Identification of key regulators for the development of Prunus leaves using single-cell RNA sequencing

Leaves require the coordinated regulation of multiple types of cells to accumulate energy for plants. Transcriptome analysis at the tissue level cannot analyze the heterogeneity of cells or reveal the molecular regulatory mechanisms of different cell types. Recently, single-cell sequencing technology has become an important tool for analyzing cell heterogeneity, identifying rare cell populations, and drawing dynamic development tracks at a single-cell resolution. However, single-cell sequencing has not been conducted in Prunus leaf, limiting our understanding of key regulatory factors and the establishment of peach leaf cell lineages. In this study, we performed single-cell RNA sequencing on young leaves in two varieties of rootstock almond and cultivated red leaf winter peach. A total of 11,132 high-quality leaf cells from both varieties were divided into seven cell clusters based on reported marker genes in Arabidopsis. Potentially useful and representative markers were obtained in each cell cluster. Reconstructing the developmental trajectory of procambial cells showed that PpAPL, expressed in phloem cells, was a good candidate gene involved in phloem development. In the epidermis cell cluster, PpCER1 was found to increase the leaf wax content, thereby enhancing drought resistance in almond leaves. Our findings reveal the heterogeneity of leaf cells and identify key regulators in peach and almond, providing a theoretical basis for peach molecular breeding to enhance drought resistance.