of Leaf Color Changes in Red-Leaf Cotton Under Drought Stress and Rewatering
Provisionally accepted
Hu Zhang1
Jinsheng Wang1Wenju Gao1Xiangyan Ma1Hongbin Wang2Wen Zhang2Qingtao Zeng2Jianping Li3
Quanjia Chen1
Qin Chen1*- 1Xinjiang Agricultural University, Ürümqi, China
- 27th Division Agricultural Research Institute, Kuitun, China
- 3Xinjiang Academy of Agricultural Sciences, Urumqi, China
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This study investigates the dynamic leaf color changes (red-green-red) in red-leaf cotton under drought stress and rewatering, and reveals the molecular and biochemical mechanisms through integrated transcriptomics and metabolomics analysis. Under mild drought stress, red-leaf cotton accumulates higher levels of anthocyanins, which coincides with better-maintained photosynthetic performance, indicating an effective photoprotective response. In contrast, under severe drought stress, anthocyanin levels decline significantly, accompanied by markedly reduced water retention and photosynthetic capacity, reflecting a shift toward survival-oriented physiological strategies.After rewatering, red-leaf cotton reactivates the flavonoid biosynthesis pathway and gradually restores anthocyanin synthesis, showing clear phenotypic recovery. Transcriptomic analysis shows reprogramming of gene expression related to flavonoid biosynthesis and drought tolerance pathways, and WGCNA analysis further identifies gene modules closely associated with anthocyanin synthesis and water retention capacity. Metabolomic analysis indicates dynamic metabolic regulation in red-leaf cotton during drought, with metabolites such as phenylalanine and 2-hydroxyquinoline providing precursors for anthocyanin synthesis. After rewatering, the recovery of metabolites lays the foundation for phenotypic restoration, revealing the strong metabolic repair and stress memory abilities of red-leaf cotton. These mechanisms provide theoretical support for the breeding of drought-resistant cotton varieties.
Keywords: Drought stress, Flavonoid biosynthesis, Metabolomics, Red-leaf cotton, Transcriptomics
Received: 13 Dec 2025; Accepted: 27 Jan 2026.
Copyright: © 2026 Zhang, Wang, Gao, Ma, Wang, Zhang, Zeng, Li, Chen and Chen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Qin Chen
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