New insights on key genes involved in drought stress response of barley: gene networks reconstruction, hub, and promoter analysis

Abstract

Background Barley (Hordeum vulgare L.) is one of the most important cereals worldwide. Although this crop is drought-tolerant, water deficiency negatively affects its growth and production. To detect key genes involved in drought tolerance in barley, a reconstruction of the related gene network and discovery of the hub genes would help. Here, drought-responsive genes in barley were collected through analysis of the available microarray datasets (− 5 ≥ Fold change ≥ 5, adjusted p value ≤ 0.05). Protein-protein interaction (PPI) networks were reconstructed. Results The hub genes were identified by Cytoscape software using three Cyto-hubba algorithms (Degree, Closeness, and MNC), leading to the identification of 17 and 16 non-redundant genes at vegetative and reproductive stages, respectively. These genes consist of some transcription factors such as HvVp1, HvERF4, HvFUS3, HvCBF6, DRF1.3, HvNAC6, HvCO5, and HvWRKY42, which belong to AP2, NAC, Zinc-finger, and WRKY families. In addition, the expression pattern of four hub genes was compared between the two studied cultivars, i.e., “Yousef” (drought-tolerant) and “Morocco” (susceptible). The results of real-time PCR revealed that the expression patterns corresponded well with those determined by the microarray. Also, promoter analysis revealed that some TF families, including AP2, NAC, Trihelix, MYB, and one modular (composed of two HD-ZIP TFs), had a binding site in 85% of promoters of the drought-responsive genes and of the hub genes in barley. Conclusions The identified hub genes, especially those from AP2 and NAC families, might be among key TFs that regulate drought-stress response in barley and are suggested as promising candidate genes for further functional analysis.

Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress

“…In Chickpea ( Cicer arietinum L.), 15 genes were down-regulated in roots and 10 genes were down-regulated in stems under abiotic stress [ 59 ]. The OsWRKY55 negatively regulates drought tolerance in transgenic rice lines [ 60 ], The transcription level of HvWRKY42 increased in Barley ( Hordeum vulgare L.) under drought stress, which indicated that HvWRKY42 was regulating the drought adaptability of barley [ 61 ]. The HvWRKY3 showed 13 fold high expression and 4 genes showed 2-fold high expression under drought stress [ 46 ].…”

Characterization of transcription factor MYB59 and expression profiling in response to low K+ and NO3− in indica rice (Oryza sativa L.)

“…To manage stress conditions, many molecular changes can take place by activating and regulating certain stress-related genes [39]. Identifying important and differentially expressed genes in response to stress environments might be a suitable approach toward a better understanding of stress responses and their mechanisms [23]. Past studies indicated that rice MYB59 is positively regulated with drought [46] and there are little studies about the regulation of OsMYB transcripts under K + and NO 3 − stress.…”

Changes in physio-biochemical parameters and expression of metallothioneins in Avena sativa L. in response to drought

“…Moreover, studies on cis -regulatory elements (CREs) provide a foundation for future experiments 54 , 72 , 73 . Regulatory elements play a crucial role in plant responses to various stresses, including drought stress 74 . There are not many studies comparing promoters of different types of MTs in one plant species 64 , 65 , 72 .…”