Transcriptomics approaches in the early Arabidopsis embryo

•The Arabidopsis embryo is an ideal model for studying plant cell fate specification.•Defining cellular transcriptomes is a major unsolved challenge in embryogenesis.•Technological advances have propelled post-embryonic developmental biology.•Using these novel tools, cellular embryo transcriptomes are coming within reach.

Early plant embryogenesis condenses the fundamental processes underlying plant development into a short sequence of predictable steps. The main tissues, as well as stem cells for their post-embryonic maintenance, are specified through genetic control networks. A key question is how cell fates are instructed by unique cellular transcriptomes, and important insights have recently been gained through cell type-specific transcriptomics during post-embryonic development. However, the poor accessibility and small size of Arabidopsis (Arabidopsis thaliana) embryos have obstructed similar progress during embryogenesis. Here, we review the current situation in plant embryo transcriptomics, and discuss how the recent development of novel cell-specific analysis technologies will enable the identification of cellular transcriptomes in the early Arabidopsis embryo.