Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of quinoa salt bladders

Abstract Salt bladders, specialized structures on the surface of quinoa leaves, secrete Na + to mitigate the effects of the plant from abiotic stresses, particularly salt exposure. Understanding the development of these structures is crucial for elucidating quinoa ’s salt tolerance mechanisms. In this study, we employed transmission electron microscopy to detail cellular differentiation across the developmental stages of quinoa salt bladders. To further explore the developmental trajectory and underlying molecular mechanisms, we conducted single-cell RNA sequencing on quinoa protoplasts derived from young leaves. This allowed us to construct a cellular atlas, identifying 13 distinct cell clusters. Through pseudotime analysis, we mapped the developmental pathways of salt bladders and identified regulatory factors involved in cell fate decisions. GO and KEGG enrichment analyses, as well as experimental results, revealed the impacts of salt stress and the deprivation of sulfur and nitrogen on the development of quinoa salt bladders. Analysis of the transcription factor interaction network in pre-stalk cells (pre-SC), stalk cells (SC), and epidermal bladder cells (EBCs) indicated that TCP5 , YAB5 , NAC078 , SCL8 , GT-3B , and T1P17.40 play crucial roles in EBC development. Based on our findings, we developed an informative model elucidating salt bladder formation. This study provides a vital resource for mapping quinoa leaf cells and contributes to our understanding of its salt tolerance mechanisms.