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<p>Abiotic stress factors such as drought, salinity, and alkaline conditions significantly reduce the productivity of cotton (<i>Gossypium hirsutum</i> L.). In this study, we applied Weighted Gene Co-expression Network Analysis (WGCNA) to unravel the molecular networks underlying cotton resilience to multiple stressors. By analyzing root and shoot transcriptomes, we identified tissue-specific modules and hub genes that regulate adaptive responses through reactive oxygen species (ROS) regulation, and abscisic acid (ABA) and ethylene signaling pathways. In shoot tissue, the enrichment of the turquoise module in ribosome biogenesis and ROS-related pathways highlights the dual role of ROS as both a signaling molecule and a mediator of oxidative stress, supporting growth and photosynthetic stability under prolonged stress. Conversely, root modules such as the brown and green clusters were enriched in nutrient uptake and chromatin remodeling processes, contributing to structural resilience and nutrient homeostasis. Hub genes, including <i>WRKY21</i> and <i>ERF-SHINE2-like</i>, showed strong discriminatory power between stressed and non-stressed conditions, positioning them as promising targets for breeding stress-resilient cultivars. Functional validation through wet-lab assays confirmed the roles of these predicted hub genes. Our results indicate that ROS and ethylene act as critical modulators of multi-stress coordination, while ABA plays a cross-tissue regulatory role. This integrative framework provides actionable genetic targets and insights into interdependent regulatory networks, bridging knowledge gaps left by single-stressor studies. Overall, the study identifies potential candidate genes for breeding cotton cultivars that can thrive under increasingly unpredictable climates and concurrent environmental stressors.</p>

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Weighted Gene Co-expression Network Analysis Identifies Functional Modules Associated with Multiple Abiotic Stressors in Cotton (Gossypium hirsutum L.)

  • 期刊论文

  • 发表日期：

    2025年10月27日

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  • Rasmieh Hamid,
  • Amir Ghaffar Shahriari,
  • Bahman Panahi

摘要

Abiotic stress factors such as drought, salinity, and alkaline conditions significantly reduce the productivity of cotton (Gossypium hirsutum L.). In this study, we applied Weighted Gene Co-expression Network Analysis (WGCNA) to unravel the molecular networks underlying cotton resilience to multiple stressors. By analyzing root and shoot transcriptomes, we identified tissue-specific modules and hub genes that regulate adaptive responses through reactive oxygen species (ROS) regulation, and abscisic acid (ABA) and ethylene signaling pathways. In shoot tissue, the enrichment of the turquoise module in ribosome biogenesis and ROS-related pathways highlights the dual role of ROS as both a signaling molecule and a mediator of oxidative stress, supporting growth and photosynthetic stability under prolonged stress. Conversely, root modules such as the brown and green clusters were enriched in nutrient uptake and chromatin remodeling processes, contributing to structural resilience and nutrient homeostasis. Hub genes, including WRKY21 and ERF-SHINE2-like, showed strong discriminatory power between stressed and non-stressed conditions, positioning them as promising targets for breeding stress-resilient cultivars. Functional validation through wet-lab assays confirmed the roles of these predicted hub genes. Our results indicate that ROS and ethylene act as critical modulators of multi-stress coordination, while ABA plays a cross-tissue regulatory role. This integrative framework provides actionable genetic targets and insights into interdependent regulatory networks, bridging knowledge gaps left by single-stressor studies. Overall, the study identifies potential candidate genes for breeding cotton cultivars that can thrive under increasingly unpredictable climates and concurrent environmental stressors.