Comparative proteomic analysis of non-embryogenic and embryogenic callus, somatic and zygotic embryos of Theobroma cacao L.

The induction, development, and maturation of somatic embryos in cocoa are subjected to numerous failures during the various development stages. Understanding the biochemical/molecular events governing somatic embryogenesis in T. cacao will help to overcome these failures. The present study focused on cocoa somatic embryogenesis proteomic variations with the aim to shed light on the constraints of somatic embryos during their development stages (induction, expression, and maturation). These were investigated using combinations of LC-MS/MS coupled with TripleTOF 5600 + and Orbitrap Fusion methods during cocoa (Theobroma cacao L.) somatic embryogenesis. Non-embryogenic callus (NC), embryogenic callus (EC), somatic embryos (ESN), and zygotic embryos (EZM) were used as samples. Sample analyses followed by bioinformatics research identified a total of 1762 proteins. The differentially expressed proteins (DEPs) were derived from NC (429), EC (301), ESN (911), and EZM (511) and classified according to ontological categories. The analysis of KEGG pathways in NC and EZM showed that they were mainly enriched in metabolic pathways and the biosynthesis of secondary metabolites. While in EC and ESN, they are enriched in endoplasmic reticulum protein processing. Based on protein-protein interaction analysis, proteins in EC and ESN were highly regulated and involved in environmental stress. On the other hand, proteins in NC and EZM, highly regulated were involved in energy metabolism. This proteomic study provides clues to understand the low rate of conversion to plant in somatic embryogenesis and helps to build a model for improved culture medium.