Comparative Transcriptome Analysis of Leaves and Roots Responses in Salt-Tolerant Barley Line CC89/Giza123 Under Salinity Stress.

Salinity stress has a debilitating effect on crop productivity and triggers complex molecular changes in plants, and understanding these responses is important for improving stress tolerance. This study investigated transcriptomic changes in the salt-tolerant barley line CC89/Giza123 by analyzing gene expression in roots and leaves following exposure to 200 mM NaCl for 12 and 24 h. The number of differentially expressed genes (DEGs) showed a much stronger response in roots than in leaves. At 12 h, roots showed 1836 DEGs, and this number increased to 2696 at 24 h, whereas leaves showed 256 DEGS at 12 h, and 787 at 24 h. The presence of strong and early activation in roots appears to indicate that roots play a key role in the adaptive response to salinity stress initiation. GO and KEGG analyses of differentially expressed genes revealed tissue- and time-specific responses. Roots showed rapid activation of ribosome and secondary-metabolite pathways at 12 h, followed by shifts toward carbon fixation and energy-related pathways at 24 h. Leaves responded early by adjusting photosynthesis-antenna proteins and later expanded their response to defense-related and amino-acid biosynthesis pathways. Important salt-responsive genes were identified in both tissues, including protein kinases, protein phosphatases 2C (PP2Cs), phospholipases, aquaporins, detoxification enzymes, molecular chaperones, and Late Embryogenesis Abundant (LEA) proteins. These results highlight clear tissue-specific and time-dependent differences in how plants respond to salt stress, providing insights into the metabolic and regulatory mechanisms involved in salt tolerance. Overall, these results provide evidence that the response of barley to salinity is achieved by using coordinated and dynamic molecular changes in different tissues. The transcriptomic dataset is a useful source of candidate genes for further functional studies and is a significant resource for breeding and biotechnological approaches to the production of salt-tolerant cereal crops.