Gene regulatory network analysis of somatic embryogenesis identifies morphogenic genes that increase maize transformation frequency

Somatic embryogenesis allows a somatic plant cell to develop into an embryo, and potentially into a fertile plant. Transcription factors such as BABY BOOM can induce somatic embryogenesis when ectopically expressed and are widely used for aiding regeneration in tissue culture for transformation and gene editing of crops. Nevertheless, regeneration remains a bottleneck and alternative morphogenic genes are highly desired. Here, we co-expressed BABY BOOM and WUSCHEL2 in zygotic maize (Zea mays L.) embryos and studied gene regulatory networks in induced somatic embryos at the single-cell level. By inferring cell-type-specific regulons, we prioritized candidate regulators and confirmed functionality of four transcription factors, bHLH48, EREB152, GRF4, and HB77, for enhanced maize transformation frequency, leading to fertile, transgenic plants. Interestingly, the basic helix-loop-helix and homeodomain-leucine zipper families had previously not been associated with induced somatic embryogenesis. Our work will contribute to more efficient transformation, much needed to deliver on the promise of gene editing for agriculture. The provided files inlude: mini-ex__input__priors.zip: list of priors used to perform MINI-EX runs mini-ex__input__seurat.zip: scRNA-seq related inputs extracted from the Seurat object for the MINI-EX runs mini-ex__output.zip: outputs provided by MINI-EX for the eight priors