Fragrance gives flowers their identity, yet the specific cells orchestrating this scent symphony have remained elusive, until now. Scientists have generated the first single-cell map of petal tissues in Prunus mume (mei), a classic ornamental tree known for its floral aroma. By integrating single-cell RNA sequencing with volatile compound profiling, researchers identified six major petal cell types and tracked how 28 scent-related genes are expressed across them. The study pinpoints where key floral volatiles, like benzyl acetate and eugenol, are produced, offering new genetic targets to enhance floral scent in horticultural breeding.

Floral scent is a hallmark of ornamental plants, influencing everything from pollinator behavior to perfume design. These fragrances arise from complex mixtures of plant volatiles—particularly benzenoids and phenylpropanoids, largely synthesized in flower petals. While prior research has cataloged many of the genes involved, most work used whole flowers, masking the precise cellular sources of fragrance production. Prunus mume, or mei, emits a particularly rich and distinct scent, making it a valuable system to decode floral aroma biology. Due to these gaps in cell-level understanding, deeper molecular and spatial analyses are urgently needed to unravel where and how these scents are made.

In a new study published in Horticulture Research, researchers from Northwest A&F University constructed a high-resolution single-cell transcriptomic atlas of Prunus mume petals. Using cutting-edge single-cell RNA sequencing and in situ hybridization, the team mapped the spatial expression of scent-related genes across individual petal cells at different stages of flowering. Their findings reveal which cell types drive the production of key aromatic compounds and uncover the cellular choreography behind mei’s distinctive fragrance.

Cell cluster identification of single-cell transcriptomes from mei petals

A Visualization of the 11 cell clusters. B Violin plots show the homologous gene expression distribution of the reported marker genes in different cell types in mei.

The team isolated nearly 17,000 high-quality cells from petals at budding and full-blooming stages using 10X Genomics scRNA-seq. These cells were categorized into six major types: epidermal cells (ECs), parenchyma cells (PCs), xylem and phloem parenchyma, xylem vessels and fibers, and sieve element companion cell complexes. Volatile profiling using GC-MS showed that floral scents peaked at full bloom. Expression of 28 genes involved in benzenoid/phenylpropanoid pathways was then examined. Notably, genes such as PmPAL2, PmCAD1, PmBAHD3, and PmEGS1 showed strong, cell-type-specific activation, particularly in ECs, PCs, and vascular tissues. Functional assays confirmed PmBAHD3 catalyzed benzyl acetate production, linking gene function to aroma synthesis. In situ hybridization further validated these spatial patterns, revealing that scent biosynthesis occurs in multiple coordinated cell types rather than a single specialized tissue.

“This study offers a high-definition snapshot of how flowers make their perfume,” said Dr. Tengxun Zhang, senior author of the study. “By combining single-cell mapping with molecular biology and chemistry, we’ve uncovered not just the ingredients of the scent, but the chefs behind them. Our findings provide critical insights for improving floral traits in ornamental breeding.” Zhang emphasized that this integrated approach could serve as a model for decoding complex traits in other non-model woody plants.

The single-cell roadmap of mei petals opens new frontiers in both basic and applied plant science. With a clearer view of where and how floral volatiles are produced, breeders can now design strategies to boost aroma intensity or diversify scent profiles in ornamental crops. This cellular insight could also benefit the fragrance and flavor industries by guiding targeted metabolic engineering. Beyond Prunus mume, the study showcases how single-cell technologies can revolutionize our understanding of plant biology—one cell at a time.

Source – Nanjing Agricultural University The Academy of Science