Identification of Key Regulatory Genes Associated with Double-Petaled Phenotype in Lycoris longituba via Transcriptome Profiling

Lycoris longituba produces a single flower bearing six tepals. The double-petaled phenotype of L. longituba has gained significant interest in China due to its ornamental and commercial value in tourism industries. This double-petal phenotype, characterized by stamen petalization, shows improved esthetic characteristics compared with conventional single-petal form. However, the molecular mechanisms underlying this floral trait remain largely undefined. In this study, RNA-based comparative transcriptomic analysis was performed between single- and double-petaled flowers of L. longituba at the fully opened flower stage. Approximately 13,848 differentially expressed genes (DEGs) were identified (6528 upregulated and 7320 downregulated genes). Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed several DEGs potentially involved in double-petal development. Six candidate genes, including the hub genes LlbHLH49, LlNAC1, LlSEP, LlTIFY, and LlAGL11, were identified based on DEG functional annotation and weighted gene co-expression network analysis (WGCNA). Transcription factors responsive to phytohormonal signaling were found to play a pivotal role in modulating double-petal development. Specifically, 123 DEGs were involved in phytohormone biosynthesis and signal transduction pathways, including those associated with auxin, cytokinin, gibberellin, ethylene, brassinosteroid, and jasmonic acid. Moreover, 521 transcription factors (TFs) were identified, including members of the MYB, WRKY, AP2/ERF, and MADS-box families. These results improve the current understanding of the genetic regulation of the double tepal trait in L. longituba and offer a base for future molecular breeding strategies to enhance ornamental characteristics.