Integrated transcriptome profiling identifies novel regulatory hubs mediating salt stress responses during germination and early seedling development in wheat

Background Soil salinity is a major abiotic stressor that severely impairs crop productivity worldwide and poses a significant threat to global food security. Wheat ( Triticum aestivum L.), one of the most widely cultivated cereal crops, is susceptible to salt stress, especially during early developmental stages, such as seed germination and seedling establishment. Results To systematically reveal the molecular mechanisms underlying salt adaptation in wheat, we performed weighted gene co-expression network analysis using transcriptomic data from salt-stressed germinating embryos and seedlings and identified a highly conserved turquoise module correlated with salinity responses across developmental stages. This module contained 432 hub genes, whose functional relevance was reinforced through an integrated analysis of 15 additional RNA sequencing datasets, yielding 74,796 differentially expressed genes (DEGs), including 6604 conserved DEGs that were identified in more than 10 datasets. Finally, we revealed the core salt-responsive regulatory network in wheat and identified 10 novel transcription factors, representing the AP2/ERF, C2C2-GATA, bHLH, bZIP, AUX/IAA, HB-HD-ZIP, and HMGB families, which were mainly downregulated under salt stress and were proposed to regulate cell wall biosynthesis coordinately. Conclusions Our work not only reveals nucleotide sugar metabolism and cell wall remodeling as central, conserved mechanisms in salt adaptation but also provides a validated set of candidate regulatory genes for functional dissection and targeted breeding.