Data mining study of hormone biosynthesis gene expression reveals new aspects of somatic embryogenesis regulation

Although the application of exogenous hormones and the status of endogenous hormones play a crucial factor in somatic embryogenesis (SE), our understanding of the status of endogenous hormones and the molecular framework for hormone biosynthesis during SE are still elusive. With a data mining approach, we analyzed public RNA-seq data of SE from two model plants, Arabidopsis thaliana and Oryza sativa var. Japonica, which showed that several plant hormone biosynthesis genes had distinct patterns during SE. The expressions of auxin, cytokinin, gibberellin, and ethylene biosynthesis genes were induced during SE in A. thaliana, while only jasmonic acid showed an expression increase during somatic embryogenesis in both plants. Furthermore, by analyzing public RNA sequencing and DNA affinity purification sequencing (DAP-seq), we revealed some possibilities of the role of ethylene during SE through the activity of EIN3, by increasing the expression level of major transcription factors of somatic embryo development such as AGL15, BBM, and FUS3.