Allelic imbalance regulation and evolution of floral specialization in Dendrobium orchids revealed by single-cell transcriptomics
Orchidaceae is one of the largest flowering plant families, yet the cell heterogeneity and molecular basis underlying pollinium formation and tepal specialization remains largely unknown. Here, we report a spatially resolved single-cell transcriptomic census of Dendrobium Chao Praya Smile flower buds, identifying 14 distinct cell types via RNA in situ hybridization. Compared to conventional pollen grains, Dendrobium meiotic cells are enriched in galactosyltransferase activity, thereby facilitating mucilage-mediated pollinium formation. Additionally, we mechanistically identify specialized cell populations driving tepal innovation, including lip-specific cells, vascular cells guiding organ curvature, and pigment cells directing localized coloration. Furthermore, haplotype-resolved expression analysis reveals that cis-regulatory structural variants favor Hap1 alleles from the pigmented parent in pigment cells. These findings illuminate cellular and genetic foundations of orchid floral specialization and demonstrate how parental genomes interact through cell type- and allele-specific expression to shape hybrid traits, offering broader insights into plant developmental biology and ornamental breeding.