Comparative transcriptome analysis reveals candidate genes and regulatory pathways underlying stamen petaloidy in Clivia miniata

Abstract Stamen petaloidy underlies double-flower formation in Clivia miniata , but its molecular basis remains poorly understood. We performed comparative transcriptome sequencing of flower buds and tepals from single-, semi-double-, and double-flowered C. miniata , assembling 127,524 unigenes and identifying 44,140 and 40,278 differentially expressed genes (DEGs) in the bud and tepal comparisons, respectively. DEGs were enriched primarily in metabolic processes and phytohormone signaling, including 209 hormone-related transcripts spanning auxin, gibberellin, jasmonic acid, and other pathways. MYB, WRKY, NAC, bHLH, and bZIP transcription factors, along with MIKC-type MADS-box genes, most notably the class B floral identity gene CmPI_1 , showed pronounced expression shifts across floral phenotypes. Weighted gene co-expression network analysis (WGCNA) identified a blue module tightly linked to stamen petaloidy, encompassing hub transcription factors, the jasmonate signaling gene CmJAR1L , and CmPI_1 . qRT-PCR validated 13 core candidates whose expression tracked petaloidy severity, with CmPI_1 markedly upregulated in double-flowered buds. Together, these results point to a regulatory network linking phytohormone signaling, transcription factors, and floral identity genes, offering candidate genes for dissecting double-flower formation and guiding molecular breeding in C. miniata .