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Abstract
BackgroundBarley (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. ResultsThe 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. ConclusionsThe 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.
Highlights
Barley (Hordeum vulgare L.) is one of the most important cereals worldwide
Identification of drought-responsive genes in barley A total of 250 differentially expressed genes (DEGs) (5 ≤ fold change ≤ − 5) were obtained, while 134 and 116 of which were upregulated and downregulated, respectively, in drought conditions based on the microarray data analysis (Table 1) after removal of the duplicated genes (Supplementary Tables 1 and 2)
A significant proportion of the hub genes was related to regulatory processes such as transcription and expression regulation (e.g., HvWRKY42, HvVP1, HvCBF6, and DRF1.3), which belong to transcription factor families
Summary
Barley (Hordeum vulgare L.) is one of the most important cereals worldwide. 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. To better understand drought tolerance and its mechanisms, the identification of DEGs in stress conditions could be a preliminary step, while reconstructing the related network and detecting the key genes would be the necessary steps. Analyzing the available microarray data revealed eight candidate WRKY genes which were upregulated under drought and salinity stresses compared to the optimum conditions at seedling stage in barley [25]. We attempted to collect highly drought-responsive genes in barley through analysis of all the available related microarray data [10,11,12,13,14]. The results of real-time PCR showed that the expression pattern of the four genes was in good agreement with the results obtained by microarray analysis
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