Coffee somatic embryogenesis, a model to decipher fundamental mechanisms associated to totipotency, somaclonal variation and photo-autotrophy acquisition

Nowadays coffee somatic embryogenesis (SE) can be considered as a model for woody perennial crops as its industrial application already allowed the dissemination of 50 millions of elite plants in the two cultivated species. The process works with high biological efficiency is observed at all developmental stages and somaclonal variation is mastered. Current research beneficiates from this regeneration model as well as from the progress of coffee genomics and biotechnologies, focuses on two distinct objectives. The recent advances of this research and their respective outputs are reviewed and discussed in this presentation. The first objective is to develop basic research based on-omics methodologies to decipher the fondamental mechanisms associated to cell reprogramming by focusing on two examples: i) Taking advantage of optimized SE protocols, we will unravel totipotency mechanisms and molecular events involved in the key developmental switches occurring during cell dedifferentiation/redifferentiation. A multi approach characterization through cell imaging, massive transcriptomic, epigenetic and metabolomic analyzes is applied at all the key developmental stages from the leaf explant to torpedo-shaped embryos (7 well characterized developmental stages). Big data integration and a system biology approach will provide a thorough knowledge of the expression of totipotency. ii) Coffee embryos acquire the capacity to photosynthetize very early in their developmental process (at the cotyledonary stage). Understanding the events leading to the acquisition of photo-autotrophy is also being studied by ecophysiological and molecular approaches applied to torpedo and cotyledonary-shaped embryo cultures under contrasted light, C02 and sugar conditions. Otherwise, the second objective is to provide - through technological approaches - powerful tools to accelerate the optimization of coffee breeding: i) The high-throughput molecular screening method has been recently developed by Nestle that allows to miniaturize the SE process and opens the way to study the biological effect of new active molecules on particular developmental switches' efficiency. It will also allow the development of miniaturized EMS (Ethyl Methyl Sulphate) mutant banks by simplifying their setting up and further management. ii) The genome editing of coffee genome by the Crispr/Cas9 technology recently described by using embryogenic tissues transformation gives us the possibility to rapidly and precisely manipulate plant genomes to introduce a trait of agronomic interest