The molecular core responses to multiple abiotic stresses in barley (Hordeum vulgare L.): Insights from global transcriptome analysis

Environmental stresses significantly affect crop yields and threaten global food security, underscoring the need for developing stress-tolerant crop varieties. This study addresses the gap in understanding stress-responsive mechanisms by analyzing 372 RNA-seq profiles from 14 barley studies on various abiotic stresses. Data quality was assessed and trimmed reads were aligned to the MorexV3 genome and quantified with HT-seq. Differential gene expression was determined, after batch effects correction. Core differentially expressed genes (DEGs) were identified through Fisher's method p-value combination method. Then, identified core genes were subjected to functional enrichment analysis via GO, KEGG, and PPI networks. Furthermore, Hub genes of constructed network were detected based on topological algorithms. Validation of core DEGs were further performed through χ2 goodness of fit test. Meta analysis identified the 360 core DEGs response to multiple abiotic stress. Functional enrichment analysis showed that these genes mostly enrich in phytohormones, calcium signaling, and secondary metabolism, starch and sucrose metabolism, and glutathione metabolism. Results of this study also showed that the upregulation of glucose-6-phosphate isomerase and sucrose synthase 4 underscores their importance in maintaining energy and osmotic balance of barley during multiple abiotic stress condition. Moreover, our survey showed that the ABC cation transporters, especially ABCC4 and ABCD1 are crucial for ion homeostasis of barley during multiple abiotic stress condition. Finally, network analysis of the identified core-DEGs highlighted the functional importance of SUS4 (Sucrose synthase 4), HSP70-4 (Heat shock protein 70 kDa 4), GLN2 (Glutamine synthetase), GAPC2 (Glyceraldehyde-3-phosphate dehydrogenase), ALDH7B4 (Aldehyde dehydrogenase family 7 member B4), and APX3 (L-ascorbate peroxidase 3) under multiple abiotic stress. Overall, this study provides a comprehensive understanding of the molecular responses to abiotic stress in barley and highlights key pathways and genes that contribute to stress adaptation and resilience.