RNA-Seq-Based Transcriptome Analysis of Barley (Hordeum vulgare) Reveals Molecular Responses to Drought Resilience

Abstract

Drought is a major abiotic stress that significantly impairs plant physiological processes and development, ultimately leading to substantial crop yield losses. As a complex quantitative trait, drought tolerance is governed by multiple genes and intricate metabolic pathways. However, the molecular mechanisms and associated morphological and physiological adaptations to drought stress in barley remain poorly understood. In this study, we employed an integrative approach combining morpho-physiological assessments and RNA-Seq-based transcriptome analysis to identify core drought-responsive genes and regulatory networks in the barley (Hordeum vulgare) cultivar ‘Giza 134’. Field trials under water-deficit conditions revealed significant reductions in crop growth rate, relative water content, leaf area duration, flag leaf area, chlorophyll (Chl) a, b, and total chlorophyll (a + b), net photosynthesis rate, and key yield components. Conversely, drought stress caused notable increases in the chlorophyll a/b ratio, stomatal resistance, and proline accumulation. Transcriptomic analysis identified 2,462 differentially expressed genes (DEGs), with 1,555 genes upregulated and 907 downregulated under drought conditions. Comparative analysis of gene expression profiles highlighted three critical metabolic pathways—carbohydrate metabolism, iron ion binding, and oxidoreductase activity—as potentially involved in the plant’s drought response. Several drought-induced marker genes were found to be associated with key physiological functions, including chlorophyll biosynthesis, photosynthesis, light harvesting, gibberellin biosynthesis, and iron homeostasis, along with distinct cis-regulatory elements. Overall, our findings provide novel insights into the molecular and physiological mechanisms underlying barley’s response to water-deficit stress.

Keywords: Carbohydrate Metabolism, Drought Stress, Photosynthesis, RNA-Sequencing, Transcription Factors