Weighted gene co-expressed network analysis in barley and expression of hub genes involved at germination stage

Seed germination is an important process that determines the beginning of the seed plant life cycle. However, the mechanism underlying seed germination in barley remains unclear. To understand the molecular mechanism of the seed germination in barley, WGCNA analysis was used to detect the hub and responsive genes and to reveal the expression of the genes on seed germination. WGCNA is a valuable tool for studying the correlation between genes, identifying modules with high correlation, and identifying Hub genes in different modules.

Raw microarray data related to germination stage were obtained from the GEO microarray database for 0h, 3h, 9h, 18h, 33h and 71h after germination stage. Then, weighted gene co-expression network analysis (WGCNA) was utilized for detection of co-expressed network genes. In the present study, a barley cultivar, Mahtab, was utilized to show expression pattern after 9h, 18h and 71h after germination stage. A total number of 4137 differentially expressed genes (DEG) were identified, with some genes showing higher expression in Mahtab and three genes verified by qRT-PCR

Most of these DEGs were involved in metabolic processes, cellular processes, glycolysis, and response to stimulus. Hub gene in MEbrown was alpha/beta-Hydrolases superfamily protein, MEpurple was U-box domain-containing protein 4, and MEdarkgrey was B3 domain-containing transcription factor ABI3 which were positively correlated with germinated seeds. The results showed a microarray database and candidate genes for further study of barley at germination stages. In addition, DEGs were divided into three modules by WGCNA. In this study, gene modules associated with seed germination during barley seed germination were identified. Transcription factor and alpha/beta-hydrolase played an important role at germination stage. Also, gene modules and hub genes at 9h, 18h, and 71h after germination were detected. As there is lack of information on seed germination requirements of barley, this research was conducted to study seed germination mechanisms as well as evaluation of hub genes to study molecular mechanism seed germination in barley.

The results of the present study provide new insights into the molecular mechanism underlying barley seed germination. Based on the network analysis, transcription factors (TFs) and ubiquitin proteins were involved in germination. Most of the genes related to each module were related to proteins involved in carbohydrate metabolism, glycolysis, and protein degradation. Our gene expression results can serve as molecular markers in barley cultivars during seed germination. These findings can be suitable for molecular assisted selection and breeding of fast germinating barley genotypes.