Molecular mechanism of drought stress tolerance in barley (Hordeum vulgare L.) via a combined analysis of the transcriptome data

Abstract

One of the main issues addressed by phytology in recent years has been plant tolerance mechanisms for abiotic stress. No combined analysis has been made to identify the genes involved in drought stress tolerance. The meta-analysis of microarray data related to drought stress was analysed by the R software packages and showed 3 029 upregulated genes and 3 017 downregulated genes. The upregulated genes were mostly related to the drought tolerance protein, abiotic stress response, and the Cys2His2 Zinc Finger Transcription Factor (C2H2 zinc finger TF). The downregulated genes were mainly related to the late embryogenesis abundant protein, abiotic stress response, and the basic leucine zipper (bZIP) TF. The common gene ontology (GO) terms in the upregulated and downregulated genes were mainly related to the metabolic process, response to stimulus, cellular metabolic process, and photorespiration. The up and down meta-differential expressed genes (meta-DEGs) mainly belonged to the those following Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including: the biosynthesis of secondary metabolites, plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signalling pathway, and RNA degradation. Moreover, in the upregulated and downregulated genes, the TFs with a high percentage mainly belonged to the Teosinte branched1/Cincinnata/proliferating cell factor (TCP), basic helix loop--helix (bHLH) and bZIP. Next, the hub upregulated genes were mainly related to the thiamine biosynthesis protein thiC, 4-hydroxyphenylpyruvate dioxygenase, ribose-5-phosphate isomerase precursor and heat shock protein. The hub downregulated genes were mainly associated with the elongation factor Ts, aldehyde dehydrogenase, and trigger factor. Finally, the data from the present meta-analysis were compared with previous studies on the qRT-PCR results and their up and down expressions were confirmed. Based on the findings of the current study, novel insights into the drought stress molecular response can be provided and various candidate genes can be introduced for barley drought stress tolerance breeding.

Understanding the Transcription Factor Mediated Regulatory Mechanism Towards Abiotic Stress Response in Cereal Crops

“…The activation domain consists of the acidic domain (acidic zone and machinery of the transcription factor), the proline-rich active domain (proteins and coactivators), and the serine-threonine-rich activation (serine and threonine). Protein-protein interaction consists of the coiled-coil domain (alphas helices zone), tetratricopeptide repeat (TPR) (repeats of a 34-amino acid motif) that act as a scaffold for the assembly of protein complexes, and WD40 repeat domain is composed of many repeats of a 40-amino acid motif (Alamholo and Tarinejad, 2023).…”

“…Common stresses include drought, temperature extremes, salinity, flooding, and limited or absent nutrients (Figure 2). Drought causes water deficiency in the soil and plant tissues, resulting in low root water uptake, reduced transpiration rates, and disrupted photosynthesis (Alamholo and Tarinejad, 2023). Drought stress affects cereal crops by reducing cell expansion, leaf area, and biomass accumulation, resulting in stunted growth and reduced yield.…”

“…This specificity allows precise control of how a gene is expressed in response to abiotic stress (Samal et al, 2021). Different sets of target genes can be activated or repressed by different transcription factors depending on which cis-regulatory regions they recognize, due to their distinct properties such as DNA-binding domains (Alamholo and Tarinejad, 2023). Examples of such domains are the APETALA2/Ethylene-Responsive Element Binding Factor (AP2/ERF) domain in the DREB family, the bZIP domain in the bZIP family, and the WRKY domain in the WRKY family.…”

“…They are No Apical Meristem (NAM), Arabidopsis Transcription Activation Factor 1 and 2 (ATAF1&2), and Cup-Shaped Cotyledon 2 (CUC2). For example, extreme temperatures activate the C-repeat binding factor/dehydration-responsive element-binding protein-1 (CBF/DREB1) TF in cereals to inhibit cold stress through a mechanistic interaction with CRT/DRE cis-elements (Alamholo and Tarinejad, 2023…”

Investigation of the morphological, physiological, biochemical, and catabolic characteristics and gene expression under drought stress in tolerant and sensitive genotypes of wild barley [Hordeum vulgare subsp. spontaneum (K. Koch) Asch. & Graebn.]

“…Manh et al [ 13 ]found that overexpression of the WHIRLY1 gene in barley delayed the onset of senescence and suppressed expression of drought-related marker genes. Alamholo and Tarinejad [ 14 ] performed a meta-analysis of microarray data and identified numerous upregulated and downregulated genes related to drought tolerance in barley. Additionally, Wang et al [ 6 ] used DNA affinity purification sequencing (DAP-seq) to identify novel transcription factors involved in drought resistance in highland barley.…”