Single Cell Multiomics of Hooked Potato Stolons Reveals Parallels to Shoot Apical Meristems in Arabidopsis

Solanum tuberosum L. (potato) is a key food crop, with its tubers serving as an important food source worldwide. Tuber development is a tightly regulated process involving the transition of a hooked stolon (a modified stem) to a tuber following the perception of mobile signals within the stolon tip. While genes like FLOWERING LOCUS T homologue StSP6A and the transcription factors (TF) StPOTH1, StBRC1b and StBEL5 have been implicated in this process, little is known about cell-type-specific gene expression and its regulation during tuber initiation. To further our understanding of tuber initiation and development, we generated single nuclei multi-ome data (gene expression and chromatin accessibility from the same nucleus) from hooked stolons of tetraploid S. tuberosum cv. Atlantic. Nuclei (20079) were assigned to 27 clusters, representing 10 annotated cell types. Differential chromatin and motif enrichment analysis revealed binding sites of TF families known to play a role in cell type development in Arabidopsis that were enriched in analogous cell types in potato stolon tips. By coupling gene co-expression and information from differential chromatin analysis, we identified novel TFs with putative roles in stolon vasculature development. Co-accessibility analysis further uncovered putative regulatory enhancers involved in stolon/tuber development. We identified cells that metabolise starch and used gene co-expression analysis to uncover novel TFs involved in the transition from source to sink. This dataset of cell-type-specific gene expression and accessible chromatin from the same nucleus is a powerful resource for discovering genes and regulatory sequences involved in the earliest stages of tuber development.