Decoding core molecular mechanisms related to multiple abiotic stress adaptation in cotton: Insights from RNA-seq data meta-analysis in combination with machine learning approach

Drought, salinity and alkaline conditions are the major constraints to cotton (Gossypium spp.) productivity and require the development of genotypes with increased resilience for sustainable cultivation. Abiotic stress tolerance in cotton involves complex gene networks and regulatory pathways. Transcriptome meta-analysis provides a robust approach to elucidate these mechanisms by integrating diverse data sets and identifying consistently responding genes. In this study, RNA-seq meta-analysis using p-value combination approach was harnessed to elucidate the core molecular mechanisms involved in adaptation to drought, salinity and alkaline stress in root and leaf tissues. Moreover, functional analysis of identified core genes were performed using GO and KEGG enrichment and protein-protein interaction network analysis. Prioritization of core genes was further performed using topological analysis of core gene networks and machine learning approach. Key genes identified as central regulatory hubs, such as Gh_A01G1844.1 (aquaporin PIP2–2), Gh_D03G1591.1 (ethylene-responsive transcription factor 5) and Gh_A05G1554.1 (dehydrin COR47), play a central role in adaptive responses, including osmotic adjustment, oxidative stress management and tissue-specific functionality. Enrichment analysis revealed that critical processes such as transcriptional regulation, macromolecular metabolism and cellular signaling pathways are crucial for stress resilience. In addition, the prediction of transcription factor (TF) networks identified the major TF families bHLH, WRKY, NAC, ERF and MYB, which integrate different regulatory mechanisms. In addition, the network analysis revealed important signaling pathways such as ethylene and nodulation, with genes such as Dehydration-Responsive Element 1 D (DRE1D) and Cycling DOF Factor 1 (CDF1) contributing to adaptive responses. This study provides a valuable resource for breeding programs aimed at improving abiotic stress tolerance in cotton and offers insights into the genetic and functional basis of adaptation in different environmental contexts.