Investigation of somatic embryogenesis, a crucial effort to jumpstart green biotechnology – SomaGreen

Somatic embryogenesis (SE) is the process by which differentiated cells resume division and form embryonic structures without fertilization. Functional modules linked to SE have been identified in plant tissue cultures, but they are not well described molecularly, and the causal chain of events driving the process is unknown. We will combine histological data with advanced single-cell profiles (gene expression, chromatin accessibility) and spatial transcriptomics to understand how cell lineages evolve in embryogenic tissues. With the integrated localization of histological, transcriptome and epigenetic data at successive stages of plant SE, we will refine or identify novel cell identities and associate multiple molecular markers with cell states and fate changes. Finally, based on our original integrated data sets, we will focus on potential key regulators and test their putative role in SE, either by phenotyping inactivation or ectopic plant lines, and by characterizing SE response of plant tissue cultures treated with specific chemical perturbators. To date, no plant developmental program has been analyzed with such a detailed multimodal approach. SE will be studied in the model grass Brachypodium distachyon as a proxy to improve vegetative multiplication, regeneration and gene editing in cereals, with the goal to promote breeding in these essential food crops. The activity of genetic or chemical factors proven to enhance SE in the Brachypodium model will be further tested on recalcitrant cereal genotypes in proof-of-concept experiments.