Somatic embryogenesis encompasses the same set of various developmental processes similar to zygotic embryogenesis. The conversion of somatic cells to embryos also requires stages of differentiation and reprogramming of cells. Since somatic embryogenesis is a complex process, a comprehensive investigation is required to identify the effective gene networks and their interactions with environmental factors. As part of this study, bioinformatics tools and molecular studies were used to gain a better understanding of Arabidopsis thaliana somatic embryogenesis. The enriched pathways of somatic embryogenesis and their core-enriched genes were identified using gene set enrichment analysis. The results indicated that significant interaction between hormones helps to induce and develop somatic embryos. The gene ontology (including biological process, molecular function and cellular compartment) of core-enriched genes revealed that lipid storage and metabolism as well as stress response are the active biological pathways during somatic embryogenesis. In the protein-protein interaction network, TIR1/AFBs as auxin receptors exhibited the greatest number of interactions and proteins involved in lipid storage and metabolism acted as mediators between auxin receptors and ethylene perception. Also, Kyoto encyclopedia of genes and genomes analysis indicated that the metabolism of membrane lipids during somatic embryogenesis of Arabidopsis is primarily related to the biosynthesis of jasmonates and their derivatives. This process is initiated by Lypooxygenase proteins in the chloroplast, while Acyl-CoA oxidase 1 (ACX1) and Oxophytodienoate reductase 3 (OPR3) proceed this process in the peroxisome. The qRT-PCR analysis also confirmed the role of these genes during somatic embryogenesis, as the activity of these genes decreased at the beginning of 2,4-D treatment, but it increased during somatic embryogenesis. According to these results, jasmonates play an important role during somatic embryogenesis by mediating auxin signaling and stress response.

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