Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis somatic embryogenesis (SE) and identification of key gene modules to uncover SE-associated hub genes

Background: Somatic embryogenesis (SE), which occurs naturally in many plant species, serves as a model to elucidate cellular and molecular mechanisms of embryo patterning in plants. Decoding the regulatory landscape of SE is essential for its further application. Hence, the present study aimed to employ Weighted Gene Correlation Network Analysis (WGCNA) to construct a gene co-expression network (GCN) for Arabidopsis SE, and then identify highly correlated gene modules to uncover the hub genes associated with SE that may serve as potential molecular targets. Results A total of 17,059 genes with a variance greater than 0.25 quantile were filtered from microarray datasets derived from Arabidopsis SE (NCBI Gene Expression Omnibus accession number: GSE48915). This included 1,711 transcription factors and 445 EMBRYO DEFECTIVE genes. GCN analysis identified a total of 26 gene modules with the module size ranging from 35 to 3,418 genes using a dynamic cut tree algorithm. The module-trait analysis revealed that four, four, seven and four modules were associated with Stage I (zygotic embryos), Stage II (proliferating tissues at 7 days of induction), Stage III (proliferating tissues at 14 days of induction) and Stage IV (mature somatic embryos), respectively. Further, we identified a total of 260 hub genes based on the degree of intramodular connectivity. Validation of the hub genes using publicly available expression datasets demonstrated that at least 78 hub genes are potentially associated with embryogenesis; of these many genes remain functionally uncharacterized thus far. In silico promoter analysis of these genes revealed the presence of EBOXBNNAPA and SEF4MOTIFGM7S motifs; this suggests these genes may play important roles in plant embryo development. Conclusion The present study successfully applied WGCNA to construct a GCN for SE in Arabidopsis and identified hub genes involved in the development of somatic embryos. These hub genes could be used as molecular targets to further elucidate the molecular mechanisms underlying SE in plants.